Psyllid ID: psy6602

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------
Protein Sequence
VQHERGPRKPKIHNAHHQDSKLEPHNPHHSPDLLPPNGISSVKIPPTVLYPPSGLKSPPPPSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYG
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHccHHHHHHHHHHHHccccccEEccccccccccccccccHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHcHHHHcccHHHHHHHHHccccccccHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHcHHHHcccHHHHHHHHHccccccccHHHHHHHHHHcccccc
Secondary Structure Prediction (SSPRO)
cccccccccHHHHHcccccccccccccccccccccccccccccccHHHHHHHHcccccccHcccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccEEEcccccccccccccHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHccHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHccHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHcccccc
Coil and Loop (DISEMBL)
vqhergprkpkihnahhqdsklephnphhspdllppngissvkipptvlyppsglksppppshhhpsmflathqppphpglLQILMSAEKCQETTARLLFMAVRWVRclapfqtlsKRDQLLLLQESWKELFLLHLAQwsipwdlsLLINCEKarerlppddvrvnNEIKLIQEILARFRqlspdgsecgcmKAVIlftpetpglvdaqpvEMLQDQAQCILGdyvrgrysrqptrfGRLLLMLPSLRAVRQSTIERLFfketigdipiqrllgdmytmeksyetpglvdaqpvEMLQDQAQCILGdyvrgrysrqptrfGRLLLMLPSLRAVRQSTIERLFfketigdipiqrllgdmytmeksyg
Flexible Loop (DISEMBL)
vqhergprkpkihnahhqDSKLEPHNPHHSPDLLPPNGISSVKIPPTVLYPPSGLKSPPPPSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARerlppddvrvnNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIErlffketigdipiqrlLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIerlffketigdipiqrllgdmytMEKSYG
Low Complexity Region (SEG)
VQHERGPRKPKIHNAHHQDSKLEPHNPHHSPDLLPPNGISSVKIPPTVLYPPSGLKsppppshhhpsMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYG
Disordered region (IsUnstruct)
********************************************************************************LLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT******
Disordered Region (DISOPRED)
VQHERGP*****************************************************************************LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCE***************EIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGD**TM*****
Disordered Region (DISEMBL)
*****************************SPDLLPPNGISSVKIPPTVLYPP************HPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYG
Disordered Region (DISPRO)
*******************************************IPPTVLYPPSGLKSPPPPSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEK***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
VQHERGPRKPKIHNAHHQDSKLEPHNPHHSPDLLPPNGISSVKIPPTVLYPPSGLKSPPPPSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYG
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	367	2.2.26 [Sep-21-2011]
Q64104	385	Nuclear receptor subfamil	yes	N/A	0.722	0.688	0.370	7e-45
Q91379	385	Nuclear receptor subfamil	yes	N/A	0.716	0.683	0.371	1e-44
Q9Y466	385	Nuclear receptor subfamil	yes	N/A	0.722	0.688	0.367	3e-44
P70052	386	Nuclear receptor subfamil	N/A	N/A	0.727	0.691	0.358	2e-42
Q9YGL3	396	Nuclear receptor subfamil	N/A	N/A	0.719	0.666	0.366	2e-41
Q9Y5X4	410	Photoreceptor-specific nu	no	N/A	0.493	0.441	0.471	2e-39
Q9TTF0	411	Photoreceptor-specific nu	no	N/A	0.749	0.669	0.374	2e-39
Q9QXZ7	395	Photoreceptor-specific nu	no	N/A	0.504	0.468	0.470	7e-37
Q9TTR8	424	COUP transcription factor	no	N/A	0.550	0.476	0.411	1e-36
P10589	423	COUP transcription factor	no	N/A	0.550	0.477	0.411	1e-36

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

 Score =  181 bits (459), Expect = 7e-45,   Method: Compositional matrix adjust.
 Identities = 113/305 (37%), Positives = 166/305 (54%), Gaps = 40/305 (13%)

Query: 1   VQHERGPRKPKIHN-------AHHQDSKLEPHNPHHSPDLLPPNGISSVKIPPTVLYPPS 53
           VQHERGPR   I          H +D+    H P  S  L  P   ++V         P 
Sbjct: 88  VQHERGPRTSTIRKQVALYFRGHKEDNGAAAHFP--STALPAPAFFTAV-----TQLEPH 140

Query: 54  GLKSPPPPSHHHPSMFLATHQPPPH--------PGLLQILMSAEKCQETTARLLFMAVRW 105
           GL+     +       ++  QP P         P  L  + +   C E+ ARLLFM+++W
Sbjct: 141 GLELAAVSATPERQTLVSLAQPTPKYPHEVNGTPMYLYEVATESVC-ESAARLLFMSIKW 199

Query: 106 VRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDV-- 163
            + +  F TLS +DQL+LL+++W+ELF+L +AQW+IP D + L+    A   +  D+   
Sbjct: 200 AKSVPAFSTLSLQDQLMLLEDAWRELFVLGIAQWAIPVDANTLL----AVSGMNTDNTDS 255

Query: 164 ----RVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTP-------ETPGLVDAQPVE 212
               ++ +EI+ +QE++ARFRQL  D +E  C+K ++ F         E     +A  + 
Sbjct: 256 QKLNKIISEIQALQEVVARFRQLRLDATEFACLKCIVTFKAVPTHSGSELRSFRNAAAIA 315

Query: 213 MLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRL 272
            LQD+AQ  L  Y+  RY  QP RFG+LLL+LP+LR++  STIE +FFK+TIG++PI RL
Sbjct: 316 ALQDEAQLTLNSYIHTRYPTQPCRFGKLLLLLPALRSISPSTIEEVFFKKTIGNVPITRL 375

Query: 273 LGDMY 277
           L DMY
Sbjct: 376 LSDMY 380

Orphan receptor that binds DNA as a monomer to hormone response elements (HRE) containing an extended core motif half-site sequence 5'-AAGGTCA-3' in which the 5' flanking nucleotides participate in determining receptor specificity (By similarity). Regulates cell cycle progression in neural stem cells of rhe developing brain. Involved in the regulation of retinal development and essential for vision. During retinogenesis, regulates PTEN-Cyclin D expression via binding to the promoter region of PTEN and suppressing its activity. May be involved in retinoic acid receptor (RAR) regulation in retinal cells.
Mus musculus (taxid: 10090)

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

 Score =  180 bits (457), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 114/307 (37%), Positives = 167/307 (54%), Gaps = 44/307 (14%)

Query: 1   VQHERGPRKPKIHN-------AHHQDSKLEPHNP---------HHSPDLLPPNGISSVKI 44
           VQHERGPR   I          H ++S   PH P           +   L P+G+    +
Sbjct: 88  VQHERGPRTSTIRKQVALYFRGHKEESSGAPHFPATALPAPAFFTAVSQLEPHGLELAAV 147

Query: 45  PPT-VLYPPSGLKSPPPPSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAV 103
             T       GL  P P    +P      H+    P  L  + +   C E+ ARLLFM++
Sbjct: 148 AGTPERQALVGLAQPTP---KYP------HEVNGTPMYLYEVATESVC-ESAARLLFMSI 197

Query: 104 RWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDV 163
           +W + +  F TLS +DQL+LL+++W+ELF+L +AQW+IP D + L+    A   +  D+ 
Sbjct: 198 KWAKSVPAFSTLSLQDQLMLLEDAWRELFVLGIAQWAIPVDANTLL----AVSGMNGDNT 253

Query: 164 ------RVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTP-------ETPGLVDAQP 210
                 ++ +EI+ +QE++ARFRQL  D +E  C+K ++ F         E     +A  
Sbjct: 254 DSQKLNKIISEIQALQEVVARFRQLRLDATEFACLKCIVTFKAVPTHSGSELRSFRNAAA 313

Query: 211 VEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQ 270
           +  LQD+AQ  L  Y+  RY  QP RFG+LLL+LP+LR++  STIE +FFK+TIG++PI 
Sbjct: 314 IAALQDEAQLTLNSYIHTRYPTQPCRFGKLLLLLPALRSISPSTIEEVFFKKTIGNVPIT 373

Query: 271 RLLGDMY 277
           RLL DMY
Sbjct: 374 RLLSDMY 380

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

Gallus gallus (taxid: 9031)

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

 Score =  179 bits (454), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 112/305 (36%), Positives = 166/305 (54%), Gaps = 40/305 (13%)

Query: 1   VQHERGPRKPKIHN-------AHHQDSKLEPHNPHHSPDLLPPNGISSVKIPPTVLYPPS 53
           VQHERGPR   I          H +++    H P  S  L  P   ++V         P 
Sbjct: 88  VQHERGPRTSTIRKQVALYFRGHKEENGAAAHFP--SAALPAPAFFTAV-----TQLEPH 140

Query: 54  GLKSPPPPSHHHPSMFLATHQPPPH--------PGLLQILMSAEKCQETTARLLFMAVRW 105
           GL+     +       ++  QP P         P  L  + +   C E+ ARLLFM+++W
Sbjct: 141 GLELAAVSTTPERQTLVSLAQPTPKYPHEVNGTPMYLYEVATESVC-ESAARLLFMSIKW 199

Query: 106 VRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDV-- 163
            + +  F TLS +DQL+LL+++W+ELF+L +AQW+IP D + L+    A   +  D+   
Sbjct: 200 AKSVPAFSTLSLQDQLMLLEDAWRELFVLGIAQWAIPVDANTLL----AVSGMNGDNTDS 255

Query: 164 ----RVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTP-------ETPGLVDAQPVE 212
               ++ +EI+ +QE++ARFRQL  D +E  C+K ++ F         E     +A  + 
Sbjct: 256 QKLNKIISEIQALQEVVARFRQLRLDATEFACLKCIVTFKAVPTHSGSELRSFRNAAAIA 315

Query: 213 MLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRL 272
            LQD+AQ  L  Y+  RY  QP RFG+LLL+LP+LR++  STIE +FFK+TIG++PI RL
Sbjct: 316 ALQDEAQLTLNSYIHTRYPTQPCRFGKLLLLLPALRSISPSTIEEVFFKKTIGNVPITRL 375

Query: 273 LGDMY 277
           L DMY
Sbjct: 376 LSDMY 380

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

Homo sapiens (taxid: 9606)

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

 Score =  173 bits (438), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 109/304 (35%), Positives = 161/304 (52%), Gaps = 37/304 (12%)

Query: 1   VQHERGPRKPKIHNA----HHQDSKLEPHNPHHSPDLLP-PNGISSVK--------IPPT 47
           VQHERGPR   I            ++     H S   LP P   ++V+        +   
Sbjct: 88  VQHERGPRTSTIRKQVALYFRGHKEVNGSTQHFSSTALPTPTFFTTVRQLEAHNLELAAI 147

Query: 48  VLYPPS----GLKSPPPPSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAV 103
              P      GL  P P    +P      H+    P  L    +   C E+ ARLLFM++
Sbjct: 148 STVPERQTLVGLAQPTP---KYP------HEVNGAPLYLYEFATESVC-ESAARLLFMSI 197

Query: 104 RWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCE--KARERLPPD 161
           +W + +  F TLS +DQL+LL+++W+ELF+L +AQW+IP D S L+            P 
Sbjct: 198 KWAKSVPAFSTLSLQDQLMLLEDAWRELFVLGIAQWAIPVDASTLLAVSGMNNENTESPK 257

Query: 162 DVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTP--------ETPGLVDAQPVEM 213
             ++ +EI+ +Q++++RFRQL  D +E  C+K ++ F          E     +A  +  
Sbjct: 258 LNKIISEIQALQDVVSRFRQLRLDATEFACLKCIVTFKAGVSTHSGSELRNFRNAAAISA 317

Query: 214 LQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLL 273
           LQD+AQ  L  Y+  RY  QP RFG+LLL+LP+LR++  STIE +FFK+TIG++PI R+L
Sbjct: 318 LQDEAQLTLNSYIHTRYPTQPCRFGKLLLLLPALRSINPSTIEEVFFKKTIGNVPITRVL 377

Query: 274 GDMY 277
            DMY
Sbjct: 378 SDMY 381

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

Xenopus laevis (taxid: 8355)

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

 Score =  170 bits (430), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 112/306 (36%), Positives = 165/306 (53%), Gaps = 42/306 (13%)

Query: 1   VQHERGPRKPKIHN-------AHHQDSKLEPHNPHHS-PDLLPPNGISSVKIPPTVLYPP 52
           VQHERGPR   I          H + +    H P  S P   PP   +  ++ P  L   
Sbjct: 99  VQHERGPRTSTIRKQVALYFRGHKEVNGSSTHFPGSSLPG--PPFFTTVTQLEPHNLEMS 156

Query: 53  SGLKSP--------PPPSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVR 104
           S   +P          P+  +P      H+    P  L  + +   C E+ ARLLFM+++
Sbjct: 157 SVATTPERQAIVGLAQPTPKYP------HEVSGTPMYLYEVATESVC-ESAARLLFMSIK 209

Query: 105 WVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDV- 163
           W + +  F TL   DQL+LL+++W+ELF+L +AQW+IP D + L+    A   L  +++ 
Sbjct: 210 WAKSVPAFSTLPLSDQLILLEDAWRELFVLGIAQWAIPVDSTTLL----AVSGLNSENME 265

Query: 164 --RVNN---EIKLIQEILARFRQLSPDGSECGCMKAVILF-------TPETPGLVDAQPV 211
             R+N    EI+ +QE++ RFRQ+  D +E  C+K ++ F       + E     +A  +
Sbjct: 266 AQRMNKIMAEIQALQEVVTRFRQMRLDATEFACLKCIVTFKAVPTQGSAELRAFRNASAI 325

Query: 212 EMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQR 271
             LQD+AQ  L  Y+  RY  QP RFG+LLL+LP+LR+V  STIE +FFK+ IG++PI R
Sbjct: 326 AALQDEAQLTLNSYIHTRYPTQPCRFGKLLLLLPALRSVSPSTIEEVFFKKNIGNVPITR 385

Query: 272 LLGDMY 277
           LL DMY
Sbjct: 386 LLSDMY 391

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

Oryzias latipes (taxid: 8090)

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

 Score =  163 bits (413), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 90/191 (47%), Positives = 127/191 (66%), Gaps = 10/191 (5%)

Query: 93  ETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN-- 150
           ET+ARLLFMAV+W + L  F +L  RDQ++LL+E+W ELFLL   QWS+P D   L+   
Sbjct: 222 ETSARLLFMAVKWAKNLPVFSSLPFRDQVILLEEAWSELFLLGAIQWSLPLDSCPLLAPP 281

Query: 151 ----CEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLV 206
                  A+ RL       + E +++QE ++RFR L+ D +E  CMKA++LF PET GL 
Sbjct: 282 EASAAGGAQGRL----TLASMETRVLQETISRFRALAVDPTEFACMKALVLFKPETRGLK 337

Query: 207 DAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGD 266
           D + VE LQDQ+Q +L  + +  +  QP RFG+LLL+LPSLR +    IE LFF++TIG+
Sbjct: 338 DPEHVEALQDQSQVMLSQHSKAHHPSQPVRFGKLLLLLPSLRFITAERIELLFFRKTIGN 397

Query: 267 IPIQRLLGDMY 277
            P+++LL DM+
Sbjct: 398 TPMEKLLCDMF 408

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

Homo sapiens (taxid: 9606)

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

 Score =  163 bits (413), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 113/302 (37%), Positives = 161/302 (53%), Gaps = 27/302 (8%)

Query: 1   VQHERGPRKPKIHNAHHQDSKLEPH-NPHHSPDLLPPNGISSVKIPPTVLYPPSGLKSPP 59
           VQ+ER PR          +S+ EP   P  +P  L   G SS    P       G ++  
Sbjct: 110 VQNERQPRSTAQVRMDSVESETEPRLQPLATPPALA--GPSSRGPTPVSAARALGPQALM 167

Query: 60  PPSHHHPSMFLATHQP----PPHPGLLQILMSA------------------EKCQETTAR 97
           PP HHH    L T +      P      I +++                  +   ET+AR
Sbjct: 168 PPGHHHFMASLITAETCTKLEPEDADENIDVTSNDPEFPSSPYSSSSPCALDSIHETSAR 227

Query: 98  LLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARER 157
           LLFMAV+W + L  F  L  RDQ++LL+E+W ELFLL   QWS+P D   L+   +A   
Sbjct: 228 LLFMAVKWAKNLPVFSNLPFRDQVILLEEAWSELFLLGAIQWSLPLDNCPLLALPEASAG 287

Query: 158 LPPDD--VRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQ 215
                  V  + E +++QE ++RFR L+ D +E  CMKA++LF PET GL D + VE LQ
Sbjct: 288 GSSQGRLVLASAETRILQETISRFRALAVDPTEFACMKALVLFKPETRGLKDPEHVEALQ 347

Query: 216 DQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGD 275
           DQ+Q +L  + +  +  Q  RFG+LLL+LPSLR +    +E LFF++TIG+ P+++LL D
Sbjct: 348 DQSQVMLSQHSKAHHPSQLVRFGKLLLLLPSLRFISSERVELLFFRKTIGNTPMEKLLCD 407

Query: 276 MY 277
           M+
Sbjct: 408 MF 409

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

Bos taurus (taxid: 9913)

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

 Score =  154 bits (390), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 87/185 (47%), Positives = 123/185 (66%)

Query: 93  ETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCE 152
           ET+ARLLFMAV+W + L  F  L  RDQ++LL+E+W ELFLL   QWS+P D   L+   
Sbjct: 209 ETSARLLFMAVKWAKNLPVFSNLPFRDQVILLEEAWNELFLLGAIQWSLPLDSCPLLAPP 268

Query: 153 KARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVE 212
           +A           + E + +QE ++RFR L+ D +E  C+KA++LF PET GL D + VE
Sbjct: 269 EASGSSQGRLALASAETRFLQETISRFRALAVDPTEFACLKALVLFKPETRGLKDPEHVE 328

Query: 213 MLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRL 272
            LQDQ+Q +L  + +  +  QP RFG+LLL+LPSLR +    IE LFF++TIG+ P+++L
Sbjct: 329 ALQDQSQVMLSQHSKAHHPSQPVRFGKLLLLLPSLRFLTAERIELLFFRKTIGNTPMEKL 388

Query: 273 LGDMY 277
           L DM+
Sbjct: 389 LCDMF 393

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

Mus musculus (taxid: 10090)

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

 Score =  154 bits (388), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 84/204 (41%), Positives = 119/204 (58%), Gaps = 2/204 (0%)

Query: 85  LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD 144
           +M  E   E  ARLLF AV W R +  F  L   DQ+ LL+ +W ELF+L+ AQ S+P  
Sbjct: 214 IMGIENICELAARLLFSAVEWARNIPFFPDLQITDQVSLLRLTWSELFVLNAAQCSMPLH 273

Query: 145 LSLLINCEKARERLPPDD--VRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPET 202
           ++ L+            D  V   + I++ QE + + + L  D +E  C+KA++LFT + 
Sbjct: 274 VAPLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDA 333

Query: 203 PGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKE 262
            GL DA  +E LQ+++QC L +YVR +Y  QP+RFG+LLL LPSLR V  S IE+LFF  
Sbjct: 334 CGLSDAAHIESLQEKSQCALEEYVRSQYPNQPSRFGKLLLRLPSLRTVSSSVIEQLFFVR 393

Query: 263 TIGDIPIQRLLGDMYTMEKSYETP 286
            +G  PI+ L+ DM     S+  P
Sbjct: 394 LVGKTPIETLIRDMLLSGSSFNWP 417

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

Bos taurus (taxid: 9913)

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

 Score =  154 bits (388), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 84/204 (41%), Positives = 119/204 (58%), Gaps = 2/204 (0%)

Query: 85  LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD 144
           +M  E   E  ARLLF AV W R +  F  L   DQ+ LL+ +W ELF+L+ AQ S+P  
Sbjct: 213 IMGIENICELAARLLFSAVEWARNIPFFPDLQITDQVSLLRLTWSELFVLNAAQCSMPLH 272

Query: 145 LSLLINCEKARERLPPDD--VRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPET 202
           ++ L+            D  V   + I++ QE + + + L  D +E  C+KA++LFT + 
Sbjct: 273 VAPLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDA 332

Query: 203 PGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKE 262
            GL DA  +E LQ+++QC L +YVR +Y  QP+RFG+LLL LPSLR V  S IE+LFF  
Sbjct: 333 CGLSDAAHIESLQEKSQCALEEYVRSQYPNQPSRFGKLLLRLPSLRTVSSSVIEQLFFVR 392

Query: 263 TIGDIPIQRLLGDMYTMEKSYETP 286
            +G  PI+ L+ DM     S+  P
Sbjct: 393 LVGKTPIETLIRDMLLSGSSFNWP 416

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

Homo sapiens (taxid: 9606)

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	367
328696467	459	PREDICTED: nuclear receptor subfamily 2	0.531	0.424	0.923	1e-100
242024443	438	Orphan nuclear receptor NR6A1, putative	0.722	0.605	0.553	3e-90
91077386	483	PREDICTED: similar to Dissatisfaction (D	0.528	0.401	0.8	6e-86
332025033	443	Photoreceptor-specific nuclear receptor	0.765	0.634	0.472	1e-72
307203729	547	Photoreceptor-specific nuclear receptor	0.749	0.502	0.479	6e-72
225581113	690	GA21482 [Drosophila miranda]	0.558	0.297	0.701	1e-71
198475944	691	GA21482 [Drosophila pseudoobscura pseudo	0.558	0.296	0.701	1e-71
194856940	693	GG25103 [Drosophila erecta] gi|190660727	0.531	0.281	0.714	1e-71
195146576	819	GL19043 [Drosophila persimilis] gi|19410	0.558	0.250	0.701	2e-71
17137164	691	dissatisfaction, isoform A [Drosophila m	0.531	0.282	0.714	2e-71

>gi|328696467|ref|XP_003240033.1| PREDICTED: nuclear receptor subfamily 2 group E member 1-like [Acyrthosiphon pisum]

 Score =  370 bits (951), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 180/195 (92%), Positives = 187/195 (95%)

Query: 89  EKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLL 148
           E  QETTARLLFMAVRWVRCLAPFQTLSK DQLLLLQESWKELFLLHLAQWSIPWDLS L
Sbjct: 264 EVLQETTARLLFMAVRWVRCLAPFQTLSKHDQLLLLQESWKELFLLHLAQWSIPWDLSPL 323

Query: 149 INCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDA 208
           +N EKARERLP DD +VNNE+K+IQEILARFRQLSPDGSECGCMKAVILFTPETPGL+DA
Sbjct: 324 LNSEKARERLPADDTKVNNEMKIIQEILARFRQLSPDGSECGCMKAVILFTPETPGLIDA 383

Query: 209 QPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIP 268
           QPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLP+LRAVRQ+TIERLFFKETIGDIP
Sbjct: 384 QPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPNLRAVRQATIERLFFKETIGDIP 443

Query: 269 IQRLLGDMYTMEKSY 283
           IQRLLGDMY MEKSY
Sbjct: 444 IQRLLGDMYHMEKSY 458

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242024443|ref|XP_002432637.1| Orphan nuclear receptor NR6A1, putative [Pediculus humanus corporis] gi|212518107|gb|EEB19899.1| Orphan nuclear receptor NR6A1, putative [Pediculus humanus corporis]

 Score =  338 bits (866), Expect = 3e-90,   Method: Compositional matrix adjust.
 Identities = 203/367 (55%), Positives = 228/367 (62%), Gaps = 102/367 (27%)

Query: 1   VQHERGPRKPKIHN-------------------AHHQDSKL------------------- 22
           VQHERGPRKPK HN                    HH +  L                   
Sbjct: 87  VQHERGPRKPK-HNITSKENNHHHHHHHHHPVLMHHSNPPLSNSAEQPSAKQPPPPPPPP 145

Query: 23  -----EPHNPH---------HSPDLLPPNGISSVKIPPTVLYPPSGLKSPPPPSHHHPSM 68
                +P NPH          S +L+P    +S    P +   PSG     PPS    +M
Sbjct: 146 GIVFPQPINPHMHYLQSPIKTSQELIP----ASENFVPNITPIPSG-----PPSA--AAM 194

Query: 69  FLATHQPPPHPGLLQILMSAEKCQE----------------------------------- 93
           FLA HQPPP PGLLQILM+AEKCQE                                   
Sbjct: 195 FLA-HQPPP-PGLLQILMTAEKCQELLWNTKLSTTERVGVPQSSPLALQPLSPSWEVLQE 252

Query: 94  TTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEK 153
           TTARLLF AVRWVR L PFQTLS+ DQLLLLQESWKELFLL+LAQWSIPWDL+ L+N  K
Sbjct: 253 TTARLLFTAVRWVRSLGPFQTLSRHDQLLLLQESWKELFLLYLAQWSIPWDLTTLLNSSK 312

Query: 154 ARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEM 213
           AR+RLP D++  N EIK IQE++ RFRQLSPD SECGCMKAVILFTPET GL D QPVEM
Sbjct: 313 ARDRLPQDEITAN-EIKTIQELIGRFRQLSPDLSECGCMKAVILFTPETAGLCDVQPVEM 371

Query: 214 LQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLL 273
           LQDQAQCILGDY+R RY RQPTRFGRLLL+LP+LR++RQ T+E+LFFKETIG+IPIQRLL
Sbjct: 372 LQDQAQCILGDYIRNRYPRQPTRFGRLLLILPNLRSIRQLTVEQLFFKETIGEIPIQRLL 431

Query: 274 GDMYTME 280
           GDMY ME
Sbjct: 432 GDMYHME 438

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91077386|ref|XP_975255.1| PREDICTED: similar to Dissatisfaction (Dsf) [Tribolium castaneum] gi|270002823|gb|EEZ99270.1| dissatisfaction [Tribolium castaneum]

 Score =  323 bits (829), Expect = 6e-86,   Method: Compositional matrix adjust.
 Identities = 156/195 (80%), Positives = 169/195 (86%), Gaps = 1/195 (0%)

Query: 92  QETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINC 151
           QETTARLLFMAVRWVRCLAPFQTLSK DQLLLLQESWKELFLLHLAQWS+PWDLS L+ C
Sbjct: 289 QETTARLLFMAVRWVRCLAPFQTLSKHDQLLLLQESWKELFLLHLAQWSVPWDLSALLGC 348

Query: 152 EKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPV 211
            +ARERLP D +    EIK IQEI+ RFRQ+SPDGSECGCMKA+ILFTPET GL D QPV
Sbjct: 349 PQARERLPAD-IHTATEIKTIQEIMCRFRQISPDGSECGCMKAIILFTPETAGLCDVQPV 407

Query: 212 EMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQR 271
           EMLQDQAQCILGDYVR RY RQPTRFGRLLL++PSLRA+R  T+E LFFKETIG+IPI +
Sbjct: 408 EMLQDQAQCILGDYVRTRYPRQPTRFGRLLLLVPSLRAIRSLTVELLFFKETIGEIPITQ 467

Query: 272 LLGDMYTMEKSYETP 286
           LLGDMY MEK    P
Sbjct: 468 LLGDMYYMEKCTSGP 482

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332025033|gb|EGI65220.1| Photoreceptor-specific nuclear receptor [Acromyrmex echinatior]

 Score =  280 bits (715), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 169/358 (47%), Positives = 197/358 (55%), Gaps = 77/358 (21%)

Query: 1   VQHERGPRKPKIH------NAHHQDSKLEPHNPHHSPDLLPPNGISSVKIPPTVLYPPSG 54
           VQHERGPRKPK H        H Q S +      HS   +  + +     PP VL P   
Sbjct: 83  VQHERGPRKPKPHAIISSEKQHQQQSPIVTQLSPHSATSVHSDRLRPALAPPYVLSPHRR 142

Query: 55  LK-----SPPPPSHH------------------HPSMFLATHQPP------PHPGLLQIL 85
           L+     +P P                      HP      +Q        P P LLQIL
Sbjct: 143 LRCDQRFTPYPRPMALVQKPPEESPSPVPLILPHPRTTTTLYQAATTVSLAPQPPLLQIL 202

Query: 86  MSAEKCQE------------------------------------------TTARLLFMAV 103
           MSAE+CQE                                          TTARLLFMAV
Sbjct: 203 MSAEECQELVWNARLQPTAEYPMEQIETETSRSPTGTVQSFSPTWEMLQETTARLLFMAV 262

Query: 104 RWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDV 163
           RWVRCL PFQT+SK DQLLLL+ SW +LFLLHLAQWS+ WD++ L+  E+ R RLP DD 
Sbjct: 263 RWVRCLPPFQTISKDDQLLLLERSWTQLFLLHLAQWSVSWDITALLEDEQVRSRLPTDDN 322

Query: 164 RVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILG 223
             N E+ LIQ I+ RFRQLSPD  ECGCMKAV LFTPET GL   QP+E+LQDQAQ IL 
Sbjct: 323 PTNQELVLIQAIICRFRQLSPDFGECGCMKAVALFTPETVGLHAVQPIEILQDQAQRILV 382

Query: 224 DYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEK 281
           DY R RY +QP+R GRL++++  LR V   T+ERLFF ETIG+IPI RLL DMY MEK
Sbjct: 383 DYTRSRYPQQPSRIGRLMILVGYLRCVSSKTVERLFFHETIGEIPISRLLVDMYQMEK 440

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307203729|gb|EFN82689.1| Photoreceptor-specific nuclear receptor [Harpegnathos saltator]

 Score =  277 bits (708), Expect = 6e-72,   Method: Compositional matrix adjust.
 Identities = 174/363 (47%), Positives = 200/363 (55%), Gaps = 88/363 (24%)

Query: 1   VQHERGPRKPKIHN-----AHHQDS----KLEPHN--PHHSPDLLPPNGISSVKIPPTVL 49
           VQHERGPRKPK H+      H Q S    +L PH+  P H+  L P         PP VL
Sbjct: 188 VQHERGPRKPKPHSIISEKQHQQQSSIVTQLSPHSGGPVHNDRLRP------ALAPPYVL 241

Query: 50  YPPSGLK-----SPPPPSHH------------------HPSMFLATHQPP------PHPG 80
            P   L+     +P P                      HP      +Q          P 
Sbjct: 242 SPHRRLRCDQRFTPYPRPMALVQKPPEESPSPVPLVLPHPRTTTTLYQAATTVSLASQPS 301

Query: 81  LLQILMSAEKCQE------------------------------------------TTARL 98
           LLQILMSAE+CQE                                          TTARL
Sbjct: 302 LLQILMSAEECQELVWNARLQPTTEYPIEQMETETSHSPTGTVQSLSPTWEMLQETTARL 361

Query: 99  LFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERL 158
           LFMAVRWVRCL PFQT+SK DQLLLL+ SW +LFLLHLAQWSI WD++ L+  E+ R RL
Sbjct: 362 LFMAVRWVRCLPPFQTISKDDQLLLLERSWTQLFLLHLAQWSISWDITALLEDEQVRSRL 421

Query: 159 PPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQA 218
           P DD   N E+ LIQ I+ RFRQLSPD  ECGCMKAV LFTPET GL   QP+E+LQDQA
Sbjct: 422 PADDNPTNQELVLIQAIICRFRQLSPDFGECGCMKAVALFTPETVGLHAVQPIEILQDQA 481

Query: 219 QCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT 278
           Q IL DY R RY +QP R GRL++++  LR V   T+ERLFF ETIG+IPI RLL DMY 
Sbjct: 482 QRILVDYTRSRYPQQPGRIGRLMILVGYLRCVSSKTVERLFFHETIGEIPISRLLVDMYQ 541

Query: 279 MEK 281
           MEK
Sbjct: 542 MEK 544

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|225581113|gb|ACN94685.1| GA21482 [Drosophila miranda]

 Score =  276 bits (707), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 146/208 (70%), Positives = 165/208 (79%), Gaps = 3/208 (1%)

Query: 75  PPPHPGLL--QILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELF 132
           PPP P  L    L+S E  QETTARLLFMAVRWV+CL PFQTLSK DQ LLLQESWKELF
Sbjct: 476 PPPLPQQLLDSRLLSWEMLQETTARLLFMAVRWVKCLMPFQTLSKNDQHLLLQESWKELF 535

Query: 133 LLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCM 192
           LL+LAQW+IP DL+ ++     +ER+  D+     E+K IQEIL RFRQ++PDGSE GCM
Sbjct: 536 LLNLAQWTIPLDLTPILESPLIKERVLQDEA-TQTEMKTIQEILCRFRQITPDGSEVGCM 594

Query: 193 KAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQ 252
           KA+ LF PET GL D QPVEMLQDQAQCIL D+VR RYSRQ TRFGRLLL+LPSLR +R 
Sbjct: 595 KAIALFAPETAGLCDVQPVEMLQDQAQCILSDHVRLRYSRQATRFGRLLLLLPSLRTIRA 654

Query: 253 STIERLFFKETIGDIPIQRLLGDMYTME 280
           STIE LFFKETIG++PI RLL DMYTME
Sbjct: 655 STIEALFFKETIGNVPIARLLRDMYTME 682

Source: Drosophila miranda

Species: Drosophila miranda

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|198475944|ref|XP_001357213.2| GA21482 [Drosophila pseudoobscura pseudoobscura] gi|198137475|gb|EAL34282.2| GA21482 [Drosophila pseudoobscura pseudoobscura]

 Score =  276 bits (706), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 146/208 (70%), Positives = 165/208 (79%), Gaps = 3/208 (1%)

Query: 75  PPPHPGLL--QILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELF 132
           PPP P  L    L+S E  QETTARLLFMAVRWV+CL PFQTLSK DQ LLLQESWKELF
Sbjct: 477 PPPLPQQLLDSRLLSWEMLQETTARLLFMAVRWVKCLMPFQTLSKNDQHLLLQESWKELF 536

Query: 133 LLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCM 192
           LL+LAQW+IP DL+ ++     +ER+  D+     E+K IQEIL RFRQ++PDGSE GCM
Sbjct: 537 LLNLAQWTIPLDLTPILESPLIKERVLQDEA-TQTEMKTIQEILCRFRQITPDGSEVGCM 595

Query: 193 KAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQ 252
           KA+ LF PET GL D QPVEMLQDQAQCIL D+VR RYSRQ TRFGRLLL+LPSLR +R 
Sbjct: 596 KAIALFAPETAGLCDVQPVEMLQDQAQCILSDHVRLRYSRQATRFGRLLLLLPSLRTIRA 655

Query: 253 STIERLFFKETIGDIPIQRLLGDMYTME 280
           STIE LFFKETIG++PI RLL DMYTME
Sbjct: 656 STIEALFFKETIGNVPIARLLRDMYTME 683

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194856940|ref|XP_001968860.1| GG25103 [Drosophila erecta] gi|190660727|gb|EDV57919.1| GG25103 [Drosophila erecta]

 Score =  276 bits (705), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 140/196 (71%), Positives = 159/196 (81%), Gaps = 1/196 (0%)

Query: 85  LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD 144
           L+S E  QETTARLLFMAVRWV+CL PFQTLSK DQ LLLQESWKELFLL+LAQW+IP D
Sbjct: 493 LLSWEMLQETTARLLFMAVRWVKCLMPFQTLSKNDQHLLLQESWKELFLLNLAQWTIPLD 552

Query: 145 LSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPG 204
           L+ ++     RER+  D+     E+K IQEIL RFRQ++PDGSE GCMKA+ LF PET G
Sbjct: 553 LTPILESPLIRERVLQDEA-TQTEMKTIQEILCRFRQITPDGSEVGCMKAIALFAPETAG 611

Query: 205 LVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETI 264
           L D QPVEMLQDQAQCIL D+VR RY RQ TRFGRLLL+LPSLR +R +TIE LFFKETI
Sbjct: 612 LCDVQPVEMLQDQAQCILSDHVRLRYPRQATRFGRLLLLLPSLRTIRAATIEALFFKETI 671

Query: 265 GDIPIQRLLGDMYTME 280
           G++PI RLL DMYTME
Sbjct: 672 GNVPIARLLRDMYTME 687

Source: Drosophila erecta

Species: Drosophila erecta

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195146576|ref|XP_002014260.1| GL19043 [Drosophila persimilis] gi|194106213|gb|EDW28256.1| GL19043 [Drosophila persimilis]

 Score =  276 bits (705), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 146/208 (70%), Positives = 165/208 (79%), Gaps = 3/208 (1%)

Query: 75  PPPHPGLL--QILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELF 132
           PPP P  L    L+S E  QETTARLLFMAVRWV+CL PFQTLSK DQ LLLQESWKELF
Sbjct: 605 PPPLPQQLLDSRLLSWEMLQETTARLLFMAVRWVKCLMPFQTLSKNDQHLLLQESWKELF 664

Query: 133 LLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCM 192
           LL+LAQW+IP DL+ ++     +ER+  D+     E+K IQEIL RFRQ++PDGSE GCM
Sbjct: 665 LLNLAQWTIPLDLTPILESPLIKERVLQDEA-TQTEMKTIQEILCRFRQITPDGSEVGCM 723

Query: 193 KAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQ 252
           KA+ LF PET GL D QPVEMLQDQAQCIL D+VR RYSRQ TRFGRLLL+LPSLR +R 
Sbjct: 724 KAIALFAPETAGLCDVQPVEMLQDQAQCILSDHVRLRYSRQATRFGRLLLLLPSLRTIRA 783

Query: 253 STIERLFFKETIGDIPIQRLLGDMYTME 280
           STIE LFFKETIG++PI RLL DMYTME
Sbjct: 784 STIEALFFKETIGNVPIARLLRDMYTME 811

Source: Drosophila persimilis

Species: Drosophila persimilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|17137164|ref|NP_477140.1| dissatisfaction, isoform A [Drosophila melanogaster] gi|442626233|ref|NP_001260109.1| dissatisfaction, isoform B [Drosophila melanogaster] gi|7297033|gb|AAF52303.1| dissatisfaction, isoform A [Drosophila melanogaster] gi|440213405|gb|AGB92645.1| dissatisfaction, isoform B [Drosophila melanogaster]

 Score =  275 bits (704), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 140/196 (71%), Positives = 159/196 (81%), Gaps = 1/196 (0%)

Query: 85  LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD 144
           L+S E  QETTARLLFMAVRWV+CL PFQTLSK DQ LLLQESWKELFLL+LAQW+IP D
Sbjct: 491 LLSWEMLQETTARLLFMAVRWVKCLMPFQTLSKNDQHLLLQESWKELFLLNLAQWTIPLD 550

Query: 145 LSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPG 204
           L+ ++     RER+  D+     E+K IQEIL RFRQ++PDGSE GCMKA+ LF PET G
Sbjct: 551 LTPILESPLIRERVLQDEA-TQTEMKTIQEILCRFRQITPDGSEVGCMKAIALFAPETAG 609

Query: 205 LVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETI 264
           L D QPVEMLQDQAQCIL D+VR RY RQ TRFGRLLL+LPSLR +R +TIE LFFKETI
Sbjct: 610 LCDVQPVEMLQDQAQCILSDHVRLRYPRQATRFGRLLLLLPSLRTIRAATIEALFFKETI 669

Query: 265 GDIPIQRLLGDMYTME 280
           G++PI RLL DMYTME
Sbjct: 670 GNVPIARLLRDMYTME 685

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	367
FB|FBgn0015381	693	dsf "dissatisfaction" [Drosoph	0.531	0.281	0.714	1.8e-76
UNIPROTKB|F1ML62	411	NR2E3 "Photoreceptor-specific	0.514	0.459	0.460	4.2e-47
UNIPROTKB|Q9TTF0	411	NR2E3 "Photoreceptor-specific	0.514	0.459	0.455	4.6e-46
MGI|MGI:1100526	385	Nr2e1 "nuclear receptor subfam	0.732	0.698	0.388	1.9e-44
UNIPROTKB|Q91379	385	NR2E1 "Nuclear receptor subfam	0.732	0.698	0.382	3.9e-44
UNIPROTKB|F1P0M4	405	NR2E3 "Uncharacterized protein	0.534	0.483	0.456	4.7e-44
UNIPROTKB|F1MN68	385	NR2E1 "Uncharacterized protein	0.738	0.703	0.391	5e-44
UNIPROTKB|F1PD89	385	NR2E1 "Uncharacterized protein	0.738	0.703	0.391	5e-44
UNIPROTKB|Q6ZMP8	422	NR2E1 "Nuclear receptor subfam	0.738	0.642	0.391	5e-44
UNIPROTKB|Q9Y466	385	NR2E1 "Nuclear receptor subfam	0.738	0.703	0.391	5e-44

FB|FBgn0015381 dsf "dissatisfaction" [Drosophila melanogaster (taxid:7227)]

 Score = 707 (253.9 bits), Expect = 1.8e-76, Sum P(2) = 1.8e-76
 Identities = 140/196 (71%), Positives = 159/196 (81%)

Query:    85 LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD 144
             L+S E  QETTARLLFMAVRWV+CL PFQTLSK DQ LLLQESWKELFLL+LAQW+IP D
Sbjct:   493 LLSWEMLQETTARLLFMAVRWVKCLMPFQTLSKNDQHLLLQESWKELFLLNLAQWTIPLD 552

Query:   145 LSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPG 204
             L+ ++     RER+  D+     E+K IQEIL RFRQ++PDGSE GCMKA+ LF PET G
Sbjct:   553 LTPILESPLIRERVLQDEA-TQTEMKTIQEILCRFRQITPDGSEVGCMKAIALFAPETAG 611

Query:   205 LVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETI 264
             L D QPVEMLQDQAQCIL D+VR RY RQ TRFGRLLL+LPSLR +R +TIE LFFKETI
Sbjct:   612 LCDVQPVEMLQDQAQCILSDHVRLRYPRQATRFGRLLLLLPSLRTIRAATIEALFFKETI 671

Query:   265 GDIPIQRLLGDMYTME 280
             G++PI RLL DMYTME
Sbjct:   672 GNVPIARLLRDMYTME 687

GO:0005634 "nucleus" evidence=IEA;ISS

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

GO:0018993 "somatic sex determination" evidence=NAS

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

GO:0007530 "sex determination" evidence=TAS

GO:0007619 "courtship behavior" evidence=NAS;TAS

GO:0007617 "mating behavior" evidence=NAS

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

GO:0007620 "copulation" evidence=NAS

GO:0018991 "oviposition" evidence=NAS;TAS

GO:0045924 "regulation of female receptivity" evidence=NAS

GO:0008049 "male courtship behavior" evidence=TAS

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

GO:0048047 "mating behavior, sex discrimination" evidence=TAS

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

GO:0035206 "regulation of hemocyte proliferation" evidence=IMP

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

 Score = 435 (158.2 bits), Expect = 4.2e-47, Sum P(3) = 4.2e-47
 Identities = 88/191 (46%), Positives = 126/191 (65%)

Query:    89 EKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLL 148
             +   ET+ARLLFMAV+W + L  F  L  RDQ++LL+E+W ELFLL   QWS+P D   L
Sbjct:   219 DSIHETSARLLFMAVKWAKNLPVFSNLPFRDQVILLEEAWSELFLLGAIQWSLPLDNCPL 278

Query:   149 INCEKARERLPPDD--VRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLV 206
             +   +A          V  + E +++QE ++RFR L+ D +E  CMKA++LF PET GL 
Sbjct:   279 LALPEASAGGSSQGRLVLASAETRILQETISRFRALAVDPTEFACMKALVLFKPETRGLK 338

Query:   207 DAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGD 266
             D + VE LQDQ+Q +L  + +  +  QP RFG+LLL+LPSLR +    +E LFF++TIG+
Sbjct:   339 DPEHVEALQDQSQVMLSQHSKAHHPSQPVRFGKLLLLLPSLRFISSERVELLFFRKTIGN 398

Query:   267 IPIQRLLGDMY 277
              P+++LL DM+
Sbjct:   399 TPMEKLLCDMF 409

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

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

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

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

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

GO:0005667 "transcription factor complex" evidence=IEA

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

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

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

 Score = 425 (154.7 bits), Expect = 4.6e-46, Sum P(3) = 4.6e-46
 Identities = 87/191 (45%), Positives = 125/191 (65%)

Query:    89 EKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLL 148
             +   ET+ARLLFMAV+W + L  F  L  RDQ++LL+E+W ELFLL   QWS+P D   L
Sbjct:   219 DSIHETSARLLFMAVKWAKNLPVFSNLPFRDQVILLEEAWSELFLLGAIQWSLPLDNCPL 278

Query:   149 INCEKARERLPPDD--VRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLV 206
             +   +A          V  + E +++QE ++RFR L+ D +E  CMKA++LF PET GL 
Sbjct:   279 LALPEASAGGSSQGRLVLASAETRILQETISRFRALAVDPTEFACMKALVLFKPETRGLK 338

Query:   207 DAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGD 266
             D + VE LQDQ+Q +L  + +  +  Q  RFG+LLL+LPSLR +    +E LFF++TIG+
Sbjct:   339 DPEHVEALQDQSQVMLSQHSKAHHPSQLVRFGKLLLLLPSLRFISSERVELLFFRKTIGN 398

Query:   267 IPIQRLLGDMY 277
              P+++LL DM+
Sbjct:   399 TPMEKLLCDMF 409

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

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

 Score = 468 (169.8 bits), Expect = 1.9e-44, P = 1.9e-44
 Identities = 117/301 (38%), Positives = 168/301 (55%)

Query:     1 VQHERGPRKPKIHN-------AHHQDSKLEPHNPHHSPDLLPPNGISSVKIPPTVLYPPS 53
             VQHERGPR   I          H +D+    H P  S  L  P   ++V    T L  P 
Sbjct:    88 VQHERGPRTSTIRKQVALYFRGHKEDNGAAAHFP--STALPAPAFFTAV----TQL-EPH 140

Query:    54 GLKXXXXXXXXXXXMFLATHQPPP-HP----GLLQIL--MSAEKCQETTARLLFMAVRWV 106
             GL+             ++  QP P +P    G    L  ++ E   E+ ARLLFM+++W 
Sbjct:   141 GLELAAVSATPERQTLVSLAQPTPKYPHEVNGTPMYLYEVATESVCESAARLLFMSIKWA 200

Query:   107 RCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVN 166
             + +  F TLS +DQL+LL+++W+ELF+L +AQW+IP D + L+           D  ++N
Sbjct:   201 KSVPAFSTLSLQDQLMLLEDAWRELFVLGIAQWAIPVDANTLL-AVSGMNTDNTDSQKLN 259

Query:   167 ---NEIKLIQEILARFRQLSPDGSECGCMKAVILF--TPETPG-----LVDAQPVEMLQD 216
                +EI+ +QE++ARFRQL  D +E  C+K ++ F   P   G       +A  +  LQD
Sbjct:   260 KIISEIQALQEVVARFRQLRLDATEFACLKCIVTFKAVPTHSGSELRSFRNAAAIAALQD 319

Query:   217 QAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDM 276
             +AQ  L  Y+  RY  QP RFG+LLL+LP+LR++  STIE +FFK+TIG++PI RLL DM
Sbjct:   320 EAQLTLNSYIHTRYPTQPCRFGKLLLLLPALRSISPSTIEEVFFKKTIGNVPITRLLSDM 379

Query:   277 Y 277
             Y
Sbjct:   380 Y 380

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

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

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

GO:0001662 "behavioral fear response" evidence=IMP

GO:0002118 "aggressive behavior" evidence=IMP

GO:0003677 "DNA binding" evidence=IDA

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0007420 "brain development" evidence=IMP

GO:0007601 "visual perception" evidence=IMP

GO:0007610 "behavior" evidence=IMP

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0008347 "glial cell migration" evidence=IMP

GO:0019899 "enzyme binding" evidence=IPI

GO:0021542 "dentate gyrus development" evidence=IMP

GO:0021764 "amygdala development" evidence=IMP

GO:0021772 "olfactory bulb development" evidence=IMP

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

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

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

GO:0021960 "anterior commissure morphogenesis" evidence=IMP

GO:0021987 "cerebral cortex development" evidence=IMP

GO:0030198 "extracellular matrix organization" evidence=IMP

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

GO:0035176 "social behavior" evidence=IMP

GO:0042826 "histone deacetylase binding" evidence=IPI

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

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

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

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

GO:0045165 "cell fate commitment" evidence=IGI

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

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

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

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

GO:0046872 "metal ion binding" evidence=IEA

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

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

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

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

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

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

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

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

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

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

UNIPROTKB|Q91379 NR2E1 "Nuclear receptor subfamily 2 group E member 1" [Gallus gallus (taxid:9031)]

 Score = 465 (168.7 bits), Expect = 3.9e-44, P = 3.9e-44
 Identities = 115/301 (38%), Positives = 166/301 (55%)

Query:     1 VQHERGPRKPKIHN-------AHHQDSKLEPHNPHHSPDLLPPNGISSVKIPPTVLYPPS 53
             VQHERGPR   I          H ++S   PH P  +  L  P   ++V         P 
Sbjct:    88 VQHERGPRTSTIRKQVALYFRGHKEESSGAPHFP--ATALPAPAFFTAVS-----QLEPH 140

Query:    54 GLKXXXXXXXXXXXMFLATHQPPP-HP----GLLQIL--MSAEKCQETTARLLFMAVRWV 106
             GL+             +   QP P +P    G    L  ++ E   E+ ARLLFM+++W 
Sbjct:   141 GLELAAVAGTPERQALVGLAQPTPKYPHEVNGTPMYLYEVATESVCESAARLLFMSIKWA 200

Query:   107 RCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVN 166
             + +  F TLS +DQL+LL+++W+ELF+L +AQW+IP D + L+           D  ++N
Sbjct:   201 KSVPAFSTLSLQDQLMLLEDAWRELFVLGIAQWAIPVDANTLL-AVSGMNGDNTDSQKLN 259

Query:   167 ---NEIKLIQEILARFRQLSPDGSECGCMKAVILF--TPETPG-----LVDAQPVEMLQD 216
                +EI+ +QE++ARFRQL  D +E  C+K ++ F   P   G       +A  +  LQD
Sbjct:   260 KIISEIQALQEVVARFRQLRLDATEFACLKCIVTFKAVPTHSGSELRSFRNAAAIAALQD 319

Query:   217 QAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDM 276
             +AQ  L  Y+  RY  QP RFG+LLL+LP+LR++  STIE +FFK+TIG++PI RLL DM
Sbjct:   320 EAQLTLNSYIHTRYPTQPCRFGKLLLLLPALRSISPSTIEEVFFKKTIGNVPITRLLSDM 379

Query:   277 Y 277
             Y
Sbjct:   380 Y 380

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

 Score = 432 (157.1 bits), Expect = 4.7e-44, Sum P(2) = 4.7e-44
 Identities = 94/206 (45%), Positives = 130/206 (63%)

Query:    73 HQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELF 132
             +Q  P+P         E   ET+  LLFMAV+W + L  F  L  RDQ++LL+E+W ELF
Sbjct:   207 YQVAPYPAA-----GPENVYETSPLLLFMAVKWAKNLPVFSNLPFRDQVILLEEAWSELF 261

Query:   133 LLHLAQWSIPWD-LSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGC 191
             LL   QWS+P +   LL   E +  +L P  V    +++ +QE L RF+ L+ D +E  C
Sbjct:   262 LLCAIQWSMPLESCPLLAVPEPSPGKLLPAAV----DVRALQETLGRFKALAVDPTEFAC 317

Query:   192 MKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVR 251
             MKAV+LF PET GL D + VE LQDQ+Q +LG + R  Y  QP RFG+LLL+LP+LR + 
Sbjct:   318 MKAVVLFKPETRGLKDPEQVENLQDQSQVMLGQHNRSHYPGQPVRFGKLLLLLPALRFLS 377

Query:   252 QSTIERLFFKETIGDIPIQRLLGDMY 277
                +E LFF+ TIG+ P+++LL DM+
Sbjct:   378 SERVELLFFRRTIGNTPMEKLLCDMF 403

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

GO:0005667 "transcription factor complex" evidence=IEA

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

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

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

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

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

UNIPROTKB|F1MN68 NR2E1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 464 (168.4 bits), Expect = 5.0e-44, P = 5.0e-44
 Identities = 117/299 (39%), Positives = 168/299 (56%)

Query:     1 VQHERGPRKPKIHNA---HHQDSKLEPHNPHHSPDL-LP-PNGISSVKIPPTVLYPPSGL 55
             VQHERGPR   I      + +  K E     H P   LP P   ++V    T L  P GL
Sbjct:    88 VQHERGPRTSTIRKQVALYFRGHKEENGAAAHFPSAALPAPAFFTAV----TQL-DPHGL 142

Query:    56 KXXXXXXXXXXXMFLATHQPPP-HP----GLLQIL--MSAEKCQETTARLLFMAVRWVRC 108
             +             ++  QP P +P    G    L  ++ E   E+ ARLLFM+++W + 
Sbjct:   143 ELAAVSATPERQTLVSLAQPTPKYPHEVNGTPMYLYEVATESVCESAARLLFMSIKWAKS 202

Query:   109 LAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVN-- 166
             +  F TLS +DQL+LL+++W+ELF+L +AQW+IP D + L+           D  ++N  
Sbjct:   203 VPAFSTLSLQDQLMLLEDAWRELFVLGIAQWAIPVDANTLL-AVSGMNGDNTDSQKLNKI 261

Query:   167 -NEIKLIQEILARFRQLSPDGSECGCMKAVILF--TPETPG-----LVDAQPVEMLQDQA 218
              +EI+ +QE++ARFRQL  D +E  C+K ++ F   P   G       +A  +  LQD+A
Sbjct:   262 ISEIQALQEVVARFRQLRLDATEFACLKCIVTFKAVPTHSGSELRSFRNAAAIAALQDEA 321

Query:   219 QCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMY 277
             Q  L  Y+  RY  QP RFG+LLL+LP+LR++  STIE +FFK+TIG++PI RLL DMY
Sbjct:   322 QLTLNSYIHTRYPTQPCRFGKLLLLLPALRSISPSTIEEVFFKKTIGNVPITRLLSDMY 380

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

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

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

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

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

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

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

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

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

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

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

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

GO:0045165 "cell fate commitment" evidence=IEA

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

GO:0042826 "histone deacetylase binding" evidence=IEA

GO:0035176 "social behavior" evidence=IEA

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

GO:0030198 "extracellular matrix organization" evidence=IEA

GO:0021960 "anterior commissure morphogenesis" evidence=IEA

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

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

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

GO:0021772 "olfactory bulb development" evidence=IEA

GO:0021764 "amygdala development" evidence=IEA

GO:0021542 "dentate gyrus development" evidence=IEA

GO:0008347 "glial cell migration" evidence=IEA

GO:0007601 "visual perception" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0002118 "aggressive behavior" evidence=IEA

GO:0001662 "behavioral fear response" evidence=IEA

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

GO:0001077 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" 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|F1PD89 NR2E1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 464 (168.4 bits), Expect = 5.0e-44, P = 5.0e-44
 Identities = 117/299 (39%), Positives = 168/299 (56%)

Query:     1 VQHERGPRKPKIHNA---HHQDSKLEPHNPHHSPDL-LP-PNGISSVKIPPTVLYPPSGL 55
             VQHERGPR   I      + +  K E     H P   LP P   ++V    T L  P GL
Sbjct:    88 VQHERGPRTSTIRKQVALYFRGHKEENGAAAHFPSAALPAPAFFTAV----TQL-EPHGL 142

Query:    56 KXXXXXXXXXXXMFLATHQPPP-HP----GLLQIL--MSAEKCQETTARLLFMAVRWVRC 108
             +             ++  QP P +P    G    L  ++ E   E+ ARLLFM+++W + 
Sbjct:   143 ELAAVSATPERQTLVSLAQPTPKYPHEVNGTPMYLYEVATESVCESAARLLFMSIKWAKS 202

Query:   109 LAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVN-- 166
             +  F TLS +DQL+LL+++W+ELF+L +AQW+IP D + L+           D  ++N  
Sbjct:   203 VPAFSTLSLQDQLMLLEDAWRELFVLGIAQWAIPVDANTLL-AVSGMNGDNTDSQKLNKI 261

Query:   167 -NEIKLIQEILARFRQLSPDGSECGCMKAVILF--TPETPG-----LVDAQPVEMLQDQA 218
              +EI+ +QE++ARFRQL  D +E  C+K ++ F   P   G       +A  +  LQD+A
Sbjct:   262 ISEIQALQEVVARFRQLRLDATEFACLKCIVTFKAVPTHSGSELRSFRNAAAIAALQDEA 321

Query:   219 QCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMY 277
             Q  L  Y+  RY  QP RFG+LLL+LP+LR++  STIE +FFK+TIG++PI RLL DMY
Sbjct:   322 QLTLNSYIHTRYPTQPCRFGKLLLLLPALRSISPSTIEEVFFKKTIGNVPITRLLSDMY 380

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

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

UNIPROTKB|Q6ZMP8 NR2E1 "Nuclear receptor subfamily 2, group E, member 1, isoform CRA_b" [Homo sapiens (taxid:9606)]

 Score = 464 (168.4 bits), Expect = 5.0e-44, P = 5.0e-44
 Identities = 117/299 (39%), Positives = 168/299 (56%)

Query:     1 VQHERGPRKPKIHNA---HHQDSKLEPHNPHHSPDL-LP-PNGISSVKIPPTVLYPPSGL 55
             VQHERGPR   I      + +  K E     H P   LP P   ++V    T L  P GL
Sbjct:   125 VQHERGPRTSTIRKQVALYFRGHKEENGAAAHFPSAALPAPAFFTAV----TQL-EPHGL 179

Query:    56 KXXXXXXXXXXXMFLATHQPPP-HP----GLLQIL--MSAEKCQETTARLLFMAVRWVRC 108
             +             ++  QP P +P    G    L  ++ E   E+ ARLLFM+++W + 
Sbjct:   180 ELAAVSTTPERQTLVSLAQPTPKYPHEVNGTPMYLYEVATESVCESAARLLFMSIKWAKS 239

Query:   109 LAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVN-- 166
             +  F TLS +DQL+LL+++W+ELF+L +AQW+IP D + L+           D  ++N  
Sbjct:   240 VPAFSTLSLQDQLMLLEDAWRELFVLGIAQWAIPVDANTLL-AVSGMNGDNTDSQKLNKI 298

Query:   167 -NEIKLIQEILARFRQLSPDGSECGCMKAVILF--TPETPG-----LVDAQPVEMLQDQA 218
              +EI+ +QE++ARFRQL  D +E  C+K ++ F   P   G       +A  +  LQD+A
Sbjct:   299 ISEIQALQEVVARFRQLRLDATEFACLKCIVTFKAVPTHSGSELRSFRNAAAIAALQDEA 358

Query:   219 QCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMY 277
             Q  L  Y+  RY  QP RFG+LLL+LP+LR++  STIE +FFK+TIG++PI RLL DMY
Sbjct:   359 QLTLNSYIHTRYPTQPCRFGKLLLLLPALRSISPSTIEEVFFKKTIGNVPITRLLSDMY 417

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

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

UNIPROTKB|Q9Y466 NR2E1 "Nuclear receptor subfamily 2 group E member 1" [Homo sapiens (taxid:9606)]

 Score = 464 (168.4 bits), Expect = 5.0e-44, P = 5.0e-44
 Identities = 117/299 (39%), Positives = 168/299 (56%)

Query:     1 VQHERGPRKPKIHNA---HHQDSKLEPHNPHHSPDL-LP-PNGISSVKIPPTVLYPPSGL 55
             VQHERGPR   I      + +  K E     H P   LP P   ++V    T L  P GL
Sbjct:    88 VQHERGPRTSTIRKQVALYFRGHKEENGAAAHFPSAALPAPAFFTAV----TQL-EPHGL 142

Query:    56 KXXXXXXXXXXXMFLATHQPPP-HP----GLLQIL--MSAEKCQETTARLLFMAVRWVRC 108
             +             ++  QP P +P    G    L  ++ E   E+ ARLLFM+++W + 
Sbjct:   143 ELAAVSTTPERQTLVSLAQPTPKYPHEVNGTPMYLYEVATESVCESAARLLFMSIKWAKS 202

Query:   109 LAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVN-- 166
             +  F TLS +DQL+LL+++W+ELF+L +AQW+IP D + L+           D  ++N  
Sbjct:   203 VPAFSTLSLQDQLMLLEDAWRELFVLGIAQWAIPVDANTLL-AVSGMNGDNTDSQKLNKI 261

Query:   167 -NEIKLIQEILARFRQLSPDGSECGCMKAVILF--TPETPG-----LVDAQPVEMLQDQA 218
              +EI+ +QE++ARFRQL  D +E  C+K ++ F   P   G       +A  +  LQD+A
Sbjct:   262 ISEIQALQEVVARFRQLRLDATEFACLKCIVTFKAVPTHSGSELRSFRNAAAIAALQDEA 321

Query:   219 QCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMY 277
             Q  L  Y+  RY  QP RFG+LLL+LP+LR++  STIE +FFK+TIG++PI RLL DMY
Sbjct:   322 QLTLNSYIHTRYPTQPCRFGKLLLLLPALRSISPSTIEEVFFKKTIGNVPITRLLSDMY 380

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

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

GO:0001662 "behavioral fear response" evidence=IEA

GO:0002118 "aggressive behavior" evidence=IEA

GO:0007601 "visual perception" evidence=IEA

GO:0008347 "glial cell migration" evidence=IEA

GO:0021542 "dentate gyrus development" evidence=IEA

GO:0021764 "amygdala development" evidence=IEA

GO:0021772 "olfactory bulb development" evidence=IEA

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

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

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

GO:0021960 "anterior commissure morphogenesis" evidence=IEA

GO:0030198 "extracellular matrix organization" evidence=IEA

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

GO:0035176 "social behavior" evidence=IEA

GO:0042826 "histone deacetylase binding" evidence=IEA

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

GO:0045165 "cell fate commitment" evidence=IEA

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

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

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

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

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

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

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

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

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

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

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

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

GO:0007399 "nervous system development" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

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

GO:0010467 "gene expression" evidence=TAS

---

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)
Q91379	NR2E1_CHICK	No assigned EC number	0.3713	0.7166	0.6831	yes	N/A
Q64104	NR2E1_MOUSE	No assigned EC number	0.3704	0.7220	0.6883	yes	N/A
Q9Y466	NR2E1_HUMAN	No assigned EC number	0.3672	0.7220	0.6883	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	367
cd06950	206	cd06950, NR_LBD_Tlx_PNR_like, The ligand binding d	3e-84
cd06948	236	cd06948, NR_LBD_COUP-TF, Ligand binding domain of	3e-53
cd06930	165	cd06930, NR_LBD_F2, Ligand-binding domain of nucle	2e-43
cd06952	222	cd06952, NR_LBD_TR2_like, The ligand binding domai	6e-32
cd06157	168	cd06157, NR_LBD, The ligand binding domain of nucl	5e-29
cd06950	206	cd06950, NR_LBD_Tlx_PNR_like, The ligand binding d	3e-28
cd06931	222	cd06931, NR_LBD_HNF4_like, The ligand binding doma	2e-26
cd06943	207	cd06943, NR_LBD_RXR_like, The ligand binding domai	3e-26
cd06951	222	cd06951, NR_LBD_Dax1_like, The ligand binding doma	3e-26
smart00430	163	smart00430, HOLI, Ligand binding domain of hormone	1e-25
cd07069	241	cd07069, NR_LBD_Lrh-1, The ligand binding domain o	6e-24
cd06948	236	cd06948, NR_LBD_COUP-TF, Ligand binding domain of	2e-23
cd07349	222	cd07349, NR_LBD_SHP, The ligand binding domain of	1e-22
cd06944	237	cd06944, NR_LBD_Ftz-F1_like, The ligand binding do	2e-22
pfam00104	186	pfam00104, Hormone_recep, Ligand-binding domain of	2e-21
cd06945	239	cd06945, NR_LBD_Nurr1_like, The ligand binding dom	6e-16
cd06953	213	cd06953, NR_LBD_DHR4_like, The ligand binding doma	3e-15
cd06946	221	cd06946, NR_LBD_ERR, The ligand binding domain of	3e-14
cd07350	232	cd07350, NR_LBD_Dax1, The ligand binding domain of	8e-14
cd07068	221	cd07068, NR_LBD_ER_like, The ligand binding domain	4e-13
cd06930	165	cd06930, NR_LBD_F2, Ligand-binding domain of nucle	2e-11
cd06931	222	cd06931, NR_LBD_HNF4_like, The ligand binding doma	1e-10
cd07069	241	cd07069, NR_LBD_Lrh-1, The ligand binding domain o	1e-09
cd06943	207	cd06943, NR_LBD_RXR_like, The ligand binding domai	4e-09
cd07070	237	cd07070, NR_LBD_SF-1, The ligand binding domain of	4e-09
cd06929	174	cd06929, NR_LBD_F1, Ligand-binding domain of nucle	5e-09
cd06941	195	cd06941, NR_LBD_DmE78_like, The ligand binding dom	6e-09
cd06952	222	cd06952, NR_LBD_TR2_like, The ligand binding domai	8e-09
cd06951	222	cd06951, NR_LBD_Dax1_like, The ligand binding doma	1e-08
cd06944	237	cd06944, NR_LBD_Ftz-F1_like, The ligand binding do	1e-08
cd07072	239	cd07072, NR_LBD_DHR38_like, Ligand binding domain	5e-08
cd06945	239	cd06945, NR_LBD_Nurr1_like, The ligand binding dom	7e-08
cd07348	238	cd07348, NR_LBD_NGFI-B, The ligand binding domain	8e-08
cd07349	222	cd07349, NR_LBD_SHP, The ligand binding domain of	1e-07
cd07071	238	cd07071, NR_LBD_Nurr1, The ligand binding domain o	4e-07
cd06937	231	cd06937, NR_LBD_RAR, The ligand binding domain (LB	1e-06
cd06954	236	cd06954, NR_LBD_LXR, The ligand binding domain of	3e-06
cd06949	235	cd06949, NR_LBD_ER, Ligand binding domain of Estro	3e-06
cd06157	168	cd06157, NR_LBD, The ligand binding domain of nucl	3e-05
cd06932	259	cd06932, NR_LBD_PPAR, The ligand binding domain of	5e-05
cd06946	221	cd06946, NR_LBD_ERR, The ligand binding domain of	2e-04
cd06935	243	cd06935, NR_LBD_TR, The ligand binding domain of t	2e-04
cd06936	221	cd06936, NR_LBD_Fxr, The ligand binding domain of	4e-04
cd06933	238	cd06933, NR_LBD_VDR, The ligand binding domain of	6e-04
cd06940	189	cd06940, NR_LBD_REV_ERB, The ligand binding domain	7e-04
smart00430	163	smart00430, HOLI, Ligand binding domain of hormone	0.002
cd06929	174	cd06929, NR_LBD_F1, Ligand-binding domain of nucle	0.003
cd06938	231	cd06938, NR_LBD_EcR, The ligand binding domain (LB	0.004

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

 Score =  254 bits (650), Expect = 3e-84
 Identities = 97/194 (50%), Positives = 126/194 (64%), Gaps = 1/194 (0%)

Query: 74  QPPPHPGLLQI-LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELF 132
           +PP   G +    +S E   E+ ARLLFMAV+W + +  F TL  RDQL+LL+ESW ELF
Sbjct: 13  RPPFPYGTISSYEVSPESVCESAARLLFMAVKWAKSIPAFSTLPFRDQLILLEESWSELF 72

Query: 133 LLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCM 192
           LL  AQWS+P D   L+            +    +E++ +QE L+RFRQL  D +E  C+
Sbjct: 73  LLGAAQWSLPLDSCPLLAVPGLSPDNTEAERTFLSEVRALQETLSRFRQLRVDATEFACL 132

Query: 193 KAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQ 252
           KA++LF PET GL D   VE LQDQAQ +L  ++R RY  QP RFG+LLL+LPSLR +  
Sbjct: 133 KAIVLFKPETRGLKDPAQVEALQDQAQLMLNKHIRTRYPTQPARFGKLLLLLPSLRFISS 192

Query: 253 STIERLFFKETIGD 266
           STIE LFFK+TIG+
Sbjct: 193 STIEELFFKKTIGN 206

The ligand binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like family: This family includes photoreceptor cell-specific nuclear receptor (PNR), Tailless (TLX), and related receptors. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular zone (SVZ) and the dentate gyrus (DG). It plays a key role in neural development by promoting cell cycle progression and preventing apoptosis in the developing brain. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX and PNR have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 206

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

 Score =  175 bits (446), Expect = 3e-53
 Identities = 84/206 (40%), Positives = 117/206 (56%), Gaps = 2/206 (0%)

Query: 85  LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD 144
           +M  +   E  ARLLF AV W R +  F  L   DQ+ LL+ SW ELF+L+ AQ  +P  
Sbjct: 29  IMGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLSWSELFVLNAAQCCMPLH 88

Query: 145 LS--LLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPET 202
           ++  L      A        V   + I++ QE + + + L  D +E  C+KA++LFT + 
Sbjct: 89  VAPLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEFSCLKAIVLFTSDA 148

Query: 203 PGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKE 262
            GL D   +E LQ+++QC L +YVR +Y  QPTRFG+LLL LPSLR V  S IE+LFF  
Sbjct: 149 CGLSDPAHIESLQEKSQCALEEYVRTQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVR 208

Query: 263 TIGDIPIQRLLGDMYTMEKSYETPGL 288
            +G  PI+ L+ DM     S+  P L
Sbjct: 209 LVGKTPIETLIRDMLLSGSSFVWPYL 234

The ligand binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs): COUP-TFs are orphan members of the steroid/thyroid hormone receptor superfamily. They are expressed in many tissues and are involved in the regulation of several important biological processes, such as neurogenesis, organogenesis, cell fate determination, and metabolic homeostasis. In mammals two isoforms named COUP-TFI and COUP-TFII have been identified. Both genes show an exceptional homology and overlapping expression patterns, suggesting that they may serve redundant functions. Although COUP-TF was originally characterized as a transcriptional activator of the chicken ovalbumin gene, COUP-TFs are generally considered to be repressors of transcription for other nuclear hormone receptors, such as retinoic acid receptor (RAR), thyroid hormone receptor (TR), vitamin D receptor (VDR), peroxisome proliferator activated receptor (PPAR), and hepatocyte nuclear factor 4 (HNF4). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, COUP-TFs have a central well cons erved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 236

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

 Score =  147 bits (374), Expect = 2e-43
 Identities = 70/166 (42%), Positives = 97/166 (58%), Gaps = 14/166 (8%)

Query: 93  ETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS------ 146
           E   R+LF  V W + L  F+ L   DQL LLQ SW EL LL LAQ S+ ++LS      
Sbjct: 6   ELADRVLFKTVDWAKNLPAFRNLPLDDQLTLLQNSWAELLLLGLAQRSVHFELSELLLPS 65

Query: 147 --LLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPG 204
             L+I  E+       + V+       +QE+L++ R L  D  E  C+KA++LF P+ PG
Sbjct: 66  PLLVILTEREALLGLAELVQR------LQELLSKLRSLQLDPKEYACLKAIVLFNPDLPG 119

Query: 205 LVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAV 250
           L + Q VE LQ++AQ  L +Y+R RY +QP RF +LLL LP LR++
Sbjct: 120 LKNQQQVEELQEKAQQALQEYIRKRYPQQPARFAKLLLRLPELRSI 165

Ligand-binding domain (LBD) of nuclear receptor (NR) family 2: This is one of the major subfamily of nuclear receptors, including some well known nuclear receptors such as glucocorticoid receptor (GR), mineralocorticoid receptor (MR), estrogen receptor (ER), progesterone receptor (PR), and androgen receptor (AR), other related receptors. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). Length = 165

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

 Score =  119 bits (300), Expect = 6e-32
 Identities = 67/185 (36%), Positives = 101/185 (54%), Gaps = 8/185 (4%)

Query: 93  ETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQ----WSIPWDLSLL 148
           E+ +RLLF+++ W R +  FQ L    Q  L++  W ELF L LAQ     S+P  L+ +
Sbjct: 28  ESASRLLFLSIHWARSIPAFQALGAETQTSLVRACWPELFTLGLAQCSQQLSLPTILAAI 87

Query: 149 INCEK---ARERLPPDDVR-VNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPG 204
           IN  +    +++L  D V+ V   I  +QE +   ++L  D  E   +KA++LF+P+ PG
Sbjct: 88  INHLQTSIQQDKLSADKVKQVMEHINKLQEFVNSMQKLDVDDHEYAYLKAIVLFSPDHPG 147

Query: 205 LVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETI 264
               Q +E LQ++A   L DYV   Y     R  +LLL LP LR++  +  E LFF   I
Sbjct: 148 QELRQQIEKLQEKALMELRDYVGKTYPEDEYRLSKLLLRLPPLRSLSPAITEELFFAGLI 207

Query: 265 GDIPI 269
           G++ I
Sbjct: 208 GNVQI 212

The ligand binding domain of the TR4 and TR2 (human testicular receptor 4 and 2): TR4 and TR2 are orphan nuclear receptors. Several isoforms of TR4 and TR2 have been isolated in various tissues. TR2 is abundantly expressed in the androgen-sensitive prostate. TR4 transcripts are expressed in many tissues, including central nervous system, adrenal gland, spleen, thyroid gland, and prostate. The expression of TR2 is negatively regulated by androgen, retinoids, and radiation. The expression of both mouse TR2 and TR4 is up-regulated by neurocytokine ciliary neurotrophic factor (CNTF) in mouse. It has shown that human TR2 binds to a wide spectrum of natural hormone response elements (HREs) with distinct affinities suggesting that TR2 may cross-talk with other gene expression regulation systems. The genes responding to TR2 or TR4 include genes that are regulated by retinoic acid receptor, vitamin D receptor, peroxisome proliferator-activated receptor. TR4/2 binds to HREs as a dimer. Like other members of the nuclea r receptor (NR) superfamily of ligand-activated transcription factors, TR2-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 222

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

 Score =  110 bits (276), Expect = 5e-29
 Identities = 55/170 (32%), Positives = 80/170 (47%), Gaps = 10/170 (5%)

Query: 89  EKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLL 148
           E   E   R L + V W + +  F+ L   DQ++LL+  W EL +L LA  S      L 
Sbjct: 1   ELLCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYK--NGLS 58

Query: 149 INCEKARERLPPDDVRVNNE------IKLIQEILARFRQLSPDGSECGCMKAVILFTPET 202
           +           D             I+L+ E +   R L  D  E   +KA++LF+P+ 
Sbjct: 59  LLLAPNGGHTDDDKEDEMKLLLKGELIRLLFEFVNPLRALKLDDEEYALLKAIVLFSPDR 118

Query: 203 P-GLVDAQPVEMLQDQAQCILGDYVRGRYS-RQPTRFGRLLLMLPSLRAV 250
              L D + VE LQ++    L DY+R  Y    P+RF +LLL+LPSLR +
Sbjct: 119 KESLEDRKIVEELQERLLEALQDYLRKNYPEEAPSRFAKLLLLLPSLRKL 168

Ligand-binding domain (LBD) of nuclear receptor (NR): Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). Length = 168

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

 Score =  108 bits (273), Expect = 3e-28
 Identities = 41/66 (62%), Positives = 49/66 (74%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           ET GL D   VE LQDQAQ +L  ++R RY  QP RFG+LLL+LPSLR +  STIE LFF
Sbjct: 141 ETRGLKDPAQVEALQDQAQLMLNKHIRTRYPTQPARFGKLLLLLPSLRFISSSTIEELFF 200

Query: 344 KETIGD 349
           K+TIG+
Sbjct: 201 KKTIGN 206

The ligand binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like family: This family includes photoreceptor cell-specific nuclear receptor (PNR), Tailless (TLX), and related receptors. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular zone (SVZ) and the dentate gyrus (DG). It plays a key role in neural development by promoting cell cycle progression and preventing apoptosis in the developing brain. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX and PNR have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 206

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

 Score =  104 bits (262), Expect = 2e-26
 Identities = 63/180 (35%), Positives = 95/180 (52%), Gaps = 4/180 (2%)

Query: 99  LFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPW-DLSLLIN-CEKARE 156
           L + V W + +  F  L   DQ+ LL+    E  LL +A+ S+P+ D+ LL N     R 
Sbjct: 45  LLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGVARRSMPYKDILLLGNDLIIPRH 104

Query: 157 RLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQD 216
              P+  RV N I  + E++   R L+ D +E  C+KA++ F P+  GL D Q ++ L+ 
Sbjct: 105 CPEPEISRVANRI--LDELVLPLRDLNIDDNEYACLKAIVFFDPDAKGLSDPQKIKRLRF 162

Query: 217 QAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDM 276
           Q Q  L DY+  R      RFG LLL+LP+L+++    IE++ F    G   I  LL +M
Sbjct: 163 QVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFARLFGVAKIDNLLQEM 222

The ligand binding domain of hepatocyte nuclear factor 4 (HNF4) like proteins: HNF4 is a member of the nuclear receptor superfamily. HNF4 plays a key role in establishing and maintenance of hepatocyte differentiation in the liver. It is also expressed in gut, kidney, and pancreatic beta cells. HNF4 was originally classified as an orphan receptor, but later it is found that HNF4 binds with very high affinity to a variety of fatty acids. However, unlike other nuclear receptors, the ligands do not act as a molecular switch for HNF4. They seem to constantly bind to the receptor, which is constitutively active as a transcription activator. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, HNF4 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). The LBD domain is also responsible for recruiting co-activator proteins. More than 280 nuclear receptors are found in C. ele gans, most of which are originated from an explosive burst of duplications of HNF4. Length = 222

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

 Score =  103 bits (260), Expect = 3e-26
 Identities = 57/171 (33%), Positives = 88/171 (51%), Gaps = 2/171 (1%)

Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
           CQ    + LF  V W + +  F  L   DQ++LL+  W EL +   A  SI     +L+ 
Sbjct: 36  CQAAD-KQLFQLVEWAKRIPHFSELPLDDQVILLRAGWNELLIAAFAHRSIAVKDGILLA 94

Query: 151 CEKARERLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
                 R       V     +++ E++ + R L  D +E GC++A+ILF P+  GL   Q
Sbjct: 95  TGLHLHRNSAHQAGVGAIFDRILTELVVKMRDLKMDRTELGCLRAIILFNPDVKGLKSRQ 154

Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 260
            VE L+++    L +Y R ++  QP RF +LLL LP+LR++    +E LFF
Sbjct: 155 EVESLREKVYASLEEYCRQKHPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 205

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

 Score =  104 bits (260), Expect = 3e-26
 Identities = 66/216 (30%), Positives = 95/216 (43%), Gaps = 17/216 (7%)

Query: 75  PPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLL 134
                  +Q+      C+  +  LL   +R+VR L  F  L   DQL LL+ SW  L LL
Sbjct: 9   SCHQHRPVQLCAPQMVCRAASQVLL-KTIRFVRNLPCFTYLPPDDQLRLLRRSWAPLLLL 67

Query: 135 HLAQWSIPWDL------SLLINC----EKARERLPPDDVRVNNEIKL-----IQEILARF 179
            LAQ  +P+D       S+L       E      PP  + +   I L     IQ+ L + 
Sbjct: 68  GLAQDKVPFDTVEVPAPSILCEILTGAEMHWGGTPPPTLTMPPCIPLADVQDIQQFLMKC 127

Query: 180 RQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGR 239
             L  D  E   +K  +LFTP  P L     +E LQ +AQ  L ++       +  R  R
Sbjct: 128 WSLDLDCKEYAYLKGAVLFTPVPPLLC-PHYIEALQKEAQQALNEHTMMTRPLEQLRSAR 186

Query: 240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGD 275
           LLLML  LR ++   +  LFF+  IG++ +  +L  
Sbjct: 187 LLLMLSLLRGIKTEPVTELFFRPIIGNVSMDDVLLQ 222

The ligand binding domain of DAX1-like proteins: This orphan nuclear receptor family includes DAX1 (dosage-sensitive sex reversal adrenal hypoplasia congenita critical region on chromosome X gene 1) and the Small Heterodimer Partner (SHP). Both receptors have a typical ligand binding domain, but lack the DNA binding domain, typical to almost all of the nuclear receptors. They function as a transcriptional coregulator by directly interacting with other nuclear receptors. DAX1 and SHP can form heterodimers with each other, as well as with many other nuclear receptors. In addition, DAX1 can also form homodimers. DAX1 plays an important role in the normal development of several hormone-producing tissues. SHP has shown to regulate a variety of target genes. Length = 222

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

 Score =  100 bits (252), Expect = 1e-25
 Identities = 53/163 (32%), Positives = 79/163 (48%), Gaps = 7/163 (4%)

Query: 95  TARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN---- 150
             R L + V W +    F+ LS  DQ++LL+  W EL LL LA  S+     LL+     
Sbjct: 1   AERQLLLTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKELLLAPDGT 60

Query: 151 CEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDA-- 208
             +    L    +      +++ E++   R+L  D  E   +KA++LF P  PGL +   
Sbjct: 61  YIRPDAVLELRKLFSPFLDRILSELVKPLRELKLDDEEYALLKAIVLFNPAVPGLSEEGK 120

Query: 209 QPVEMLQDQAQCILGDYVRGRYSRQ-PTRFGRLLLMLPSLRAV 250
           + VE LQ++    L DY    Y    P RF +LLL+LP LR +
Sbjct: 121 EIVEKLQEKYANALHDYYLKNYPMNYPGRFAKLLLILPELRKI 163

Length = 163

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

 Score = 98.6 bits (245), Expect = 6e-24
 Identities = 62/188 (32%), Positives = 92/188 (48%), Gaps = 15/188 (7%)

Query: 99  LFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLL--------HLAQWSIPWDLSLLIN 150
           LF  V W R    F+ L   DQ+ LLQ  W EL +L        H  + SI      L+ 
Sbjct: 53  LFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSI-----FLVT 107

Query: 151 CEKARERL--PPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDA 208
            ++    +        +NN +   QE++A+ R L  D  E  C+K ++LF+ +   L + 
Sbjct: 108 GQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENF 167

Query: 209 QPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIP 268
           Q VE +Q+Q    L DY    Y +Q  +FG+LLL LP +RA+     E L++K   GD+P
Sbjct: 168 QLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVP 227

Query: 269 IQRLLGDM 276
              LL +M
Sbjct: 228 YNNLLIEM 235

The ligand binding domain (LBD) of the liver receptor homolog-1 (LRH-1): LRH-1 belongs to nuclear hormone receptor superfamily, and is expressed mainly in the liver, intestine, exocrine pancreas, and ovary. Most nuclear receptors function as homodimer or heterodimers. However, LRH-1 binds DNA as a monomer, and is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development. Recently, phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, LRH-1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 241

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

 Score = 96.8 bits (241), Expect = 2e-23
 Identities = 40/76 (52%), Positives = 52/76 (68%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           +  GL D   +E LQ+++QC L +YVR +Y  QPTRFG+LLL LPSLR V  S IE+LFF
Sbjct: 147 DACGLSDPAHIESLQEKSQCALEEYVRTQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFF 206

Query: 344 KETIGDIPIQRLLGDM 359
              +G  PI+ L+ DM
Sbjct: 207 VRLVGKTPIETLIRDM 222

The ligand binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs): COUP-TFs are orphan members of the steroid/thyroid hormone receptor superfamily. They are expressed in many tissues and are involved in the regulation of several important biological processes, such as neurogenesis, organogenesis, cell fate determination, and metabolic homeostasis. In mammals two isoforms named COUP-TFI and COUP-TFII have been identified. Both genes show an exceptional homology and overlapping expression patterns, suggesting that they may serve redundant functions. Although COUP-TF was originally characterized as a transcriptional activator of the chicken ovalbumin gene, COUP-TFs are generally considered to be repressors of transcription for other nuclear hormone receptors, such as retinoic acid receptor (RAR), thyroid hormone receptor (TR), vitamin D receptor (VDR), peroxisome proliferator activated receptor (PPAR), and hepatocyte nuclear factor 4 (HNF4). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, COUP-TFs have a central well cons erved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 236

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

 Score = 94.5 bits (235), Expect = 1e-22
 Identities = 65/200 (32%), Positives = 97/200 (48%), Gaps = 13/200 (6%)

Query: 89  EKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS-- 146
             C+   + +L   V ++R L  F  L  +DQLLLLQ  W  LFLL LAQ  + ++++  
Sbjct: 23  RTCR-EASDVLVKTVAFMRNLPSFWQLPPQDQLLLLQNCWGPLFLLGLAQDRVTFEVAEA 81

Query: 147 ---------LLINCEKARERLPPDDVRVN-NEIKLIQEILARFRQLSPDGSECGCMKAVI 196
                    LL     +     PD  + +   ++ +Q  L +F  L     E   +K  I
Sbjct: 82  PVPSMLKKILLEGQSSSGGSGQPDRPQPSLAAVQWLQCCLNKFWSLDLSPKEYAYLKGTI 141

Query: 197 LFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIE 256
           LF P+ PGL  +  V  LQ +AQ  L + +   + +   RF R+LL   +L+++  S I 
Sbjct: 142 LFNPDVPGLTASSHVGHLQQEAQWALCEVLEPLHPQDQGRFARILLTASTLKSIPPSLIT 201

Query: 257 RLFFKETIGDIPIQRLLGDM 276
            LFF+  IGD  I  LLGDM
Sbjct: 202 DLFFRPIIGDADIAELLGDM 221

The ligand binding domain of the Small Heterodimer Partner (SHP): SHP is a member of the nuclear receptor superfamily. SHP has a ligand binding domain, but lacks the DNA binding domain, typical to almost all of the nuclear receptors. It functions as a transcriptional coregulator by directly interacting with other nuclear receptors through its AF-2 motif. The closest relative of SHP is DAX1 and they can form heterodimer. SHP is an orphan receptor, lacking an identified ligand. Length = 222

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

 Score = 94.3 bits (235), Expect = 2e-22
 Identities = 62/188 (32%), Positives = 95/188 (50%), Gaps = 15/188 (7%)

Query: 99  LFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLL-HLAQW-------SIPWDLSLLIN 150
           LF  V W R    F+ L   DQ+ LLQ  W EL +L H+ +        SI     LL+ 
Sbjct: 51  LFSIVEWARNSVFFKELKVDDQMKLLQNCWSELLVLDHIYRQVHHGKEDSI-----LLVT 105

Query: 151 CEKARERLPPDD--VRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDA 208
            ++           + +++ +   QE++ + R+L  D  E  C+K +ILF P+  GL + 
Sbjct: 106 GQEVDLSTLASQAGLGLSSLVDRAQELVNKLRELQFDRQEFVCLKFLILFNPDVKGLENR 165

Query: 209 QPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIP 268
           Q VE +Q+Q    L DY    Y +Q  +FG+LLL LP +RA+     E L++K   G++P
Sbjct: 166 QLVESVQEQVNAALLDYTLCNYPQQTDKFGQLLLRLPEIRAISMQAEEYLYYKHLNGEVP 225

Query: 269 IQRLLGDM 276
              LL +M
Sbjct: 226 CNNLLIEM 233

The ligand binding domain of FTZ-F1 like nuclear receptors: This nuclear receptor family includes at least three subgroups of receptors that function in embryo development and differentiation, and other processes. FTZ-F1 interacts with the cis-acting DNA motif of ftz gene, which required at several stages of development. Particularly, FTZ-F1 genes are strongly linked to steroid biosynthesis and sex-determination; LRH-1 is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development. SF-1 is an essential regulator of endocrine development and function and is considered a master regulator of reproduction; SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). However, the ligand for FTZ-F1 has not yet been identified. Most nuclear receptors function as homodimer or heterodimers. However, LRH-1 and SF-1 bind to DNA as a monomer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, receptors in this family have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 237

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

 Score = 90.1 bits (224), Expect = 2e-21
 Identities = 50/182 (27%), Positives = 78/182 (42%), Gaps = 8/182 (4%)

Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS-LLI 149
             E   R L + V W +    F+ LS  DQL LL+ SW E   L LA  S   +   LL 
Sbjct: 5   LFEIWERDLLLVVEWAKRFPGFRELSLDDQLALLKSSWFEWLRLELASRSAECEKDDLLF 64

Query: 150 NCEKARERLPPDDVRVN---NEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLV 206
           +     +R     + VN    +I+ + E++   ++L     E   +KA++LF P    L 
Sbjct: 65  SNGLYLDRDELKSIEVNYINEQIRQLFELVQPLKELKLTDEELAALKALLLFNPAGKRLS 124

Query: 207 DAQP--VEMLQDQAQCILGDYVRG--RYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKE 262
                 VE LQ+     L +Y +          R  +LL +LP+LR + +   E+L   +
Sbjct: 125 GEILEVVEKLQEVIANALHNYYKDENSPPNYSGRLAKLLKLLPALRKISRKLREKLELAK 184

Query: 263 TI 264
             
Sbjct: 185 LF 186

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

>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 = 75.9 bits (187), Expect = 6e-16
 Identities = 59/194 (30%), Positives = 89/194 (45%), Gaps = 9/194 (4%)

Query: 97  RLLFMAVRWVRCLAP----FQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCE 152
            LL  +V  +R  A     F+ L + DQ LLL+ ++ ELF+L LA  S P D  L+    
Sbjct: 48  DLLTGSVDVIRQWAEKIPGFKDLHREDQDLLLESAFLELFVLRLAYRSNPVDGKLVFCNG 107

Query: 153 KARERLPPDDVRVNNE-IKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPV 211
               RL    VR   E +  I    +  + L  D     C  A++L   E  GL + + V
Sbjct: 108 LVLHRL--QCVRGFGEWLDSILAFSSSLQSLLLDDISAFCCLALLLLITERHGLKEPKKV 165

Query: 212 EMLQDQAQCILGDYVRGRYSRQ--PTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
           E LQ++    L D+V   Y  Q  P R  +LLL LP LR + +  ++R+FF +    +P 
Sbjct: 166 EELQNKIISCLRDHVTSNYPGQDKPNRLSKLLLKLPELRTLSKKGLQRIFFLKLEDLLPP 225

Query: 270 QRLLGDMYTMEKSY 283
             L+   +     +
Sbjct: 226 PPLIDKRFLDTLPF 239

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

 Score = 73.6 bits (181), Expect = 3e-15
 Identities = 52/161 (32%), Positives = 74/161 (45%), Gaps = 10/161 (6%)

Query: 97  RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINC----- 151
            LLF  ++W + L  F  LS +D   LL   W EL LL     +   +L LL +C     
Sbjct: 38  ELLFRQIQWTKKLPFFTELSIKDHTHLLTTKWAELILLSTITVASLQNLGLLQDCLSKYL 97

Query: 152 --EKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
             E   ER   +   V   ++ +  +LA+FRQL     E  C+K +     +  GL +A 
Sbjct: 98  PSEDELERFGDEGGEV---VERLTYLLAKFRQLKVSNEEYVCLKVINFLNQDIDGLTNAS 154

Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAV 250
            +E LQ +   +L D+    Y  QP RF  LL  LP +RA 
Sbjct: 155 QLESLQKRYWYVLQDFTELNYPNQPNRFSDLLSCLPEIRAA 195

The ligand binding domain of Ecdysone-induced receptor DHR4: Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). . Length = 213

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

 Score = 70.9 bits (174), Expect = 3e-14
 Identities = 53/187 (28%), Positives = 88/187 (47%), Gaps = 13/187 (6%)

Query: 97  RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE 156
           R L + + W + +  F +LS  DQ+ LLQ +W E+  L +   S+P++  L         
Sbjct: 38  RELVVIIGWAKHIPGFSSLSLNDQMSLLQSAWMEILTLGVVFRSLPFNGEL---VFAEDF 94

Query: 157 RLPPDDVRVNNEIKL---IQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEM 213
            L  +  R    ++L     +++ R ++L  +  E   +KA+ L   ++  + D + V  
Sbjct: 95  ILDEELAREAGLLELYSACLQLVRRLQRLRLEKEEYVLLKALALANSDSVHIEDVEAVRQ 154

Query: 214 LQDQAQCILGDYVRGRYSRQ-PTRFGRLLLMLPSLRAVRQSTIERLFF---KETIGDIPI 269
           L+D     L DY  GR+  + P R G+LLL LP LR        R FF   K   G +P+
Sbjct: 155 LRDALLEALSDYEAGRHPGEAPRRAGQLLLTLPLLRQT--DGKARRFFYGVKRE-GKVPM 211

Query: 270 QRLLGDM 276
            +L  +M
Sbjct: 212 HKLFLEM 218

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

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

 Score = 69.9 bits (171), Expect = 8e-14
 Identities = 55/213 (25%), Positives = 94/213 (44%), Gaps = 24/213 (11%)

Query: 85  LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD 144
           L S +   +  + +L   +R+V+ +  FQ L   DQL+L++  W  L +L LAQ  + ++
Sbjct: 18  LKSPQVTCKAASAVLVKTLRFVKGVPCFQELPLDDQLVLVRSCWAPLLVLGLAQDGVDFE 77

Query: 145 L----------SLLINCEKARERLPPDDVRVNN--------------EIKLIQEILARFR 180
                       +L           P + +                 +I+ I+  LA+  
Sbjct: 78  TVETSEPSMLQRILTTRPPPTSGAEPGEPQALPQMPQAEASHLPSAADIRAIKAFLAKCW 137

Query: 181 QLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRL 240
            L     E   +K  +LF P+ PGL   Q ++ LQ +AQ  L ++VR  +     RF +L
Sbjct: 138 SLDISTKEYAYLKGTVLFNPDLPGLQCVQYIQGLQWEAQQALNEHVRMIHRGDQARFAKL 197

Query: 241 LLMLPSLRAVRQSTIERLFFKETIGDIPIQRLL 273
            + L  LRA+  + I  LFF+  IG + +  +L
Sbjct: 198 NIALSLLRAINANVIAELFFRPIIGTVNMDDML 230

The ligand binding domain of the DAX1 protein: DAX1 (dosage-sensitive sex reversal adrenal hypoplasia congenita critical region on chromosome X gene 1) is a nuclear receptor with a typical ligand binding domain, but lacks the DNA binding domain. DAX1 plays an important role in the normal development of several hormone-producing tissues. Duplications of the region of the X chromosome containing DAX1 cause dosage sensitive sex reversal. DAX1 acts as a global repressor of many nuclear receptors, including SF-1, LRH-1, ERR, ER, AR and PR. DAX1 can form homodimer and heterodimerizes with its alternatively spliced isoform DAX1A and other nuclear receptors such as SHP, ERalpha and SF-1. Length = 232

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

 Score = 67.6 bits (166), Expect = 4e-13
 Identities = 48/141 (34%), Positives = 70/141 (49%), Gaps = 7/141 (4%)

Query: 112 FQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKL 171
           F  LS  DQ+ LLQ +W E+ +L L   S+P    L+         L  +  RV   +++
Sbjct: 53  FSDLSLNDQMHLLQSAWLEILMLGLVWRSLPHPGKLVF---APDLLLDREQARVEGLLEI 109

Query: 172 IQEILA---RFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRG 228
              +L    RFR+L     E  C+KA+IL   +   L D + V+ L+D     L D    
Sbjct: 110 FDMLLQLVRRFRELGLQREEYVCLKAIILANSDVRHLEDREAVQQLRDAILDALVDVEAK 169

Query: 229 RY-SRQPTRFGRLLLMLPSLR 248
           R+ S+QP R  +LLL+LP LR
Sbjct: 170 RHGSQQPRRLAQLLLLLPHLR 190

The ligand binding domain of estrogen receptor (ER) and estrogen receptor-related receptors (ERRs): Estrogen receptors are a group of receptors which are activated by the hormone estrogen. Estrogen regulates many physiological processes including reproduction, bone integrity, cardiovascular health, and behavior. The main mechanism of action of the estrogen receptor is as a transcription factor by binding to the estrogen response element of target genes upon activation by estrogen and then recruiting coactivator proteins which are responsible for the transcription of target genes. Additionally some ERs may associate with other membrane proteins and can be rapidly activated by exposure of cells to estrogen. ERRs are closely related to the estrogen receptor (ER) family. But, it lacks the ability to bind estrogen. ERRs can interfere with the classic ER-mediated estrogen signaling pathway, positively or negatively. ERRs share target genes, co-regulators and promoters with the estrogen receptor (ER) family. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER and ERRs have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). Length = 221

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

 Score = 61.9 bits (151), Expect = 2e-11
 Identities = 26/49 (53%), Positives = 35/49 (71%)

Query: 285 TPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAV 333
            PGL + Q VE LQ++AQ  L +Y+R RY +QP RF +LLL LP LR++
Sbjct: 117 LPGLKNQQQVEELQEKAQQALQEYIRKRYPQQPARFAKLLLRLPELRSI 165

Ligand-binding domain (LBD) of nuclear receptor (NR) family 2: This is one of the major subfamily of nuclear receptors, including some well known nuclear receptors such as glucocorticoid receptor (GR), mineralocorticoid receptor (MR), estrogen receptor (ER), progesterone receptor (PR), and androgen receptor (AR), other related receptors. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). Length = 165

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

 Score = 60.5 bits (147), Expect = 1e-10
 Identities = 28/76 (36%), Positives = 41/76 (53%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           +  GL D Q ++ L+ Q Q  L DY+  R      RFG LLL+LP+L+++    IE++ F
Sbjct: 147 DAKGLSDPQKIKRLRFQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQF 206

Query: 344 KETIGDIPIQRLLGDM 359
               G   I  LL +M
Sbjct: 207 ARLFGVAKIDNLLQEM 222

The ligand binding domain of hepatocyte nuclear factor 4 (HNF4) like proteins: HNF4 is a member of the nuclear receptor superfamily. HNF4 plays a key role in establishing and maintenance of hepatocyte differentiation in the liver. It is also expressed in gut, kidney, and pancreatic beta cells. HNF4 was originally classified as an orphan receptor, but later it is found that HNF4 binds with very high affinity to a variety of fatty acids. However, unlike other nuclear receptors, the ligands do not act as a molecular switch for HNF4. They seem to constantly bind to the receptor, which is constitutively active as a transcription activator. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, HNF4 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). The LBD domain is also responsible for recruiting co-activator proteins. More than 280 nuclear receptors are found in C. ele gans, most of which are originated from an explosive burst of duplications of HNF4. Length = 222

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

 Score = 57.7 bits (139), Expect = 1e-09
 Identities = 30/78 (38%), Positives = 43/78 (55%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
           S +   L + Q VE +Q+Q    L DY    Y +Q  +FG+LLL LP +RA+     E L
Sbjct: 158 SLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYL 217

Query: 342 FFKETIGDIPIQRLLGDM 359
           ++K   GD+P   LL +M
Sbjct: 218 YYKHLNGDVPYNNLLIEM 235

The ligand binding domain (LBD) of the liver receptor homolog-1 (LRH-1): LRH-1 belongs to nuclear hormone receptor superfamily, and is expressed mainly in the liver, intestine, exocrine pancreas, and ovary. Most nuclear receptors function as homodimer or heterodimers. However, LRH-1 binds DNA as a monomer, and is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development. Recently, phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, LRH-1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 241

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

 Score = 55.8 bits (135), Expect = 4e-09
 Identities = 24/57 (42%), Positives = 35/57 (61%)

Query: 287 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           GL   Q VE L+++    L +Y R ++  QP RF +LLL LP+LR++    +E LFF
Sbjct: 149 GLKSRQEVESLREKVYASLEEYCRQKHPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 205

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

 Score = 56.1 bits (135), Expect = 4e-09
 Identities = 50/188 (26%), Positives = 80/188 (42%), Gaps = 15/188 (7%)

Query: 99  LFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLL--------HLAQWSIPWDLSLLIN 150
               V W R    F+ L   DQ+ LLQ  W EL +         H  + SI     LL+ 
Sbjct: 51  FISIVDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQHGKEGSI-----LLVT 105

Query: 151 CEKARERLPPDDV--RVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDA 208
            ++             +++ +   QE++ +   L  D  E  C+K +ILF+ +   L + 
Sbjct: 106 GQEVELSTVAAQAGSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILFSLDVKFLNNH 165

Query: 209 QPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIP 268
             V+  Q++A   L DY    Y     +F +LLL L  +RA+     E L+ K    ++P
Sbjct: 166 SLVKDAQEKANAALLDYTLCHYPHCGDKFQQLLLRLVEVRALSMQAKEYLYHKHLGNEMP 225

Query: 269 IQRLLGDM 276
              LL +M
Sbjct: 226 RNNLLIEM 233

The ligand binding domain of nuclear receptor steroidogenic factor 1 (SF-1): SF-1, a member of the nuclear hormone receptor superfamily, is an essential regulator of endocrine development and function and is considered a master regulator of reproduction. Most nuclear receptors function as homodimer or heterodimers, however SF-1 binds to its target genes as a monomer, recognizing the variations of the DNA sequence motif, T/CCA AGGTCA. SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been determined as potential ligands of SF-1. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, SF-1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 237

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

 Score = 54.9 bits (133), Expect = 5e-09
 Identities = 42/143 (29%), Positives = 67/143 (46%), Gaps = 8/143 (5%)

Query: 112 FQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKL 171
           F+ LS+ DQ+ LL+    E+ LL  A    P   SL     K   R   D +      + 
Sbjct: 28  FRELSQEDQIALLKGGCFEILLLRSATLYDPEKNSLTFGDGKGNSR---DVLLNGGFGEF 84

Query: 172 IQEILA---RFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQ-AQCILGDYVR 227
           I+ +     +  +L  D +E   + A++LF+P+ PGL D   VE LQ++  +  L  Y++
Sbjct: 85  IEPLFEFAEKMNKLQLDDNEYALLTAIVLFSPDRPGLQDVDTVEKLQERLLEA-LQRYLK 143

Query: 228 GRYSRQPTRFGRLLLMLPSLRAV 250
             +   P  F +LL  L  LR +
Sbjct: 144 VNHPDAPQMFAKLLKKLTELRTL 166

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

 Score = 55.1 bits (133), Expect = 6e-09
 Identities = 36/139 (25%), Positives = 67/139 (48%)

Query: 112 FQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKL 171
           F  LS+ DQLLL++  + E++L+ +++       S+  +   +  R   D +  ++ +K 
Sbjct: 28  FCDLSQDDQLLLIKAGFFEVWLVRISRLINSKSGSITFDDGISISRQQLDIIYDSDFVKA 87

Query: 172 IQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYS 231
           + E    F  L    +E     AV+L +P+  GL + + V +LQD+    L   V     
Sbjct: 88  LFEFSDSFNSLGLSDTEVALFCAVVLLSPDRIGLSEPKKVAILQDRVLEALKVQVSRNRP 147

Query: 232 RQPTRFGRLLLMLPSLRAV 250
            +   F  LL+ +P LR++
Sbjct: 148 AEAQLFASLLMKIPELRSI 166

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

 Score = 55.0 bits (133), Expect = 8e-09
 Identities = 27/67 (40%), Positives = 36/67 (53%)

Query: 286 PGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKE 345
           PG    Q +E LQ++A   L DYV   Y     R  +LLL LP LR++  +  E LFF  
Sbjct: 146 PGQELRQQIEKLQEKALMELRDYVGKTYPEDEYRLSKLLLRLPPLRSLSPAITEELFFAG 205

Query: 346 TIGDIPI 352
            IG++ I
Sbjct: 206 LIGNVQI 212

The ligand binding domain of the TR4 and TR2 (human testicular receptor 4 and 2): TR4 and TR2 are orphan nuclear receptors. Several isoforms of TR4 and TR2 have been isolated in various tissues. TR2 is abundantly expressed in the androgen-sensitive prostate. TR4 transcripts are expressed in many tissues, including central nervous system, adrenal gland, spleen, thyroid gland, and prostate. The expression of TR2 is negatively regulated by androgen, retinoids, and radiation. The expression of both mouse TR2 and TR4 is up-regulated by neurocytokine ciliary neurotrophic factor (CNTF) in mouse. It has shown that human TR2 binds to a wide spectrum of natural hormone response elements (HREs) with distinct affinities suggesting that TR2 may cross-talk with other gene expression regulation systems. The genes responding to TR2 or TR4 include genes that are regulated by retinoic acid receptor, vitamin D receptor, peroxisome proliferator-activated receptor. TR4/2 binds to HREs as a dimer. Like other members of the nuclea r receptor (NR) superfamily of ligand-activated transcription factors, TR2-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 222

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

 Score = 54.4 bits (131), Expect = 1e-08
 Identities = 23/73 (31%), Positives = 37/73 (50%)

Query: 286 PGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKE 345
           P L+    +E LQ +AQ  L ++       +  R  RLLLML  LR ++   +  LFF+ 
Sbjct: 150 PPLLCPHYIEALQKEAQQALNEHTMMTRPLEQLRSARLLLMLSLLRGIKTEPVTELFFRP 209

Query: 346 TIGDIPIQRLLGD 358
            IG++ +  +L  
Sbjct: 210 IIGNVSMDDVLLQ 222

The ligand binding domain of DAX1-like proteins: This orphan nuclear receptor family includes DAX1 (dosage-sensitive sex reversal adrenal hypoplasia congenita critical region on chromosome X gene 1) and the Small Heterodimer Partner (SHP). Both receptors have a typical ligand binding domain, but lack the DNA binding domain, typical to almost all of the nuclear receptors. They function as a transcriptional coregulator by directly interacting with other nuclear receptors. DAX1 and SHP can form heterodimers with each other, as well as with many other nuclear receptors. In addition, DAX1 can also form homodimers. DAX1 plays an important role in the normal development of several hormone-producing tissues. SHP has shown to regulate a variety of target genes. Length = 222

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

 Score = 54.6 bits (132), Expect = 1e-08
 Identities = 29/76 (38%), Positives = 43/76 (56%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           +  GL + Q VE +Q+Q    L DY    Y +Q  +FG+LLL LP +RA+     E L++
Sbjct: 158 DVKGLENRQLVESVQEQVNAALLDYTLCNYPQQTDKFGQLLLRLPEIRAISMQAEEYLYY 217

Query: 344 KETIGDIPIQRLLGDM 359
           K   G++P   LL +M
Sbjct: 218 KHLNGEVPCNNLLIEM 233

The ligand binding domain of FTZ-F1 like nuclear receptors: This nuclear receptor family includes at least three subgroups of receptors that function in embryo development and differentiation, and other processes. FTZ-F1 interacts with the cis-acting DNA motif of ftz gene, which required at several stages of development. Particularly, FTZ-F1 genes are strongly linked to steroid biosynthesis and sex-determination; LRH-1 is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development. SF-1 is an essential regulator of endocrine development and function and is considered a master regulator of reproduction; SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). However, the ligand for FTZ-F1 has not yet been identified. Most nuclear receptors function as homodimer or heterodimers. However, LRH-1 and SF-1 bind to DNA as a monomer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, receptors in this family have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 237

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

 Score = 52.9 bits (127), Expect = 5e-08
 Identities = 64/228 (28%), Positives = 99/228 (43%), Gaps = 18/228 (7%)

Query: 57  SPPPPSHHHPSMFLATHQPPPHPGLLQILMS-AEKCQETTARLLFMAVRWVRCLAP---- 111
           SP   +  +        +P P    L+  MS AEK Q+  + LL  ++  ++  A     
Sbjct: 17  SPDFANLDYSQY----REPSP----LEPPMSEAEKVQQFYS-LLTSSIDVIKTFAEKIPG 67

Query: 112 FQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKL 171
           F  L K DQ LL Q +  ELF+L LA  + P D + L  C               + +  
Sbjct: 68  FPDLCKEDQELLFQSASLELFVLRLAYRTAPED-TKLTFCNGVVLHKQQCQRSFGDWLHA 126

Query: 172 IQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYV--RGR 229
           I E       +  D S   C+ A+ L T E  GL +   VE LQ +    L D+V     
Sbjct: 127 ILEFSKSLHAMDIDISAFACLCALTLIT-ERHGLKEPHKVEQLQMKIISSLRDHVTYNAE 185

Query: 230 YSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMY 277
             ++P  F RLL  LP LR++    ++R+F+ +    +P   L+ +M+
Sbjct: 186 AQKKPHYFSRLLGKLPELRSLSVQGLQRIFYLKLEDLVPAPPLIENMF 233

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

 Score = 52.4 bits (126), Expect = 7e-08
 Identities = 26/85 (30%), Positives = 42/85 (49%), Gaps = 2/85 (2%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQ--PTRFGRLLLMLPSLRAVRQSTIERL 341
           E  GL + + VE LQ++    L D+V   Y  Q  P R  +LLL LP LR + +  ++R+
Sbjct: 155 ERHGLKEPKKVEELQNKIISCLRDHVTSNYPGQDKPNRLSKLLLKLPELRTLSKKGLQRI 214

Query: 342 FFKETIGDIPIQRLLGDMYTMEKSY 366
           FF +    +P   L+   +     +
Sbjct: 215 FFLKLEDLLPPPPLIDKRFLDTLPF 239

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

 Score = 52.5 bits (126), Expect = 8e-08
 Identities = 48/160 (30%), Positives = 78/160 (48%), Gaps = 6/160 (3%)

Query: 104 RWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDV 163
           +W   +  F    K DQ LLL+ ++ ELF+L LA  S P +  L+        R     V
Sbjct: 59  KWAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNPEEGKLIFCNGVVLHRT--QCV 116

Query: 164 RVNNE-IKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCIL 222
           R   + I  I E      +++ D S   C+ A+++ T +  GL + + VE LQ++    L
Sbjct: 117 RGFGDWIDSILEFSQSLHRMNLDVSAFSCLAALVIIT-DRHGLKEPKRVEELQNRLISCL 175

Query: 223 GDYVRGRYS--RQPTRFGRLLLMLPSLRAVRQSTIERLFF 260
            ++V G  S  ++P    RLL  LP LR +    ++R+F+
Sbjct: 176 KEHVSGSASEPQRPNCLSRLLGKLPELRTLCTQGLQRIFY 215

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

 Score = 51.4 bits (123), Expect = 1e-07
 Identities = 29/76 (38%), Positives = 42/76 (55%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           + PGL  +  V  LQ +AQ  L + +   + +   RF R+LL   +L+++  S I  LFF
Sbjct: 146 DVPGLTASSHVGHLQQEAQWALCEVLEPLHPQDQGRFARILLTASTLKSIPPSLITDLFF 205

Query: 344 KETIGDIPIQRLLGDM 359
           +  IGD  I  LLGDM
Sbjct: 206 RPIIGDADIAELLGDM 221

The ligand binding domain of the Small Heterodimer Partner (SHP): SHP is a member of the nuclear receptor superfamily. SHP has a ligand binding domain, but lacks the DNA binding domain, typical to almost all of the nuclear receptors. It functions as a transcriptional coregulator by directly interacting with other nuclear receptors through its AF-2 motif. The closest relative of SHP is DAX1 and they can form heterodimer. SHP is an orphan receptor, lacking an identified ligand. Length = 222

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

 Score = 50.0 bits (119), Expect = 4e-07
 Identities = 49/159 (30%), Positives = 75/159 (47%), Gaps = 6/159 (3%)

Query: 105 WVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVR 164
           W   +  F  L K DQ LL + ++ ELF+L LA  S P +  L+        RL    VR
Sbjct: 60  WAEKIPGFTDLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIFCNGVVLHRL--QCVR 117

Query: 165 VNNE-IKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILG 223
              E I  I E  +  + ++ D S   C+ A+ + T E  GL + + VE LQ++    L 
Sbjct: 118 GFGEWIDSIVEFSSNLQNMNIDISAFSCIAALAMVT-ERHGLKEPKRVEELQNKIVNCLK 176

Query: 224 DYV--RGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 260
           D+V        +P    +LL  LP LR +    ++R+F+
Sbjct: 177 DHVTFNNGGLNRPNYLSKLLGKLPELRTLCTQGLQRIFY 215

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

 Score = 48.7 bits (116), Expect = 1e-06
 Identities = 39/174 (22%), Positives = 72/174 (41%), Gaps = 6/174 (3%)

Query: 89  EKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLL 148
           +K  E + + +   V + + L  F TL+  DQ+ LL+ +  ++ +L +     P   ++ 
Sbjct: 41  DKFSELSTKCIIKIVEFAKRLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMT 100

Query: 149 INCEKARERLPPDDVRVNNEIKLIQEILARFRQLSP---DGSECGCMKAVILFTPETPGL 205
            +      R     +       L   +     QL P   D +E G + A+ L   +   L
Sbjct: 101 FSDGLTLNR---TQMHNAGFGPLTDLVFTFANQLLPLEMDDTEIGLLSAICLICGDRQDL 157

Query: 206 VDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLF 259
            +   VE LQ+     L  Y R R   +P  F ++L+ +  LR++     ER+ 
Sbjct: 158 EEPDRVEKLQEPLLEALKIYARKRRPDKPHMFPKMLMKITDLRSISAKGAERVI 211

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

 Score = 47.8 bits (114), Expect = 3e-06
 Identities = 41/151 (27%), Positives = 70/151 (46%), Gaps = 5/151 (3%)

Query: 112 FQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKL 171
           F TL++ DQ+ LL+ S  E+ LL  A+   P   ++    +    R   D  R   +++ 
Sbjct: 69  FLTLTREDQIALLKASTIEVMLLETARRYNPESEAITFLKDFPYSR--DDFARAGLQVEF 126

Query: 172 IQEIL---ARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRG 228
           I  I       R+L  D +E   + A+ +F+ + P + D   VE LQ+     L  Y++ 
Sbjct: 127 INPIFEFSKSMRELQLDDAEYALLIAINIFSADRPNVQDHHRVERLQETYVEALHSYIKI 186

Query: 229 RYSRQPTRFGRLLLMLPSLRAVRQSTIERLF 259
           +       F R+L+ L SLR +     E++F
Sbjct: 187 KRPSDRLMFPRMLMKLVSLRTLSSVHSEQVF 217

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

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

 Score = 47.4 bits (113), Expect = 3e-06
 Identities = 58/240 (24%), Positives = 95/240 (39%), Gaps = 41/240 (17%)

Query: 59  PPP--SHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLS 116
           PP   S + P+      +P     L+ +L +         R L   + W + +  F  LS
Sbjct: 15  PPHIYSEYDPT------RPFTEASLMMLLTN------LADRELVHMINWAKKIPGFVDLS 62

Query: 117 KRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEIL 176
             DQ+ LL+ +W EL +L L   S+     LL           PD +   N+   ++ ++
Sbjct: 63  LHDQVHLLESAWLELLMLGLVWRSMEHPGKLL---------FAPDLLLDRNQGSCVEGMV 113

Query: 177 ----------ARFRQLSPDGSECGCMKAVILFT-----PETPGLVDAQPVEMLQDQAQCI 221
                     +RFR+L     E  C+KA+IL            L   + V+ L D+    
Sbjct: 114 EIFDMLLATASRFRELQLQREEYVCLKAIILLNSSVYTFLLESLESRRQVQRLLDKITDA 173

Query: 222 LGDYVRGRY---SRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT 278
           L      R     +Q  R  +LLL+L  +R V    +E L+  +    +P+  LL +M  
Sbjct: 174 LVHACSKRGLSLQQQSRRLAQLLLILSHIRHVSNKGMEHLYSMKCKNVVPLYDLLLEMLD 233

The ligand binding domain (LBD) of Estrogen receptor (ER): Estrogen receptor, a member of nuclear receptor superfamily, is activated by the hormone estrogen. Estrogen regulates many physiological processes including reproduction, bone integrity, cardiovascular health, and behavior. The main mechanism of action of the estrogen receptor is as a transcription factor by binding to the estrogen response element of target genes upon activation by estrogen and then recruiting coactivator proteins which are responsible for the transcription of target genes. Additionally some ERs may associate with other membrane proteins and can be rapidly activated by exposure of cells to estrogen. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). The C-terminal LBD also contains AF-2 activation motif, the dimerization motif, and part of the nuclear localization region. Estrogen receptor has been linked to aging, cancer, obesity and other diseases. Length = 235

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

 Score = 43.4 bits (103), Expect = 3e-05
 Identities = 22/50 (44%), Positives = 30/50 (60%), Gaps = 1/50 (2%)

Query: 285 TPGLVDAQPVEMLQDQAQCILGDYVRGRYS-RQPTRFGRLLLMLPSLRAV 333
              L D + VE LQ++    L DY+R  Y    P+RF +LLL+LPSLR +
Sbjct: 119 KESLEDRKIVEELQERLLEALQDYLRKNYPEEAPSRFAKLLLLLPSLRKL 168

Ligand-binding domain (LBD) of nuclear receptor (NR): Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). Length = 168

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

 Score = 43.9 bits (104), Expect = 5e-05
 Identities = 44/209 (21%), Positives = 77/209 (36%), Gaps = 23/209 (11%)

Query: 52  PSGLKSPPPPSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAP 111
            +G  +   P   +    L  ++          +   ++CQ  +   +     + + L  
Sbjct: 29  LTGKTTDHAPFVIYDIESLKLNKDGQPQEKTIRIRLFQRCQVRSVETIRELTEFAKSLPG 88

Query: 112 FQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNE--- 168
           F+ L   DQ+ LL+    E+    LA          L N  K     P  +  V  E   
Sbjct: 89  FRNLDLNDQVTLLKYGVHEVIFTMLAS---------LYN--KDGLLFPEGNGYVTREFLE 137

Query: 169 ---------IKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQ 219
                    ++   E   +F  L    SE     AVI+ +P+ PGL++ +PVE +Q+   
Sbjct: 138 SLRKPFCDIMEPKFEFAEKFNALELTDSELALFCAVIILSPDRPGLINRKPVERIQEHVL 197

Query: 220 CILGDYVRGRYSRQPTRFGRLLLMLPSLR 248
             L   ++  +   P  F +LL  +  LR
Sbjct: 198 QALELQLKKNHPDSPQLFAKLLQKMVDLR 226

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

 Score = 41.6 bits (98), Expect = 2e-04
 Identities = 27/74 (36%), Positives = 36/74 (48%), Gaps = 7/74 (9%)

Query: 290 DAQPVEMLQDQAQCILGDYVRGRYSRQ-PTRFGRLLLMLPSLRAVRQSTIERLFF---KE 345
           D + V  L+D     L DY  GR+  + P R G+LLL LP LR        R FF   K 
Sbjct: 148 DVEAVRQLRDALLEALSDYEAGRHPGEAPRRAGQLLLTLPLLRQT--DGKARRFFYGVKR 205

Query: 346 TIGDIPIQRLLGDM 359
             G +P+ +L  +M
Sbjct: 206 E-GKVPMHKLFLEM 218

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

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

 Score = 42.5 bits (100), Expect = 2e-04
 Identities = 37/156 (23%), Positives = 65/156 (41%)

Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDD 162
           V + + L  F  L   DQ++LL+    E+  L  A    P   +L ++ E A  R    +
Sbjct: 69  VDFAKKLPMFTELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLSGEMAVTREQLKN 128

Query: 163 VRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCIL 222
             +      I ++       + D +E   ++AV+L + + PGL   + +E LQD      
Sbjct: 129 GGLGVVSDAIFDLGVSLSSFNLDDTEVALLQAVLLMSSDRPGLACVERIEKLQDSFLLAF 188

Query: 223 GDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 258
             Y+  R    P  + +LL+ +  LR +      R 
Sbjct: 189 EHYINYRKHHVPHFWPKLLMKVTDLRMIGACHASRF 224

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

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

 Score = 41.0 bits (96), Expect = 4e-04
 Identities = 39/156 (25%), Positives = 62/156 (39%), Gaps = 3/156 (1%)

Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDD 162
           V + + L  F+TL   DQ+ LL+ S  E   L  AQ  I        + +   ER+    
Sbjct: 53  VEFTKGLPGFETLDHEDQIALLKGSAVEAMFLRSAQ--IYNKKLPAGHADLLEERIRSSG 110

Query: 163 VRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCIL 222
           +  +  I  +        +L     E   + A+ +  P+ P L D + VE LQ+    +L
Sbjct: 111 I-SDEFITPMFNFYKSMGELKMTQEEYALLTAITILFPDRPYLKDKEAVEKLQEPLLDLL 169

Query: 223 GDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 258
             + +  +   P  F  LL  L  LR +     E L
Sbjct: 170 QKFCKLYHPEDPQHFACLLGRLTELRTLNHHHAEML 205

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

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

 Score = 40.3 bits (94), Expect = 6e-04
 Identities = 35/147 (23%), Positives = 73/147 (49%), Gaps = 8/147 (5%)

Query: 112 FQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKL 171
           F+ L+  DQ+ LL+ S  E+ +L   Q     D+S        + ++  D  +  + ++L
Sbjct: 63  FRDLTAEDQIALLKSSAIEVIMLRSNQSFSLDDMSWTCGSPDFKYKVS-DVTKAGHSLEL 121

Query: 172 IQEILARF----RQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVR 227
           + E L +F    ++L+    E   + A+ + +P+ PG+ D   +E +QD+    L  Y+R
Sbjct: 122 L-EPLVKFQVGLKKLNLHEEEHVLLMAICILSPDRPGVQDHALIEAIQDRLSDTLQTYIR 180

Query: 228 GRYSRQPTR--FGRLLLMLPSLRAVRQ 252
            R+    +R  + +++  L  LR++ +
Sbjct: 181 CRHPPPGSRLLYAKMIQKLADLRSLNE 207

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

 Score = 39.8 bits (93), Expect = 7e-04
 Identities = 37/150 (24%), Positives = 63/150 (42%), Gaps = 6/150 (4%)

Query: 112 FQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKL 171
           F+ LS+ DQ+ LL+    E+ ++  A      + S+     +       DD+       L
Sbjct: 38  FRDLSQHDQVTLLKAGTFEVLMVRFASLFDAKERSVTFLSGQKYSV---DDLHSMGAGDL 94

Query: 172 IQ---EILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRG 228
           +    +   +   L     E G   AV+L + +  GL +   VE LQ+     L   +  
Sbjct: 95  LNSMFDFSEKLNSLQLSDEEMGLFTAVVLVSADRSGLENVNLVEALQETLIRALRTLIAK 154

Query: 229 RYSRQPTRFGRLLLMLPSLRAVRQSTIERL 258
            +  +P+ F +LLL LP LR +     E+L
Sbjct: 155 NHPNEPSIFTKLLLKLPDLRTLNNLHSEKL 184

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|214658 smart00430, HOLI, Ligand binding domain of hormone receptors

 Score = 38.1 bits (89), Expect = 0.002
 Identities = 21/55 (38%), Positives = 29/55 (52%), Gaps = 3/55 (5%)

Query: 282 SYETPGLVDA--QPVEMLQDQAQCILGDYVRGRYSRQ-PTRFGRLLLMLPSLRAV 333
           +   PGL +   + VE LQ++    L DY    Y    P RF +LLL+LP LR +
Sbjct: 109 NPAVPGLSEEGKEIVEKLQEKYANALHDYYLKNYPMNYPGRFAKLLLILPELRKI 163

Length = 163

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

 Score = 38.0 bits (89), Expect = 0.003
 Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 2/49 (4%)

Query: 286 PGLVDAQPVEMLQDQ-AQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAV 333
           PGL D   VE LQ++  +  L  Y++  +   P  F +LL  L  LR +
Sbjct: 119 PGLQDVDTVEKLQERLLEA-LQRYLKVNHPDAPQMFAKLLKKLTELRTL 166

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

 Score = 38.2 bits (89), Expect = 0.004
 Identities = 41/145 (28%), Positives = 65/145 (44%), Gaps = 10/145 (6%)

Query: 109 LAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNE 168
           L  F  LS+ DQ+ LL+    E+ +L +A+       S++    +   R   D  R    
Sbjct: 62  LPGFDKLSREDQITLLKACSSEVMMLRVARRYDAKTDSIVFANNQPYTR---DSYRKAGM 118

Query: 169 IKLIQEILARF-RQLSP---DGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGD 224
                E L RF R +     D +E   + A+++F+ + PGL+  + VE +Q+     L  
Sbjct: 119 GDSA-EDLFRFCRAMCSMKVDNAEYALLTAIVIFS-DRPGLLQPKKVEKIQEIYLEALRA 176

Query: 225 YVRGRYS-RQPTRFGRLLLMLPSLR 248
           YV  R    Q   F +LL +L  LR
Sbjct: 177 YVDNRRPPSQRVIFAKLLSILTELR 201

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	367
cd07076	247	NR_LBD_GR Ligand binding domain of the glucocortic	100.0
cd06949	235	NR_LBD_ER Ligand binding domain of Estrogen recept	100.0
cd06937	231	NR_LBD_RAR The ligand binding domain (LBD) of reti	100.0
cd07348	238	NR_LBD_NGFI-B The ligand binding domain of Nurr1,	100.0
cd06947	246	NR_LBD_GR_Like Ligand binding domain of nuclear ho	100.0
cd07071	238	NR_LBD_Nurr1 The ligand binding domain of Nurr1, a	100.0
cd06935	243	NR_LBD_TR The ligand binding domain of thyroid hor	100.0
cd06945	239	NR_LBD_Nurr1_like The ligand binding domain of Nur	100.0
cd07073	246	NR_LBD_AR Ligand binding domain of the nuclear rec	100.0
cd07075	248	NR_LBD_MR Ligand binding domain of the mineralocor	100.0
cd07069	241	NR_LBD_Lrh-1 The ligand binding domain of the live	100.0
cd07349	222	NR_LBD_SHP The ligand binding domain of DAX1 prote	100.0
cd07072	239	NR_LBD_DHR38_like Ligand binding domain of DHR38_l	100.0
cd06950	206	NR_LBD_Tlx_PNR_like The ligand binding domain of T	100.0
cd06946	221	NR_LBD_ERR The ligand binding domain of estrogen r	100.0
cd07070	237	NR_LBD_SF-1 The ligand binding domain of nuclear r	100.0
cd06944	237	NR_LBD_Ftz-F1_like The ligand binding domain of FT	100.0
cd07068	221	NR_LBD_ER_like The ligand binding domain of estrog	100.0
cd06941	195	NR_LBD_DmE78_like The ligand binding domain of Dro	100.0
cd07350	232	NR_LBD_Dax1 The ligand binding domain of DAX1 prot	100.0
cd06951	222	NR_LBD_Dax1_like The ligand binding domain of DAX1	100.0
cd06948	236	NR_LBD_COUP-TF Ligand binding domain of chicken ov	100.0
cd07074	248	NR_LBD_PR Ligand binding domain of the progesteron	100.0
cd06940	189	NR_LBD_REV_ERB The ligand binding domain of REV-ER	100.0
cd06939	241	NR_LBD_ROR_like The ligand binding domain of Retin	100.0
cd06954	236	NR_LBD_LXR The ligand binding domain of Liver X re	100.0
cd06938	231	NR_LBD_EcR The ligand binding domain (LBD) of the	100.0
cd06932	259	NR_LBD_PPAR The ligand binding domain of peroxisom	100.0
cd06933	238	NR_LBD_VDR The ligand binding domain of vitamin D	100.0
cd06934	226	NR_LBD_PXR_like The ligand binding domain of xenob	100.0
cd06943	207	NR_LBD_RXR_like The ligand binding domain of the r	100.0
cd06952	222	NR_LBD_TR2_like The ligand binding domain of the o	100.0
cd06936	221	NR_LBD_Fxr The ligand binding domain of Farnesoid	100.0
cd06953	213	NR_LBD_DHR4_like The ligand binding domain of orph	100.0
cd06931	222	NR_LBD_HNF4_like The ligand binding domain of hept	100.0
cd06929	174	NR_LBD_F1 Ligand-binding domain of nuclear recepto	100.0
KOG4215|consensus	432		100.0
cd06942	191	NR_LBD_Sex_1_like The ligand binding domain of Cae	100.0
cd06930	165	NR_LBD_F2 Ligand-binding domain of nuclear recepto	99.98
cd06157	168	NR_LBD The ligand binding domain of nuclear recept	99.94
PF00104	203	Hormone_recep: Ligand-binding domain of nuclear ho	99.93
smart00430	163	HOLI Ligand binding domain of hormone receptors.	99.92
KOG4218|consensus	475		99.92
KOG4217|consensus	605		99.88
KOG4216|consensus	479		99.85
cd07069	241	NR_LBD_Lrh-1 The ligand binding domain of the live	99.77
cd07349	222	NR_LBD_SHP The ligand binding domain of DAX1 prote	99.77
cd06937	231	NR_LBD_RAR The ligand binding domain (LBD) of reti	99.75
cd07070	237	NR_LBD_SF-1 The ligand binding domain of nuclear r	99.75
cd07348	238	NR_LBD_NGFI-B The ligand binding domain of Nurr1,	99.72
cd06944	237	NR_LBD_Ftz-F1_like The ligand binding domain of FT	99.72
cd06949	235	NR_LBD_ER Ligand binding domain of Estrogen recept	99.72
cd07350	232	NR_LBD_Dax1 The ligand binding domain of DAX1 prot	99.71
cd06945	239	NR_LBD_Nurr1_like The ligand binding domain of Nur	99.69
cd06951	222	NR_LBD_Dax1_like The ligand binding domain of DAX1	99.69
cd07071	238	NR_LBD_Nurr1 The ligand binding domain of Nurr1, a	99.68
cd07072	239	NR_LBD_DHR38_like Ligand binding domain of DHR38_l	99.68
cd06932	259	NR_LBD_PPAR The ligand binding domain of peroxisom	99.65
cd06948	236	NR_LBD_COUP-TF Ligand binding domain of chicken ov	99.64
cd06935	243	NR_LBD_TR The ligand binding domain of thyroid hor	99.63
cd06941	195	NR_LBD_DmE78_like The ligand binding domain of Dro	99.59
cd07068	221	NR_LBD_ER_like The ligand binding domain of estrog	99.59
cd06946	221	NR_LBD_ERR The ligand binding domain of estrogen r	99.57
cd06939	241	NR_LBD_ROR_like The ligand binding domain of Retin	99.56
cd07076	247	NR_LBD_GR Ligand binding domain of the glucocortic	99.56
cd06952	222	NR_LBD_TR2_like The ligand binding domain of the o	99.55
cd07073	246	NR_LBD_AR Ligand binding domain of the nuclear rec	99.55
cd06954	236	NR_LBD_LXR The ligand binding domain of Liver X re	99.53
cd06947	246	NR_LBD_GR_Like Ligand binding domain of nuclear ho	99.52
cd06933	238	NR_LBD_VDR The ligand binding domain of vitamin D	99.52
cd06950	206	NR_LBD_Tlx_PNR_like The ligand binding domain of T	99.48
cd06936	221	NR_LBD_Fxr The ligand binding domain of Farnesoid	99.46
cd06938	231	NR_LBD_EcR The ligand binding domain (LBD) of the	99.46
cd06940	189	NR_LBD_REV_ERB The ligand binding domain of REV-ER	99.45
cd06934	226	NR_LBD_PXR_like The ligand binding domain of xenob	99.41
cd07075	248	NR_LBD_MR Ligand binding domain of the mineralocor	99.31
KOG4215|consensus	432		99.28
cd06943	207	NR_LBD_RXR_like The ligand binding domain of the r	99.28
cd06931	222	NR_LBD_HNF4_like The ligand binding domain of hept	99.28
cd06953	213	NR_LBD_DHR4_like The ligand binding domain of orph	99.15
cd06929	174	NR_LBD_F1 Ligand-binding domain of nuclear recepto	98.92
cd06942	191	NR_LBD_Sex_1_like The ligand binding domain of Cae	98.92
KOG4217|consensus	605		98.67
cd06930	165	NR_LBD_F2 Ligand-binding domain of nuclear recepto	98.57
cd07074	248	NR_LBD_PR Ligand binding domain of the progesteron	98.28
KOG4216|consensus	479		98.02
PF00104	203	Hormone_recep: Ligand-binding domain of nuclear ho	97.93
smart00430	163	HOLI Ligand binding domain of hormone receptors.	97.7
cd06157	168	NR_LBD The ligand binding domain of nuclear recept	97.61
KOG4846|consensus	538		96.85
KOG4218|consensus	475		95.96
KOG4846|consensus	538		94.84

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

Probab=100.00  E-value=7.8e-41  Score=302.60  Aligned_cols=210  Identities=20%  Similarity=0.253  Sum_probs=182.3

Q ss_pred             CCCcccccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccC
Q psy6602          64 HHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPW  143 (367)
Q Consensus        64 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~  143 (367)
                      .+|..++++|++..|++....   +..+|+++++.++.+|+|||++|||.+|+.+||++|||+||+|++++++|||+.+.
T Consensus         9 ~ep~~~~~~~d~~~p~~~~~~---~~~l~~la~r~L~~~VeWAK~IPgF~~L~l~DQi~LLk~sW~Ellvl~~a~rs~~~   85 (247)
T cd07076           9 IEPEVLYSGYDSSVPDSTWRI---MSTLNMLGGRQVVAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMAFALGWRSYRQ   85 (247)
T ss_pred             cCCCcccCCCCCCCCCcHHHH---HHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHhccCC
Confidence            577889999999999998666   45699999999999999999999999999999999999999999999999999986


Q ss_pred             CCc-eE-ecCCccccCCCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCC-CCCCCCChhHHHHHHHHHHH
Q psy6602         144 DLS-LL-INCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTP-ETPGLVDAQPVEMLQDQAQC  220 (367)
Q Consensus       144 ~~~-~l-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~p-d~~~L~~~~~v~~~q~~~~~  220 (367)
                      .+. .+ +.++...++......+..+.++.+.+++.+|++|++|.+||+|||||+||+| |++|++++..|+++|++|..
T Consensus        86 ~~~~~l~fa~~~~~~~~~~~~~~~~~~~~~l~e~~~~~r~L~ld~~EfacLKAIvLfnp~d~~GL~~~~~Ve~lqe~~~~  165 (247)
T cd07076          86 SNGNLLCFAPDLIINEQRMTLPCMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSTVPKDGLKSQELFDEIRMTYIK  165 (247)
T ss_pred             CCCceEEecCCeeecHHHHhhhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHHH
Confidence            654 34 4455555544434445666678899999999999999999999999999999 99999999999999999999


Q ss_pred             HHHHHHHhhCCCcc---hHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHc
Q psy6602         221 ILGDYVRGRYSRQP---TRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT  278 (367)
Q Consensus       221 ~L~~y~~~~~~~~~---~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~  278 (367)
                      +|.+|+..++++.+   .|||+|+++|+++|+++....|  |+.+.+++.++..++.+|+.
T Consensus       166 aL~~yi~~~~p~~~~~~~RF~kLLllLp~Lr~i~~~~~e--f~~~~~~~~~~~~~~~~ml~  224 (247)
T cd07076         166 ELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEVVENLLN--FCFQTFLDKTMSIEFPEMLA  224 (247)
T ss_pred             HHHHHHHhcCCCcchhhhHHHHHHHHHHHHHHHHHHHHH--HHHHHhcccchhhhhHHHHH
Confidence            99999999987654   4999999999999999999999  66667777777666666654

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

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

Probab=100.00  E-value=2.8e-40  Score=299.66  Aligned_cols=213  Identities=24%  Similarity=0.329  Sum_probs=192.4

Q ss_pred             CCCcccccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccC
Q psy6602          64 HHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPW  143 (367)
Q Consensus        64 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~  143 (367)
                      .+|..+++.|+|..+++....   ++.+++++++.++.+|+|||++|||.+|+.+||++|||++|+|+++|+.|||+...
T Consensus        13 ~~~~~~~~~~~~~~~~~~~~~---~~~l~~la~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w~el~~L~~a~rs~~~   89 (235)
T cd06949          13 AEPPHIYSEYDPTRPFTEASL---MMLLTNLADRELVHMINWAKKIPGFVDLSLHDQVHLLESAWLELLMLGLVWRSMEH   89 (235)
T ss_pred             hCCCcCcCCCCCCCCCChHHH---HHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcCC
Confidence            466777788887777776555   77899999999999999999999999999999999999999999999999999988


Q ss_pred             CCceEecCCccccCCCCC-ccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCC-----CCChhHHHHHHHH
Q psy6602         144 DLSLLINCEKARERLPPD-DVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPG-----LVDAQPVEMLQDQ  217 (367)
Q Consensus       144 ~~~~l~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~-----L~~~~~v~~~q~~  217 (367)
                      ++..++.++......... ..+..+..+.+.+++.+|++|++|.+||+|||||+|||||++|     +.++.+|+++|++
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~EyalLKAIvLfnpd~~g~~~~~l~~~~~Ve~lq~~  169 (235)
T cd06949          90 PGKLLFAPDLLLDRNQGSCVEGMVEIFDMLLATASRFRELQLQREEYVCLKAIILLNSSVYTFLLESLESRRQVQRLLDK  169 (235)
T ss_pred             CCeEEeeCCceecHHHhhhcccHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHcCCCcCCcccccccCHHHHHHHHHH
Confidence            777777777665544332 3345667788999999999999999999999999999999999     8899999999999


Q ss_pred             HHHHHHHHHHhhC---CCcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcc
Q psy6602         218 AQCILGDYVRGRY---SRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM  279 (367)
Q Consensus       218 ~~~~L~~y~~~~~---~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~  279 (367)
                      +..+|++||..++   ++++.||++|+++++.+|+++..+.|.+++.+.++..++++++.||++.
T Consensus       170 ~~~aL~~y~~~~~~~~p~~~~Rf~~LLl~Lp~LR~l~~~~~e~l~~~k~~~~~~~~~Ll~Eml~~  234 (235)
T cd06949         170 ITDALVHACSKRGLSLQQQSRRLAQLLLILSHIRHVSNKGMEHLYSMKCKNVVPLYDLLLEMLDA  234 (235)
T ss_pred             HHHHHHHHHHhcCCCCCCcccHHHHHHHhchHHHHhhHHHHHHHHHHHhCCCCChHHHHHHHhcC
Confidence            9999999999998   8999999999999999999999999999999999999999999999974

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

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

Probab=100.00  E-value=4e-40  Score=297.90  Aligned_cols=194  Identities=21%  Similarity=0.301  Sum_probs=178.0

Q ss_pred             ccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccc
Q psy6602          85 LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVR  164 (367)
Q Consensus        85 ~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~  164 (367)
                      ...++++++++++.++.+|+|||++|||.+|+.+||++|||+||+|+++++.||++.+.++...+.++....+......+
T Consensus        37 ~~~~~~l~e~~~~~l~~~V~wAK~iPgF~~L~~~DQi~LLk~~w~El~~L~~a~~~~~~~~~l~~~~~~~~~~~~~~~~~  116 (231)
T cd06937          37 LGLWDKFSELSTKCIIKIVEFAKRLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMHNAG  116 (231)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEecCCceecHHHHhhcC
Confidence            34488999999999999999999999999999999999999999999999999999887777666665444444333344


Q ss_pred             hHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhh
Q psy6602         165 VNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLML  244 (367)
Q Consensus       165 ~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l  244 (367)
                      ....++.+.+|+.+|++|++|.+||+|||||+||+||++|+.+..+|+++|+++.++|+.|+..+||+.+.||++||++|
T Consensus       117 ~~~~~~~~~~~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~p~rf~kLLl~L  196 (231)
T cd06937         117 FGPLTDLVFTFANQLLPLEMDDTEIGLLSAICLICGDRQDLEEPDRVEKLQEPLLEALKIYARKRRPDKPHMFPKMLMKI  196 (231)
T ss_pred             hHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCccCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHh
Confidence            56677889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHc
Q psy6602         245 PSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT  278 (367)
Q Consensus       245 ~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~  278 (367)
                      +.||+++..++|.+++.+..+..++++++.||++
T Consensus       197 p~LR~l~~~~~e~l~~~k~~~~~~~~~Ll~Eml~  230 (231)
T cd06937         197 TDLRSISAKGAERVITLKMEIPGPMPPLISEMLE  230 (231)
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHhc
Confidence            9999999999999999999999999999999986

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

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

Probab=100.00  E-value=1.5e-39  Score=294.11  Aligned_cols=193  Identities=24%  Similarity=0.367  Sum_probs=177.8

Q ss_pred             cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccch
Q psy6602          86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRV  165 (367)
Q Consensus        86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~  165 (367)
                      ..++++++++++.++.+|+|||++|||.+|+.+||++|||+||+|+++|+.|||+.+.++..++.++...++... ..+.
T Consensus        41 ~~~~~~~el~t~~l~~iVewAK~iPgF~~L~~~DQi~LLk~~w~El~vL~~a~r~~~~~~~l~f~~~~~~~r~~~-~~~~  119 (238)
T cd07348          41 SDIQQFYDLLSGSLEVIRKWAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNPEEGKLIFCNGVVLHRTQC-VRGF  119 (238)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHccCCCccCCChHHHHHHHHHHHHHHHHHHHHHHcCCCCCeEEeeCCeeecHHHH-HhhH
Confidence            448999999999999999999999999999999999999999999999999999999887777777665555442 3456


Q ss_pred             HHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhC--CCcchHHHHHHHh
Q psy6602         166 NNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRY--SRQPTRFGRLLLM  243 (367)
Q Consensus       166 ~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~--~~~~~Rf~~LL~~  243 (367)
                      .+.++.+.+|+.+|++|++|.+||+|||||+|| ||++|+++..+|+++|+++.++|+.|+..++  |+.+.||++||++
T Consensus       120 ~~~~~~i~ef~~~l~~L~ld~~E~a~LkAIvLf-~Dr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~p~~p~rf~kLLl~  198 (238)
T cd07348         120 GDWIDSILEFSQSLHRMNLDVSAFSCLAALVII-TDRHGLKEPKRVEELQNRLISCLKEHVSGSASEPQRPNCLSRLLGK  198 (238)
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc-CCCcCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccccHHHHHHHH
Confidence            778889999999999999999999999999999 7999999999999999999999999999864  8999999999999


Q ss_pred             hhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHccc
Q psy6602         244 LPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  280 (367)
Q Consensus       244 l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~  280 (367)
                      |+.||+++..+.|.+++.+..+..++++++.|||...
T Consensus       199 Lp~LRsl~~~~~e~lf~~kl~~~~~~~pLl~e~~~~~  235 (238)
T cd07348         199 LPELRTLCTQGLQRIFYLKLEDLVPPPPIVDKIFMDT  235 (238)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHhcc
Confidence            9999999999999999999999999999999999743

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

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

Probab=100.00  E-value=9.1e-39  Score=290.38  Aligned_cols=223  Identities=18%  Similarity=0.233  Sum_probs=188.2

Q ss_pred             CCCcccccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccC
Q psy6602          64 HHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPW  143 (367)
Q Consensus        64 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~  143 (367)
                      .+|..++++|++..|++....   ++++++++++.++.+|+|||++|||.+|+.+||++|||+||+|+++++.|||+...
T Consensus         9 ~ep~~~~~~~~~~~p~~~~~~---~~~l~ela~~~L~~~VeWAK~iPgF~~L~~~DQi~LLk~~w~ElliL~~a~rs~~~   85 (246)
T cd06947           9 IEPEVVYAGYDNSQPDTTARL---LSSLNRLGERQLVSVVKWAKALPGFRNLHLDDQMTLIQYSWMSLMVFALGWRSYKH   85 (246)
T ss_pred             cCCCcccCCCCCCCCCchhHH---HHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHhhccC
Confidence            455667788888888876544   67799999999999999999999999999999999999999999999999998875


Q ss_pred             CCc-eE-ecCCccccCCCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCC-CCCCCCChhHHHHHHHHHHH
Q psy6602         144 DLS-LL-INCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTP-ETPGLVDAQPVEMLQDQAQC  220 (367)
Q Consensus       144 ~~~-~l-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~p-d~~~L~~~~~v~~~q~~~~~  220 (367)
                      .+. .+ +.++...++......+..+.+..+.+++.+|++|++|.+||+|||||+|||| |++|+.++..|+++|+++..
T Consensus        86 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~L~ld~~E~acLKAIvLfn~~d~~gL~~~~~Ve~lqe~i~~  165 (246)
T cd06947          86 VNSQMLYFAPDLVFNEQRMHQSAMYSLCLGMRQISQEFVRLQVTYEEFLCMKVLLLLSTIPKDGLKSQAAFDEMRMNYIK  165 (246)
T ss_pred             CCCCeEEecCCeeecHHHhhhccHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHcCCCccccccCHHHHHHHHHHHHH
Confidence            543 34 4455555544433444566667788999999999999999999999999999 89999999999999999999


Q ss_pred             HHHHHHHhhCC---CcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccC---CchhHhHHHHHHcccCCCCCCCCC
Q psy6602         221 ILGDYVRGRYS---RQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIG---DIPIQRLLGDMYTMEKSYETPGLV  289 (367)
Q Consensus       221 ~L~~y~~~~~~---~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~---~~~~~~Ll~eml~~~~s~d~~gl~  289 (367)
                      +|.+|+.++++   +.+.|||+|+++|+.+|+++....|+++......   .+++++++.|||+.....-..|..
T Consensus       166 AL~~yi~~~~~~~~~~~~Rf~kLLllLp~Lr~i~~~~~e~~~~~~~~~~~~~v~~~~ll~ei~~~~~~~~~~~~~  240 (246)
T cd06947         166 ELRKAIVKREKNSSQSWQRFYQLTKLLDSMHDLVKNLLQFCFYTFIQSHALSVEFPEMLVEIISDQLPKVLSGNV  240 (246)
T ss_pred             HHHHHHHHhCCCCcccchHHHHHHHhhhhHHHHHHHHHHHHHHHHhhcCCCccccHHHHHHHHHcccchhhcCCc
Confidence            99999998863   5689999999999999999999999998774433   368999999999977654455543

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

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

Probab=100.00  E-value=7.8e-39  Score=289.69  Aligned_cols=192  Identities=24%  Similarity=0.334  Sum_probs=176.2

Q ss_pred             cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccch
Q psy6602          86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRV  165 (367)
Q Consensus        86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~  165 (367)
                      ..++++++++++.++.+|+|||++|||.+|+.+||++|||+||+|+++++.||++++.++..++.++..+.+... ..++
T Consensus        41 ~~~~~~~e~~~~~i~~iVewAK~iPgF~~L~~~DQi~LLk~~~~Ell~L~~a~~~~~~~~~l~~~~g~~~~~~~~-~~~~  119 (238)
T cd07071          41 QHIQQFYDLLTGSMEIIRGWAEKIPGFTDLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIFCNGVVLHRLQC-VRGF  119 (238)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCCceEeeCCceechhhh-hhcH
Confidence            448899999999999999999999999999999999999999999999999999998887777766655555442 3456


Q ss_pred             HHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhC--CCcchHHHHHHHh
Q psy6602         166 NNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRY--SRQPTRFGRLLLM  243 (367)
Q Consensus       166 ~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~--~~~~~Rf~~LL~~  243 (367)
                      .+.++.+.+|+.+|++|++|.+||+|||||+|| +|++|+.+..+|+++|+++..+|++|+..++  ++.+.||++||++
T Consensus       120 ~~~~~~i~ef~~~l~~L~ld~~E~alLkAIvLf-~D~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~p~~~~rf~kLLl~  198 (238)
T cd07071         120 GEWIDSIVEFSSNLQNMNIDISAFSCIAALAMV-TERHGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLGK  198 (238)
T ss_pred             HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHc-CCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCCcccHHHHHHHH
Confidence            777888999999999999999999999999999 5999999999999999999999999999774  5899999999999


Q ss_pred             hhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcc
Q psy6602         244 LPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM  279 (367)
Q Consensus       244 l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~  279 (367)
                      |+.||+++..+.|.+++.+..+..++++++.+||..
T Consensus       199 Lp~LRsl~~~~~e~l~~~k~~~~~p~~~Ll~e~~~~  234 (238)
T cd07071         199 LPELRTLCTQGLQRIFYLKLEDLVPPPAIIDKLFLD  234 (238)
T ss_pred             hHHHHHHHHHHHHHHHHHHcCCCCCCcHHHHHHHHh
Confidence            999999999999999999999999999999999863

The ligand binding domain of nuclear receptor Nurr1: Nurr1 belongs to the conserved family of nuclear receptors. It is a transcription factor that is expressed in the embryonic ventral midbrain and is critical for the development of dopamine (DA) neurons. Structural studies have shown that the ligand binding pocket of Nurr1 is filled by bulky hydrophobic residues, making it unable to bind to ligands. Therefore, it belongs to the class of orphan receptors. However, Nurr1 forms heterodimers with RXR and can promote signaling via its partner, RXR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, Nurr1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).

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

Probab=100.00  E-value=1.9e-39  Score=295.70  Aligned_cols=203  Identities=20%  Similarity=0.239  Sum_probs=180.4

Q ss_pred             CCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCc
Q psy6602          74 QPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEK  153 (367)
Q Consensus        74 ~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~  153 (367)
                      .++.+++.......|.++++++++.++.+|+|||++|||.+|+.+||++|||+||+|+++++.||++...++...+.++.
T Consensus        40 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~iVefAK~iPgF~~L~~~DQi~LLk~~~~ElliL~~a~~~~~~~~~~~~~~~~  119 (243)
T cd06935          40 IVSAPDGDKVDLEAFSHFTKIITPAITRVVDFAKKLPMFTELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLSGEM  119 (243)
T ss_pred             CCCCCccccccHHHHHHHHHHHHHHHHHHHHHHhcCCccccCChHHHHHHHHHhHHHHHHHHHHHHhCcCCCeEEeeCCe
Confidence            33445545555666999999999999999999999999999999999999999999999999999998776666666655


Q ss_pred             cccCCCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCc
Q psy6602         154 ARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQ  233 (367)
Q Consensus       154 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~  233 (367)
                      .+.+......+....++.+.+|+.+|++|++|++||+|||||+||+||++|+.+..+|+++|+.+..+|+.|+..++|+.
T Consensus       120 ~~~~~~~~~~~~~~~~~~i~~f~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~  199 (243)
T cd06935         120 AVTREQLKNGGLGVVSDAIFDLGVSLSSFNLDDTEVALLQAVLLMSSDRPGLACVERIEKLQDSFLLAFEHYINYRKHHV  199 (243)
T ss_pred             EeeHHHHHhcChHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCC
Confidence            44554443445667788999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             chHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchh-HhHHHHH
Q psy6602         234 PTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI-QRLLGDM  276 (367)
Q Consensus       234 ~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~-~~Ll~em  276 (367)
                      +.||++||++++.||+++..+.|.+++.+..+..++ ++|+.||
T Consensus       200 ~~rf~kLL~~L~~LR~i~~~~~e~l~~~k~~~~~~~~~~L~~Em  243 (243)
T cd06935         200 PHFWPKLLMKVTDLRMIGACHASRFLHMKVECPTELFPPLFLEV  243 (243)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCChhhhcC
Confidence            999999999999999999999999999999988775 8888775

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

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

Probab=100.00  E-value=1.8e-38  Score=288.40  Aligned_cols=193  Identities=26%  Similarity=0.384  Sum_probs=178.0

Q ss_pred             cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccch
Q psy6602          86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRV  165 (367)
Q Consensus        86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~  165 (367)
                      ..++++++++++.++.+|+|||++|||.+|+.+||++|||+||+|+++|+.|||+++.++..++.++....+... ..+.
T Consensus        41 ~~~~~~~~~~~~~l~~iv~wAK~IPgF~~L~~~DQi~LLk~~w~El~~L~~a~r~~~~~~~l~~~~~~~~~~~~~-~~~~  119 (239)
T cd06945          41 QQVQQFYDLLTGSVDVIRQWAEKIPGFKDLHREDQDLLLESAFLELFVLRLAYRSNPVDGKLVFCNGLVLHRLQC-VRGF  119 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCceEeeCCceecHHHH-HHhH
Confidence            348899999999999999999999999999999999999999999999999999998877766766655544332 2346


Q ss_pred             HHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCC--CcchHHHHHHHh
Q psy6602         166 NNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYS--RQPTRFGRLLLM  243 (367)
Q Consensus       166 ~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~--~~~~Rf~~LL~~  243 (367)
                      .+.++.+.+|+.+|++|++|++||+|||||+||+||++|+.+..+|+++|+++.++|++|+..++|  +.+.||++||++
T Consensus       120 ~~~~~~i~~f~~~l~~L~ld~~E~~~LkaivL~~pD~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~~~rf~kLLl~  199 (239)
T cd06945         120 GEWLDSILAFSSSLQSLLLDDISAFCCLALLLLITERHGLKEPKKVEELQNKIISCLRDHVTSNYPGQDKPNRLSKLLLK  199 (239)
T ss_pred             HHHHHHHHHHHHHHHHHhCChHHHHHHHHHHHhCCCccccCCHHHHHHHHHHHHHHHHHHHHHhCCCcccccHHHHHHHH
Confidence            677889999999999999999999999999999999999999999999999999999999999999  899999999999


Q ss_pred             hhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcc
Q psy6602         244 LPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM  279 (367)
Q Consensus       244 l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~  279 (367)
                      |+.||+++..+.|.+++.+.++..++++++.+||..
T Consensus       200 Lp~LR~ls~~~~e~l~~~k~~~~~~~~~Ll~e~~~~  235 (239)
T cd06945         200 LPELRTLSKKGLQRIFFLKLEDLLPPPPLIDKRFLD  235 (239)
T ss_pred             hHHHHHHHHHHHHHHHHHHccCCCCCChHHHHHHHh
Confidence            999999999999999999999999999999999974

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

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

Probab=100.00  E-value=3.7e-38  Score=286.43  Aligned_cols=220  Identities=18%  Similarity=0.266  Sum_probs=181.0

Q ss_pred             CCCcccccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccC
Q psy6602          64 HHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPW  143 (367)
Q Consensus        64 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~  143 (367)
                      .+|..+++++++..+++.   ...++++++++++.++.+|+|||++|||.+|+.+||++|||+||+|+++|+.|||+.+.
T Consensus         9 ~ep~~~~~~~~~~~~~~~---~~~~~~l~~la~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~w~ElliL~~a~rs~~~   85 (246)
T cd07073           9 IEPGVVCAGHDNNQPDSF---AALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTN   85 (246)
T ss_pred             cCCccccCCCCCCCCCch---hHHHHHHHHHHHHHHHHHHHHHHcCCCccCCCHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            466677788777766663   34478899999999999999999999999999999999999999999999999999875


Q ss_pred             -CCceE-ecCCccccCCCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCC-CCCCCCChhHHHHHHHHHHH
Q psy6602         144 -DLSLL-INCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTP-ETPGLVDAQPVEMLQDQAQC  220 (367)
Q Consensus       144 -~~~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~p-d~~~L~~~~~v~~~q~~~~~  220 (367)
                       +...+ +.++...++......+..+.+..+.+++.+|++|++|.+||+|||||+|||| |++|+.++..|+.+|+++..
T Consensus        86 ~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~L~ld~~EyacLKAIiLfnp~d~~gL~~~~~Ve~lQe~~~~  165 (246)
T cd07073          86 VNSRMLYFAPDLVFNEYRMHKSRMYSQCVRMRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFFDELRMNYIK  165 (246)
T ss_pred             CCCCeEEecCCeeechhhhccccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCcccccCHHHHHHHHHHHHH
Confidence             44434 4444444443333334555666678999999999999999999999999999 99999999999999999999


Q ss_pred             HHHHHHHhhC---CCcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCc-----hhHhHHHHHHcccCCCCCCCC
Q psy6602         221 ILGDYVRGRY---SRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDI-----PIQRLLGDMYTMEKSYETPGL  288 (367)
Q Consensus       221 ~L~~y~~~~~---~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~-----~~~~Ll~eml~~~~s~d~~gl  288 (367)
                      +|.+|+..++   +..+.||++||++|+.+|+++...  .+++.++++..     .+++++.||++.....-..|.
T Consensus       166 aL~~yi~~~~~~~~~~~~Rf~kLLl~Lp~LRsi~~~~--~~~~~~l~~~~~~~~~~~~pll~ei~~~~~~~~~~~~  239 (246)
T cd07073         166 ELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPIAREL--HQFTFDLLIKSHMVSVDFPEMMAEIISVQVPKILSGK  239 (246)
T ss_pred             HHHHHHHhcCCCCcccchHHHHHHHHHHHHHHHHHHH--HHHHHHHhCccccCccCccHHHHHHHHhccchhhcCC
Confidence            9999999874   366899999999999999999988  55666666554     689999999996654333343

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

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

Probab=100.00  E-value=3.7e-38  Score=285.33  Aligned_cols=198  Identities=19%  Similarity=0.213  Sum_probs=170.8

Q ss_pred             CCCcccccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccC
Q psy6602          64 HHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPW  143 (367)
Q Consensus        64 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~  143 (367)
                      .++..+++++++..|++....   +.++|+++++.++.+|+|||++|||.+|+.+||++|||+||+|+++++.|||+.+.
T Consensus         9 ~e~~~~~~~~~~~~p~~~~~~---~~~l~ela~~~L~~iVeWAK~IPgF~~L~~~DQi~LLk~~w~EllvL~~a~rs~~~   85 (248)
T cd07075           9 IEPEIVYAGYDSSKPDTAENL---LSTLNRLAGKQMIQVVKWAKVLPGFRNLPLEDQITLIQYSWMCLSSFALSWRSYKH   85 (248)
T ss_pred             cCCCcccCCCCCCCCCchhHH---HHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhccCC
Confidence            455666678888888776544   67799999999999999999999999999999999999999999999999999876


Q ss_pred             CCc-eE-ecCCccccCCCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCC-CCCCCChhHHHHHHHHHHH
Q psy6602         144 DLS-LL-INCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPE-TPGLVDAQPVEMLQDQAQC  220 (367)
Q Consensus       144 ~~~-~l-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd-~~~L~~~~~v~~~q~~~~~  220 (367)
                      ++. .+ +.++..++.......+..+.++.+.+++.+|++|++|.+||+|||||+||||| ++|++++..|+++|++|..
T Consensus        86 ~~~~~l~fa~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~L~Ld~~E~acLKAIvLfn~d~~~gL~~~~~Ve~lqe~~~~  165 (248)
T cd07075          86 TNSQFLYFAPDLVFNEERMHQSAMYELCQGMHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKDGLKSQAAFEEMRTNYIK  165 (248)
T ss_pred             CCCceEEecCCccccHHHHhhccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHH
Confidence            544 34 44555455544334456677788999999999999999999999999999996 7999999999999999999


Q ss_pred             HHHHHHHhhCC---CcchHHHHHHHhhhHhHhhhhhHHHHHHhhhcc
Q psy6602         221 ILGDYVRGRYS---RQPTRFGRLLLMLPSLRAVRQSTIERLFFKETI  264 (367)
Q Consensus       221 ~L~~y~~~~~~---~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~  264 (367)
                      +|.+|+.++++   ..+.|||+|+++|+.+|+++....|++||....
T Consensus       166 aL~~yi~~~~~~~~~~~~RF~~LLllLp~Lr~i~~k~iE~lff~~~~  212 (248)
T cd07075         166 ELRKMVTKAPNNSGQSWQRFYQLTKLLDSMHDLVSDLLEFCFYTFRE  212 (248)
T ss_pred             HHHHHHHHcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence            99999996654   456899999999999999999999999887553

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

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

Probab=100.00  E-value=6e-38  Score=285.10  Aligned_cols=197  Identities=30%  Similarity=0.473  Sum_probs=173.1

Q ss_pred             ccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCC--CceEecCCccccCCC---
Q psy6602          85 LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD--LSLLINCEKARERLP---  159 (367)
Q Consensus        85 ~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~--~~~l~~~~~~~~~~~---  159 (367)
                      ...+..+|+++++.++.+|+|||++|||.+|+.+||++|||+||+|+++++.||++....  +..++.++.......   
T Consensus        39 ~~~~~~i~~~a~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~w~EllvL~~a~~s~~~~~~~~~ll~~~~~~~~~~~~~  118 (241)
T cd07069          39 LSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIAS  118 (241)
T ss_pred             cchHHHHHHHHHHHHHHHHHHHhhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCeeEecCCCccCchhhhh
Confidence            445788999999999999999999999999999999999999999999999999987542  334444433222211   


Q ss_pred             CCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHH
Q psy6602         160 PDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGR  239 (367)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~  239 (367)
                      ....+....++.+.+++.+|++|++|.+||||||||+|||||++|+.+..+|+.+|+++..+|++|+..+||+.+.||++
T Consensus       119 ~~~~~~~~~~~~~~e~~~~lr~L~ld~~E~a~LKaivLfnpd~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~Rf~k  198 (241)
T cd07069         119 QAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQ  198 (241)
T ss_pred             hhhhHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCchhHHHH
Confidence            11223445567889999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccC
Q psy6602         240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEK  281 (367)
Q Consensus       240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~  281 (367)
                      |+++|++||+++....|.+++++.++..++++++.||+....
T Consensus       199 LLl~Lp~LR~is~~~~e~l~~~~l~g~~~~~~Ll~Eml~~~~  240 (241)
T cd07069         199 LLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHAKR  240 (241)
T ss_pred             HHHHhHHHHHhhHHHHHHHHhccccCCCcHHHHHHHHHhccc
Confidence            999999999999999999999999999999999999998653

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).

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

Probab=100.00  E-value=4.7e-38  Score=281.95  Aligned_cols=193  Identities=32%  Similarity=0.494  Sum_probs=168.0

Q ss_pred             ccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCce---------EecCCccc
Q psy6602          85 LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSL---------LINCEKAR  155 (367)
Q Consensus        85 ~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~---------l~~~~~~~  155 (367)
                      +.+++.+|+++++.++.+|+|||++|+|.+|+.+||++|||++|.|+++|+.||++.+.+...         ++..+...
T Consensus        18 ~~~~~~ice~a~~~L~~~V~WAK~iP~F~~L~~~DQi~LLk~~W~EL~iL~laq~s~~~~~~~~~~~~~~~~~l~~~~~~   97 (222)
T cd07349          18 LCTPHRTCREASDVLVKTVAFMRNLPSFWQLPPQDQLLLLQNCWGPLFLLGLAQDRVTFEVAEAPVPSMLKKILLEGQSS   97 (222)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHhcCCCcccCChHHHHHHHHHccHHHHHHHHHHHccccccccccchhHHHHHHhccccc
Confidence            345888999999999999999999999999999999999999999999999999997765432         22222111


Q ss_pred             cCCCC---CccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCC
Q psy6602         156 ERLPP---DDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSR  232 (367)
Q Consensus       156 ~~~~~---~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~  232 (367)
                      .....   ........++.+.+++.+|++|++|.+||+|||||+||+||++|+.+...|+.+|+++..+|++|+..+||+
T Consensus        98 ~~~~~~~~~~~~~~~~~~~l~e~~~~l~~L~ld~~Eya~LkaivLf~pd~~gl~~~~~V~~lqe~~~~aL~~~~~~~~p~  177 (222)
T cd07349          98 SGGSGQPDRPQPSLAAVQWLQCCLNKFWSLDLSPKEYAYLKGTILFNPDVPGLTASSHVGHLQQEAQWALCEVLEPLHPQ  177 (222)
T ss_pred             ccccchhhhhhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCcccCCCHHHHHHHHHHHHHHHHHHHHHHCCC
Confidence            11110   111123445678899999999999999999999999999999999999999999999999999999999999


Q ss_pred             cchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHH
Q psy6602         233 QPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMY  277 (367)
Q Consensus       233 ~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml  277 (367)
                      .+.||++|+++|+.+|+++...+|.+||.+.+|..++++++.||+
T Consensus       178 ~~~r~~kLLl~Lp~LR~i~~~~ie~lff~~~~g~~~i~~Ll~eml  222 (222)
T cd07349         178 DQGRFARILLTASTLKSIPPSLITDLFFRPIIGDADIAELLGDML  222 (222)
T ss_pred             cccHHHHHHHHhHHHhcCCHHHHHHHhCccccCCCcHHHHHHHhC
Confidence            999999999999999999999999999999999999999999985

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.

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

Probab=100.00  E-value=5.7e-38  Score=283.97  Aligned_cols=193  Identities=25%  Similarity=0.329  Sum_probs=174.6

Q ss_pred             cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccch
Q psy6602          86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRV  165 (367)
Q Consensus        86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~  165 (367)
                      ..++++++++++.++.+|+|||++|||.+|+.+||++|||+||+|+++|+.|||+.+.++..++.++....+.... .+.
T Consensus        42 ~~~~~~~~l~t~~i~~iv~wAK~IPgF~~L~~~DQi~LLk~~w~Ell~L~~a~r~~~~~~~l~~~~g~~~~~~~~~-~~~  120 (239)
T cd07072          42 EKVQQFYSLLTSSIDVIKTFAEKIPGFPDLCKEDQELLFQSASLELFVLRLAYRTAPEDTKLTFCNGVVLHKQQCQ-RSF  120 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHHHHHHhHHHHHHHHHHHHccCCCCeEEeeCCeeecHHHHH-hhH
Confidence            3489999999999999999999999999999999999999999999999999999988777666665544444322 246


Q ss_pred             HHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhC--CCcchHHHHHHHh
Q psy6602         166 NNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRY--SRQPTRFGRLLLM  243 (367)
Q Consensus       166 ~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~--~~~~~Rf~~LL~~  243 (367)
                      ++.++.+++|+.+|++|++|.+||+|||||+||+ |++|+.+..+|+++|+++..+|++|+..++  ++.+.||++||++
T Consensus       121 ~~~~~~i~ef~~~l~~L~ld~~E~a~LkAivLf~-dr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~~~~rf~kLLl~  199 (239)
T cd07072         121 GDWLHAILEFSKSLHAMDIDISAFACLCALTLIT-ERHGLKEPHKVEQLQMKIISSLRDHVTYNAEAQKKPHYFSRLLGK  199 (239)
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhC-CCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcccccHHHHHHHH
Confidence            6777889999999999999999999999999995 999999999999999999999999999765  4788999999999


Q ss_pred             hhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHccc
Q psy6602         244 LPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  280 (367)
Q Consensus       244 l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~  280 (367)
                      |+.||+++..+.|.+++.+..+..++++++.|||..+
T Consensus       200 Lp~LRsl~~~~~e~lf~~k~~~~~p~~~Ll~Em~~~~  236 (239)
T cd07072         200 LPELRSLSVQGLQRIFYLKLEDLVPAPPLIENMFVAS  236 (239)
T ss_pred             hHHHHhhHHHHHHHHHHHHcCCCCCCcHHHHHHHhcc
Confidence            9999999999999999999999999999999999753

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).

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

Probab=100.00  E-value=3.8e-37  Score=274.24  Aligned_cols=189  Identities=50%  Similarity=0.799  Sum_probs=169.1

Q ss_pred             CCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccC
Q psy6602          78 HPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARER  157 (367)
Q Consensus        78 ~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~  157 (367)
                      +++......+.+++|+++++.++.+|+|||++|||.+|+.+||++|||+||+|+++++.||++...+...++.+++....
T Consensus        18 ~~~~~~~~~~~~~~~~~a~~~L~~~VewaK~ip~F~~L~~~DQi~LLk~~w~el~iL~~a~~s~~~~~~~ll~~~~~~~~   97 (206)
T cd06950          18 YGTISSYEVSPESVCESAARLLFMAVKWAKSIPAFSTLPFRDQLILLEESWSELFLLGAAQWSLPLDSCPLLAVPGLSPD   97 (206)
T ss_pred             cccccccccCHHHHHHHHHHHHHHHHHHHHhCCccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCcceeecCCccccc
Confidence            45666778889999999999999999999999999999999999999999999999999999988777777776554333


Q ss_pred             CCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHH
Q psy6602         158 LPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRF  237 (367)
Q Consensus       158 ~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf  237 (367)
                      ...........++.+.+++.+|++|++|++||+|||||+||+||++|+++...|+++|+++..+|++|+..+|+.++.||
T Consensus        98 ~~~~~~~~~~~~~~i~~~~~~~~~L~ld~~EyalLKai~L~npd~~~L~~~~~Ve~lq~~~~~aL~~y~~~~~~~~~~Rf  177 (206)
T cd06950          98 NTEAERTFLSEVRALQETLSRFRQLRVDATEFACLKAIVLFKPETRGLKDPAQVEALQDQAQLMLNKHIRTRYPTQPARF  177 (206)
T ss_pred             ccchhhHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcccHH
Confidence            22222234455577899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhhHhHhhhhhHHHHHHhhhccCC
Q psy6602         238 GRLLLMLPSLRAVRQSTIERLFFKETIGD  266 (367)
Q Consensus       238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~  266 (367)
                      ++|+++|+.+|+++..+.|.+++.+++|+
T Consensus       178 ~kLLl~Lp~lr~ls~~~~e~l~~~~~~g~  206 (206)
T cd06950         178 GKLLLLLPSLRFISSSTIEELFFKKTIGN  206 (206)
T ss_pred             HHHHHHHHHHHhhhHHHHHHHhccCcCCC
Confidence            99999999999999999999999988763

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

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

Probab=100.00  E-value=4.2e-37  Score=277.32  Aligned_cols=212  Identities=23%  Similarity=0.381  Sum_probs=185.5

Q ss_pred             CCCcccccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccC
Q psy6602          64 HHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPW  143 (367)
Q Consensus        64 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~  143 (367)
                      .+|.+..++|.|..+++....   ++++++++++.++.+|+|||++|||..|+.+||++|||++|+++++++.||++++.
T Consensus         8 ~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~l~~~Ve~aK~lp~F~~L~~~DQi~LLk~~~~el~lL~~a~~s~~~   84 (221)
T cd06946           8 AEPDKLFAMPDPALPDSDIKA---LTTLSDLADRELVVIIGWAKHIPGFSSLSLNDQMSLLQSAWMEILTLGVVFRSLPF   84 (221)
T ss_pred             cCCccccCCCCCCCCCCchHH---HHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHccCC
Confidence            445555556565555554433   78899999999999999999999999999999999999999999999999999988


Q ss_pred             CCceEecCCccccCCCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHH
Q psy6602         144 DLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILG  223 (367)
Q Consensus       144 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~  223 (367)
                      ++..++.++....+......+.....+.+.+++.+|++|++|.+||+|||||+||+||+.|+.+...|+++|++|.++|.
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~l~~~E~~lLkai~L~npd~~~l~~~~~v~~~q~~~~~aL~  164 (221)
T cd06946          85 NGELVFAEDFILDEELAREAGLLELYSACLQLVRRLQRLRLEKEEYVLLKALALANSDSVHIEDVEAVRQLRDALLEALS  164 (221)
T ss_pred             CCceeecCCeEEcHHHHhhcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHH
Confidence            76666656554443332333455666788899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhCC-CcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHc
Q psy6602         224 DYVRGRYS-RQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT  278 (367)
Q Consensus       224 ~y~~~~~~-~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~  278 (367)
                      +||..+|+ ++|.||++|+++++.+|+++..+.|++++.+..+..++++++.||+.
T Consensus       165 ~y~~~~~~~~~p~Rf~~LL~~l~~Lr~~~~~~~e~l~~~~~~~~~~~~~Ll~eml~  220 (221)
T cd06946         165 DYEAGRHPGEAPRRAGQLLLTLPLLRQTDGKARRFFYGVKREGKVPMHKLFLEMLE  220 (221)
T ss_pred             HHHHHhCCCcchhHHHHHHhhchhHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHhc
Confidence            99999988 89999999999999999999999999999999999999999999986

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

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

Probab=100.00  E-value=1.9e-37  Score=281.44  Aligned_cols=195  Identities=24%  Similarity=0.317  Sum_probs=169.4

Q ss_pred             ccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCC-CceEecCCcc-ccCCCCC-
Q psy6602          85 LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD-LSLLINCEKA-RERLPPD-  161 (367)
Q Consensus        85 ~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~-~~~l~~~~~~-~~~~~~~-  161 (367)
                      ...+..+|+++++.++.+|+|||++|||.+|+.+||++|||+||+|+++|+.|||+.... .+.+.++++. +...... 
T Consensus        37 ~~~~~~l~~~a~~~L~~~VeWaK~lP~F~~L~~~DQi~LLk~~w~el~vL~~a~rs~~~~~~~~l~~~~g~~~~~~~~~~  116 (237)
T cd07070          37 PAPFGLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQHGKEGSILLVTGQEVELSTVAA  116 (237)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCceeecCCCeechhHHHH
Confidence            344788999999999999999999999999999999999999999999999999998543 3334444433 2222111 


Q ss_pred             ccc--hHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHH
Q psy6602         162 DVR--VNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGR  239 (367)
Q Consensus       162 ~~~--~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~  239 (367)
                      ..+  ....+..+.+++.+|++|++|.+||+|||||+|||||++|+++...|+++|++|..+|.+||..+||..+.||++
T Consensus       117 ~~~~~~~~~~~~~~e~~~kl~~L~ld~~Ey~~LkaIiLfnpd~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~Rf~k  196 (237)
T cd07070         117 QAGSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILFSLDVKFLNNHSLVKDAQEKANAALLDYTLCHYPHCGDKFQQ  196 (237)
T ss_pred             HHhHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHhcCCCccCCCCHHHHHHHHHHHHHHHHHHHHhcCCCcchHHHH
Confidence            111  123334567899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcc
Q psy6602         240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM  279 (367)
Q Consensus       240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~  279 (367)
                      ||++|+.||+++....|++++.+.++..++++++.||++.
T Consensus       197 LLl~Lp~LRsis~~~~e~l~~~~l~g~~~~~~Ll~eml~~  236 (237)
T cd07070         197 LLLRLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIEMLQA  236 (237)
T ss_pred             HHHHhHHHHHhhHHHHHHHHHhcccCCCcHHHHHHHHhcC
Confidence            9999999999999999999999999999999999999874

The ligand binding domain of nuclear receptor steroidogenic factor 1 (SF-1): SF-1, a member of the nuclear hormone receptor superfamily, is an essential regulator of endocrine development and function and is considered a master regulator of reproduction. Most nuclear receptors function as homodimer or heterodimers, however SF-1 binds to its target genes as a monomer, recognizing the variations of the DNA sequence motif, T/CCA AGGTCA. SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been determined as potential ligands of SF-1. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, SF-1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).

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

Probab=100.00  E-value=3.7e-37  Score=279.94  Aligned_cols=195  Identities=30%  Similarity=0.476  Sum_probs=173.9

Q ss_pred             ccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCC-CceEecCCcc-ccCCCC--
Q psy6602          85 LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD-LSLLINCEKA-RERLPP--  160 (367)
Q Consensus        85 ~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~-~~~l~~~~~~-~~~~~~--  160 (367)
                      ...++.+++++.+.++.+|+|||++|+|.+|+.+||++|||++|+++++|+.||++...+ .+.+...++. ......  
T Consensus        37 ~~~~~~~~~~a~~~l~~~VewaK~lp~F~~L~~~DQi~LLk~~w~el~~L~~a~rs~~~~~~~~l~~~~g~~~~~~~~~~  116 (237)
T cd06944          37 LDTFGLMCKMADQTLFSIVEWARNSVFFKELKVDDQMKLLQNCWSELLVLDHIYRQVHHGKEDSILLVTGQEVDLSTLAS  116 (237)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHhCCChhcCCHHHHHHHHHHHhHHHHHHHHHHHhcccCCCCceeecCCCccchhhhhh
Confidence            345788999999999999999999999999999999999999999999999999998765 4445444443 222221  


Q ss_pred             -CccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHH
Q psy6602         161 -DDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGR  239 (367)
Q Consensus       161 -~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~  239 (367)
                       ...+..+.++.+.+++.+|++|++|++||+|||||+|||||++|++++..|+++|++|.++|.+||..+++.++.||++
T Consensus       117 ~~~~~~~~~~~~i~~~~~~l~~L~ld~~E~~lLkaIiL~npd~~gL~~~~~Ve~~q~~~~~aL~~y~~~~~~~~~~Rf~~  196 (237)
T cd06944         117 QAGLGLSSLVDRAQELVNKLRELQFDRQEFVCLKFLILFNPDVKGLENRQLVESVQEQVNAALLDYTLCNYPQQTDKFGQ  196 (237)
T ss_pred             hccccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCcCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccHHHH
Confidence             1123455677889999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcc
Q psy6602         240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM  279 (367)
Q Consensus       240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~  279 (367)
                      |+++++.+|+++....|++++++.++..++++++.||++.
T Consensus       197 LL~~Lp~Lr~is~~~~e~l~~~~l~g~~~~~~Ll~eml~~  236 (237)
T cd06944         197 LLLRLPEIRAISMQAEEYLYYKHLNGEVPCNNLLIEMLHA  236 (237)
T ss_pred             HHHHhHHHHHHHHHHHHHHHhcccCCCCcHHHHHHHHHcC
Confidence            9999999999999999999999999999999999999874

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=100.00  E-value=7.1e-37  Score=275.74  Aligned_cols=212  Identities=26%  Similarity=0.420  Sum_probs=185.0

Q ss_pred             CCCcccccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccC
Q psy6602          64 HHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPW  143 (367)
Q Consensus        64 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~  143 (367)
                      .+|...++++++..+++..   ..++++|+++.+.++.+|+|||++|+|..|+.+||++|+|++|++++++..||+++..
T Consensus         8 ~~~~~~~~~~~~~~~~~~~---~~~~~~~~~a~~~l~~~vewaK~lp~F~~L~~~DQi~LLk~~~~~~~~l~~a~~s~~~   84 (221)
T cd07068           8 AEPDKLYAMNDPTGPDTEV---SLLATLSDLADRELVHIISWAKHIPGFSDLSLNDQMHLLQSAWLEILMLGLVWRSLPH   84 (221)
T ss_pred             hCCCcccCCCCCCCCCCch---HHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHhhHHHHHHHHHHhhcCC
Confidence            3455555554444444443   3488999999999999999999999999999999999999999999999999999887


Q ss_pred             CCceEecCCccccCCCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHH
Q psy6602         144 DLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILG  223 (367)
Q Consensus       144 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~  223 (367)
                      +....+.++....+......+..+..+.+.+++.+|++|++|++||+|||||+||+||++|+.++..|++.|++|.++|.
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~~lLkaIil~npd~~~L~~~~~V~~~q~~~~~aL~  164 (221)
T cd07068          85 PGKLVFAPDLLLDREQARVEGLLEIFDMLLQLVRRFRELGLQREEYVCLKAIILANSDVRHLEDREAVQQLRDAILDALV  164 (221)
T ss_pred             CCeEEeCCCceECHHHHhhccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCccCccCHHHHHHHHHHHHHHHH
Confidence            77555555555444333334455666788999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhCC-CcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHc
Q psy6602         224 DYVRGRYS-RQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT  278 (367)
Q Consensus       224 ~y~~~~~~-~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~  278 (367)
                      +||..+++ .++.||++|+++++.+|+++..++|++++.+..+..++++++.||+.
T Consensus       165 ~y~~~~~~~~~~~Rf~~LL~~l~~Lr~~~~~~~e~l~~~k~~~~~~~~~Ll~e~l~  220 (221)
T cd07068         165 DVEAKRHGSQQPRRLAQLLLLLPHLRQASNKGVRHLYSVKCEGKVPMYKLFLEMLE  220 (221)
T ss_pred             HHHHHhCCCccccHHHHHHHhccHHHHHHHHHHHHHHHHHHcCCccHHHHHHHHhc
Confidence            99999999 99999999999999999999999999999999999999999999986

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

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

Probab=100.00  E-value=3.1e-37  Score=273.01  Aligned_cols=192  Identities=21%  Similarity=0.304  Sum_probs=169.0

Q ss_pred             CHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccchH
Q psy6602          87 SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVN  166 (367)
Q Consensus        87 ~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  166 (367)
                      -|.++++.+++.++.+|+|||++|||++|+.+||++|||+||+|++++++++++...++...+.++..+.+......+..
T Consensus         3 ~w~~~~~~~~~~l~~iI~waK~iP~F~~L~~~DQi~LLk~~~~el~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (195)
T cd06941           3 LWQQLSEALTPSVQRVVEFAKRIPGFCDLSQDDQLLLIKAGFFEVWLVRISRLINSKSGSITFDDGISISRQQLDIIYDS   82 (195)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHcCCCCeEEecCCeEeeHHHHHhccch
Confidence            37899999999999999999999999999999999999999999999999998877655555555444443322222234


Q ss_pred             HHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhhhH
Q psy6602         167 NEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPS  246 (367)
Q Consensus       167 ~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~~  246 (367)
                      +..+.+.+|+.+|++|++|++||+|||||+||+||++|+.+...|+++|+++.++|++|+..++|+.+.||++|+++++.
T Consensus        83 ~~~~~~~~~~~~l~~L~ld~~E~allkAi~Lf~pd~~gl~~~~~Ve~lq~~~~~aL~~~i~~~~p~~~~rf~~Ll~~Lp~  162 (195)
T cd06941          83 DFVKALFEFSDSFNSLGLSDTEVALFCAVVLLSPDRIGLSEPKKVAILQDRVLEALKVQVSRNRPAEAQLFASLLMKIPE  162 (195)
T ss_pred             HHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHhHH
Confidence            56788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHhhhhhHHHHHH-hhhccCCchhHhHHHHHHc
Q psy6602         247 LRAVRQSTIERLF-FKETIGDIPIQRLLGDMYT  278 (367)
Q Consensus       247 Lr~l~~~~~e~l~-~~~~~~~~~~~~Ll~eml~  278 (367)
                      ||+++..+.|.+. ++...+..++++|+.|||+
T Consensus       163 Lr~l~~~~~e~l~~~~~~~~~~~~p~L~~E~~~  195 (195)
T cd06941         163 LRSIGAKHQMHLDWYRVNWPLLRLPPLFAEIYD  195 (195)
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCCCCcHHHHhcC
Confidence            9999999999997 4445566789999999986

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

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

Probab=100.00  E-value=3.2e-37  Score=278.17  Aligned_cols=193  Identities=28%  Similarity=0.438  Sum_probs=166.0

Q ss_pred             hhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCc---------
Q psy6602          83 QILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEK---------  153 (367)
Q Consensus        83 ~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~---------  153 (367)
                      .++.+++++|+++++.++.+|+|||++|+|.+|+.+||++|||+||.|+++|+.||++.+.+....+.++.         
T Consensus        16 ~~l~~~~~~ce~a~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~W~El~iL~~a~~s~~~~~~~~~~~~~~~~~l~~~~   95 (232)
T cd07350          16 VTLKSPQVTCKAASAVLVKTLRFVKGVPCFQELPLDDQLVLVRSCWAPLLVLGLAQDGVDFETVETSEPSMLQRILTTRP   95 (232)
T ss_pred             cccCCHHHHHHHHHHHHHHHHHHHHhCcCcccCChHHHHHHHHHhhHHHHHHHHHHHcCCCccccccchhHHHHHHhccc
Confidence            34566899999999999999999999999999999999999999999999999999998766543221111         


Q ss_pred             ccc------------CCCCCc---cchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHH
Q psy6602         154 ARE------------RLPPDD---VRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQA  218 (367)
Q Consensus       154 ~~~------------~~~~~~---~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~  218 (367)
                      ...            ......   ......++.+.+|+.+|++|++|.+||||||||+||+||++|+.+..+|+++|+++
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~e~~~~l~~L~ld~~E~a~LkAivLf~pD~~~L~~~~~Ve~lQe~~  175 (232)
T cd07350          96 PPTSGAEPGEPQALPQMPQAEASHLPSAADIRAIKAFLAKCWSLDISTKEYAYLKGTVLFNPDLPGLQCVQYIQGLQWEA  175 (232)
T ss_pred             ccccccccccccccccccchhhccccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcccCCCHHHHHHHHHHH
Confidence            000            000000   01123457799999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhCCCcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHH
Q psy6602         219 QCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGD  275 (367)
Q Consensus       219 ~~~L~~y~~~~~~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~e  275 (367)
                      ..+|++|+..+||+++.||++|+++|+.||+++...+|.+||++.+|.+++++++.|
T Consensus       176 ~~aL~~yi~~~~p~~~~rf~kLLl~Lp~LRsi~~~~iE~lff~~l~g~v~i~~ll~E  232 (232)
T cd07350         176 QQALNEHVRMIHRGDQARFAKLNIALSLLRAINANVIAELFFRPIIGTVNMDDMLLE  232 (232)
T ss_pred             HHHHHHHHHhhCCChhhHHHHHHHHhHHHHccCHHHHHHHhccccCCCCcHHHHhcC
Confidence            999999999999999999999999999999999999999999999999999988753

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.

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

Probab=100.00  E-value=3.3e-37  Score=277.06  Aligned_cols=189  Identities=31%  Similarity=0.456  Sum_probs=163.8

Q ss_pred             ccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEe---------cCCccc
Q psy6602          85 LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLI---------NCEKAR  155 (367)
Q Consensus        85 ~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~---------~~~~~~  155 (367)
                      +..++++|+++++.++.+|+|||++|||.+|+.+||++|||++|+|+++|+.||++.+.+.....         ..++..
T Consensus        18 ~~~~~~~ce~a~~~L~~~V~wAK~iP~F~~L~~~DQi~LLk~~w~El~iL~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~   97 (222)
T cd06951          18 LCAPQMVCRAASQVLLKTIRFVRNLPCFTYLPPDDQLRLLRRSWAPLLLLGLAQDKVPFDTVEVPAPSILCEILTGAEMH   97 (222)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHhCCCcccCChHHHHHHHHHHhHHHHHHHHHHHhccccccccccchHHHHHHhccccc
Confidence            55688999999999999999999999999999999999999999999999999999876543221         112111


Q ss_pred             -cCCCC----Ccc-chHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhh
Q psy6602         156 -ERLPP----DDV-RVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGR  229 (367)
Q Consensus       156 -~~~~~----~~~-~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~  229 (367)
                       .....    ... .....++.+++|+.+|++|++|.+||||||||+||+||++|+ +...|+++|+++..+|++|+..+
T Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~l~e~~~~l~~L~ld~~Eya~LkAivLfnpD~~gl-~~~~Ve~lQe~~~~aL~~yi~~~  176 (222)
T cd06951          98 WGGTPPPTLTMPPCIPLADVQDIQQFLMKCWSLDLDCKEYAYLKGAVLFTPVPPLL-CPHYIEALQKEAQQALNEHTMMT  176 (222)
T ss_pred             cccccccccccchhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCcc-CHHHHHHHHHHHHHHHHHHHHhh
Confidence             11110    011 122346789999999999999999999999999999999999 99999999999999999999999


Q ss_pred             CCCcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHH
Q psy6602         230 YSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLG  274 (367)
Q Consensus       230 ~~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~  274 (367)
                      ||+.+.||++||++|+.||+++...+|.+++.+.+|..++++++.
T Consensus       177 ~p~~~~Rf~kLLl~Lp~LRsl~~~~~e~lff~~~~g~~~i~~ll~  221 (222)
T cd06951         177 RPLEQLRSARLLLMLSLLRGIKTEPVTELFFRPIIGNVSMDDVLL  221 (222)
T ss_pred             CCCcccHHHHHHHHhHHhhcCCHHHHHHHhCccccCCCcHHHHhc
Confidence            999999999999999999999999999999999999999998875

The ligand binding domain of DAX1-like proteins: This orphan nuclear receptor family includes DAX1 (dosage-sensitive sex reversal adrenal hypoplasia congenita critical region on chromosome X gene 1) and the Small Heterodimer Partner (SHP). Both receptors have a typical ligand binding domain, but lack the DNA binding domain, typical to almost all of the nuclear receptors. They function as a transcriptional coregulator by directly interacting with other nuclear receptors. DAX1 and SHP can form heterodimers with each other, as well as with many other nuclear receptors. In addition, DAX1 can also form homodimers. DAX1 plays an important role in the normal development of several hormone-producing tissues. SHP has shown to regulate a variety of target genes.

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

Probab=100.00  E-value=1.9e-36  Score=275.24  Aligned_cols=201  Identities=41%  Similarity=0.718  Sum_probs=177.6

Q ss_pred             cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccC-CCCCc-c
Q psy6602          86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARER-LPPDD-V  163 (367)
Q Consensus        86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~-~~~~~-~  163 (367)
                      +.++++|+++++.++.+|+|||++|||..|+.+||++|||+||+|+++|+.|+++.+.+.+.++.+++.... ..... .
T Consensus        30 ~~~~~l~~~a~~~L~~~VewaK~lp~F~~L~~~DQi~LLk~~w~el~lL~~a~~s~~~~~~~~~~~~g~~~~~~~~~~~~  109 (236)
T cd06948          30 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLSWSELFVLNAAQCCMPLHVAPLLAAAGLHASPMSADRVV  109 (236)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHhhHHHHHHHHHHHcccccchhhhhccccccCccchhhHh
Confidence            448899999999999999999999999999999999999999999999999999988777766666554321 11111 1


Q ss_pred             chHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHh
Q psy6602         164 RVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLM  243 (367)
Q Consensus       164 ~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~  243 (367)
                      ...+.++.+.+++.+|++|++|++||+|||||+||+||++|+++..+|+++|++|.++|++||..++++++.||++|+++
T Consensus       110 ~~~~~~~~~~~l~~~l~~L~ld~~E~~lLkaiiL~npd~~~L~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LLl~  189 (236)
T cd06948         110 AFMDHIRIFQEQVEKLKALHVDSAEFSCLKAIVLFTSDACGLSDPAHIESLQEKSQCALEEYVRTQYPNQPTRFGKLLLR  189 (236)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCcccccccCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHH
Confidence            12334456778999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCC
Q psy6602         244 LPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETP  286 (367)
Q Consensus       244 l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~  286 (367)
                      ++.+|+++..+.|.+++.+.++..++++++.+|+....+++.+
T Consensus       190 Lp~Lr~is~~~~e~l~~~~l~g~~~~~~ll~e~l~~~~~~~~~  232 (236)
T cd06948         190 LPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDMLLSGSSFVWP  232 (236)
T ss_pred             HHHHHhccHHHHHHhhcccccCCCcHHHHHHHHHhCCCCCccc
Confidence            9999999999999999999999999999999999876665543

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

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

Probab=100.00  E-value=5.7e-36  Score=270.77  Aligned_cols=215  Identities=16%  Similarity=0.200  Sum_probs=180.4

Q ss_pred             CCCcccccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccC
Q psy6602          64 HHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPW  143 (367)
Q Consensus        64 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~  143 (367)
                      .+|..++++|++..|++....   +..+++++++.++.+|+|||++|||.+|+.+||++|||++|+|+++++.|||+...
T Consensus         9 ~ep~~~~~~~d~~~p~~~~~~---~~~l~~la~r~L~~vVeWAK~lPgF~~L~~~DQi~LLk~sw~ellvL~~a~rS~~~   85 (248)
T cd07074           9 IEPDVVYAGYDNTKPETPSSL---LTSLNQLCERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKH   85 (248)
T ss_pred             hCCCcccCCCCCCCCCCchhh---HHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence            577888999999999887666   45599999999999999999999999999999999999999999999999999876


Q ss_pred             CC-ceE-ecCCccccCCCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCC-CCCCCCChhHHHHHHHHHHH
Q psy6602         144 DL-SLL-INCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTP-ETPGLVDAQPVEMLQDQAQC  220 (367)
Q Consensus       144 ~~-~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~p-d~~~L~~~~~v~~~q~~~~~  220 (367)
                      .. +.+ +.+|+..++......+..+.+..+.+++.+|++|++|.+||+|||||+|||| |++||+++..|+++|++|.+
T Consensus        86 ~~~~~l~fa~d~~~~~~~~~~~~~~~~~~~m~e~~~~~~~L~ld~~Ey~cLKAIvLfnp~d~~gL~~q~~Ve~lR~~y~~  165 (248)
T cd07074          86 VSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKALLLLNTIPLEGLRSQTQFDEMRSSYIR  165 (248)
T ss_pred             CCCCeEEecCCcccchhhhhhccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHCCCCcCCCCCCHHHHHHHHHHHHH
Confidence            43 333 5566666655433334556667788999999999999999999999999999 89999999999999999999


Q ss_pred             HHHHHHHhhC---CCcchHHHHHHHhhhHhHhhhhhHHHHHHhhhc---cCCchhHhHHHHHHcccC
Q psy6602         221 ILGDYVRGRY---SRQPTRFGRLLLMLPSLRAVRQSTIERLFFKET---IGDIPIQRLLGDMYTMEK  281 (367)
Q Consensus       221 ~L~~y~~~~~---~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~---~~~~~~~~Ll~eml~~~~  281 (367)
                      +|.+|+..++   .+++.||++|+.+++.++.+..+...+++....   ...+.++.++.|+.....
T Consensus       166 aL~~yi~~~~~~~~~~~~RF~~Ll~ll~~l~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  232 (248)
T cd07074         166 ELIKAIGLRQKGVVASSQRFYQLTKLMDNMHDLVKQLHLYCLNTFIQSRALSVEFPEMMSEVIAAQL  232 (248)
T ss_pred             HHHHHHHHcCCCCccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhheeecHHHHHHHHHhcc
Confidence            9999977664   378999999999999999888888777754432   335667777877776433

The ligand binding domain of the progesterone receptor (PR): PR is a member of the nuclear receptor superfamily of ligand dependent transcription factors, mediating the biological actions of progesterone. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, protein processing, and metabolism. When no binding hormone is present the carboxyl terminal inhibits transcription. Binding to a hormone induces a structural change that removes the inhibitory action. After progesterone binds to the receptor, PR forms a dimer and the complex enters the nucleus where it interacts with the hormone response element (HRE) in the promoters of progesterone responsive genes and alters their transcription. In addition, rapid actions of PR that occur independent of transcription, have also been observed in several tissues

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

Probab=100.00  E-value=2.7e-36  Score=265.06  Aligned_cols=177  Identities=20%  Similarity=0.268  Sum_probs=159.2

Q ss_pred             cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccch
Q psy6602          86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRV  165 (367)
Q Consensus        86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~  165 (367)
                      .-|+++++.++..|+.+|+|||++|||.+|+.+||++|||+||+|+++++.++++....+...+.++..+++......+.
T Consensus        12 ~~~~~~~~~~~~~i~~~V~waK~iPgF~~L~~~DQi~LLk~~w~Ell~L~~a~~~~~~~~~l~~~~~~~~~~~~~~~~~~   91 (189)
T cd06940          12 EIWEEFSMSFTPAVREVVEFAKRIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFDAKERSVTFLSGQKYSVDDLHSMGA   91 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCcccCChhhHHHHHHHhhHHHHHHHHHHHhccCCCeEEecCCcEEcHHHHHHcCc
Confidence            33889999999999999999999999999999999999999999999999999988766665555544444333223345


Q ss_pred             HHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhhh
Q psy6602         166 NNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLP  245 (367)
Q Consensus       166 ~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~  245 (367)
                      .+.++.+.+++.+|++|++|.+||+|||||+||+||++|+.++.+|+++|+++.++|++|+..++|+++.||++|+++++
T Consensus        92 ~~~~~~~~~~~~~l~~L~ld~~E~a~LkAivLf~pd~~~L~~~~~Ve~lq~~~~~aL~~~~~~~~p~~~~rf~kLL~~L~  171 (189)
T cd06940          92 GDLLNSMFDFSEKLNSLQLSDEEMGLFTAVVLVSADRSGLENVNLVEALQETLIRALRTLIAKNHPNEPSIFTKLLLKLP  171 (189)
T ss_pred             HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCcCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHH
Confidence            67788899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhHhhhhhHHHHHHhhh
Q psy6602         246 SLRAVRQSTIERLFFKE  262 (367)
Q Consensus       246 ~Lr~l~~~~~e~l~~~~  262 (367)
                      .+|+++..+.|.+++.+
T Consensus       172 ~LR~l~~~~~e~l~~~~  188 (189)
T cd06940         172 DLRTLNNLHSEKLLAFK  188 (189)
T ss_pred             HHHHHHHHHHHHHHHhh
Confidence            99999999999998865

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

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

Probab=100.00  E-value=2.8e-36  Score=274.16  Aligned_cols=190  Identities=19%  Similarity=0.269  Sum_probs=168.0

Q ss_pred             cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccch
Q psy6602          86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRV  165 (367)
Q Consensus        86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~  165 (367)
                      .-|.++++..+..|+.+|+|||++|||.+|+.+||++|||+||+|++++++|++++..++.. ++++....+......+.
T Consensus        48 ~~~~~~~~~~t~~i~~vVefAK~IPgF~~L~~~DQi~LLk~~~~Ellll~~a~~~~~~~~~~-~~~~~~~~~~~~~~~~~  126 (241)
T cd06939          48 EMWQLCAEKITEAIQYVVEFAKRIPGFMELCQNDQIVLLKAGSLEVVLVRMSRAFNPSNNTV-LFDGKYAPIDLFKSLGC  126 (241)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhCCCCCEE-EECCccccHHHHHHcCc
Confidence            44899999999999999999999999999999999999999999999999998887655554 44444333332222345


Q ss_pred             HHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhhh
Q psy6602         166 NNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLP  245 (367)
Q Consensus       166 ~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~  245 (367)
                      .+.++.+++|+.+|+.|++|++||+|||||+||+||++|+.+..+|+++|+++..+|+.|+..+| +.+.||++||++++
T Consensus       127 ~~~~~~~~~f~~~l~~L~ld~~E~all~AivL~~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~-~~~~rf~kLL~~Lp  205 (241)
T cd06939         127 DDLISAVFDFAKSLCELKLTEDEIALFSALVLISADRPGLQEKRKVEKLQQKIELALRHVLQKNH-GDDTILTKLLAKMP  205 (241)
T ss_pred             HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHhcCCCcCCCCHHHHHHHHHHHHHHHHHHHHHhC-CCccHHHHHHHHHH
Confidence            67788999999999999999999999999999999999999999999999999999999999998 89999999999999


Q ss_pred             HhHhhhhhHHHHHHhhhccCC----chhHhHHHHHH
Q psy6602         246 SLRAVRQSTIERLFFKETIGD----IPIQRLLGDMY  277 (367)
Q Consensus       246 ~Lr~l~~~~~e~l~~~~~~~~----~~~~~Ll~eml  277 (367)
                      .||+++..+.|.+++.+..+.    ..+++|+.|||
T Consensus       206 ~LR~l~~~~~e~l~~~k~~~p~~~~~~~ppL~~Elf  241 (241)
T cd06939         206 TLRALCSLHMEKLQKFKQSYPDIVHLEFPPLYKELF  241 (241)
T ss_pred             HHHHHHHHHHHHHHHHhccCCCcccCCCCcHHHhhC
Confidence            999999999999999988743    35889998885

The ligand binding domain (LBD) of Retinoid-related orphan receptors (RORs): Retinoid-related orphan receptors (RORs) are transcription factors belonging to the nuclear receptor superfamily. RORs are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. Transcription regulation by RORs is mediated through certain corepressors, as well as coactivators. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma that differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum, particularly in the regulation of the maturation and survival of Purkinje cells. RORbeta expression is largely r

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

Probab=100.00  E-value=1e-35  Score=270.86  Aligned_cols=193  Identities=23%  Similarity=0.265  Sum_probs=170.7

Q ss_pred             ccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccc
Q psy6602          85 LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVR  164 (367)
Q Consensus        85 ~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~  164 (367)
                      ...+.++++++.+.++.+|+|||++|||..|+.+||++|||++|+|+++|+.||++....+...+.++..+.+......+
T Consensus        42 ~~~~~~~~~~~~~~i~~~VefaK~lP~F~~L~~~DQi~LLK~~~~el~iL~~a~~~~~~~~~~~~~~g~~~~~~~~~~~~  121 (236)
T cd06954          42 QQRFAHFTELAILSVQEIVDFAKQLPGFLTLTREDQIALLKASTIEVMLLETARRYNPESEAITFLKDFPYSRDDFARAG  121 (236)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCCCcccCChHHHHHHHHHhHHHHHHHHHHHHhcCCCCeEEeeCCccccHHHHHHhc
Confidence            35588999999999999999999999999999999999999999999999999998876555555444333332211112


Q ss_pred             -hHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHh
Q psy6602         165 -VNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLM  243 (367)
Q Consensus       165 -~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~  243 (367)
                       ..+..+.+.+|+.+|++|++|++||+|||||+||+||++|+++...|+++|++|..+|++||..+||+.+.||++++++
T Consensus       122 ~~~~~~~~i~~~~~~l~~L~ld~~E~~lL~aivLf~pd~~gL~~~~~V~~lQ~~~~~aL~~y~~~~~p~~~~rf~klL~~  201 (236)
T cd06954         122 LQVEFINPIFEFSKSMRELQLDDAEYALLIAINIFSADRPNVQDHHRVERLQETYVEALHSYIKIKRPSDRLMFPRMLMK  201 (236)
T ss_pred             ChHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhhccCCcccCCCHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHH
Confidence             3456788999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHc
Q psy6602         244 LPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT  278 (367)
Q Consensus       244 l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~  278 (367)
                      |+.||+++..+.|.+++.+..+ .++++++.|||+
T Consensus       202 L~~Lr~l~~~~~e~l~~~k~~~-~~~~~L~~El~~  235 (236)
T cd06954         202 LVSLRTLSSVHSEQVFALRLQD-KKLPPLLSEIWD  235 (236)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcC-CCCCcHHHHHhc
Confidence            9999999999999999888764 689999999987

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

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

Probab=100.00  E-value=1.5e-35  Score=268.75  Aligned_cols=194  Identities=21%  Similarity=0.308  Sum_probs=172.3

Q ss_pred             hccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCcc
Q psy6602          84 ILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDV  163 (367)
Q Consensus        84 ~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~  163 (367)
                      ....+.++++++...++.+|+|||++|||..|+.+||++|||+||+|+++|+.||++....+...+.++..+.+......
T Consensus        37 ~~~~~~~~~~~~~~~i~~iIefaK~lp~F~~L~~~DQi~LLK~~~~el~~L~~a~~~~~~~~~~~f~~g~~~~~~~~~~~  116 (231)
T cd06938          37 SDMRFRHITEMTILTVQLIVEFAKRLPGFDKLSREDQITLLKACSSEVMMLRVARRYDAKTDSIVFANNQPYTRDSYRKA  116 (231)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHhcCCccccCChhHHHHHHHHHHHHHHHHHHHHHhCCCCCeEEeeCCEEecHHHHhhc
Confidence            44668999999999999999999999999999999999999999999999999999877666555555443444332233


Q ss_pred             chHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCC-cchHHHHHHH
Q psy6602         164 RVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSR-QPTRFGRLLL  242 (367)
Q Consensus       164 ~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~-~~~Rf~~LL~  242 (367)
                      +.....+.+.+|+.+|++|++|++||+|||||+||+ |++|+++...|+.+|++|.++|+.||..+|+. ++.||++||+
T Consensus       117 ~~~~~~~~l~~~~~~l~~L~ld~~E~~lL~AI~Lf~-d~~~L~~~~~Ve~~Q~~~~~aL~~y~~~~~~~~~~~rf~kLL~  195 (231)
T cd06938         117 GMGDSAEDLFRFCRAMCSMKVDNAEYALLTAIVIFS-DRPGLLQPKKVEKIQEIYLEALRAYVDNRRPPSQRVIFAKLLS  195 (231)
T ss_pred             CHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcc-CCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCcccHHHHHHH
Confidence            455667889999999999999999999999999998 77899999999999999999999999999986 8999999999


Q ss_pred             hhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcc
Q psy6602         243 MLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM  279 (367)
Q Consensus       243 ~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~  279 (367)
                      +++.||+++..+.|.+++.+.. ...+++++.|+++.
T Consensus       196 ~L~~Lr~l~~~~~e~~~~~k~~-~~~~~pl~~Ei~d~  231 (231)
T cd06938         196 ILTELRTLGNQNSEMCFSLKLK-NRKLPPFLAEIWDV  231 (231)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHh-CCCCCcHHHHHhCC
Confidence            9999999999999999999988 67899999999873

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

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

Probab=100.00  E-value=2e-35  Score=271.08  Aligned_cols=196  Identities=21%  Similarity=0.294  Sum_probs=168.9

Q ss_pred             hhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccc-cCCC
Q psy6602          81 LLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKAR-ERLP  159 (367)
Q Consensus        81 ~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~-~~~~  159 (367)
                      ......-|.++.......++.+|+|||++|||.+|+.+||++|||++|+|+++++.|++++  .+..++..++.+ .+..
T Consensus        58 ~~~~~~~~~~~~~~~~~~i~~vVewAK~IPgF~~L~~~DQi~LLk~~~~Ellil~~a~~~~--~~~~~~~~~~~~~~~~~  135 (259)
T cd06932          58 KTIRIRLFQRCQVRSVETIRELTEFAKSLPGFRNLDLNDQVTLLKYGVHEVIFTMLASLYN--KDGLLFPEGNGYVTREF  135 (259)
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCChhHHHHHHHHhhHHHHHHHHHHhcC--CCCeEEeCCCEEeeHHH
Confidence            3334445888999999999999999999999999999999999999999999999998764  334455544332 2222


Q ss_pred             CCc--cchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHH
Q psy6602         160 PDD--VRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRF  237 (367)
Q Consensus       160 ~~~--~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf  237 (367)
                      ...  .+..+.++.+++|+.+|++|++|++||+|||||+||+||++|+.++..|+++|+++..+|+.|+..+||+.+.||
T Consensus       136 ~~~~~~~~~~~~~~~~e~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~~i~~~~p~~~~rf  215 (259)
T cd06932         136 LESLRKPFCDIMEPKFEFAEKFNALELTDSELALFCAVIILSPDRPGLINRKPVERIQEHVLQALELQLKKNHPDSPQLF  215 (259)
T ss_pred             HHHhcccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcccCcCHHHHHHHHHHHHHHHHHHHhhhCCCcccHH
Confidence            111  123466788899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhhHhHhhhhhHHHHHHhhhc-cCCchhHhHHHHHHc
Q psy6602         238 GRLLLMLPSLRAVRQSTIERLFFKET-IGDIPIQRLLGDMYT  278 (367)
Q Consensus       238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~-~~~~~~~~Ll~eml~  278 (367)
                      ++||++|+.||+++..+.|.+++.+. .+..++++|+.|||+
T Consensus       216 ~kLLl~L~~LRsl~~~~~e~l~~~k~~~~~~~~~pLl~Ei~~  257 (259)
T cd06932         216 AKLLQKMVDLRQLVTDHVQMVQQIKKTETDASLPPLLQEIYK  257 (259)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCCcHHHHHhh
Confidence            99999999999999999999997764 557889999999986

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

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

Probab=100.00  E-value=2e-35  Score=268.39  Aligned_cols=193  Identities=15%  Similarity=0.205  Sum_probs=160.5

Q ss_pred             cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCc-eEecCCcc-ccCCCCCcc
Q psy6602          86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS-LLINCEKA-RERLPPDDV  163 (367)
Q Consensus        86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~-~l~~~~~~-~~~~~~~~~  163 (367)
                      .-+.++++++++.++.+|+|||++|||.+|+.+||++|||+||+|+++++.++++.. ++. ..+.+... +........
T Consensus        37 ~l~~~l~~l~~~~l~~iI~wAK~iPgF~~L~~~DQi~LLk~~~~ElliL~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~  115 (238)
T cd06933          37 SMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEVIMLRSNQSFSL-DDMSWTCGSPDFKYKVSDVTKA  115 (238)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCCccccCChHHHHHHHHHhHHHHHHHHHHHhcCc-CCCeeEecCCceeecHHHHHHc
Confidence            336889999999999999999999999999999999999999999999999986543 443 33333221 222111111


Q ss_pred             c-hHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCC--CcchHHHHH
Q psy6602         164 R-VNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYS--RQPTRFGRL  240 (367)
Q Consensus       164 ~-~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~--~~~~Rf~~L  240 (367)
                      + ..+.++.+.+|..+|++|++|.+||+|||||+||+||++|+.+...|+.+|+++.++|++|+..+||  ..+.||++|
T Consensus       116 g~~~~~~~~l~~~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~~~~f~kL  195 (238)
T cd06933         116 GHSLELLEPLVKFQVGLKKLNLHEEEHVLLMAICILSPDRPGVQDHALIEAIQDRLSDTLQTYIRCRHPPPGSRLLYAKM  195 (238)
T ss_pred             cCcHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHCCCCCCCcchHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHH
Confidence            2 2356788999999999999999999999999999999999999999999999999999999999986  456689999


Q ss_pred             HHhhhHhHhhhhhHHHHHHhhhccC--CchhHhHHHHHHcc
Q psy6602         241 LLMLPSLRAVRQSTIERLFFKETIG--DIPIQRLLGDMYTM  279 (367)
Q Consensus       241 L~~l~~Lr~l~~~~~e~l~~~~~~~--~~~~~~Ll~eml~~  279 (367)
                      |++|+.||+++..+.|.+...+...  ...+++|+.|+|+.
T Consensus       196 Ll~L~~LRsi~~~h~~~~~~~~~~~~~~~~~~pL~~Ei~~~  236 (238)
T cd06933         196 IQKLADLRSLNEEHSKQYRSLSFQPEHSMKLTPLVLEVFGN  236 (238)
T ss_pred             HHHhHHHHhhhHHHHHHHHHHHhccCCCCCCCcHHHHHhcc
Confidence            9999999999999999876544432  33589999999973

The ligand binding domain of vitamin D receptors (VDR): VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of corepressors. Upon ligand binding, VDR forms heterodimer with the retinoid X receptor (RXR) that binds to vitamin D response elements (VDREs), recruits coactivators. This leads to the expression of a large number of genes. Approximately 200 human genes are considered to be primary targets of VDR and

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

Probab=100.00  E-value=3.6e-35  Score=264.73  Aligned_cols=188  Identities=15%  Similarity=0.224  Sum_probs=157.3

Q ss_pred             cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccch
Q psy6602          86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRV  165 (367)
Q Consensus        86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~  165 (367)
                      ..+.++++.+.+.++.+|+|||++|||.+|+.+||++|||+||+|+++++.+++++.. ...+++++..+........+.
T Consensus        35 ~~~~~~~~~~~~~l~~iV~wAK~iPgF~~L~~~DQi~LLk~~~~Ellil~~~~~~~~~-~~~~~~~~~~~~~~~~~~~g~  113 (226)
T cd06934          35 SLLPHFADLTTYMIKQIIKFAKDLPYFRSLPIEDQISLLKGATFEICQIRFNTVFNEE-TGTWECGPLTYCIEDAARAGF  113 (226)
T ss_pred             hHHHHHHHHHHHHHHHHHHHhcCCcccccCCcchHHHHHHHhHHHHHHHHHHHHhccc-CCeEeeCCEeecHHHHHHccc
Confidence            3478999999999999999999999999999999999999999999999999988764 344555554433222222233


Q ss_pred             HH-HHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcc--hHHHHHHH
Q psy6602         166 NN-EIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP--TRFGRLLL  242 (367)
Q Consensus       166 ~~-~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~--~Rf~~LL~  242 (367)
                      .. ..+.+.+|+.+|++|++|++||+|||||+||+||++|+.+...|+++|+++.++|++|+..+||..+  .||++||+
T Consensus       114 ~~~~~~~~~~~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~r~~f~kLLl  193 (226)
T cd06934         114 QQLLLEPLLRFHYTLRKLQLQEEEYVLMQAMSLFSPDRPGVTQHDVIDQLQEKMALTLKSYIDSKRPGPEKRFLYPKILA  193 (226)
T ss_pred             hHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCcCCcChHHHHHHHHHHHHHHHHHHHHcCCCCCcccHHHHHHH
Confidence            33 4578999999999999999999999999999999999999999999999999999999999987544  45999999


Q ss_pred             hhhHhHhhhhhHHHHHHhhhccCCch-hHhHHHHH
Q psy6602         243 MLPSLRAVRQSTIERLFFKETIGDIP-IQRLLGDM  276 (367)
Q Consensus       243 ~l~~Lr~l~~~~~e~l~~~~~~~~~~-~~~Ll~em  276 (367)
                      +|+.||+++..+.|.+...+  +..+ +++|+.|+
T Consensus       194 ~L~~LRsl~~~~~~~~~~~~--~~~~~~~pl~~Ei  226 (226)
T cd06934         194 CLTELRTINEEYTKQILHIQ--DIQPMATPLMQEI  226 (226)
T ss_pred             HhHHHhcchHHHHHHHHHHh--ccCCCCCchhhcC
Confidence            99999999999999875433  3334 47777664

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

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

Probab=100.00  E-value=2.8e-34  Score=256.62  Aligned_cols=176  Identities=31%  Similarity=0.578  Sum_probs=157.2

Q ss_pred             CHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccchH
Q psy6602          87 SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVN  166 (367)
Q Consensus        87 ~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  166 (367)
                      +++++|+++.+.++.+|+|||++|+|.+|+.+||++|+|++|+++++++.||++....+..++.++....+......+..
T Consensus        31 ~~~~~~~~~~~~l~~~Iewak~lp~F~~L~~~DQ~~LLk~~~~e~~~l~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~~  110 (207)
T cd06943          31 PVSNICQAADKQLFQLVEWAKRIPHFSELPLDDQVILLRAGWNELLIAAFAHRSIAVKDGILLATGLHLHRNSAHQAGVG  110 (207)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHhCchhhccChhhhHHHHHHHHHHHHHHHHHHHccCCCCeeEecCCceeccchhhhccch
Confidence            47889999999999999999999999999999999999999999999999999998777777776655444332233334


Q ss_pred             HHHHH-HHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhhh
Q psy6602         167 NEIKL-IQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLP  245 (367)
Q Consensus       167 ~~~~~-~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~  245 (367)
                      ..... +.+++.+|++|++|++||+|||||+||+||++|+++...|+++|++|.++|++||..++++++.||++|+++++
T Consensus       111 ~~~~~~~~~~~~~l~~L~ld~~E~~lLkaI~L~~pd~~~L~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LLl~L~  190 (207)
T cd06943         111 AIFDRILTELVVKMRDLKMDRTELGCLRAIILFNPDVKGLKSRQEVESLREKVYASLEEYCRQKHPEQPGRFAKLLLRLP  190 (207)
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHHH
Confidence            44444 56899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhHhhhhhHHHHHHhhh
Q psy6602         246 SLRAVRQSTIERLFFKE  262 (367)
Q Consensus       246 ~Lr~l~~~~~e~l~~~~  262 (367)
                      .+|+++..+.|.+++.+
T Consensus       191 ~lr~l~~~~~e~l~~~~  207 (207)
T cd06943         191 ALRSIGLKCLEHLFFFK  207 (207)
T ss_pred             HHHhHhHHHHHHHhhcC
Confidence            99999999999998853

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

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

Probab=100.00  E-value=4.1e-34  Score=258.09  Aligned_cols=195  Identities=31%  Similarity=0.526  Sum_probs=168.4

Q ss_pred             hccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCcccc-----CC
Q psy6602          84 ILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE-----RL  158 (367)
Q Consensus        84 ~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~-----~~  158 (367)
                      ...+++++++++.+.++.+|+|||++|+|..|+.+||++|+|++|.|+++++.+|++...+...++...+.+.     ..
T Consensus        19 ~~~~~~~~~~~a~~~l~~~v~wak~iP~F~~L~~~DQ~~LLk~~w~el~lL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (222)
T cd06952          19 SYLNVHYICESASRLLFLSIHWARSIPAFQALGAETQTSLVRACWPELFTLGLAQCSQQLSLPTILAAIINHLQTSIQQD   98 (222)
T ss_pred             ccCCHHHHHHHHHHHHHHHHHHHHhCCchhhCChHHHHHHHHHHhHHHHHHHHHHHhcccCchHHhhhhhhhhhhhHhcC
Confidence            3445888999999999999999999999999999999999999999999999998887655554443321110     11


Q ss_pred             CCCcc---chHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcch
Q psy6602         159 PPDDV---RVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPT  235 (367)
Q Consensus       159 ~~~~~---~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~  235 (367)
                      .....   ...+.+..+.+++.+|++|++|..||+|||||+||+||++|+.+...|+++|+++.++|.+|+..++++.+.
T Consensus        99 ~~~~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~~~LkaiiLf~~d~~~l~~~~~v~~lq~~i~~aL~~y~~~~~p~~~~  178 (222)
T cd06952          99 KLSADKVKQVMEHINKLQEFVNSMQKLDVDDHEYAYLKAIVLFSPDHPGQELRQQIEKLQEKALMELRDYVGKTYPEDEY  178 (222)
T ss_pred             CCchhhhHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCcCCcCHHHHHHHHHHHHHHHHHHHHHhCCCccc
Confidence            11111   122334557889999999999999999999999999999999999999999999999999999998999999


Q ss_pred             HHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHc
Q psy6602         236 RFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT  278 (367)
Q Consensus       236 Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~  278 (367)
                      ||++|+++|+.+|+++..+.|.+++.+.+|..+++.++..++.
T Consensus       179 R~~klLl~Lp~Lr~~~~~~~e~l~~~~~~g~~~~~~ll~~~~~  221 (222)
T cd06952         179 RLSKLLLRLPPLRSLSPAITEELFFAGLIGNVQIDSVIPYILR  221 (222)
T ss_pred             HHHHHHHHhHHhhhcCHHHHHHHhcccccCCCcHHHHHHHHHh
Confidence            9999999999999999999999999999999999999998874

The ligand binding domain of the TR4 and TR2 (human testicular receptor 4 and 2): TR4 and TR2 are orphan nuclear receptors. Several isoforms of TR4 and TR2 have been isolated in various tissues. TR2 is abundantly expressed in the androgen-sensitive prostate. TR4 transcripts are expressed in many tissues, including central nervous system, adrenal gland, spleen, thyroid gland, and prostate. The expression of TR2 is negatively regulated by androgen, retinoids, and radiation. The expression of both mouse TR2 and TR4 is up-regulated by neurocytokine ciliary neurotrophic factor (CNTF) in mouse. It has shown that human TR2 binds to a wide spectrum of natural hormone response elements (HREs) with distinct affinities suggesting that TR2 may cross-talk with other gene expression regulation systems. The genes responding to TR2 or TR4 include genes that are regulated by retinoic acid receptor, vitamin D

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

Probab=100.00  E-value=1.4e-33  Score=253.79  Aligned_cols=184  Identities=22%  Similarity=0.206  Sum_probs=156.6

Q ss_pred             cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccc-
Q psy6602          86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVR-  164 (367)
Q Consensus        86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~-  164 (367)
                      ..+.++++++.+.++.+|+|||++|||..|+.+||++|||+||+|+++++.|++++..    ...+............+ 
T Consensus        36 ~~~~~~~e~a~~~l~~~IefaK~iP~F~~L~~~DQi~LLk~~~~el~iL~~a~~~~~~----~~~~~~~~~~~~~~~~~~  111 (221)
T cd06936          36 ENFLILTEMATSHVQVLVEFTKGLPGFETLDHEDQIALLKGSAVEAMFLRSAQIYNKK----LPAGHADLLEERIRSSGI  111 (221)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCCchhhCChhHHHHHHHHhHHHHHHHHHHHHhccc----ccCCCchhhHHHHHhccc
Confidence            4488899999999999999999999999999999999999999999999999776531    10011011110001112 


Q ss_pred             hHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhh
Q psy6602         165 VNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLML  244 (367)
Q Consensus       165 ~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l  244 (367)
                      ..+.++.+++|+.+|++|++|.+||+|||||+||+||++|++++..|+.+|++|.++|++||..+||+.+.||++||+++
T Consensus       112 ~~e~~~~i~~~~~kl~~L~l~~~E~~lLkaIvL~npd~~gL~~~~~Ve~~Q~~~~~aL~~y~~~~~p~~p~rf~~LL~~L  191 (221)
T cd06936         112 SDEFITPMFNFYKSMGELKMTQEEYALLTAITILFPDRPYLKDKEAVEKLQEPLLDLLQKFCKLYHPEDPQHFACLLGRL  191 (221)
T ss_pred             hHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCcCCCCHHHHHHHHHHHHHHHHHHHHhhCCCchhHHHHHHHHh
Confidence            34567888899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHhHhhhhhHHHHHHhhhccCCchhHhHHH
Q psy6602         245 PSLRAVRQSTIERLFFKETIGDIPIQRLLG  274 (367)
Q Consensus       245 ~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~  274 (367)
                      +.||+++..+.|.+++.+... ..+++|+.
T Consensus       192 ~~LR~l~~~~~e~l~~~k~~~-~~~~pl~~  220 (221)
T cd06936         192 TELRTLNHHHAEMLMSWKVND-HKFTPLLC  220 (221)
T ss_pred             HHHHHHHHHHHHHHHHHHccC-CCCCcccc
Confidence            999999999999999998875 46777764

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

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

Probab=100.00  E-value=6.9e-33  Score=247.96  Aligned_cols=175  Identities=28%  Similarity=0.421  Sum_probs=147.6

Q ss_pred             cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCc-cccCCC---CC
Q psy6602          86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEK-ARERLP---PD  161 (367)
Q Consensus        86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~-~~~~~~---~~  161 (367)
                      ..+..+++++++.++.+|+|||++|||.+|+.+||++|||++|+|+++++.||+++..+...+....+ ......   ..
T Consensus        27 ~~~~~l~~la~~~l~~~I~waK~lp~F~~L~~~DQi~LLk~~w~el~iL~~a~~s~~~~~~~l~~~~~~~~~~~~~~~~~  106 (213)
T cd06953          27 ELFALLCRLGDELLFRQIQWTKKLPFFTELSIKDHTHLLTTKWAELILLSTITVASLQNLGLLQDCLSKYLPSEDELERF  106 (213)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhcCCchhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHhhhccCCchhhHHHH
Confidence            34788999999999999999999999999999999999999999999999999998644322111000 000100   00


Q ss_pred             ccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHH
Q psy6602         162 DVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLL  241 (367)
Q Consensus       162 ~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL  241 (367)
                      .....+.++.+.+++.+|++|++|.+||+|||||+||+||++|+++...|+++|++|.++|++||..++++++.||++||
T Consensus       107 ~~~~~~~~~~i~~l~~~l~~L~ld~eEy~lLkAIvLfnpd~~gLs~~~~Ve~lQ~~~~~aL~~y~~~~~~~~p~Rf~~LL  186 (213)
T cd06953         107 GDEGGEVVERLTYLLAKFRQLKVSNEEYVCLKVINFLNQDIDGLTNASQLESLQKRYWYVLQDFTELNYPNQPNRFSDLL  186 (213)
T ss_pred             HhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcchHHHHHH
Confidence            11234566788899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhhHhHhhhhhHHHHHHh
Q psy6602         242 LMLPSLRAVRQSTIERLFF  260 (367)
Q Consensus       242 ~~l~~Lr~l~~~~~e~l~~  260 (367)
                      ++++.+|+++....|.-.+
T Consensus       187 ~~L~~Lr~l~~~~~e~~~~  205 (213)
T cd06953         187 SCLPEIRAAAGKLLHSKLF  205 (213)
T ss_pred             HHhHHHHHHHHHHHHHHHH
Confidence            9999999999988876543

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).

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

Probab=100.00  E-value=2.6e-32  Score=246.46  Aligned_cols=193  Identities=31%  Similarity=0.536  Sum_probs=171.3

Q ss_pred             hhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCc
Q psy6602          83 QILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDD  162 (367)
Q Consensus        83 ~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~  162 (367)
                      .+.++++++++.+.+.++.+|+|||++|+|..|+.+||++|+|++|++++++..||++...++..++.++..+...... 
T Consensus        29 ~~~~~~~~~~~~~~~~l~~~vewak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~s~~~~~~l~~~~g~~~~~~~~~-  107 (222)
T cd06931          29 KKIASINDVCESMKQQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGVARRSMPYKDILLLGNDLIIPRHCPE-  107 (222)
T ss_pred             cccCCHHHHHHHHHHHHHHHHHHHHhCCccccCChHHHHHHHHHHHHHHHHHHHHHhccCCCCeeeeCCCccccccccc-
Confidence            5677799999999999999999999999999999999999999999999999999999876666566655544443322 


Q ss_pred             cchHHHH-HHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHH
Q psy6602         163 VRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLL  241 (367)
Q Consensus       163 ~~~~~~~-~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL  241 (367)
                      .+..... +.+.+++.+|++|++|++||+|||||++|+||++|+++...++++|+++.++|.+|+..++++++.||++|+
T Consensus       108 ~~~~~~~~~~~~~~~~~l~~L~l~~~E~~lLkaiil~~p~~~~ls~~~~i~~~r~~~~~aL~~y~~~~~~~~~~Rf~~LL  187 (222)
T cd06931         108 PEISRVANRILDELVLPLRDLNIDDNEYACLKAIVFFDPDAKGLSDPQKIKRLRFQVQVSLEDYINDRQYDSRGRFGELL  187 (222)
T ss_pred             chHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCccCCCCHHHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHH
Confidence            2233334 345689999999999999999999999999999999999999999999999999999888889999999999


Q ss_pred             HhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHH
Q psy6602         242 LMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDM  276 (367)
Q Consensus       242 ~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~em  276 (367)
                      .+++.+++++....|.+++.++++..++++++.+|
T Consensus       188 ~~l~~lr~~~~~~~e~l~~~~lf~~~~~~~L~~e~  222 (222)
T cd06931         188 LLLPTLQSITWQMIEQIQFARLFGVAKIDNLLQEM  222 (222)
T ss_pred             HHHHHHHHHHHHHHHHHhhhhhcCCCcHHHHHhhC
Confidence            99999999999999999999999999999999875

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

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

Probab=100.00  E-value=6.9e-33  Score=240.99  Aligned_cols=170  Identities=25%  Similarity=0.333  Sum_probs=150.2

Q ss_pred             CHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccc-cCCCCCccch
Q psy6602          87 SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKAR-ERLPPDDVRV  165 (367)
Q Consensus        87 ~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~-~~~~~~~~~~  165 (367)
                      .++++++.+++.++.+|+|||++|+|..|+.+||++|+|++|+++++++.||++....+ .+.++++.. ........+.
T Consensus         3 ~~~~~~~~~~~~l~~~v~~ak~ip~F~~L~~~Dq~~Llk~~~~~l~~l~~a~~~~~~~~-~~~~~~~~~~~~~~~~~~~~   81 (174)
T cd06929           3 KFDHFTEIMTVAIRRVVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATLYDPEKN-SLTFGDGKGNSRDVLLNGGF   81 (174)
T ss_pred             HHHHHHHHHHHHHHHHHhhccCCcCcccCChhHHHHHHHhcHHHHHHHHHHHHhcccCC-eEEecCCceecHHHHHHccc
Confidence            37889999999999999999999999999999999999999999999999998876444 455555443 2222122234


Q ss_pred             HHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhhh
Q psy6602         166 NNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLP  245 (367)
Q Consensus       166 ~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~  245 (367)
                      ....+.+.+++.+|++|++|.+||+|||||+||+||++|++++..|++.|++|.++|++||..++++++.||++|+.+++
T Consensus        82 ~~~~~~~~~~~~~l~~L~l~~~E~~llkai~l~~pd~~~l~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~Ll~~l~  161 (174)
T cd06929          82 GEFIEPLFEFAEKMNKLQLDDNEYALLTAIVLFSPDRPGLQDVDTVEKLQERLLEALQRYLKVNHPDAPQMFAKLLKKLT  161 (174)
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcccCcCHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHHhH
Confidence            56778899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhHhhhhhHHHH
Q psy6602         246 SLRAVRQSTIER  257 (367)
Q Consensus       246 ~Lr~l~~~~~e~  257 (367)
                      .+|.++..+.|.
T Consensus       162 ~lr~l~~~~~e~  173 (174)
T cd06929         162 ELRTLNELHAEL  173 (174)
T ss_pred             HHHHHHHHHHhc
Confidence            999999998874

Ligand-binding domain (LBD) of nuclear receptor (NR) family 1: This is one of the major subfamily of nuclear receptors, including thyroid receptor, retinoid acid receptor, ecdysone receptor, farnesoid X receptor, vitamin D receptor, and other related receptors. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).

>KOG4215|consensus

Probab=100.00  E-value=1.2e-31  Score=244.25  Aligned_cols=206  Identities=26%  Similarity=0.433  Sum_probs=183.9

Q ss_pred             hhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCC
Q psy6602          82 LQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPD  161 (367)
Q Consensus        82 ~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~  161 (367)
                      ....++..++++...+++...|||||.||+|.+|+.+||++|||+...+.++|..++|+...++-.++.++++..+....
T Consensus       150 n~~~at~~Dv~eSm~qqLlllVEWAK~i~~F~el~l~DqvaLLk~~a~~hllLg~a~RSm~l~~v~ll~N~~v~~~~~~~  229 (432)
T KOG4215|consen  150 NKKIATENDVCESMKQQLLLLVEWAKYIPPFCELPLDDQVALLKAHAGQHLLLGAAFRSMHLKDVCLLNNTYVLHRHAPD  229 (432)
T ss_pred             ccccccHHHHHHHHHHHHHHHHHHHHhccchhcCCchhHHHHHHccchhhhhhhhhhccccccceEEecCceeeccCCCC
Confidence            34677889999999999999999999999999999999999999999999999999999988777777777776655544


Q ss_pred             ccchHHH-HHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChh--HHHHHHHHHHHHHHHHHHhhCC-CcchHH
Q psy6602         162 DVRVNNE-IKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ--PVEMLQDQAQCILGDYVRGRYS-RQPTRF  237 (367)
Q Consensus       162 ~~~~~~~-~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~--~v~~~q~~~~~~L~~y~~~~~~-~~~~Rf  237 (367)
                      ....... .+.+.+++.+|++|++|+.||+|||||++|+||..|+++..  .|+++|++++.+|..|+..+.+ +.+.||
T Consensus       230 ~~eis~v~~RIiDElv~Pmr~L~md~~Ey~cLKAi~FfdP~akGis~~s~~~I~~aR~~vl~sLe~yi~d~q~~d~~~R~  309 (432)
T KOG4215|consen  230 LPEISRVAPRIIDELVNPMRRLQMDEIEYVCLKAIAFFDPDAKGLSDPSQIRIREARNRVLKSLEAYISDRQPYDAPGRF  309 (432)
T ss_pred             hHHHHHHHHHHHHHHhhHHHHhccchHHHHHHHHHHhcCccccccCCchHhHHHHHHHHHHHHHHHHHhhcCccccccch
Confidence            3323333 37888999999999999999999999999999999999966  9999999999999999999985 778999


Q ss_pred             HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCC
Q psy6602         238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPG  287 (367)
Q Consensus       238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~g  287 (367)
                      |+||+++|.|+.++.+.+|++.+.++||...++.++.+++.-....|.+.
T Consensus       310 g~LLLllPsLqsIt~qliE~iqlaklFGla~vDsll~e~~l~~~~~d~~~  359 (432)
T KOG4215|consen  310 GNLLLLLPSLQSITQQLIEQIQLAKLFGLAKVDSLLQEFLLGGEPNDHSH  359 (432)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHhHHHHHhhcCCCCccCCC
Confidence            99999999999999999999999999999999999999998766555443

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

Probab=100.00  E-value=8.8e-32  Score=237.22  Aligned_cols=171  Identities=16%  Similarity=0.120  Sum_probs=148.9

Q ss_pred             HHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCC-CccchH
Q psy6602          88 AEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPP-DDVRVN  166 (367)
Q Consensus        88 ~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~-~~~~~~  166 (367)
                      |.++++.+++.++.+|+|||++|||.+|+.+||++|||++|+|+++++.+++++..  ..++.++........ ...+..
T Consensus         4 w~~~~~~~~~~i~~~IefaK~iPgF~~L~~~DQi~LLk~~~~e~~ll~~~~~~~~~--~~~~~~g~~~~~~~~~~~~~~~   81 (191)
T cd06942           4 WGHFAHEFEMHIQEIVQFVKSIPGFNQLSGEDRAQLLKGNMFPLYLLRLSRDYNNE--GTVLCDFRPVEFASLLSQLLHG   81 (191)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCcccCChhHHHHHHHHHHHHHHHHHHHHHhCcC--CeEEeCCccccHHHHHHhcchH
Confidence            88999999999999999999999999999999999999999999999998877654  334433322222111 111234


Q ss_pred             HHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCC--CCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhh
Q psy6602         167 NEIKLIQEILARFRQLSPDGSECGCMKAVILFTPE--TPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLML  244 (367)
Q Consensus       167 ~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd--~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l  244 (367)
                      +.++.+.+++.+|++|++|++||+||+||+||+||  ++|+++..+|+.+|+.+.++|.+||..+|++.+.||++|+.++
T Consensus        82 ~~~~~~~~~~~~l~~L~l~~~E~~lL~Aivl~~pd~~~~~l~~~~~v~~~q~~l~~~L~~~~~~~~~~~~~rf~kLL~~l  161 (191)
T cd06942          82 KLIDEMLQFANKILTLNLTNAELALLCAAELLQPDSLGIQLEETAKSNLQLSVLFQFLKSVLFKDGEDTEQRLQKLFDIL  161 (191)
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCCccchHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHH
Confidence            66777889999999999999999999999999999  9999999999999999999999999999999999999999999


Q ss_pred             hHhHhhhhhHHHHHHh
Q psy6602         245 PSLRAVRQSTIERLFF  260 (367)
Q Consensus       245 ~~Lr~l~~~~~e~l~~  260 (367)
                      +.+|+++..+.+.+..
T Consensus       162 ~~Lr~~~~~~~~~l~~  177 (191)
T cd06942         162 NRLRNMNKEHQNILAD  177 (191)
T ss_pred             HHHHHHHHHHHHHHHc
Confidence            9999999999997665

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

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

Probab=99.98  E-value=2.2e-31  Score=229.46  Aligned_cols=162  Identities=41%  Similarity=0.691  Sum_probs=141.9

Q ss_pred             HHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCC-CceEecCCc-cccCCCCCccchH
Q psy6602          89 EKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD-LSLLINCEK-ARERLPPDDVRVN  166 (367)
Q Consensus        89 ~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~-~~~l~~~~~-~~~~~~~~~~~~~  166 (367)
                      +++++++++.++.+|+|||++|+|..|+.+||++|+|++|++++++..||++.... ...+..+++ ..........+..
T Consensus         2 ~~~~~~~~~~l~~~ie~ak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (165)
T cd06930           2 ESLCELADRVLFKTVDWAKNLPAFRNLPLDDQLTLLQNSWAELLLLGLAQRSVHFELSELLLPSPLLVILTEREALLGLA   81 (165)
T ss_pred             hhHHHHHHHHHHHHHHHHHcCCccccCChHHHHHHHHHHHHHHHHHHHHHHHhccCCCcceeecCCcccchhhhhhhhHH
Confidence            46899999999999999999999999999999999999999999999999998763 334444443 3333322223355


Q ss_pred             HHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhhhH
Q psy6602         167 NEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPS  246 (367)
Q Consensus       167 ~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~~  246 (367)
                      +..+.+.+++.+|++|++|++||+|||||++|+||++|+++...|++.|++|.++|..||..++++++.||++|+.+++.
T Consensus        82 ~~~~~~~~~~~~l~~L~l~~~E~~lLkai~l~~p~~~~l~~~~~v~~~q~~~~~aL~~~~~~~~~~~~~R~~~ll~~l~~  161 (165)
T cd06930          82 ELVQRLQELLSKLRSLQLDPKEYACLKAIVLFNPDLPGLKNQQQVEELQEKAQQALQEYIRKRYPQQPARFAKLLLRLPE  161 (165)
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHHHHHHHHHHHhhCCCchhHHHHHHHHhHh
Confidence            66788899999999999999999999999999999999999999999999999999999999989999999999999999


Q ss_pred             hHhh
Q psy6602         247 LRAV  250 (367)
Q Consensus       247 Lr~l  250 (367)
                      +|++
T Consensus       162 lr~~  165 (165)
T cd06930         162 LRSI  165 (165)
T ss_pred             hccC
Confidence            9864

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).

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

Probab=99.94  E-value=9.6e-26  Score=193.71  Aligned_cols=161  Identities=35%  Similarity=0.548  Sum_probs=138.7

Q ss_pred             HHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccc----cCCCCCccch
Q psy6602          90 KCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKAR----ERLPPDDVRV  165 (367)
Q Consensus        90 ~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~----~~~~~~~~~~  165 (367)
                      ++++++.+.+..+++|||++|+|..|+.+||+.|+|++|+++++|+.+|++........+..++..    ..........
T Consensus         2 ~~~~~~~~~~~~~i~~~~~~~~f~~L~~~dq~~Llk~~~~~~~~L~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (168)
T cd06157           2 LLCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLLLAPNGGHTDDDKEDEMKLLLK   81 (168)
T ss_pred             cHHHHHHHHHHHHHHHHHcCCchhcCChHHHHHHHHHHhHHHHHHHHHHHHHhcCCCcEEeecccccccCchHHHHHhHH
Confidence            478999999999999999999999999999999999999999999999999987776666554432    1111111223


Q ss_pred             HHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCC-CCCChhHHHHHHHHHHHHHHHHHHhhCC-CcchHHHHHHHh
Q psy6602         166 NNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP-GLVDAQPVEMLQDQAQCILGDYVRGRYS-RQPTRFGRLLLM  243 (367)
Q Consensus       166 ~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~-~L~~~~~v~~~q~~~~~~L~~y~~~~~~-~~~~Rf~~LL~~  243 (367)
                      ....+.+.+++.+|.+|++|++||++||||++|+|+.+ +......+++.|++|.++|+.|+..+++ +++.||++|+.+
T Consensus        82 ~~~~~~~~~~~~~~~~L~l~~~E~~~l~ai~l~~~~~~~s~~~~~~~~~~~~~~~~~L~~y~~~~~~~~~~~R~~~ll~~  161 (168)
T cd06157          82 GELIRLLFEFVNPLRALKLDDEEYALLKAIVLFSPDRKESLEDRKIVEELQERLLEALQDYLRKNYPEEAPSRFAKLLLL  161 (168)
T ss_pred             HHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHhCCccchhHHHHHHHh
Confidence            34457788999999999999999999999999999998 6777999999999999999999999986 899999999999


Q ss_pred             hhHhHhh
Q psy6602         244 LPSLRAV  250 (367)
Q Consensus       244 l~~Lr~l  250 (367)
                      ++.++++
T Consensus       162 l~~l~~~  168 (168)
T cd06157         162 LPSLRKL  168 (168)
T ss_pred             chhcccC
Confidence            9999863

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

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

Probab=99.93  E-value=5.4e-25  Score=195.01  Aligned_cols=181  Identities=33%  Similarity=0.490  Sum_probs=149.4

Q ss_pred             hhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccc-cCCC--
Q psy6602          83 QILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKAR-ERLP--  159 (367)
Q Consensus        83 ~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~-~~~~--  159 (367)
                      .+..+++++++++.+.+..+|+|||.+|+|..|+.+||++|+|++|+++++|..++++.......+...++.. ....  
T Consensus        14 ~~~~~~~~~~~~~~~~~~~~v~~~k~~p~f~~L~~~dk~~Llk~~~~~~~~l~~~~~s~~~~~~~~~~~~~~~~~~~~~~   93 (203)
T PF00104_consen   14 LRPATFEDLCEIWRRELRLIVDWAKSFPEFSELSMEDKIALLKSSWFELFILELAYRSYQCNQDQLMFPNGTFIDKDSFD   93 (203)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGS-HHHHHHHHHHHHHHHHHHHHHHHEEHTTTTEEEETTTEEEEHHHHH
T ss_pred             CcHhhHHHHHHHHHHHHHHHHHHHHhCcCHHhhhhhhhhhHHhhhcccccchhhhhhhcccccccccccccccccccccc
Confidence            4455688999999999999999999999999999999999999999999999999999833344444444332 2111  


Q ss_pred             -CCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCC-Ch-hHHHHHHHHHHHHHHHHH-HhhCC-Ccc
Q psy6602         160 -PDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLV-DA-QPVEMLQDQAQCILGDYV-RGRYS-RQP  234 (367)
Q Consensus       160 -~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~-~~-~~v~~~q~~~~~~L~~y~-~~~~~-~~~  234 (367)
                       .......+.++.+.+++.+|+++++|++||++|+|+++|+|+.++++ +. ..++++|+++.++|+.|+ ...++ +.+
T Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~l~l~~~E~~~l~~l~l~~~~~~~~~~~~~~~~~~~r~~~~~~L~~y~~~~~~~~~~~  173 (203)
T PF00104_consen   94 DFITGIFSEFIQYMNEVLRPFRRLKLDEEEFALLKALILFNPDYPGLSEETREIVEELRDRIIQALHSYYNQSKGPEDYA  173 (203)
T ss_dssp             HTSTTTHHHHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHSSTTSTTHS-SHHHHHHHHHHHHHHHHHHHHHHHHSTTTHT
T ss_pred             cccccccccchhHHHHHHHHHHHhhhhhHHHHHHHHHhhhcccccccccchhHHHHHHHHHHHHHHHHHHhccCCCccHH
Confidence             01123456678899999999999999999999999999999999998 54 459999999999999999 66665 458


Q ss_pred             hHHHHHHHhhhHhHhhhhhHHHHHHhhhc
Q psy6602         235 TRFGRLLLMLPSLRAVRQSTIERLFFKET  263 (367)
Q Consensus       235 ~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~  263 (367)
                      .||++|+.+++.++.+.....|.+++..+
T Consensus       174 ~R~~~ll~ll~~l~~~~~~~~e~~~~~~l  202 (203)
T PF00104_consen  174 QRFGKLLLLLPSLRKISEKHIENMFLSDL  202 (203)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhHHhh
Confidence            99999999999999999999999877654

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

>smart00430 HOLI Ligand binding domain of hormone receptors

Probab=99.92  E-value=1.1e-24  Score=186.18  Aligned_cols=154  Identities=33%  Similarity=0.514  Sum_probs=134.9

Q ss_pred             HHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCc----cchHHHHHH
Q psy6602          96 ARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDD----VRVNNEIKL  171 (367)
Q Consensus        96 ~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~----~~~~~~~~~  171 (367)
                      .+.+..+|+|||++|+|++|+.+||+.|+|++|++++++..++++.......++.+++.+.......    .......+.
T Consensus         2 ~~~~~~~~~~~~~~~~f~~L~~~dq~~Llk~~~~~~~~l~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (163)
T smart00430        2 ERDLLLAVEWAKTFPFFRELSQEDKLILLKHFWFEWLLLESAYRSAKMKKSLLLLPDGTFIDNDKVDLLRKLFSPFLDRI   81 (163)
T ss_pred             hhHHHHHHHHHHhChhHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEeCCCcccCcchhHHHHHHHHHHHHHH
Confidence            4678999999999999999999999999999999999999999998877777787877655433221    112334477


Q ss_pred             HHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCCh--hHHHHHHHHHHHHHHHHHHhhCC-CcchHHHHHHHhhhHhH
Q psy6602         172 IQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDA--QPVEMLQDQAQCILGDYVRGRYS-RQPTRFGRLLLMLPSLR  248 (367)
Q Consensus       172 ~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~--~~v~~~q~~~~~~L~~y~~~~~~-~~~~Rf~~LL~~l~~Lr  248 (367)
                      +.+++.+|++|++|++||++|+|+++|+|+.+|+.+.  ..++++|+.+.++|+.|+..+++ +.+.||++|+.+++.++
T Consensus        82 ~~~~~~~l~~L~l~~~E~~~l~ai~l~~~~~~~l~~~~~~~~~~~~~~~~~~L~~y~~~~~~~~~~~R~~~ll~~l~~i~  161 (163)
T smart00430       82 LQELVKPLRELKLDDEEYALLKAILLFNPAGPGLSEEGKEILEKLQEKLANALHDYYLKNYPMNYPGRFGELLLILNAIQ  161 (163)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHcChhhhhhChHHHHHHHHHHHHHHHHHHHHHHHcCCCcchhHHHHHHHHHHHhh
Confidence            8899999999999999999999999999999999986  89999999999999999999887 67899999999999987


Q ss_pred             h
Q psy6602         249 A  249 (367)
Q Consensus       249 ~  249 (367)
                      .
T Consensus       162 ~  162 (163)
T smart00430      162 K  162 (163)
T ss_pred             c
Confidence            5

>KOG4218|consensus

Probab=99.92  E-value=1.3e-24  Score=196.43  Aligned_cols=196  Identities=26%  Similarity=0.327  Sum_probs=162.0

Q ss_pred             cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCC--CceEecCC-ccccCC--CC
Q psy6602          86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD--LSLLINCE-KARERL--PP  160 (367)
Q Consensus        86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~--~~~l~~~~-~~~~~~--~~  160 (367)
                      .++--.|.++++.++.+|+|||+--.|.+|+.+||++||++||.|+.+++..|+.+..+  +++.+.++ .+.-..  ..
T Consensus       274 ~~fgl~c~mAdqtl~sIV~WAr~~~~F~eL~vdDQM~LLQncWselli~DhiyrqV~hgkegsi~lvtGqeV~~~~vA~q  353 (475)
T KOG4218|consen  274 EKFGLSCQMADQTLKSIVIWARNDQLFSELSVDDQMILLQNCWSELLIVDHIYRQVHHGKEGSIKLVTGQEVPVGLVALQ  353 (475)
T ss_pred             hhhhhhhhhhHhHHHHHHHHHhhhhHHHhcchhhHHHHHHHhhHHHHHHHHHHHHHhcCcccceEEecCCcccchhHhhh
Confidence            34445799999999999999999999999999999999999999999999999988543  33333332 221111  11


Q ss_pred             CccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHH
Q psy6602         161 DDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRL  240 (367)
Q Consensus       161 ~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~L  240 (367)
                      ........+...++++.+++.|++|+.||+|||-|+||+-|..                                     
T Consensus       354 ags~l~tlvs~aqelV~~Lr~lqfd~~efvclkFl~LFsld~k-------------------------------------  396 (475)
T KOG4218|consen  354 AGSLLQTLVSSAQELVIRLRNLQFDNFEFVCLKFLALFSLDMK-------------------------------------  396 (475)
T ss_pred             hhhHHHHHHHHHHHHHHHHHhcCCccchhhHHHHHHHHhhhHH-------------------------------------
Confidence            1111334456778999999999999999999999999995531                                     


Q ss_pred             HHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcChH
Q psy6602         241 LLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRF  320 (367)
Q Consensus       241 L~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r~  320 (367)
                                                                    .|++-..|+++|+++..||-+|...+||+....|
T Consensus       397 ----------------------------------------------fLenf~lv~~~qe~~naaLldyt~c~yp~~~~kF  430 (475)
T KOG4218|consen  397 ----------------------------------------------FLENFELVRRLQEDSNAALLDYTSCCYPNWEQKF  430 (475)
T ss_pred             ----------------------------------------------HHHHHHHHHHHHHHHHHHHHHhhccCCccHHHHH
Confidence                                                          1122336889999999999999999999999999


Q ss_pred             HHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhccc
Q psy6602         321 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEK  364 (367)
Q Consensus       321 ~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~~  364 (367)
                      +++|++|+++|+++.+..|+++.+++.|++|-++|+.|||.++.
T Consensus       431 ~qllL~L~eiRa~smqa~eyly~khl~~~~p~nnllieml~Ak~  474 (475)
T KOG4218|consen  431 PQLLLVLEEIRATSMQAAEYLYTKHLQVPAPQNNLLIEMLTAKP  474 (475)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhCCCccccchHHHHhhccC
Confidence            99999999999999999999999999999999999999999985

>KOG4217|consensus

Probab=99.88  E-value=3e-22  Score=187.87  Aligned_cols=190  Identities=27%  Similarity=0.382  Sum_probs=173.5

Q ss_pred             CHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccchH
Q psy6602          87 SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVN  166 (367)
Q Consensus        87 ~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  166 (367)
                      .+..++++..-.+-.+-.||.+||||.+|..+||-.||.++++|+|+|+.|||+.+.++..+|+++.+..+.+... +++
T Consensus       409 ~vqqfy~lLtgsl~virk~aekiPgf~el~paDq~lLlesaflelfvlRlAyRs~~~e~kliFcsG~vlhr~qC~r-gfg  487 (605)
T KOG4217|consen  409 HVQQFYDLLTGSLEVIRKWAEKIPGFAELPPADQDLLLESAFLELFVLRLAYRSNPSEDKLIFCSGLVLHRLQCLR-GFG  487 (605)
T ss_pred             HHHHHHHHhhhhHHHHHHHHHhCcCcccCChhhHHHHHHHHHHHHHHHHHHHhcCCCCCeEEEecchhhhHHHHHH-HHH
Confidence            3677899999999999999999999999999999999999999999999999999988888898888877754333 477


Q ss_pred             HHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhC--CCcchHHHHHHHhh
Q psy6602         167 NEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRY--SRQPTRFGRLLLML  244 (367)
Q Consensus       167 ~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~--~~~~~Rf~~LL~~l  244 (367)
                      +.++.+.+|...+..|.+|-.-|+||.|+.+.. ++-||.+...||++|++++.+|.+|+....  ...+.++.+++..+
T Consensus       488 ewidsi~~FS~~l~~l~idi~AfacL~aLa~iT-ErhGL~epkrVeelqnkIi~~LKDHvt~~~~~~~k~~~lSrllgkl  566 (605)
T KOG4217|consen  488 EWIDSIREFSRSLHSLNIDISAFACLSALALIT-ERHGLKEPKRVEELQNKIINCLKDHVTGSAGKLAKPVYLSRLLGKL  566 (605)
T ss_pred             HHHHHHHHHHHHhhhchhhHHHHHHHHHHHhhh-hhhcCCCcchHHHHHHHHHHHHHHHhhhcccccccchHHHHHhhhh
Confidence            889999999999999999999999999999987 889999999999999999999999997554  46788999999999


Q ss_pred             hHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHc
Q psy6602         245 PSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT  278 (367)
Q Consensus       245 ~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~  278 (367)
                      ++||.+..+....+|+.+....++.+.++..||.
T Consensus       567 peLr~l~tqgLqrifyLklEdlvp~p~iidklf~  600 (605)
T KOG4217|consen  567 PELRTLCTQGLQRIFYLKLEDLVPPPAIIDKLFL  600 (605)
T ss_pred             HHHHHHHHHhhhhhhcccHhhccCchhhhhhhhh
Confidence            9999999999999999999988888888887775

>KOG4216|consensus

Probab=99.85  E-value=3.1e-21  Score=177.39  Aligned_cols=189  Identities=17%  Similarity=0.188  Sum_probs=160.2

Q ss_pred             HHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccchHH
Q psy6602          88 AEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNN  167 (367)
Q Consensus        88 ~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~  167 (367)
                      |+.+..-....|+.+|||||.|+||.+|+++|||+|||.+.+|+.+.++++.++..++.+.+..+..- .......+..+
T Consensus       284 We~cA~~lt~~IQ~vVEFAK~I~GFM~L~Q~dQI~LLKaGsfEv~lvrm~r~~~v~~ntV~~e~~~~g-~~~f~a~~~~e  362 (479)
T KOG4216|consen  284 WELCAIKLTPAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSFEVVLVRMCRAFDVDNNTVYFEGKYAG-PEVFYALGCEE  362 (479)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhhHhhccCccceEEeeecCceeeeHHHHHHhhcccccceeecccccc-hhheeccChHH
Confidence            45566666778999999999999999999999999999999999999999988876666665554432 22223344677


Q ss_pred             HHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhhhHh
Q psy6602         168 EIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSL  247 (367)
Q Consensus       168 ~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~~L  247 (367)
                      ++..++++...+..|++++.|.|++.|++|.+||++|+.+..+|++++++...++++.+.+++.. ..-..+|+...+.+
T Consensus       363 lis~vf~~~ksL~~Lq~te~EiAL~~alVL~~~~r~gl~e~~ki~~lq~~~~~a~qhvl~knh~~-~~~l~kl~~k~~~~  441 (479)
T KOG4216|consen  363 LISRVFEFGKSLCSLQLTEDEIALFSALVLMSADRSGLQEKVKIEKLQQKIQLALQHVLQKNHRE-DGILTKLICKVSTL  441 (479)
T ss_pred             HHHHHHhhhHHHHhhccCcHHHHHHHHHHhhCCccccccchHHHHHHHHHHHHHHHHHHHhcCCh-hhhHHHhhcccchH
Confidence            88999999999999999999999999999999999999999999999999999999999988632 23689999999999


Q ss_pred             HhhhhhHHHHHHhhhccCCchh---HhHHHHHHc
Q psy6602         248 RAVRQSTIERLFFKETIGDIPI---QRLLGDMYT  278 (367)
Q Consensus       248 r~l~~~~~e~l~~~~~~~~~~~---~~Ll~eml~  278 (367)
                      |.+...+.|.+..++..+...+   ++|..|+|.
T Consensus       442 r~~~~lH~E~Lq~Fk~~hP~iv~~fP~LYKELFt  475 (479)
T KOG4216|consen  442 RALCGLHTEKLQAFKASHPDIVRHFPPLYKELFT  475 (479)
T ss_pred             HHHHHHHHHHHHHHhhcCchHHhhccHHHHHHhc
Confidence            9999999999998888766554   556666654

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

Probab=99.77  E-value=9.4e-19  Score=159.27  Aligned_cols=111  Identities=31%  Similarity=0.448  Sum_probs=103.2

Q ss_pred             HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcCh
Q psy6602         240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTR  319 (367)
Q Consensus       240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r  319 (367)
                      +..+...+|.+..+..|+++++...-               .+||++|+.+..+|+++|++++.||++|+..+||+++.|
T Consensus       131 ~~e~~~~lr~L~ld~~E~a~LKaivL---------------fnpd~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~R  195 (241)
T cd07069         131 AQELVAKLRSLQFDQREFVCLKFLVL---------------FSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEK  195 (241)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHH---------------cCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCchhH
Confidence            34567789999999999999998863               348999999999999999999999999999999999999


Q ss_pred             HHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhcccc
Q psy6602         320 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKS  365 (367)
Q Consensus       320 ~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~~~  365 (367)
                      |+|||++||+||+++..++|++||++++|.+|+++|+.||+++|+.
T Consensus       196 f~kLLl~Lp~LR~is~~~~e~l~~~~l~g~~~~~~Ll~Eml~~~~~  241 (241)
T cd07069         196 FGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHAKRA  241 (241)
T ss_pred             HHHHHHHhHHHHHhhHHHHHHHHhccccCCCcHHHHHHHHHhcccC
Confidence            9999999999999999999999999999999999999999999863

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).

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

Probab=99.77  E-value=1e-18  Score=156.93  Aligned_cols=107  Identities=34%  Similarity=0.466  Sum_probs=99.3

Q ss_pred             HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcC
Q psy6602         239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPT  318 (367)
Q Consensus       239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~  318 (367)
                      .+......++.+..+..|+.+++.+.-               .+||++|+++..+|+++|++++.||++|+..+||+++.
T Consensus       116 ~l~e~~~~l~~L~ld~~Eya~LkaivL---------------f~pd~~gl~~~~~V~~lqe~~~~aL~~~~~~~~p~~~~  180 (222)
T cd07349         116 WLQCCLNKFWSLDLSPKEYAYLKGTIL---------------FNPDVPGLTASSHVGHLQQEAQWALCEVLEPLHPQDQG  180 (222)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHH---------------cCCCcccCCCHHHHHHHHHHHHHHHHHHHHHHCCCccc
Confidence            344577789999999999999997753               24799999999999999999999999999999999999


Q ss_pred             hHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHH
Q psy6602         319 RFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMY  360 (367)
Q Consensus       319 r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml  360 (367)
                      ||+|||++||+||+++.+++|++||++++|++||++|+.|||
T Consensus       181 r~~kLLl~Lp~LR~i~~~~ie~lff~~~~g~~~i~~Ll~eml  222 (222)
T cd07349         181 RFARILLTASTLKSIPPSLITDLFFRPIIGDADIAELLGDML  222 (222)
T ss_pred             HHHHHHHHhHHHhcCCHHHHHHHhCccccCCCcHHHHHHHhC
Confidence            999999999999999999999999999999999999999996

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.

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

Probab=99.75  E-value=1.3e-17  Score=151.07  Aligned_cols=109  Identities=19%  Similarity=0.237  Sum_probs=99.4

Q ss_pred             HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCc
Q psy6602         238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP  317 (367)
Q Consensus       238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~  317 (367)
                      ..+......++.+..+..|+.+++...-               .+||++|+++..+|+++|+++..||++|+..+||++|
T Consensus       122 ~~~~~~~~~l~~L~ld~~E~alLkAivL---------------f~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~p  186 (231)
T cd06937         122 DLVFTFANQLLPLEMDDTEIGLLSAICL---------------ICGDRQDLEEPDRVEKLQEPLLEALKIYARKRRPDKP  186 (231)
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHH---------------cCCCCccCCCHHHHHHHHHHHHHHHHHHHHhhCCCcc
Confidence            3345566678888889999988887753               2489999999999999999999999999999999999


Q ss_pred             ChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHh
Q psy6602         318 TRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT  361 (367)
Q Consensus       318 ~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~  361 (367)
                      .||+|||++||+||+++.+++|++|+.|++|.+|+++|+.|||+
T Consensus       187 ~rf~kLLl~Lp~LR~l~~~~~e~l~~~k~~~~~~~~~Ll~Eml~  230 (231)
T cd06937         187 HMFPKMLMKITDLRSISAKGAERVITLKMEIPGPMPPLISEMLE  230 (231)
T ss_pred             cHHHHHHHHhHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHhc
Confidence            99999999999999999999999999999999999999999996

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

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

Probab=99.75  E-value=4.1e-18  Score=154.91  Aligned_cols=107  Identities=26%  Similarity=0.284  Sum_probs=100.1

Q ss_pred             HhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcChHH
Q psy6602         242 LMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFG  321 (367)
Q Consensus       242 ~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r~~  321 (367)
                      .+...++.+..+..|+++++...-               .+||++|+.+...|+.+|+++..||.+|+..+||+.+.||+
T Consensus       131 e~~~kl~~L~ld~~Ey~~LkaIiL---------------fnpd~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~Rf~  195 (237)
T cd07070         131 ELVLQLHALQLDRQEFVCLKFLIL---------------FSLDVKFLNNHSLVKDAQEKANAALLDYTLCHYPHCGDKFQ  195 (237)
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHHh---------------cCCCccCCCCHHHHHHHHHHHHHHHHHHHHhcCCCcchHHH
Confidence            466678899999999999988753               24899999999999999999999999999999999999999


Q ss_pred             HHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhcc
Q psy6602         322 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  363 (367)
Q Consensus       322 ~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~  363 (367)
                      +||++||+||+++.+++|++||.+++|.+|+++|+.||+++|
T Consensus       196 kLLl~Lp~LRsis~~~~e~l~~~~l~g~~~~~~Ll~eml~~~  237 (237)
T cd07070         196 QLLLRLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIEMLQAK  237 (237)
T ss_pred             HHHHHhHHHHHhhHHHHHHHHHhcccCCCcHHHHHHHHhcCC
Confidence            999999999999999999999999999999999999999875

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).

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

Probab=99.72  E-value=9.8e-17  Score=145.41  Aligned_cols=108  Identities=21%  Similarity=0.322  Sum_probs=95.9

Q ss_pred             HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhh--CCCC
Q psy6602         239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGR--YSRQ  316 (367)
Q Consensus       239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~--~p~~  316 (367)
                      .+......++.+..+..|+.+++.+.-           |     +|++||++..+||++|+++..||++|+..+  +|++
T Consensus       125 ~i~ef~~~l~~L~ld~~E~a~LkAIvL-----------f-----~Dr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~p~~  188 (238)
T cd07348         125 SILEFSQSLHRMNLDVSAFSCLAALVI-----------I-----TDRHGLKEPKRVEELQNRLISCLKEHVSGSASEPQR  188 (238)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHH-----------c-----CCCcCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCcc
Confidence            344566677888888888888876642           1     499999999999999999999999999985  4999


Q ss_pred             cChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhc
Q psy6602         317 PTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM  362 (367)
Q Consensus       317 ~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~  362 (367)
                      +.||+|||++||+||+++.+++|++|+.|++|.+|+++|+.|||..
T Consensus       189 p~rf~kLLl~Lp~LRsl~~~~~e~lf~~kl~~~~~~~pLl~e~~~~  234 (238)
T cd07348         189 PNCLSRLLGKLPELRTLCTQGLQRIFYLKLEDLVPPPPIVDKIFMD  234 (238)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHhc
Confidence            9999999999999999999999999999999999999999999964

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

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

Probab=99.72  E-value=2.6e-17  Score=149.79  Aligned_cols=109  Identities=31%  Similarity=0.450  Sum_probs=101.4

Q ss_pred             HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcCh
Q psy6602         240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTR  319 (367)
Q Consensus       240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r  319 (367)
                      +..+...++.+..+..|+++++..+-               .+||++|+++...|+++|+++..||.+|+..+||+.+.|
T Consensus       129 i~~~~~~l~~L~ld~~E~~lLkaIiL---------------~npd~~gL~~~~~Ve~~q~~~~~aL~~y~~~~~~~~~~R  193 (237)
T cd06944         129 AQELVNKLRELQFDRQEFVCLKFLIL---------------FNPDVKGLENRQLVESVQEQVNAALLDYTLCNYPQQTDK  193 (237)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHH---------------cCCCcCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccH
Confidence            44567788999999999999998763               347899999999999999999999999999999999999


Q ss_pred             HHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhcc
Q psy6602         320 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  363 (367)
Q Consensus       320 ~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~  363 (367)
                      |++||++||+||+++.+++|++||++++|.+|+++|+.||+++|
T Consensus       194 f~~LL~~Lp~Lr~is~~~~e~l~~~~l~g~~~~~~Ll~eml~~~  237 (237)
T cd06944         194 FGQLLLRLPEIRAISMQAEEYLYYKHLNGEVPCNNLLIEMLHAK  237 (237)
T ss_pred             HHHHHHHhHHHHHHHHHHHHHHHhcccCCCCcHHHHHHHHHcCC
Confidence            99999999999999999999999999999999999999999876

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

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

Probab=99.72  E-value=2.9e-17  Score=149.13  Aligned_cols=113  Identities=24%  Similarity=0.278  Sum_probs=102.6

Q ss_pred             HHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCC-----CCCCchhhhhHHHHHHHHHHHHH
Q psy6602         236 RFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPG-----LVDAQPVEMLQDQAQCILGDYVR  310 (367)
Q Consensus       236 Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~g-----l~~~~~ve~lq~~~~~aL~~~~~  310 (367)
                      .+..+......++++..+..|+++++.+.-               .+||++|     +++..+|+++|+++..||.+|+.
T Consensus       115 ~~~~~~~~~~~l~~L~ld~~EyalLKAIvL---------------fnpd~~g~~~~~l~~~~~Ve~lq~~~~~aL~~y~~  179 (235)
T cd06949         115 IFDMLLATASRFRELQLQREEYVCLKAIIL---------------LNSSVYTFLLESLESRRQVQRLLDKITDALVHACS  179 (235)
T ss_pred             HHHHHHHHHHHHHHhCCCHHHHHHHHHHHH---------------cCCCcCCcccccccCHHHHHHHHHHHHHHHHHHHH
Confidence            344566677788999999999999988753               2478999     99999999999999999999999


Q ss_pred             hhC---CCCcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhcc
Q psy6602         311 GRY---SRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  363 (367)
Q Consensus       311 ~~~---p~~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~  363 (367)
                      ++|   |+++.||++||++||+||+++++++|+||++|++|.+|+++|+.|||+++
T Consensus       180 ~~~~~~p~~~~Rf~~LLl~Lp~LR~l~~~~~e~l~~~k~~~~~~~~~Ll~Eml~~~  235 (235)
T cd06949         180 KRGLSLQQQSRRLAQLLLILSHIRHVSNKGMEHLYSMKCKNVVPLYDLLLEMLDAH  235 (235)
T ss_pred             hcCCCCCCcccHHHHHHHhchHHHHhhHHHHHHHHHHHhCCCCChHHHHHHHhcCC
Confidence            999   99999999999999999999999999999999999999999999999863

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

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

Probab=99.71  E-value=1.6e-17  Score=150.07  Aligned_cols=106  Identities=29%  Similarity=0.367  Sum_probs=97.7

Q ss_pred             HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCc
Q psy6602         238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP  317 (367)
Q Consensus       238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~  317 (367)
                      ..+......++.+..+..|+++++.+.-               .+||++|+++..+|+++|++++.||.+|+..+||+++
T Consensus       127 ~~l~e~~~~l~~L~ld~~E~a~LkAivL---------------f~pD~~~L~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~  191 (232)
T cd07350         127 RAIKAFLAKCWSLDISTKEYAYLKGTVL---------------FNPDLPGLQCVQYIQGLQWEAQQALNEHVRMIHRGDQ  191 (232)
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHH---------------hCCCcccCCCHHHHHHHHHHHHHHHHHHHHhhCCChh
Confidence            3455677789999999999999998752               2479999999999999999999999999999999999


Q ss_pred             ChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHH
Q psy6602         318 TRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGD  358 (367)
Q Consensus       318 ~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~e  358 (367)
                      .||+|||++||+||+++.+++|++||++++|.++|++|+.|
T Consensus       192 ~rf~kLLl~Lp~LRsi~~~~iE~lff~~l~g~v~i~~ll~E  232 (232)
T cd07350         192 ARFAKLNIALSLLRAINANVIAELFFRPIIGTVNMDDMLLE  232 (232)
T ss_pred             hHHHHHHHHhHHHHccCHHHHHHHhccccCCCCcHHHHhcC
Confidence            99999999999999999999999999999999999999975

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.

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

Probab=99.69  E-value=6.1e-17  Score=147.29  Aligned_cols=110  Identities=26%  Similarity=0.405  Sum_probs=98.2

Q ss_pred             HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCC--CC
Q psy6602         239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYS--RQ  316 (367)
Q Consensus       239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p--~~  316 (367)
                      .++.....++++.....|+++++...-               .++|++||++..+|+++|+++..||++|+..+||  ++
T Consensus       125 ~i~~f~~~l~~L~ld~~E~~~LkaivL---------------~~pD~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~  189 (239)
T cd06945         125 SILAFSSSLQSLLLDDISAFCCLALLL---------------LITERHGLKEPKKVEELQNKIISCLRDHVTSNYPGQDK  189 (239)
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHH---------------hCCCccccCCHHHHHHHHHHHHHHHHHHHHHhCCCccc
Confidence            344555677778888888888876642               2479999999999999999999999999999999  99


Q ss_pred             cChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhcc
Q psy6602         317 PTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  363 (367)
Q Consensus       317 ~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~  363 (367)
                      +.||+|||++||+||+++.+++|++||.|++|.+|+++|+.|||...
T Consensus       190 ~~rf~kLLl~Lp~LR~ls~~~~e~l~~~k~~~~~~~~~Ll~e~~~~~  236 (239)
T cd06945         190 PNRLSKLLLKLPELRTLSKKGLQRIFFLKLEDLLPPPPLIDKRFLDT  236 (239)
T ss_pred             ccHHHHHHHHhHHHHHHHHHHHHHHHHHHccCCCCCChHHHHHHHhc
Confidence            99999999999999999999999999999999999999999999754

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

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

Probab=99.69  E-value=4.5e-17  Score=146.57  Aligned_cols=104  Identities=25%  Similarity=0.329  Sum_probs=95.6

Q ss_pred             HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcC
Q psy6602         239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPT  318 (367)
Q Consensus       239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~  318 (367)
                      .+..+...++.+..+..|+++++.+.-               .+||++|+ +..+|+++|++++.||++|+..+||+++.
T Consensus       119 ~l~e~~~~l~~L~ld~~Eya~LkAivL---------------fnpD~~gl-~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~  182 (222)
T cd06951         119 DIQQFLMKCWSLDLDCKEYAYLKGAVL---------------FTPVPPLL-CPHYIEALQKEAQQALNEHTMMTRPLEQL  182 (222)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHH---------------hCCCCCcc-CHHHHHHHHHHHHHHHHHHHHhhCCCccc
Confidence            345677788999999999999988753               34899999 99999999999999999999999999999


Q ss_pred             hHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHH
Q psy6602         319 RFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGD  358 (367)
Q Consensus       319 r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~e  358 (367)
                      ||+|||++||+||+++.+++|++||.+++|.+||++++.|
T Consensus       183 Rf~kLLl~Lp~LRsl~~~~~e~lff~~~~g~~~i~~ll~~  222 (222)
T cd06951         183 RSARLLLMLSLLRGIKTEPVTELFFRPIIGNVSMDDVLLQ  222 (222)
T ss_pred             HHHHHHHHhHHhhcCCHHHHHHHhCccccCCCcHHHHhcC
Confidence            9999999999999999999999999999999999999864

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.

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

Probab=99.68  E-value=1.6e-16  Score=144.17  Aligned_cols=109  Identities=19%  Similarity=0.252  Sum_probs=96.8

Q ss_pred             HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhh--CCC
Q psy6602         238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGR--YSR  315 (367)
Q Consensus       238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~--~p~  315 (367)
                      ..+......++.+..+..|+.+++.+.-           |     +|++||++..+|+++|++++.||++|+..+  +|+
T Consensus       124 ~~i~ef~~~l~~L~ld~~E~alLkAIvL-----------f-----~D~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~p~  187 (238)
T cd07071         124 DSIVEFSSNLQNMNIDISAFSCIAALAM-----------V-----TERHGLKEPKRVEELQNKIVNCLKDHVTFNNGGLN  187 (238)
T ss_pred             HHHHHHHHHHHhcCCCHHHHHHHHHHHH-----------c-----CCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCC
Confidence            3345667788888999999998876642           1     389999999999999999999999999977  468


Q ss_pred             CcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhc
Q psy6602         316 QPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM  362 (367)
Q Consensus       316 ~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~  362 (367)
                      ++.||+|||++||+||+++.+++|++|+.+++|.+|+++|+.||+..
T Consensus       188 ~~~rf~kLLl~Lp~LRsl~~~~~e~l~~~k~~~~~p~~~Ll~e~~~~  234 (238)
T cd07071         188 RPNYLSKLLGKLPELRTLCTQGLQRIFYLKLEDLVPPPAIIDKLFLD  234 (238)
T ss_pred             cccHHHHHHHHhHHHHHHHHHHHHHHHHHHcCCCCCCcHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999854

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).

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

Probab=99.68  E-value=4e-15  Score=134.96  Aligned_cols=107  Identities=26%  Similarity=0.329  Sum_probs=93.9

Q ss_pred             HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhC--CCCc
Q psy6602         240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRY--SRQP  317 (367)
Q Consensus       240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~--p~~~  317 (367)
                      +......++.+..+..|+.+++.+.-           |     +|++|+++..+|+++|+++..||++|+..++  |+++
T Consensus       127 i~ef~~~l~~L~ld~~E~a~LkAivL-----------f-----~dr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~~~  190 (239)
T cd07072         127 ILEFSKSLHAMDIDISAFACLCALTL-----------I-----TERHGLKEPHKVEQLQMKIISSLRDHVTYNAEAQKKP  190 (239)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHH-----------h-----CCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcccc
Confidence            34555667778888888888876641           1     3899999999999999999999999999765  4789


Q ss_pred             ChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhc
Q psy6602         318 TRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM  362 (367)
Q Consensus       318 ~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~  362 (367)
                      .||+|||++||+||+++.+++|++||.|++|.+|+++|+.||+.+
T Consensus       191 ~rf~kLLl~Lp~LRsl~~~~~e~lf~~k~~~~~p~~~Ll~Em~~~  235 (239)
T cd07072         191 HYFSRLLGKLPELRSLSVQGLQRIFYLKLEDLVPAPPLIENMFVA  235 (239)
T ss_pred             cHHHHHHHHhHHHHhhHHHHHHHHHHHHcCCCCCCcHHHHHHHhc
Confidence            999999999999999999999999999999999999999999974

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).

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

Probab=99.65  E-value=1.8e-15  Score=139.20  Aligned_cols=107  Identities=22%  Similarity=0.322  Sum_probs=95.4

Q ss_pred             HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcCh
Q psy6602         240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTR  319 (367)
Q Consensus       240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r  319 (367)
                      +......++.+..+..|+.+++...-               .+||++||++..+|+++|+++..||+.|+..+||+++.|
T Consensus       150 ~~e~~~~l~~L~ld~~E~alLkAivL---------------f~pDr~gL~~~~~Ve~lQe~~~~aL~~~i~~~~p~~~~r  214 (259)
T cd06932         150 KFEFAEKFNALELTDSELALFCAVII---------------LSPDRPGLINRKPVERIQEHVLQALELQLKKNHPDSPQL  214 (259)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHH---------------hCCCcccCcCHHHHHHHHHHHHHHHHHHHhhhCCCcccH
Confidence            44566777888888888888877652               248999999999999999999999999999999999999


Q ss_pred             HHHHHhhchhhhhhchhhHHHHHHhh-hcCCCChHHHHHHHHh
Q psy6602         320 FGRLLLMLPSLRAVRQSTIERLFFKE-TIGDIPIQRLLGDMYT  361 (367)
Q Consensus       320 ~~~lLl~Lp~lr~i~~~~~e~l~~~~-~~g~~~i~~ll~eml~  361 (367)
                      |+|||++||+||+++.+++|.+++.+ ..|.+++++|+.|||+
T Consensus       215 f~kLLl~L~~LRsl~~~~~e~l~~~k~~~~~~~~~pLl~Ei~~  257 (259)
T cd06932         215 FAKLLQKMVDLRQLVTDHVQMVQQIKKTETDASLPPLLQEIYK  257 (259)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCCcHHHHHhh
Confidence            99999999999999999999999766 5678999999999996

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

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

Probab=99.64  E-value=5.7e-16  Score=140.94  Aligned_cols=108  Identities=41%  Similarity=0.655  Sum_probs=99.7

Q ss_pred             HhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcChHH
Q psy6602         242 LMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFG  321 (367)
Q Consensus       242 ~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r~~  321 (367)
                      .++..++.+..+..|+++++.++-               .+||++|+.+..+|+++|+++..||.+|+..+||+.+.||+
T Consensus       120 ~l~~~l~~L~ld~~E~~lLkaiiL---------------~npd~~~L~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~  184 (236)
T cd06948         120 EQVEKLKALHVDSAEFSCLKAIVL---------------FTSDACGLSDPAHIESLQEKSQCALEEYVRTQYPNQPTRFG  184 (236)
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHH---------------cCcccccccCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHH
Confidence            355678999999999999987752               24789999999999999999999999999999999999999


Q ss_pred             HHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhccc
Q psy6602         322 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEK  364 (367)
Q Consensus       322 ~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~~  364 (367)
                      +||++||+||+++..++|++||.+++|.+++++|+.||+.++.
T Consensus       185 ~LLl~Lp~Lr~is~~~~e~l~~~~l~g~~~~~~ll~e~l~~~~  227 (236)
T cd06948         185 KLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDMLLSGS  227 (236)
T ss_pred             HHHHHHHHHHhccHHHHHHhhcccccCCCcHHHHHHHHHhCCC
Confidence            9999999999999999999999999999999999999998763

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

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

Probab=99.63  E-value=2.9e-15  Score=136.74  Aligned_cols=106  Identities=19%  Similarity=0.267  Sum_probs=94.9

Q ss_pred             HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcC
Q psy6602         239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPT  318 (367)
Q Consensus       239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~  318 (367)
                      .+......++.+..+..|+++++...-               .+||++||++..+|+++|+.+..||++|+..+||+.+.
T Consensus       137 ~i~~f~~~l~~L~ld~~E~alLkAivL---------------f~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~  201 (243)
T cd06935         137 AIFDLGVSLSSFNLDDTEVALLQAVLL---------------MSSDRPGLACVERIEKLQDSFLLAFEHYINYRKHHVPH  201 (243)
T ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHH---------------hCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCcc
Confidence            344466667778888888888877642               25899999999999999999999999999999999999


Q ss_pred             hHHHHHhhchhhhhhchhhHHHHHHhhhcCCCCh-HHHHHHH
Q psy6602         319 RFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI-QRLLGDM  359 (367)
Q Consensus       319 r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i-~~ll~em  359 (367)
                      ||+|||++||+||+++.+++|++++.|+.|..++ ++|+.||
T Consensus       202 rf~kLL~~L~~LR~i~~~~~e~l~~~k~~~~~~~~~~L~~Em  243 (243)
T cd06935         202 FWPKLLMKVTDLRMIGACHASRFLHMKVECPTELFPPLFLEV  243 (243)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCChhhhcC
Confidence            9999999999999999999999999999999996 9999997

The ligand binding domain (LBD) of thyroid hormone receptors: Thyroid hormone receptors are members of a superfamily of nuclear receptors. Thyroid hormone receptors (TR) mediate the actions of thyroid hormones, which play critical roles in growth, development, and homeostasis in mammals. They regulate overall metabolic rate, cholesterol and triglyceride levels, and heart rate, and affect mood. TRs are expressed from two separate genes (alpha and beta) in human and each gene generates two isoforms of the receptor through differential promoter usage or splicing. TRalpha functions in the heart to regulate heart rate and rhythm and TRbeta is active in the liver and other tissues. The unliganded TRs function as transcription repressors, by binding to thyroid hormone response elements (TRE) predominantly as homodimers, or as heterodimers with retinoid X-receptors (RXR), a

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

Probab=99.59  E-value=1.7e-14  Score=127.57  Aligned_cols=109  Identities=21%  Similarity=0.282  Sum_probs=95.9

Q ss_pred             HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCc
Q psy6602         238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP  317 (367)
Q Consensus       238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~  317 (367)
                      ..+......++.+..+..|+.+++...-               .+||++|+++..+|+++|+.+..||++|+..+||+.+
T Consensus        86 ~~~~~~~~~l~~L~ld~~E~allkAi~L---------------f~pd~~gl~~~~~Ve~lq~~~~~aL~~~i~~~~p~~~  150 (195)
T cd06941          86 KALFEFSDSFNSLGLSDTEVALFCAVVL---------------LSPDRIGLSEPKKVAILQDRVLEALKVQVSRNRPAEA  150 (195)
T ss_pred             HHHHHHHHHHHhcCCCHHHHHHHHHHHH---------------cCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCcc
Confidence            3445566678888888888888876642               2479999999999999999999999999999999999


Q ss_pred             ChHHHHHhhchhhhhhchhhHHHHH-HhhhcCCCChHHHHHHHHh
Q psy6602         318 TRFGRLLLMLPSLRAVRQSTIERLF-FKETIGDIPIQRLLGDMYT  361 (367)
Q Consensus       318 ~r~~~lLl~Lp~lr~i~~~~~e~l~-~~~~~g~~~i~~ll~eml~  361 (367)
                      .||++||++||+||+++..+.++++ |+...+.+++++|+.|||+
T Consensus       151 ~rf~~Ll~~Lp~Lr~l~~~~~e~l~~~~~~~~~~~~p~L~~E~~~  195 (195)
T cd06941         151 QLFASLLMKIPELRSIGAKHQMHLDWYRVNWPLLRLPPLFAEIYD  195 (195)
T ss_pred             cHHHHHHHHhHHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHhcC
Confidence            9999999999999999999999998 6777788999999999985

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

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

Probab=99.59  E-value=5.8e-15  Score=133.11  Aligned_cols=110  Identities=26%  Similarity=0.387  Sum_probs=100.1

Q ss_pred             HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCC-CC
Q psy6602         238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYS-RQ  316 (367)
Q Consensus       238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p-~~  316 (367)
                      ..+...+..++++..+..|+++++...-               .+||++|+++...|+++|+++..||.+|+..+|| +.
T Consensus       111 ~~~~~~~~~l~~L~ld~~E~~lLkaIil---------------~npd~~~L~~~~~V~~~q~~~~~aL~~y~~~~~~~~~  175 (221)
T cd07068         111 DMLLQLVRRFRELGLQREEYVCLKAIIL---------------ANSDVRHLEDREAVQQLRDAILDALVDVEAKRHGSQQ  175 (221)
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHH---------------cCCCccCccCHHHHHHHHHHHHHHHHHHHHHhCCCcc
Confidence            3445567789999999999999887652               2489999999999999999999999999999999 99


Q ss_pred             cChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhc
Q psy6602         317 PTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM  362 (367)
Q Consensus       317 ~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~  362 (367)
                      +.||++||++||+||+++..++|++++.+++|.+|+++|+.|||++
T Consensus       176 ~~Rf~~LL~~l~~Lr~~~~~~~e~l~~~k~~~~~~~~~Ll~e~l~~  221 (221)
T cd07068         176 PRRLAQLLLLLPHLRQASNKGVRHLYSVKCEGKVPMYKLFLEMLEA  221 (221)
T ss_pred             ccHHHHHHHhccHHHHHHHHHHHHHHHHHHcCCccHHHHHHHHhcC
Confidence            9999999999999999999999999999999999999999999975

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=99.57  E-value=1.1e-14  Score=131.38  Aligned_cols=110  Identities=25%  Similarity=0.381  Sum_probs=99.7

Q ss_pred             HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCC-CC
Q psy6602         238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYS-RQ  316 (367)
Q Consensus       238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p-~~  316 (367)
                      ..+..+...++.+..+..|+++++..+-               .+||+.|+++...|+++|+.+..||.+|+..+|| +.
T Consensus       111 ~~~~~~~~~l~~L~l~~~E~~lLkai~L---------------~npd~~~l~~~~~v~~~q~~~~~aL~~y~~~~~~~~~  175 (221)
T cd06946         111 SACLQLVRRLQRLRLEKEEYVLLKALAL---------------ANSDSVHIEDVEAVRQLRDALLEALSDYEAGRHPGEA  175 (221)
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHH---------------cCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcc
Confidence            3345567788999999999999887752               3478899999999999999999999999999999 78


Q ss_pred             cChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhc
Q psy6602         317 PTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM  362 (367)
Q Consensus       317 ~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~  362 (367)
                      |.||++||+++|+||+++.++++++++.+++|.+|+++|+.|||++
T Consensus       176 p~Rf~~LL~~l~~Lr~~~~~~~e~l~~~~~~~~~~~~~Ll~eml~~  221 (221)
T cd06946         176 PRRAGQLLLTLPLLRQTDGKARRFFYGVKREGKVPMHKLFLEMLEA  221 (221)
T ss_pred             hhHHHHHHhhchhHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHhcC
Confidence            9999999999999999999999999999999999999999999974

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-

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

Probab=99.56  E-value=3.3e-14  Score=129.46  Aligned_cols=106  Identities=22%  Similarity=0.281  Sum_probs=91.8

Q ss_pred             HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcC
Q psy6602         239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPT  318 (367)
Q Consensus       239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~  318 (367)
                      .+......++.+..+..|+.+++...-               .+||++||++..+|+++|+++..||++|+..+| +++.
T Consensus       132 ~~~~f~~~l~~L~ld~~E~all~AivL---------------~~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~-~~~~  195 (241)
T cd06939         132 AVFDFAKSLCELKLTEDEIALFSALVL---------------ISADRPGLQEKRKVEKLQQKIELALRHVLQKNH-GDDT  195 (241)
T ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHH---------------hcCCCcCCCCHHHHHHHHHHHHHHHHHHHHHhC-CCcc
Confidence            344556667777778888887776642               248999999999999999999999999999999 8999


Q ss_pred             hHHHHHhhchhhhhhchhhHHHHHHhhhcCC----CChHHHHHHHH
Q psy6602         319 RFGRLLLMLPSLRAVRQSTIERLFFKETIGD----IPIQRLLGDMY  360 (367)
Q Consensus       319 r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~----~~i~~ll~eml  360 (367)
                      ||+|||++||+||+++..++|+|++.|+..+    .++++|+.|||
T Consensus       196 rf~kLL~~Lp~LR~l~~~~~e~l~~~k~~~p~~~~~~~ppL~~Elf  241 (241)
T cd06939         196 ILTKLLAKMPTLRALCSLHMEKLQKFKQSYPDIVHLEFPPLYKELF  241 (241)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcccCCCCcHHHhhC
Confidence            9999999999999999999999999999843    47899999986

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

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

Probab=99.56  E-value=1.3e-14  Score=131.66  Aligned_cols=105  Identities=21%  Similarity=0.215  Sum_probs=93.6

Q ss_pred             HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCC-CCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcC
Q psy6602         240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSY-ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPT  318 (367)
Q Consensus       240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~-d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~  318 (367)
                      +..+...++.+..+..|+++++.+.-               .++ |++||++...|+++|+++..||++|+.++||+.+.
T Consensus       116 l~e~~~~~r~L~ld~~EfacLKAIvL---------------fnp~d~~GL~~~~~Ve~lqe~~~~aL~~yi~~~~p~~~~  180 (247)
T cd07076         116 MLYVSSELHRLQVSYEEYLCMKTLLL---------------LSTVPKDGLKSQELFDEIRMTYIKELGKAIVKREGNSSQ  180 (247)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHh---------------CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCcch
Confidence            44566778889999999999988763               125 89999999999999999999999999999987655


Q ss_pred             ---hHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHh
Q psy6602         319 ---RFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT  361 (367)
Q Consensus       319 ---r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~  361 (367)
                         ||+|||++||+||+|+.+..|  ||++++|+.|+..++.|||.
T Consensus       181 ~~~RF~kLLllLp~Lr~i~~~~~e--f~~~~~~~~~~~~~~~~ml~  224 (247)
T cd07076         181 NWQRFYQLTKLLDSMHEVVENLLN--FCFQTFLDKTMSIEFPEMLA  224 (247)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHH--HHHHHhcccchhhhhHHHHH
Confidence               999999999999999999999  99999999999999988874

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

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

Probab=99.55  E-value=1.4e-14  Score=130.82  Aligned_cols=108  Identities=30%  Similarity=0.457  Sum_probs=98.6

Q ss_pred             HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcC
Q psy6602         239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPT  318 (367)
Q Consensus       239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~  318 (367)
                      .+..+...++.+..+..|+++.+.+.-               .++|++|+++...|+++|+++..||.+|+..+||+++.
T Consensus       114 ~l~~~~~~l~~L~ld~~E~~~LkaiiL---------------f~~d~~~l~~~~~v~~lq~~i~~aL~~y~~~~~p~~~~  178 (222)
T cd06952         114 KLQEFVNSMQKLDVDDHEYAYLKAIVL---------------FSPDHPGQELRQQIEKLQEKALMELRDYVGKTYPEDEY  178 (222)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHH---------------hCCCCcCCcCHHHHHHHHHHHHHHHHHHHHHhCCCccc
Confidence            344567788899999999999987752               23789999999999999999999999999999999999


Q ss_pred             hHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHh
Q psy6602         319 RFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT  361 (367)
Q Consensus       319 r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~  361 (367)
                      ||++||++||+||+++.+++|++||.+++|.+++++++..+|.
T Consensus       179 R~~klLl~Lp~Lr~~~~~~~e~l~~~~~~g~~~~~~ll~~~~~  221 (222)
T cd06952         179 RLSKLLLRLPPLRSLSPAITEELFFAGLIGNVQIDSVIPYILR  221 (222)
T ss_pred             HHHHHHHHhHHhhhcCHHHHHHHhcccccCCCcHHHHHHHHHh
Confidence            9999999999999999999999999999999999999998874

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

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

Probab=99.55  E-value=1.4e-14  Score=132.01  Aligned_cols=107  Identities=13%  Similarity=0.147  Sum_probs=92.5

Q ss_pred             HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCC-CCCCCCCCchhhhhHHHHHHHHHHHHHhhC---CC
Q psy6602         240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSY-ETPGLVDAQPVEMLQDQAQCILGDYVRGRY---SR  315 (367)
Q Consensus       240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~-d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~---p~  315 (367)
                      +..+...++.+..+..|+++++.+.-               .++ |++||+++.+|+++|++++.||.+|+.+++   |+
T Consensus       116 l~~~~~~l~~L~ld~~EyacLKAIiL---------------fnp~d~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~~  180 (246)
T cd07073         116 MRHLSQEFGWLQITPQEFLCMKALLL---------------FSIIPVDGLKNQKFFDELRMNYIKELDRIIACKRKNPTS  180 (246)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHH---------------cCCCCcccccCHHHHHHHHHHHHHHHHHHHHhcCCCCcc
Confidence            44557778889999999999988753               225 789999999999999999999999998875   36


Q ss_pred             CcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCC-----ChHHHHHHHHhcc
Q psy6602         316 QPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDI-----PIQRLLGDMYTME  363 (367)
Q Consensus       316 ~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~-----~i~~ll~eml~~~  363 (367)
                      ++.||+|||++||+||+|+.++  .+||.+++|..     ++++||.|||..+
T Consensus       181 ~~~Rf~kLLl~Lp~LRsi~~~~--~~~~~~l~~~~~~~~~~~~pll~ei~~~~  231 (246)
T cd07073         181 CSRRFYQLTKLLDSVQPIAREL--HQFTFDLLIKSHMVSVDFPEMMAEIISVQ  231 (246)
T ss_pred             cchHHHHHHHHHHHHHHHHHHH--HHHHHHHhCccccCccCccHHHHHHHHhc
Confidence            6899999999999999999998  77888888875     7999999999854

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

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

Probab=99.53  E-value=3.1e-14  Score=129.71  Aligned_cols=106  Identities=22%  Similarity=0.285  Sum_probs=96.8

Q ss_pred             HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcCh
Q psy6602         240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTR  319 (367)
Q Consensus       240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r  319 (367)
                      +......++.+..+..|+++++..+-               .+||++||.+...|+.+|+.+..||.+|+..+||+++.|
T Consensus       130 i~~~~~~l~~L~ld~~E~~lL~aivL---------------f~pd~~gL~~~~~V~~lQ~~~~~aL~~y~~~~~p~~~~r  194 (236)
T cd06954         130 IFEFSKSMRELQLDDAEYALLIAINI---------------FSADRPNVQDHHRVERLQETYVEALHSYIKIKRPSDRLM  194 (236)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHhh---------------ccCCcccCCCHHHHHHHHHHHHHHHHHHHHhcCCCcccH
Confidence            44566788999999999999887753               348999999999999999999999999999999999999


Q ss_pred             HHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHh
Q psy6602         320 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT  361 (367)
Q Consensus       320 ~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~  361 (367)
                      |++||++||+||+++..++|++|+.++.+ .++++|+.|||+
T Consensus       195 f~klL~~L~~Lr~l~~~~~e~l~~~k~~~-~~~~~L~~El~~  235 (236)
T cd06954         195 FPRMLMKLVSLRTLSSVHSEQVFALRLQD-KKLPPLLSEIWD  235 (236)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCCCcHHHHHhc
Confidence            99999999999999999999999999976 699999999996

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

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

Probab=99.52  E-value=5e-14  Score=128.35  Aligned_cols=107  Identities=14%  Similarity=0.129  Sum_probs=93.3

Q ss_pred             HhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCC-CCCCCCCCchhhhhHHHHHHHHHHHHHhhCC---CCc
Q psy6602         242 LMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSY-ETPGLVDAQPVEMLQDQAQCILGDYVRGRYS---RQP  317 (367)
Q Consensus       242 ~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~-d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p---~~~  317 (367)
                      .+...++.+..+..|+++++.++-               .++ |++|+++...|+++|++++.||++|+.++||   +.+
T Consensus       118 e~~~~l~~L~ld~~E~acLKAIvL---------------fn~~d~~gL~~~~~Ve~lqe~i~~AL~~yi~~~~~~~~~~~  182 (246)
T cd06947         118 QISQEFVRLQVTYEEFLCMKVLLL---------------LSTIPKDGLKSQAAFDEMRMNYIKELRKAIVKREKNSSQSW  182 (246)
T ss_pred             HHHHHHHhcCCCHHHHHHHHHHHH---------------cCCCccccccCHHHHHHHHHHHHHHHHHHHHHhCCCCcccc
Confidence            456778889999999999887752               124 6899999999999999999999999998874   558


Q ss_pred             ChHHHHHhhchhhhhhchhhHHHHHHhhhcC---CCChHHHHHHHHhcc
Q psy6602         318 TRFGRLLLMLPSLRAVRQSTIERLFFKETIG---DIPIQRLLGDMYTME  363 (367)
Q Consensus       318 ~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g---~~~i~~ll~eml~~~  363 (367)
                      .||+|||++||+||+++.+++|++|++....   .|++++|+.|||+++
T Consensus       183 ~Rf~kLLllLp~Lr~i~~~~~e~~~~~~~~~~~~~v~~~~ll~ei~~~~  231 (246)
T cd06947         183 QRFYQLTKLLDSMHDLVKNLLQFCFYTFIQSHALSVEFPEMLVEIISDQ  231 (246)
T ss_pred             hHHHHHHHhhhhHHHHHHHHHHHHHHHHhhcCCCccccHHHHHHHHHcc
Confidence            9999999999999999999999999885544   489999999999966

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

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

Probab=99.52  E-value=4e-14  Score=128.81  Aligned_cols=109  Identities=17%  Similarity=0.242  Sum_probs=92.9

Q ss_pred             HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCC--C
Q psy6602         239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSR--Q  316 (367)
Q Consensus       239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~--~  316 (367)
                      .+......++.+..+..|+++++...-               .+||++||++...|+++|+++..||++|+..+||.  .
T Consensus       124 ~l~~~~~~l~~L~ld~~E~alLkAivL---------------f~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~  188 (238)
T cd06933         124 PLVKFQVGLKKLNLHEEEHVLLMAICI---------------LSPDRPGVQDHALIEAIQDRLSDTLQTYIRCRHPPPGS  188 (238)
T ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHH---------------HCCCCCCCcchHHHHHHHHHHHHHHHHHHHhcCCCCCc
Confidence            344555678889999999999887752               24799999999999999999999999999999984  4


Q ss_pred             cChHHHHHhhchhhhhhchhhHHHHHHhhhcC--CCChHHHHHHHHhc
Q psy6602         317 PTRFGRLLLMLPSLRAVRQSTIERLFFKETIG--DIPIQRLLGDMYTM  362 (367)
Q Consensus       317 ~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g--~~~i~~ll~eml~~  362 (367)
                      +.||+|||++||+||+|+.+|.+.++..++.+  +.++++|+.|||+.
T Consensus       189 ~~~f~kLLl~L~~LRsi~~~h~~~~~~~~~~~~~~~~~~pL~~Ei~~~  236 (238)
T cd06933         189 RLLYAKMIQKLADLRSLNEEHSKQYRSLSFQPEHSMKLTPLVLEVFGN  236 (238)
T ss_pred             hhHHHHHHHHhHHHHhhhHHHHHHHHHHHhccCCCCCCCcHHHHHhcc
Confidence            56799999999999999999999987766655  44699999999975

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

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

Probab=99.48  E-value=9.8e-14  Score=123.69  Aligned_cols=95  Identities=49%  Similarity=0.696  Sum_probs=86.7

Q ss_pred             HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcCh
Q psy6602         240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTR  319 (367)
Q Consensus       240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r  319 (367)
                      +...+..++.+..+..|+++++...-               .+||++|+++...|+++|+++..||.+|+..+||+++.|
T Consensus       112 i~~~~~~~~~L~ld~~EyalLKai~L---------------~npd~~~L~~~~~Ve~lq~~~~~aL~~y~~~~~~~~~~R  176 (206)
T cd06950         112 LQETLSRFRQLRVDATEFACLKAIVL---------------FKPETRGLKDPAQVEALQDQAQLMLNKHIRTRYPTQPAR  176 (206)
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHH---------------hCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcccH
Confidence            44566678999999999999987752               247999999999999999999999999999999999999


Q ss_pred             HHHHHhhchhhhhhchhhHHHHHHhhhcCC
Q psy6602         320 FGRLLLMLPSLRAVRQSTIERLFFKETIGD  349 (367)
Q Consensus       320 ~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~  349 (367)
                      |++||++||+||+++++++|++||.+++|.
T Consensus       177 f~kLLl~Lp~lr~ls~~~~e~l~~~~~~g~  206 (206)
T cd06950         177 FGKLLLLLPSLRFISSSTIEELFFKKTIGN  206 (206)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHhccCcCCC
Confidence            999999999999999999999999999985

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

>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=99.46  E-value=4.6e-13  Score=120.60  Aligned_cols=103  Identities=20%  Similarity=0.221  Sum_probs=91.1

Q ss_pred             HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcCh
Q psy6602         240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTR  319 (367)
Q Consensus       240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r  319 (367)
                      +..+...++.+..+..|+++++..+-               .+||++||.+...|+.+|+.+..||.+|+..+||++|.|
T Consensus       119 i~~~~~kl~~L~l~~~E~~lLkaIvL---------------~npd~~gL~~~~~Ve~~Q~~~~~aL~~y~~~~~p~~p~r  183 (221)
T cd06936         119 MFNFYKSMGELKMTQEEYALLTAITI---------------LFPDRPYLKDKEAVEKLQEPLLDLLQKFCKLYHPEDPQH  183 (221)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHH---------------hcCCCcCCCCHHHHHHHHHHHHHHHHHHHHhhCCCchhH
Confidence            33455667888888888888877652               248999999999999999999999999999999999999


Q ss_pred             HHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHH
Q psy6602         320 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGD  358 (367)
Q Consensus       320 ~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~e  358 (367)
                      |++||++||+||+++..++|+|++.|+.. .++++|+.|
T Consensus       184 f~~LL~~L~~LR~l~~~~~e~l~~~k~~~-~~~~pl~~e  221 (221)
T cd06936         184 FACLLGRLTELRTLNHHHAEMLMSWKVND-HKFTPLLCE  221 (221)
T ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHHccC-CCCCccccC
Confidence            99999999999999999999999999975 589999875

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

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

Probab=99.46  E-value=1.1e-12  Score=119.16  Aligned_cols=105  Identities=21%  Similarity=0.347  Sum_probs=92.3

Q ss_pred             HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCC-CcC
Q psy6602         240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSR-QPT  318 (367)
Q Consensus       240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~-~~~  318 (367)
                      +......++.+..+..|+++++...-           +     +|++||.+...|+++|+.+..||..|+..+||. .+.
T Consensus       125 l~~~~~~l~~L~ld~~E~~lL~AI~L-----------f-----~d~~~L~~~~~Ve~~Q~~~~~aL~~y~~~~~~~~~~~  188 (231)
T cd06938         125 LFRFCRAMCSMKVDNAEYALLTAIVI-----------F-----SDRPGLLQPKKVEKIQEIYLEALRAYVDNRRPPSQRV  188 (231)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHH-----------c-----cCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCccc
Confidence            44456677888888888888766541           1     268899999999999999999999999999998 899


Q ss_pred             hHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHh
Q psy6602         319 RFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT  361 (367)
Q Consensus       319 r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~  361 (367)
                      ||++||++|++||+++..+.|.+|+.+++ .+++++|+.|+|+
T Consensus       189 rf~kLL~~L~~Lr~l~~~~~e~~~~~k~~-~~~~~pl~~Ei~d  230 (231)
T cd06938         189 IFAKLLSILTELRTLGNQNSEMCFSLKLK-NRKLPPFLAEIWD  230 (231)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCCcHHHHHhC
Confidence            99999999999999999999999999999 6799999999996

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

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

Probab=99.45  E-value=9.4e-13  Score=115.74  Aligned_cols=95  Identities=24%  Similarity=0.327  Sum_probs=84.3

Q ss_pred             HHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCC
Q psy6602         237 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQ  316 (367)
Q Consensus       237 f~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~  316 (367)
                      ...+......++++..+..|+.+++.+.-               .+||++|+++..+|+++|+.+..||++|+..+||++
T Consensus        95 ~~~~~~~~~~l~~L~ld~~E~a~LkAivL---------------f~pd~~~L~~~~~Ve~lq~~~~~aL~~~~~~~~p~~  159 (189)
T cd06940          95 LNSMFDFSEKLNSLQLSDEEMGLFTAVVL---------------VSADRSGLENVNLVEALQETLIRALRTLIAKNHPNE  159 (189)
T ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHH---------------hCCCCcCCCCHHHHHHHHHHHHHHHHHHHHHhCCCC
Confidence            34455667778888888889888887752               247999999999999999999999999999999999


Q ss_pred             cChHHHHHhhchhhhhhchhhHHHHHHhhh
Q psy6602         317 PTRFGRLLLMLPSLRAVRQSTIERLFFKET  346 (367)
Q Consensus       317 ~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~  346 (367)
                      +.||+|||++||+||++++.++|++||.|+
T Consensus       160 ~~rf~kLL~~L~~LR~l~~~~~e~l~~~~~  189 (189)
T cd06940         160 PSIFTKLLLKLPDLRTLNNLHSEKLLAFKV  189 (189)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            999999999999999999999999999863

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

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

Probab=99.41  E-value=4.1e-13  Score=121.30  Aligned_cols=103  Identities=18%  Similarity=0.343  Sum_probs=88.0

Q ss_pred             HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcCh
Q psy6602         240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTR  319 (367)
Q Consensus       240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r  319 (367)
                      +......++.+..+..|+.+++...-               .+||++||++...|+++|+++..||++|+..+||..+.|
T Consensus       121 ~~~~~~~l~~L~ld~~E~alLkAivL---------------f~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~r  185 (226)
T cd06934         121 LLRFHYTLRKLQLQEEEYVLMQAMSL---------------FSPDRPGVTQHDVIDQLQEKMALTLKSYIDSKRPGPEKR  185 (226)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHH---------------hCCCCcCCcChHHHHHHHHHHHHHHHHHHHHcCCCCCcc
Confidence            44556678888999999999887752               248999999999999999999999999999999876555


Q ss_pred             --HHHHHhhchhhhhhchhhHHHHHHhhhcCCCCh-HHHHHHH
Q psy6602         320 --FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI-QRLLGDM  359 (367)
Q Consensus       320 --~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i-~~ll~em  359 (367)
                        |+|||++||+||+++..+.+.++  +++|..|+ ++|+.|+
T Consensus       186 ~~f~kLLl~L~~LRsl~~~~~~~~~--~~~~~~~~~~pl~~Ei  226 (226)
T cd06934         186 FLYPKILACLTELRTINEEYTKQIL--HIQDIQPMATPLMQEI  226 (226)
T ss_pred             cHHHHHHHHhHHHhcchHHHHHHHH--HHhccCCCCCchhhcC
Confidence              99999999999999999999885  45566675 9999885

The ligand binding domain of xenobiotic receptors: This xenobiotic receptor family includes pregnane X receptor (PXR), constitutive androstane receptor (CAR) and other related nuclear receptors. They function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The nuclear receptor pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. The ligand binding domain of PXR shows remarkable flexibility to accommodate both large and small molecules. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and elimination of

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

Probab=99.31  E-value=4.5e-12  Score=115.29  Aligned_cols=104  Identities=15%  Similarity=0.091  Sum_probs=87.2

Q ss_pred             HhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCC-CCCCCCCchhhhhHHHHHHHHHHHHHhhCC---CCc
Q psy6602         242 LMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYE-TPGLVDAQPVEMLQDQAQCILGDYVRGRYS---RQP  317 (367)
Q Consensus       242 ~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d-~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p---~~~  317 (367)
                      .....++.+..+..|+++++...-               .++| ++||++...|+++|+++..||++|+.++++   +.+
T Consensus       118 e~~~~l~~L~Ld~~E~acLKAIvL---------------fn~d~~~gL~~~~~Ve~lqe~~~~aL~~yi~~~~~~~~~~~  182 (248)
T cd07075         118 QISLQFVRLQLTFEEYTIMKVLLL---------------LSTIPKDGLKSQAAFEEMRTNYIKELRKMVTKAPNNSGQSW  182 (248)
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHH---------------hCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCCcccch
Confidence            345677888888999998887752               1354 799999999999999999999999997765   456


Q ss_pred             ChHHHHHhhchhhhhhchhhHHHHHHhhhc-CCCChHHHHHHHHhc
Q psy6602         318 TRFGRLLLMLPSLRAVRQSTIERLFFKETI-GDIPIQRLLGDMYTM  362 (367)
Q Consensus       318 ~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~-g~~~i~~ll~eml~~  362 (367)
                      .||++||++||.||+++.+++|++||.-.. +.+++  .+.||+..
T Consensus       183 ~RF~~LLllLp~Lr~i~~k~iE~lff~~~~~~~~~~--~~~~~~~~  226 (248)
T cd07075         183 QRFYQLTKLLDSMHDLVSDLLEFCFYTFRESQALKV--EFPAMLVE  226 (248)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHccccceee--ehHHHHHH
Confidence            999999999999999999999999987666 67777  77787764

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

>KOG4215|consensus

Probab=99.28  E-value=9.6e-12  Score=114.58  Aligned_cols=107  Identities=25%  Similarity=0.418  Sum_probs=97.7

Q ss_pred             hhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCc--hhhhhHHHHHHHHHHHHHhhCCCC-cCh
Q psy6602         243 MLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQ--PVEMLQDQAQCILGDYVRGRYSRQ-PTR  319 (367)
Q Consensus       243 ~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~--~ve~lq~~~~~aL~~~~~~~~p~~-~~r  319 (367)
                      ++.-+|.+..+..||++.+.+.-               .+|+..|+.+..  .|+.++.+++.+|++||..+.|.+ ++|
T Consensus       244 lv~Pmr~L~md~~Ey~cLKAi~F---------------fdP~akGis~~s~~~I~~aR~~vl~sLe~yi~d~q~~d~~~R  308 (432)
T KOG4215|consen  244 LVNPMRRLQMDEIEYVCLKAIAF---------------FDPDAKGLSDPSQIRIREARNRVLKSLEAYISDRQPYDAPGR  308 (432)
T ss_pred             HhhHHHHhccchHHHHHHHHHHh---------------cCccccccCCchHhHHHHHHHHHHHHHHHHHhhcCccccccc
Confidence            55678999999999999998742               248999999999  799999999999999999999755 689


Q ss_pred             HHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhccc
Q psy6602         320 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEK  364 (367)
Q Consensus       320 ~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~~  364 (367)
                      |++||++||+|.+|+...+|...+.+++|-+.|++|+.||+..+.
T Consensus       309 ~g~LLLllPsLqsIt~qliE~iqlaklFGla~vDsll~e~~l~~~  353 (432)
T KOG4215|consen  309 FGNLLLLLPSLQSITQQLIEQIQLAKLFGLAKVDSLLQEFLLGGE  353 (432)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHhHHHHHhhcCCC
Confidence            999999999999999999999999999999999999999998753

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

Probab=99.28  E-value=9.7e-12  Score=111.04  Aligned_cols=89  Identities=30%  Similarity=0.484  Sum_probs=81.6

Q ss_pred             HhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcChHH
Q psy6602         242 LMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFG  321 (367)
Q Consensus       242 ~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r~~  321 (367)
                      .+...++.+..+..|+++++.++-               .+||++|+.+...|+++|+++..||.+|+..+||+.+.||+
T Consensus       119 ~~~~~l~~L~ld~~E~~lLkaI~L---------------~~pd~~~L~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~  183 (207)
T cd06943         119 ELVVKMRDLKMDRTELGCLRAIIL---------------FNPDVKGLKSRQEVESLREKVYASLEEYCRQKHPEQPGRFA  183 (207)
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHh---------------cCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHH
Confidence            466789999999999999987753               23789999999999999999999999999999999999999


Q ss_pred             HHHhhchhhhhhchhhHHHHHHhh
Q psy6602         322 RLLLMLPSLRAVRQSTIERLFFKE  345 (367)
Q Consensus       322 ~lLl~Lp~lr~i~~~~~e~l~~~~  345 (367)
                      +||++||+||+++.+++|+|||.+
T Consensus       184 ~LLl~L~~lr~l~~~~~e~l~~~~  207 (207)
T cd06943         184 KLLLRLPALRSIGLKCLEHLFFFK  207 (207)
T ss_pred             HHHHHHHHHHhHhHHHHHHHhhcC
Confidence            999999999999999999999875

The ligand binding domain of the retinoid X receptor (RXR) and Ultraspiracle (USP): This family includes two evolutionary related nuclear receptors: retinoid X receptor (RXR) and Ultraspiracle (USP). RXR is a nuclear receptor in mammalian and USP is its counterpart in invertebrates. The native ligand of retinoid X receptor is 9-cis retinoic acid (RA). RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. RXRs can play different roles in these heterodimers. It acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, func

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

Probab=99.28  E-value=9.1e-12  Score=112.45  Aligned_cols=102  Identities=31%  Similarity=0.461  Sum_probs=93.3

Q ss_pred             hhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcChHHH
Q psy6602         243 MLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGR  322 (367)
Q Consensus       243 ~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r~~~  322 (367)
                      ++..++.+..+..|+++.+.+.-               .+|+++|+.+...|+.+|+++..||.+|+..++|+.+.||++
T Consensus       121 ~~~~l~~L~l~~~E~~lLkaiil---------------~~p~~~~ls~~~~i~~~r~~~~~aL~~y~~~~~~~~~~Rf~~  185 (222)
T cd06931         121 LVLPLRDLNIDDNEYACLKAIVF---------------FDPDAKGLSDPQKIKRLRFQVQVSLEDYINDRQYDSRGRFGE  185 (222)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHH---------------cCCCccCCCCHHHHHHHHHHHHHHHHHHHHhcCCchhhHHHH
Confidence            55678888888889888877652               237899999999999999999999999999999999999999


Q ss_pred             HHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHH
Q psy6602         323 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDM  359 (367)
Q Consensus       323 lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~em  359 (367)
                      ||+++|+||.++..+.|++++.+++|.+|+++|+.||
T Consensus       186 LL~~l~~lr~~~~~~~e~l~~~~lf~~~~~~~L~~e~  222 (222)
T cd06931         186 LLLLLPTLQSITWQMIEQIQFARLFGVAKIDNLLQEM  222 (222)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhcCCCcHHHHHhhC
Confidence            9999999999999999999999999999999999987

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

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

Probab=99.15  E-value=1e-10  Score=104.81  Aligned_cols=94  Identities=30%  Similarity=0.442  Sum_probs=81.1

Q ss_pred             HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCc
Q psy6602         238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP  317 (367)
Q Consensus       238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~  317 (367)
                      ..+..++..++.+..+..|+++.+..+-               .+||++|+.+..+|+++|+.+..||.+|+..+||+.|
T Consensus       115 ~~i~~l~~~l~~L~ld~eEy~lLkAIvL---------------fnpd~~gLs~~~~Ve~lQ~~~~~aL~~y~~~~~~~~p  179 (213)
T cd06953         115 ERLTYLLAKFRQLKVSNEEYVCLKVINF---------------LNQDIDGLTNASQLESLQKRYWYVLQDFTELNYPNQP  179 (213)
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHH---------------hCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcc
Confidence            3345677788889999999999887752               3478999999999999999999999999999999999


Q ss_pred             ChHHHHHhhchhhhhhchhhHHH-HHHhhh
Q psy6602         318 TRFGRLLLMLPSLRAVRQSTIER-LFFKET  346 (367)
Q Consensus       318 ~r~~~lLl~Lp~lr~i~~~~~e~-l~~~~~  346 (367)
                      .||++||++||+||+++.+.+|. +++.|.
T Consensus       180 ~Rf~~LL~~L~~Lr~l~~~~~e~~~~~~~~  209 (213)
T cd06953         180 NRFSDLLSCLPEIRAAAGKLLHSKLFYLPL  209 (213)
T ss_pred             hHHHHHHHHhHHHHHHHHHHHHHHHHhhhh
Confidence            99999999999999999999854 455553

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).

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

Probab=98.92  E-value=2.2e-09  Score=93.03  Aligned_cols=90  Identities=23%  Similarity=0.301  Sum_probs=79.4

Q ss_pred             HHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCC
Q psy6602         236 RFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSR  315 (367)
Q Consensus       236 Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~  315 (367)
                      -+..+......++++..+..|+++++...-               .+||++|+.+...|+..|+++..||.+|+..+||+
T Consensus        84 ~~~~~~~~~~~l~~L~l~~~E~~llkai~l---------------~~pd~~~l~~~~~v~~~q~~~~~aL~~y~~~~~~~  148 (174)
T cd06929          84 FIEPLFEFAEKMNKLQLDDNEYALLTAIVL---------------FSPDRPGLQDVDTVEKLQERLLEALQRYLKVNHPD  148 (174)
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHHHHH---------------hCCCcccCcCHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence            344555677889999999999998887652               24788999999999999999999999999999999


Q ss_pred             CcChHHHHHhhchhhhhhchhhHHH
Q psy6602         316 QPTRFGRLLLMLPSLRAVRQSTIER  340 (367)
Q Consensus       316 ~~~r~~~lLl~Lp~lr~i~~~~~e~  340 (367)
                      .+.||++||+++|+||.++..+.|.
T Consensus       149 ~~~Rf~~Ll~~l~~lr~l~~~~~e~  173 (174)
T cd06929         149 APQMFAKLLKKLTELRTLNELHAEL  173 (174)
T ss_pred             ChhHHHHHHHHhHHHHHHHHHHHhc
Confidence            9999999999999999999999875

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).

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

Probab=98.92  E-value=1e-08  Score=90.33  Aligned_cols=89  Identities=11%  Similarity=0.039  Sum_probs=78.8

Q ss_pred             HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCC--CCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCc
Q psy6602         240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYE--TPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP  317 (367)
Q Consensus       240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d--~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~  317 (367)
                      +......++.+..+..|+++++...-               .+||  ++|+.+...|+.+|+.+..+|.+|+..+||+.+
T Consensus        87 ~~~~~~~l~~L~l~~~E~~lL~Aivl---------------~~pd~~~~~l~~~~~v~~~q~~l~~~L~~~~~~~~~~~~  151 (191)
T cd06942          87 MLQFANKILTLNLTNAELALLCAAEL---------------LQPDSLGIQLEETAKSNLQLSVLFQFLKSVLFKDGEDTE  151 (191)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHH---------------hCCCCCCCCccchHHHHHHHHHHHHHHHHHHHhcCCChH
Confidence            44566778888888888888877652               2478  999999999999999999999999999999999


Q ss_pred             ChHHHHHhhchhhhhhchhhHHHHHH
Q psy6602         318 TRFGRLLLMLPSLRAVRQSTIERLFF  343 (367)
Q Consensus       318 ~r~~~lLl~Lp~lr~i~~~~~e~l~~  343 (367)
                      .||+|||+++++||+++..+.+.+..
T Consensus       152 ~rf~kLL~~l~~Lr~~~~~~~~~l~~  177 (191)
T cd06942         152 QRLQKLFDILNRLRNMNKEHQNILAD  177 (191)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            99999999999999999999997775

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).

>KOG4217|consensus

Probab=98.67  E-value=2.9e-07  Score=87.81  Aligned_cols=123  Identities=24%  Similarity=0.338  Sum_probs=96.9

Q ss_pred             HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHh-HHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhh--CC
Q psy6602         238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQR-LLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGR--YS  314 (367)
Q Consensus       238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~-Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~--~p  314 (367)
                      |.++.++.-+|.++.+.....-|....+...++- -+..+--....+||-||+++..||+||.++..+|++|+...  .+
T Consensus       474 G~vlhr~qC~rgfgewidsi~~FS~~l~~l~idi~AfacL~aLa~iTErhGL~epkrVeelqnkIi~~LKDHvt~~~~~~  553 (605)
T KOG4217|consen  474 GLVLHRLQCLRGFGEWIDSIREFSRSLHSLNIDISAFACLSALALITERHGLKEPKRVEELQNKIINCLKDHVTGSAGKL  553 (605)
T ss_pred             chhhhHHHHHHHHHHHHHHHHHHHHHhhhchhhHHHHHHHHHHHhhhhhhcCCCcchHHHHHHHHHHHHHHHhhhccccc
Confidence            6677777778888755555555655555544441 12222223446899999999999999999999999999544  46


Q ss_pred             CCcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHH
Q psy6602         315 RQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMY  360 (367)
Q Consensus       315 ~~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml  360 (367)
                      ..+.++.|+|.+||+||.++..+....|+.|+...||++.++..|+
T Consensus       554 ~k~~~lSrllgklpeLr~l~tqgLqrifyLklEdlvp~p~iidklf  599 (605)
T KOG4217|consen  554 AKPVYLSRLLGKLPELRTLCTQGLQRIFYLKLEDLVPPPAIIDKLF  599 (605)
T ss_pred             ccchHHHHHhhhhHHHHHHHHHhhhhhhcccHhhccCchhhhhhhh
Confidence            7889999999999999999999999999999999999988887765

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

Probab=98.57  E-value=1.5e-07  Score=80.63  Aligned_cols=80  Identities=41%  Similarity=0.645  Sum_probs=69.7

Q ss_pred             HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcC
Q psy6602         239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPT  318 (367)
Q Consensus       239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~  318 (367)
                      .+..+...++.+..+..|+++++...-               .+||++|+.+...|+..|+.+..||..|+..+||+.+.
T Consensus        86 ~~~~~~~~l~~L~l~~~E~~lLkai~l---------------~~p~~~~l~~~~~v~~~q~~~~~aL~~~~~~~~~~~~~  150 (165)
T cd06930          86 RLQELLSKLRSLQLDPKEYACLKAIVL---------------FNPDLPGLKNQQQVEELQEKAQQALQEYIRKRYPQQPA  150 (165)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHH---------------cCCCCCCCcCHHHHHHHHHHHHHHHHHHHHhhCCCchh
Confidence            334466778889999999998887752               23788999999999999999999999999999999999


Q ss_pred             hHHHHHhhchhhhhh
Q psy6602         319 RFGRLLLMLPSLRAV  333 (367)
Q Consensus       319 r~~~lLl~Lp~lr~i  333 (367)
                      ||++||+.||+||++
T Consensus       151 R~~~ll~~l~~lr~~  165 (165)
T cd06930         151 RFAKLLLRLPELRSI  165 (165)
T ss_pred             HHHHHHHHhHhhccC
Confidence            999999999999975

Ligand-binding domain (LBD) of nuclear receptor (NR) family 2: This is one of the major subfamily of nuclear receptors, including some well known nuclear receptors such as glucocorticoid receptor (GR), mineralocorticoid receptor (MR), estrogen receptor (ER), progesterone receptor (PR), and androgen receptor (AR), other related receptors. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).

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

Probab=98.28  E-value=5e-06  Score=75.82  Aligned_cols=105  Identities=10%  Similarity=0.056  Sum_probs=80.1

Q ss_pred             hhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCC-CCCCCCCCchhhhhHHHHHHHHHHHHHhhC---CCCcC
Q psy6602         243 MLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSY-ETPGLVDAQPVEMLQDQAQCILGDYVRGRY---SRQPT  318 (367)
Q Consensus       243 ~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~-d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~---p~~~~  318 (367)
                      ....++.+..+..|+++++.+.-               .++ |++||++...|+++|+++..||.+|+..++   ++.|+
T Consensus       119 ~~~~~~~L~ld~~Ey~cLKAIvL---------------fnp~d~~gL~~q~~Ve~lR~~y~~aL~~yi~~~~~~~~~~~~  183 (248)
T cd07074         119 IPQEFVKLQVSQEEFLCMKALLL---------------LNTIPLEGLRSQTQFDEMRSSYIRELIKAIGLRQKGVVASSQ  183 (248)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHH---------------CCCCcCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCCCccCcH
Confidence            56788889999999999998753               235 789999999999999999999999987775   35789


Q ss_pred             hHHHHHhhchhhhhhchhhHHHHHHhhhc---CCCChHHHHHHHHhc
Q psy6602         319 RFGRLLLMLPSLRAVRQSTIERLFFKETI---GDIPIQRLLGDMYTM  362 (367)
Q Consensus       319 r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~---g~~~i~~ll~eml~~  362 (367)
                      ||++|++.++.|+.+-...-...|.....   -.|..+..+.|+.-.
T Consensus       184 RF~~Ll~ll~~l~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  230 (248)
T cd07074         184 RFYQLTKLMDNMHDLVKQLHLYCLNTFIQSRALSVEFPEMMSEVIAA  230 (248)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhheeecHHHHHHHHHh
Confidence            99999999999995444444433322221   256667777777653

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

>KOG4216|consensus

Probab=98.02  E-value=4.1e-05  Score=71.84  Aligned_cols=196  Identities=15%  Similarity=0.087  Sum_probs=119.2

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccchHHHHHHHHHHHHHH------------Hh
Q psy6602         114 TLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARF------------RQ  181 (367)
Q Consensus       114 ~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l------------~~  181 (367)
                      +...-+-+.-+++...|.||..+|....                         ..+..+.+|++.+            .-
T Consensus       265 ~~~~~e~I~~yq~k~~e~mWe~cA~~lt-------------------------~~IQ~vVEFAK~I~GFM~L~Q~dQI~L  319 (479)
T KOG4216|consen  265 QTFDQEEIENYQNKGREEMWELCAIKLT-------------------------PAIQYVVEFAKRIDGFMELCQNDQIVL  319 (479)
T ss_pred             ccCCHHHHHHHHhhhHHHHHHHHHHHHH-------------------------HHHHHHHHHHHhhhHhhccCccceEEe
Confidence            3344556666777777777777775432                         3344555555544            23


Q ss_pred             cCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhhhHhHhhhhhHHHHHHhh
Q psy6602         182 LSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFK  261 (367)
Q Consensus       182 L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~  261 (367)
                      |+-...|.++..+-.+++.|....---.+.--..--|...+           ..-...+.....+|..+...-.|...+.
T Consensus       320 LKaGsfEv~lvrm~r~~~v~~ntV~~e~~~~g~~~f~a~~~-----------~elis~vf~~~ksL~~Lq~te~EiAL~~  388 (479)
T KOG4216|consen  320 LKAGSFEVVLVRMCRAFDVDNNTVYFEGKYAGPEVFYALGC-----------EELISRVFEFGKSLCSLQLTEDEIALFS  388 (479)
T ss_pred             eecCceeeeHHHHHHhhcccccceeecccccchhheeccCh-----------HHHHHHHHhhhHHHHhhccCcHHHHHHH
Confidence            44555666666666666665422211111100001011111           1112222333344444444444544444


Q ss_pred             hccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcChHHHHHhhchhhhhhchhhHHHH
Q psy6602         262 ETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL  341 (367)
Q Consensus       262 ~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r~~~lLl~Lp~lr~i~~~~~e~l  341 (367)
                      .++.               .+++|+||.+..+|++||..+..|++.++.++|. +.+-++||+-+.|.||+++..|.|.|
T Consensus       389 alVL---------------~~~~r~gl~e~~ki~~lq~~~~~a~qhvl~knh~-~~~~l~kl~~k~~~~r~~~~lH~E~L  452 (479)
T KOG4216|consen  389 ALVL---------------MSADRSGLQEKVKIEKLQQKIQLALQHVLQKNHR-EDGILTKLICKVSTLRALCGLHTEKL  452 (479)
T ss_pred             HHHh---------------hCCccccccchHHHHHHHHHHHHHHHHHHHhcCC-hhhhHHHhhcccchHHHHHHHHHHHH
Confidence            3321               2578999999999999999999999999999985 34489999999999999999999999


Q ss_pred             HHhhhcCCCCh---HHHHHHHHh
Q psy6602         342 FFKETIGDIPI---QRLLGDMYT  361 (367)
Q Consensus       342 ~~~~~~g~~~i---~~ll~eml~  361 (367)
                      ..++..-+.-+   ++|--|++.
T Consensus       453 q~Fk~~hP~iv~~fP~LYKELFt  475 (479)
T KOG4216|consen  453 QAFKASHPDIVRHFPPLYKELFT  475 (479)
T ss_pred             HHHhhcCchHHhhccHHHHHHhc
Confidence            98888765444   344444443

>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=97.93  E-value=3e-05  Score=68.12  Aligned_cols=94  Identities=30%  Similarity=0.484  Sum_probs=76.2

Q ss_pred             HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCC-CCch-hhhhHHHHHHHHHHHH-HhhCCC
Q psy6602         239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLV-DAQP-VEMLQDQAQCILGDYV-RGRYSR  315 (367)
Q Consensus       239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~-~~~~-ve~lq~~~~~aL~~~~-~~~~p~  315 (367)
                      .+...+..++.+..+..|+++++...-               -+++.+++. +... ++++|+.+..+|..|+ ...++.
T Consensus       106 ~~~~~~~~~~~l~l~~~E~~~l~~l~l---------------~~~~~~~~~~~~~~~~~~~r~~~~~~L~~y~~~~~~~~  170 (203)
T PF00104_consen  106 YMNEVLRPFRRLKLDEEEFALLKALIL---------------FNPDYPGLSEETREIVEELRDRIIQALHSYYNQSKGPE  170 (203)
T ss_dssp             HHHHHHHHHHHTT-BHHHHHHHHHHHH---------------SSTTSTTHS-SHHHHHHHHHHHHHHHHHHHHHHHHSTT
T ss_pred             HHHHHHHHHHHhhhhhHHHHHHHHHhh---------------hcccccccccchhHHHHHHHHHHHHHHHHHHhccCCCc
Confidence            445566678888888888888876641               235777877 5555 9999999999999999 878887


Q ss_pred             C-cChHHHHHhhchhhhhhchhhHHHHHHhhhc
Q psy6602         316 Q-PTRFGRLLLMLPSLRAVRQSTIERLFFKETI  347 (367)
Q Consensus       316 ~-~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~  347 (367)
                      + +.||++|++.+|.++.++..+.|+.++..++
T Consensus       171 ~~~~R~~~ll~ll~~l~~~~~~~~e~~~~~~lf  203 (203)
T PF00104_consen  171 DYAQRFGKLLLLLPSLRKISEKHIENMFLSDLF  203 (203)
T ss_dssp             THTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHhhHHhhC
Confidence            7 7999999999999999999999998887653

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

>smart00430 HOLI Ligand binding domain of hormone receptors

Probab=97.70  E-value=6.2e-05  Score=63.57  Aligned_cols=76  Identities=29%  Similarity=0.489  Sum_probs=63.6

Q ss_pred             hhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCC--chhhhhHHHHHHHHHHHHHhhCC-CCcCh
Q psy6602         243 MLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDA--QPVEMLQDQAQCILGDYVRGRYS-RQPTR  319 (367)
Q Consensus       243 ~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~--~~ve~lq~~~~~aL~~~~~~~~p-~~~~r  319 (367)
                      ....++.+.....|+++++...-               .+++++++.+.  ..++++|+.+..+|..|+..++| +.+.|
T Consensus        85 ~~~~l~~L~l~~~E~~~l~ai~l---------------~~~~~~~l~~~~~~~~~~~~~~~~~~L~~y~~~~~~~~~~~R  149 (163)
T smart00430       85 LVKPLRELKLDDEEYALLKAILL---------------FNPAGPGLSEEGKEILEKLQEKLANALHDYYLKNYPMNYPGR  149 (163)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHH---------------cChhhhhhChHHHHHHHHHHHHHHHHHHHHHHHcCCCcchhH
Confidence            45567888888899888876642               12567888888  78999999999999999999998 56899


Q ss_pred             HHHHHhhchhhhhh
Q psy6602         320 FGRLLLMLPSLRAV  333 (367)
Q Consensus       320 ~~~lLl~Lp~lr~i  333 (367)
                      |++|++++|++|.+
T Consensus       150 ~~~ll~~l~~i~~~  163 (163)
T smart00430      150 FGELLLILNAIQKI  163 (163)
T ss_pred             HHHHHHHHHHhhcC
Confidence            99999999999863

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

Probab=97.61  E-value=0.00013  Score=62.00  Aligned_cols=77  Identities=36%  Similarity=0.568  Sum_probs=63.9

Q ss_pred             HhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCC-CCCCCchhhhhHHHHHHHHHHHHHhhCC-CCcCh
Q psy6602         242 LMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETP-GLVDAQPVEMLQDQAQCILGDYVRGRYS-RQPTR  319 (367)
Q Consensus       242 ~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~-gl~~~~~ve~lq~~~~~aL~~~~~~~~p-~~~~r  319 (367)
                      .++..++.+..+..|+++.+...-           |    +++.+ +..+...+++.|+.+..+|..|+..+++ +.+.|
T Consensus        90 ~~~~~~~~L~l~~~E~~~l~ai~l-----------~----~~~~~~s~~~~~~~~~~~~~~~~~L~~y~~~~~~~~~~~R  154 (168)
T cd06157          90 EFVNPLRALKLDDEEYALLKAIVL-----------F----SPDRKESLEDRKIVEELQERLLEALQDYLRKNYPEEAPSR  154 (168)
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHHH-----------h----CCCCCCCccCHHHHHHHHHHHHHHHHHHHHHhCCccchhH
Confidence            355677788888888888877642           1    24444 7889999999999999999999999997 88999


Q ss_pred             HHHHHhhchhhhhh
Q psy6602         320 FGRLLLMLPSLRAV  333 (367)
Q Consensus       320 ~~~lLl~Lp~lr~i  333 (367)
                      |++|+++++++|.+
T Consensus       155 ~~~ll~~l~~l~~~  168 (168)
T cd06157         155 FAKLLLLLPSLRKL  168 (168)
T ss_pred             HHHHHHhchhcccC
Confidence            99999999999864

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

>KOG4846|consensus

Probab=96.85  E-value=0.0036  Score=59.59  Aligned_cols=158  Identities=9%  Similarity=0.016  Sum_probs=113.4

Q ss_pred             hHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCC------CCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHH
Q psy6602         165 VNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPG------LVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFG  238 (367)
Q Consensus       165 ~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~------L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~  238 (367)
                      +....+.+..|.+....+...+...+++..+.++.+....      .....+..++...+..-+.++...+. .+ .-+.
T Consensus       371 ~~~av~e~~~fa~hi~~~~~~~~~~~~~~~L~~~q~l~t~~~f~t~f~~~~Q~~~mfl~~~~~~~Q~~~~~~-~g-d~~~  448 (538)
T KOG4846|consen  371 YGSAVDEMLAFANHIITIGCTDGDIALFIVLILCQPLTTEQQFSTNFKSQLQLLEMFLFYKKVLFQKMTCRI-DG-DTYK  448 (538)
T ss_pred             hhHHHHHHHHhhhccCCccccccchhHHHHHhccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh-ch-HHHH
Confidence            3455688899999999999999999999888888874321      11233444455556666665555542 22 5577


Q ss_pred             HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcC
Q psy6602         239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPT  318 (367)
Q Consensus       239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~  318 (367)
                      .++.++-.+..++..+.+.+-..                   .+.++.+.+....||.|||....++  ..-.+.|-...
T Consensus       449 a~~~~~~~ln~L~~~~~~~~~~l-------------------~s~~s~~~e~~~sVe~lqe~~lr~~--~~~~n~pl~~s  507 (538)
T KOG4846|consen  449 ALMKCIHELNRLNELHKQQLNIL-------------------RSNLSFLNEPPLSVEMLQESTLRLP--VNHNNQPLNQS  507 (538)
T ss_pred             HHHHhhcchhhcCchHHHHHHHH-------------------HHhhhhhccCCchHHHHHhhhhhcc--ccccCCccccc
Confidence            77777777777777766653332                   2345677888889999999998888  44455677788


Q ss_pred             hHHHHHhhchhhhhhchhhHHHHHHhh
Q psy6602         319 RFGRLLLMLPSLRAVRQSTIERLFFKE  345 (367)
Q Consensus       319 r~~~lLl~Lp~lr~i~~~~~e~l~~~~  345 (367)
                      ++.+.++.++++|++.+.+.+.+...+
T Consensus       508 ~~~~~~~~~~d~~sl~~lhs~kv~~~~  534 (538)
T KOG4846|consen  508 LPHVRHQVKRDVQSLENLHSMKVHPVP  534 (538)
T ss_pred             CcchhhccCCcCCcccchhcccccccc
Confidence            999999999999999998888776544

>KOG4218|consensus

Probab=95.96  E-value=0.021  Score=53.16  Aligned_cols=72  Identities=31%  Similarity=0.401  Sum_probs=65.7

Q ss_pred             hHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHccc
Q psy6602         209 QPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  280 (367)
Q Consensus       209 ~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~  280 (367)
                      ..|+.+|+....+|-+|-...||+....|+++++.|.++|.++....|+++.+.+-...+-..++.+|+...
T Consensus       402 ~lv~~~qe~~naaLldyt~c~yp~~~~kF~qllL~L~eiRa~smqa~eyly~khl~~~~p~nnllieml~Ak  473 (475)
T KOG4218|consen  402 ELVRRLQEDSNAALLDYTSCCYPNWEQKFPQLLLVLEEIRATSMQAAEYLYTKHLQVPAPQNNLLIEMLTAK  473 (475)
T ss_pred             HHHHHHHHHHHHHHHHhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCccccchHHHHhhcc
Confidence            468899999999999999999999999999999999999999999999999999888877778888887643

>KOG4846|consensus

Probab=94.84  E-value=0.0064  Score=57.93  Aligned_cols=163  Identities=7%  Similarity=-0.078  Sum_probs=111.1

Q ss_pred             HHHHHHHHHHHHHHHHHHhhcCCCCCCCC-HHHHHHHHHHHHHHHHHHHHHHhhccCCC---ceEecCCccccCCCCCcc
Q psy6602          88 AEKCQETTARLLFMAVRWVRCLAPFQTLS-KRDQLLLLQESWKELFLLHLAQWSIPWDL---SLLINCEKARERLPPDDV  163 (367)
Q Consensus        88 ~~~l~e~~~~~l~~~V~waK~lp~F~~L~-~~DQ~~LLk~~~~el~lL~~a~~~~~~~~---~~l~~~~~~~~~~~~~~~  163 (367)
                      |+++.-+....+-.+++||+.+++|..++ ..++..+|+.+-++...-..+-.......   ..++..........  +.
T Consensus       364 ~~~~~ll~~~av~e~~~fa~hi~~~~~~~~~~~~~~~L~~~q~l~t~~~f~t~f~~~~Q~~~mfl~~~~~~~Q~~~--~~  441 (538)
T KOG4846|consen  364 FKSLQLLYGSAVDEMLAFANHIITIGCTDGDIALFIVLILCQPLTTEQQFSTNFKSQLQLLEMFLFYKKVLFQKMT--CR  441 (538)
T ss_pred             cchhhhhhhHHHHHHHHhhhccCCccccccchhHHHHHhccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--hh
Confidence            66777788888889999999999999999 89999999998888776655532221000   00000001111111  11


Q ss_pred             chHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHh
Q psy6602         164 RVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLM  243 (367)
Q Consensus       164 ~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~  243 (367)
                      ++++....+..++.++..|.....|.    +.++-+-+..+......|+.+|+....++-  ...+.|-...++......
T Consensus       442 ~~gd~~~a~~~~~~~ln~L~~~~~~~----~~~l~s~~s~~~e~~~sVe~lqe~~lr~~~--~~~n~pl~~s~~~~~~~~  515 (538)
T KOG4846|consen  442 IDGDTYKALMKCIHELNRLNELHKQQ----LNILRSNLSFLNEPPLSVEMLQESTLRLPV--NHNNQPLNQSLPHVRHQV  515 (538)
T ss_pred             hchHHHHHHHHhhcchhhcCchHHHH----HHHHHHhhhhhccCCchHHHHHhhhhhccc--cccCCcccccCcchhhcc
Confidence            24567788889999999999988886    556666677777778999999999888772  222234455677777778


Q ss_pred             hhHhHhhhhhHHHHH
Q psy6602         244 LPSLRAVRQSTIERL  258 (367)
Q Consensus       244 l~~Lr~l~~~~~e~l  258 (367)
                      .+.++++...+.+.+
T Consensus       516 ~~d~~sl~~lhs~kv  530 (538)
T KOG4846|consen  516 KRDVQSLENLHSMKV  530 (538)
T ss_pred             CCcCCcccchhcccc
Confidence            888887776666544

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	367
3cjw_A	244	Crystal Structure Of The Human Coup-Tfii Ligand Bin		7e-38
3cjw_A	244	Crystal Structure Of The Human Coup-Tfii Ligand Bin		2e-17
3p0u_A	249	Crystal Structure Of The Ligand Binding Domain Of H		5e-26
3p0u_A	249	Crystal Structure Of The Ligand Binding Domain Of H		2e-09
1xiu_A	230	Crystal Structure Of The Agonist-Bound Ligand-Bindi		2e-25
1xiu_A	230	Crystal Structure Of The Agonist-Bound Ligand-Bindi		2e-10
2gl8_A	241	Human Retinoic Acid Receptor Rxr-Gamma Ligand-Bindi		3e-25
2gl8_A	241	Human Retinoic Acid Receptor Rxr-Gamma Ligand-Bindi		7e-10
2nxx_A	235	Crystal Structure Of The Ligand-Binding Domains Of		5e-25
2nxx_A	235	Crystal Structure Of The Ligand-Binding Domains Of		2e-10
3dzu_A	467	Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp		2e-24
3dzu_A	467	Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp		1e-09
3e94_A	244	Crystal Structure Of Rxralpha Ligand Binding Domain		2e-24
3e94_A	244	Crystal Structure Of Rxralpha Ligand Binding Domain		8e-10
3eyb_A	219	Structural And Functional Insights Into The Ligand		2e-24
3eyb_A	219	Structural And Functional Insights Into The Ligand		6e-10
1lbd_A	282	Ligand-Binding Domain Of The Human Nuclear Receptor		2e-24
1lbd_A	282	Ligand-Binding Domain Of The Human Nuclear Receptor		1e-09
3uvv_B	244	Crystal Structure Of The Ligand Binding Domains Of		2e-24
3uvv_B	244	Crystal Structure Of The Ligand Binding Domains Of		9e-10
1rdt_A	242	Crystal Structure Of A New Rexinoid Bound To The Rx		3e-24
1rdt_A	242	Crystal Structure Of A New Rexinoid Bound To The Rx		9e-10
1fm6_A	238	The 2.1 Angstrom Resolution Crystal Structure Of Th		3e-24
1fm6_A	238	The 2.1 Angstrom Resolution Crystal Structure Of Th		8e-10
1mv9_A	240	Crystal Structure Of The Human Rxr Alpha Ligand Bin		3e-24
1mv9_A	240	Crystal Structure Of The Human Rxr Alpha Ligand Bin		8e-10
1xdk_A	238	Crystal Structure Of The RarbetaRXRALPHA LIGAND BIN		3e-24
1xdk_A	238	Crystal Structure Of The RarbetaRXRALPHA LIGAND BIN		8e-10
1xv9_A	236	Crystal Structure Of CarRXR HETERODIMER BOUND WITH		3e-24
1xv9_A	236	Crystal Structure Of CarRXR HETERODIMER BOUND WITH		9e-10
3a9e_A	240	Crystal Structure Of A Mixed Agonist-Bound Rar-Alph		3e-24
3a9e_A	240	Crystal Structure Of A Mixed Agonist-Bound Rar-Alph		8e-10
1fby_A	239	Crystal Structure Of The Human Rxr Alpha Ligand Bin		3e-24
1fby_A	239	Crystal Structure Of The Human Rxr Alpha Ligand Bin		9e-10
3pcu_A	230	Crystal Structure Of Human Retinoic X Receptor Alph		3e-24
3pcu_A	230	Crystal Structure Of Human Retinoic X Receptor Alph		9e-10
1xls_A	232	Crystal Structure Of The Mouse CarRXR LBD HETERODIM		3e-24
1xls_A	232	Crystal Structure Of The Mouse CarRXR LBD HETERODIM		9e-10
3oap_A	231	Crystal Structure Of Human Retinoid X Receptor Alph		4e-24
3oap_A	231	Crystal Structure Of Human Retinoid X Receptor Alph		9e-10
3h0a_A	228	Crystal Structure Of Peroxisome Proliferator-Activa		4e-24
3h0a_A	228	Crystal Structure Of Peroxisome Proliferator-Activa		1e-09
1dkf_A	233	Crystal Structure Of A Heterodimeric Complex Of Rar		5e-24
1dkf_A	233	Crystal Structure Of A Heterodimeric Complex Of Rar		8e-10
2q60_A	258	Crystal Structure Of The Ligand Binding Domain Of P		9e-24
2q60_A	258	Crystal Structure Of The Ligand Binding Domain Of P		7e-10
1uhl_A	236	Crystal Structure Of The Lxralfa-Rxrbeta Lbd Hetero		4e-23
1uhl_A	236	Crystal Structure Of The Lxralfa-Rxrbeta Lbd Hetero		1e-08
1h9u_A	224	The Structure Of The Human Retinoid-X-Receptor Beta		1e-22
1h9u_A	224	The Structure Of The Human Retinoid-X-Receptor Beta		3e-08
1z5x_U	262	Hemipteran Ecdysone Receptor Ligand-Binding Domain		3e-22
1z5x_U	262	Hemipteran Ecdysone Receptor Ligand-Binding Domain		2e-08
1pk5_A	248	Crystal Structure Of The Orphan Nuclear Receptor Lr		4e-22
1pk5_A	248	Crystal Structure Of The Orphan Nuclear Receptor Lr		4e-09
1zh7_A	243	Structural And Biochemical Basis For Selective Repr		8e-22
1zh7_A	243	Structural And Biochemical Basis For Selective Repr		8e-09
3tx7_B	352	Crystal Structure Of Lrh-1BETA-Catenin Complex Leng		4e-21
3tx7_B	352	Crystal Structure Of Lrh-1BETA-Catenin Complex Leng		5e-09
1yuc_A	255	Human Nuclear Receptor Liver Receptor Homologue-1,		1e-20
1yuc_A	255	Human Nuclear Receptor Liver Receptor Homologue-1,		5e-09
4dos_A	242	Human Nuclear Receptor Liver Receptor Homologue-1,		2e-20
4dos_A	242	Human Nuclear Receptor Liver Receptor Homologue-1,		5e-09
1zdu_A	245	The Crystal Structure Of Human Liver Receptor Homol		2e-20
1zdu_A	245	The Crystal Structure Of Human Liver Receptor Homol		5e-09
3plz_A	257	Human Lrh1 Lbd Bound To Gr470 Length = 257		2e-20
3plz_A	257	Human Lrh1 Lbd Bound To Gr470 Length = 257		7e-09
1yok_A	256	Crystal Structure Of Human Lrh-1 Bound With Tif-2 P		2e-20
1yok_A	256	Crystal Structure Of Human Lrh-1 Bound With Tif-2 P		6e-09
1m7w_A	250	Hnf4a Ligand Binding Domain With Bound Fatty Acid L		5e-16
1pzl_A	237	Crystal Structure Of Hnf4a Lbd In Complex With The		1e-14
3fs1_A	230	Crystal Structure Of Hnf4a Lbd In Complex With The		1e-14
1vjb_A	251	Crystal Structure Of The Ligand-Binding Domain Of T		4e-14
1vjb_A	251	Crystal Structure Of The Ligand-Binding Domain Of T		1e-04
1s9q_A	251	Crystal Structure Of The Ligand-Binding Domain Of T		4e-14
1s9q_A	251	Crystal Structure Of The Ligand-Binding Domain Of T		1e-04
1kv6_A	230	X-Ray Structure Of The Orphan Nuclear Receptor Err3		5e-14
1kv6_A	230	X-Ray Structure Of The Orphan Nuclear Receptor Err3		1e-04
1lv2_A	229	Hepatocyte Nuclear Factor 4 Is A Transcription Fact		6e-14
1s9p_A	227	Crystal Structure Of The Ligand-Binding Domain Of T		6e-14
1s9p_A	227	Crystal Structure Of The Ligand-Binding Domain Of T		1e-04
2ewp_A	226	Crystal Structure Of Estrogen Related Receptor-3 (E		6e-14
2ewp_A	226	Crystal Structure Of Estrogen Related Receptor-3 (E		1e-04
2e2r_A	244	Crystal Structure Of Human Estrogen-Related Recepto		6e-14
2e2r_A	244	Crystal Structure Of Human Estrogen-Related Recepto		1e-04
1hg4_A	279	Ultraspiracle Ligand Binding Domain From Drosophila		7e-11
3f7d_A	244	Sf-1 Lbd Bound By Phosphatidylcholine Length = 244		7e-11
1ymt_A	246	Mouse Sf-1 Lbd Length = 246		9e-11
1r1k_A	263	Crystal Structure Of The Ligand-Binding Domains Of		1e-10
1g2n_A	264	Crystal Structure Of The Ligand Binding Domain Of T		1e-10
2xhs_A	245	Crystal Structure Of The Ligand Binding Domain Of F		2e-09
1yp0_A	239	Structure Of The Steroidogenic Factor-1 Ligand Bind		2e-09
3f5c_B	268	Structure Of Dax-1:lrh-1 Complex Length = 268		5e-09
1ovl_B	271	Crystal Structure Of Nurr1 Lbd Length = 271		3e-07
1ovl_A	271	Crystal Structure Of Nurr1 Lbd Length = 271		3e-07
2qw4_A	273	Human Nr4a1 Ligand-Binding Domain Length = 273		2e-06
3v3e_B	257	Crystal Structure Of The Human Nur77 Ligand-Binding		3e-06
1yje_A	264	Crystal Structure Of The Rngfi-B Ligand-Binding Dom		4e-06
3fc6_B	266	Hrxralpha & Mlxralpha With An Indole Pharmacophore,		5e-06
2zl9_A	271	2-Substituted-16-Ene-22-Thia-1alpha,25-Dihydroxy-26		6e-06
2zfx_A	265	Crystal Structure Of The Rat Vitamin D Receptor Lig		7e-06
2acl_B	244	Liver X-Receptor Alpha Ligand Binding Domain With S		8e-06
1rjk_A	292	Crystal Structure Of The Rat Vitamin D Receptor Lig		8e-06
3p8x_A	280	Synthesis, Structure, And Biological Activity Of De		1e-05
3kmr_A	266	Crystal Structure Of Raralpha Ligand Binding Domain		1e-05
2fsz_A	246	A Second Binding Site For Hydroxytamoxifen Within T		1e-05
1xv9_B	246	Crystal Structure Of CarRXR HETERODIMER BOUND WITH		1e-05
1s0z_A	263	Crystal Structure Of The Vdr Lbd Complexed To Seoca		1e-05
3b0t_A	254	Human Vdr Ligand Binding Domain In Complex With Max		2e-05
1db1_A	259	Crystal Structure Of The Nuclear Receptor For Vitam		2e-05
3az1_A	253	Crystal Structure Analysis Of Vitamin D Receptor Le		2e-05
4dqm_A	234	Revealing A Marine Natural Product As A Novel Agoni		2e-05
1dkf_B	235	Crystal Structure Of A Heterodimeric Complex Of Rar		2e-05
3m7r_A	253	Crystal Structure Of Vdr H305q Mutant Length = 253		3e-05
3a9e_B	269	Crystal Structure Of A Mixed Agonist-Bound Rar-Alph		3e-05
1zdt_A	241	The Crystal Structure Of Human Steroidogenic Factor		3e-05
3d24_A	253	Crystal Structure Of Ligand-Binding Domain Of Estro		3e-05
3a2i_A	263	Crystal Structure Of The Human Vitamin D Receptor (		4e-05
1pdu_A	244	Ligand-Binding Domain Of Drosophila Orphan Nuclear		4e-05
3a2j_A	263	Crystal Structure Of The Human Vitamin D Receptor (		4e-05
1l2j_A	271	Human Estrogen Receptor Beta Ligand-Binding Domain		5e-05
3ipq_A	283	X-Ray Structure Of Gw3965 Synthetic Agonist Bound T		5e-05
2yly_A	240	Sulfonamides As Selective Estrogen Receptor Beta Ag		5e-05
2pjl_A	247	Crystal Structure Of Human Estrogen-Related Recepto		5e-05
1xls_E	242	Crystal Structure Of The Mouse CarRXR LBD HETERODIM		5e-05
1xnx_A	256	Crystal Structure Of Constitutive Androstane Recept		5e-05
3et0_A	292	Structure Of Ppargamma With 3-(5-Methoxy-1h-Indol-3		5e-05
3bc5_A	296	X-Ray Crystal Structure Of Human Ppar Gamma With 2-		6e-05
3k6p_A	248	Estrogen Related Receptor Alpha In Complex With An		6e-05
2nv7_A	238	Crystal Structure Of Estrogen Receptor Beta Complex		6e-05
3oll_A	240	Crystal Structure Of Phosphorylated Estrogen Recept		6e-05
1xb7_A	247	X-Ray Structure Of Erralpha Lbd In Complex With A P		6e-05
1x76_A	240	Crystal Structure Of Estrogen Receptor Beta Complex		6e-05
3n00_A	245	Crystal Structure Of A Deletion Mutant Of Human Rev		6e-05
1yy4_A	268	Crystal Structure Of Estrogen Receptor Beta Complex		6e-05
3et3_A	292	Structure Of Ppargamma With 3-[5-Methoxy-1-(4-Metho		6e-05
1zaf_A	238	Crystal Structure Of Estrogen Receptor Beta Complex		7e-05
2giu_A	241	Human Estrogen Receptor Beta Ligand-Binding Domain		7e-05
1u9e_A	241	Crystal Structure Of Estrogen Receptor Beta Complex		7e-05
2om9_A	278	Ajulemic Acid, A Synthetic Cannabinoid Bound To Ppa		7e-05
1qkm_A	255	Human Oestrogen Receptor Beta Ligand-Binding Domain		7e-05
1k74_D	283	The 2.3 Angstrom Resolution Crystal Structure Of Th		7e-05
1uhl_B	242	Crystal Structure Of The Lxralfa-Rxrbeta Lbd Hetero		7e-05
2i0g_A	257	Benzopyrans Are Selective Estrogen Receptor Beta Ag		8e-05
1yow_A	242	Human Steroidogenic Factor 1 Lbd With Bound Co-Fact		8e-05
3prg_A	278	Ligand Binding Domain Of Human Peroxisome Prolifera		8e-05
3s9s_A	284	Ligand Binding Domain Of Ppargamma Complexed With A		8e-05
2q59_A	274	Crystal Structure Of Ppargamma Lbd Bound To Full Ag		8e-05
1i7i_A	292	Crystal Structure Of The Ligand Binding Domain Of H		8e-05
3b0q_A	274	Human Ppar Gamma Ligand Binding Domain In Complex W		8e-05
3cs8_A	275	Structural And Biochemical Basis For The Binding Se		8e-05
2q59_B	274	Crystal Structure Of Ppargamma Lbd Bound To Full Ag		8e-05
3vn2_A	285	Crystal Structure Of Ppargamma Complexed With Telmi		8e-05
3lmp_A	283	Crystal Structure Of The Ppargamma-Lbd Complexed Wi		8e-05
2vv4_B	276	Hppargamma Ligand Binding Domain In Complex With 6-		8e-05
1nde_A	255	Estrogen Receptor Beta With Selective Triazine Modu		8e-05
3osi_A	285	Crystal Structure Of Ppargamma Ligand Binding Domai		8e-05
3ads_A	287	Human Ppargamma Ligand-Binding Domain In Complex Wi		8e-05
2zvt_A	286	Cys285ser Mutant Ppargamma Ligand-Binding Domain Co		8e-05
1knu_A	274	Ligand Binding Domain Of The Human Peroxisome Proli		8e-05
2hfp_A	282	Crystal Structure Of Ppar Gamma With N-Sulfonyl-2-I		9e-05
3pba_A	286	Crystal Structure Of Ppargamma Ligand Binding Domai		9e-05
3t03_A	284	Crystal Structure Of Ppar Gamma Ligand Binding Doma		9e-05
2vsr_A	276	Hppargamma Ligand Binding Domain In Complex With 9-		9e-05
1nyx_A	276	Ligand Binding Domain Of The Human Peroxisome Proli		9e-05
2vv1_B	276	Hppargamma Ligand Binding Domain In Complex With 4-		9e-05
2i4j_A	286	Crystal Structure Of The Complex Between Ppargamma		9e-05
1zeo_A	277	Crystal Structure Of Human Ppar-Gamma Ligand Bindin		9e-05
1fm6_D	272	The 2.1 Angstrom Resolution Crystal Structure Of Th		9e-05
1qkn_A	255	Rat Oestrogen Receptor Beta Ligand-Binding Domain I		9e-05
2j7x_A	255	Structure Of Estradiol-bound Estrogen Receptor Beta		9e-05
3r8a_A	282	X-Ray Crystal Structure Of The Nuclear Hormone Rece		1e-04
1wm0_X	292	Ppargamma In Complex With A 2-Baba Compound Length		1e-04
3u9q_A	269	Ligand Binding Domain Of Ppargamma Complexed With D		1e-04
4prg_A	270	0072 Partial Agonist Ppar Gamma Cocrystal Length =		1e-04
3cwd_A	270	Molecular Recognition Of Nitro-Fatty Acids By Ppar		1e-04
1rdt_D	284	Crystal Structure Of A New Rexinoid Bound To The Rx		1e-04
2prg_A	271	Ligand-Binding Domain Of The Human Peroxisome Proli		1e-04
1uom_A	254	The Structure Of Estrogen Receptor In Complex With		1e-04
1nuo_A	261	Two Rth Mutants With Impaired Hormone Binding Lengt		1e-04
1qkt_A	248	Mutant Estrogen Nuclear Receptor Ligand Binding Dom		2e-04
2yat_A	252	Crystal Structure Of Estradiol Derived Metal Chelat		2e-04
1pcg_A	244	Helix-Stabilized Cyclic Peptides As Selective Inhib		2e-04
2ocf_A	298	Human Estrogen Receptor Alpha Ligand-Binding Domain		2e-04
3dzu_D	419	Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp		2e-04
3jzc_A	263	Crystal Structure Of Tr-Beta Bound To The Selective		3e-04
1zky_A	257	Human Estrogen Receptor Alpha Ligand-Binding Domain		3e-04
1xap_A	267	Structure Of The Ligand Binding Domain Of The Retin		3e-04
3uu7_B	251	Crystal Structure Of Hera-Lbd (Y537s) In Complex Wi		3e-04
3q97_A	260	Crystal Structure Of Human Estrogen Receptor Alpha		3e-04
3uu7_A	251	Crystal Structure Of Hera-Lbd (Y537s) In Complex Wi		4e-04
3q95_B	260	Crystal Structure Of Human Estrogen Receptor Alpha		4e-04
2hbh_A	302	Crystal Structure Of Vitamin D Nuclear Receptor Lig		4e-04
4fhh_A	300	Development Of Synthetically Accessible Non-Secoste		4e-04
3hm1_A	253	Crystal Structure Of Human Estrogen Receptor Alpha		4e-04
1xdk_B	303	Crystal Structure Of The RarbetaRXRALPHA LIGAND BIN		5e-04
3imy_A	261	Structure Of Tr-Beta Bound To Selective Thyromimeti		5e-04
3gws_X	259	Crystal Structure Of T3-Bound Thyroid Hormone Recep		6e-04
3uua_B	251	Crystal Structure Of Hera-Lbd (Y537s) In Complex Wi		6e-04
2qzo_B	258	Crystal Structure Of The Estrogen Receptor Alpha Li		6e-04
3h52_A	254	Crystal Structure Of The Antagonist Form Of Human G		6e-04
3uua_A	251	Crystal Structure Of Hera-Lbd (Y537s) In Complex Wi		6e-04
2h79_A	269	Crystal Structure Of Human Tr Alpha Bound T3 In Ort		6e-04
3jzb_A	267	Crystal Structure Of Tr-Alfa Bound To The Selective		6e-04
3hzf_A	269	Structure Of Tr-alfa Bound To Selective Thyromimeti		7e-04
2qa8_B	258	Crystal Structure Of The Estrogen Receptor Alpha Li		7e-04
3l0e_A	253	X-Ray Crystal Structure Of A Potent Liver X Recepto		7e-04
3q95_A	260	Crystal Structure Of Human Estrogen Receptor Alpha		8e-04
1err_A	253	Human Estrogen Receptor Ligand-Binding Domain In Co		8e-04
1x7e_A	245	Crystal Structure Of Estrogen Receptor Alpha Comple		9e-04

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

Iteration: 1
 Score =  154 bits (389), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 84/204 (41%), Positives = 118/204 (57%), Gaps = 2/204 (0%)
Query: 85  LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD 144
           +M  E   E  AR+LF AV W R +  F  L   DQ+ LL+ +W ELF+L+ AQ S+P  
Sbjct: 36  IMGIENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLH 95
Query: 145 LSLLINCEKARERLPPDD--VRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPET 202
           ++ L+            D  V   + I++ QE + + + L  D +E  C+KA++LFT + 
Sbjct: 96  VAPLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDA 155
Query: 203 PGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKE 262
            GL D   VE LQ+++QC L +YVR +Y  QPTRFG+LLL LPSLR V  S IE+LFF  
Sbjct: 156 CGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVR 215
Query: 263 TIGDIPIQRLLGDMYTMEKSYETP 286
            +G  PI+ L+ DM     S+  P
Sbjct: 216 LVGKTPIETLIRDMLLSGSSFNWP 239

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

Iteration: 1
 Score = 86.7 bits (213), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 42/81 (51%), Positives = 53/81 (65%)
Query: 287 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKET 346
           GL D   VE LQ+++QC L +YVR +Y  QPTRFG+LLL LPSLR V  S IE+LFF   
Sbjct: 157 GLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVRL 216
Query: 347 IGDIPIQRLLGDMYTMEKSYG 367
           +G  PI+ L+ DM     S+ 
Sbjct: 217 VGKTPIETLIRDMLLSGSSFN 237

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

Iteration: 1
 Score =  115 bits (287), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 69/216 (31%), Positives = 107/216 (49%), Gaps = 12/216 (5%)
Query: 75  PPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLL 134
           P P P  L +        E+ +RLLF+++ W R +  FQ L +     L++  W ELF L
Sbjct: 27  PSPMPEYLNV----HYICESASRLLFLSMHWARSIPAFQALGQDCNTSLVRACWNELFTL 82
Query: 135 HLAQWSIPWDLSLLINC-------EKARERLPPDDVR-VNNEIKLIQEILARFRQLSPDG 186
            LAQ +    LS ++             ++L  D ++ V   I  +QE      +L  DG
Sbjct: 83  GLAQCAQVMSLSTILAAIVNHLQNSIQEDKLSGDRIKQVMEHIWKLQEFCNSMAKLDIDG 142
Query: 187 SECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPS 246
            E   +KA++LF+P+ PGL     +E  Q+ AQ  L DYV+  YS    R  R+L+ LP+
Sbjct: 143 YEYAYLKAIVLFSPDHPGLTSTSQIEKFQEAAQMELQDYVQATYSEDTYRLARILVRLPA 202
Query: 247 LRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKS 282
           LR +  +  E LFF   IG++ I  ++  +  ME +
Sbjct: 203 LRLMSSNITEELFFTGLIGNVSIDSIIPYILKMETA 238

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

Iteration: 1
 Score = 60.1 bits (144), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 29/80 (36%), Positives = 43/80 (53%)
Query: 286 PGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKE 345
           PGL     +E  Q+ AQ  L DYV+  YS    R  R+L+ LP+LR +  +  E LFF  
Sbjct: 159 PGLTSTSQIEKFQEAAQMELQDYVQATYSEDTYRLARILVRLPALRLMSSNITEELFFTG 218
Query: 346 TIGDIPIQRLLGDMYTMEKS 365
            IG++ I  ++  +  ME +
Sbjct: 219 LIGNVSIDSIIPYILKMETA 238

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

Iteration: 1
 Score =  112 bits (281), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 63/187 (33%), Positives = 98/187 (52%), Gaps = 2/187 (1%)
Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
           CQ    +L F  V W + +  F  L   DQ++LL+  W EL +   +  SI     +L+ 
Sbjct: 37  CQAADKQL-FTLVEWAKRIPHFTELPLEDQVILLRAGWNELLIAGFSHRSIMAKDGILLA 95
Query: 151 CEKARERLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
                 R       V     +++ E++A+ R +  D +E GC++AV+LF P+  GL   Q
Sbjct: 96  TGLHVHRSSAHQAGVGTIFDRVLTELVAKMRDMKMDKTELGCLRAVVLFNPDAKGLTAVQ 155
Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
            VE L+++    L +Y + RY  +P RF +LLL LP+LR++    +E LFF + IGD PI
Sbjct: 156 EVEQLREKVYASLEEYTKSRYPEEPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDQPI 215
Query: 270 QRLLGDM 276
              L +M
Sbjct: 216 DTFLMEM 222

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

Iteration: 1
 Score = 63.2 bits (152), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 31/76 (40%), Positives = 45/76 (59%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           +  GL   Q VE L+++    L +Y + RY  +P RF +LLL LP+LR++    +E LFF
Sbjct: 147 DAKGLTAVQEVEQLREKVYASLEEYTKSRYPEEPGRFAKLLLRLPALRSIGLKCLEHLFF 206
Query: 344 KETIGDIPIQRLLGDM 359
            + IGD PI   L +M
Sbjct: 207 FKLIGDQPIDTFLMEM 222

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

Iteration: 1
 Score =  112 bits (280), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 57/179 (31%), Positives = 96/179 (53%), Gaps = 1/179 (0%)
Query: 99  LFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERL 158
           LF  V W + +  F  L+  DQ++LL+  W EL +   +  S+     +L+       R 
Sbjct: 55  LFTLVEWAKRIPHFSDLTLEDQVILLRAGWNELLIASFSHRSVSVQDGILLATGLHVHRS 114
Query: 159 PPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQ 217
                 V +   +++ E++++ + +  D SE GC++A++LF P+  GL +   VE L+++
Sbjct: 115 SAHSAGVGSIFDRVLTELVSKMKDMQMDKSELGCLRAIVLFNPDAKGLSNPSEVETLREK 174
Query: 218 AQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDM 276
               L  Y + +Y  QP RF +LLL LP+LR++    +E LFF + IGD PI   L +M
Sbjct: 175 VYATLEAYTKQKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEM 233

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

Iteration: 1
 Score = 61.6 bits (148), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 44/76 (57%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           +  GL +   VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF
Sbjct: 158 DAKGLSNPSEVETLREKVYATLEAYTKQKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 217
Query: 344 KETIGDIPIQRLLGDM 359
            + IGD PI   L +M
Sbjct: 218 FKLIGDTPIDTFLMEM 233

>pdb|2NXX|A Chain A, Crystal Structure Of The Ligand-Binding Domains Of The T.Castaneum (Coleoptera) Heterodimer Ecrusp Bound To Ponasterone A Length = 235

Iteration: 1
 Score =  111 bits (278), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 59/187 (31%), Positives = 105/187 (56%), Gaps = 2/187 (1%)
Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
           CQ  T + LF  V+W + +  F +L   DQ+ LL+  W EL +   +  S+    ++++ 
Sbjct: 43  CQ-ATHKQLFQLVQWAKLVPHFTSLPLTDQVQLLRAGWNELLIAAFSHRSMQAQDAIVLA 101
Query: 151 CEKARERLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
                 +     V V N   +++ E++ + +++  D +E GC++A+IL+ P+  G+   Q
Sbjct: 102 TGLTVNKSTAHAVGVGNIYDRVLSELVNKMKEMKMDKTELGCLRAIILYNPDVRGIKSVQ 161
Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
            VEML+++   +L +Y R  +  +P RF +LLL LP+LR++    +E LFF + IGD+PI
Sbjct: 162 EVEMLREKIYGVLEEYTRTTHPNEPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDVPI 221
Query: 270 QRLLGDM 276
              L +M
Sbjct: 222 DTFLMEM 228

>pdb|2NXX|A Chain A, Crystal Structure Of The Ligand-Binding Domains Of The T.Castaneum (Coleoptera) Heterodimer Ecrusp Bound To Ponasterone A Length = 235

Iteration: 1
 Score = 63.5 bits (153), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 30/73 (41%), Positives = 46/73 (63%)
Query: 287 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKET 346
           G+   Q VEML+++   +L +Y R  +  +P RF +LLL LP+LR++    +E LFF + 
Sbjct: 156 GIKSVQEVEMLREKIYGVLEEYTRTTHPNEPGRFAKLLLRLPALRSIGLKCLEHLFFFKL 215
Query: 347 IGDIPIQRLLGDM 359
           IGD+PI   L +M
Sbjct: 216 IGDVPIDTFLMEM 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 =  110 bits (274), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 60/187 (32%), Positives = 98/187 (52%), Gaps = 2/187 (1%)
Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
           CQ    + LF  V W + +  F  L   DQ++LL+  W EL +   +  SI     +L+ 
Sbjct: 274 CQ-AADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLA 332
Query: 151 CEKARERLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
                 R       V     +++ E++++ R +  D +E GC++A++LF P++ GL +  
Sbjct: 333 TGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPA 392
Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
            VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF + IGD PI
Sbjct: 393 EVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPI 452
Query: 270 QRLLGDM 276
              L +M
Sbjct: 453 DTFLMEM 459

>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 = 60.8 bits (146), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 45/76 (59%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           ++ GL +   VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF
Sbjct: 384 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 443
Query: 344 KETIGDIPIQRLLGDM 359
            + IGD PI   L +M
Sbjct: 444 FKLIGDTPIDTFLMEM 459

>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 =  109 bits (273), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 60/187 (32%), Positives = 98/187 (52%), Gaps = 2/187 (1%)
Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
           CQ    +L F  V W + +  F  L   DQ++LL+  W EL +   +  SI     +L+ 
Sbjct: 51  CQAADKQL-FTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLA 109
Query: 151 CEKARERLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
                 R       V     +++ E++++ R +  D +E GC++A++LF P++ GL +  
Sbjct: 110 TGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPA 169
Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
            VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF + IGD PI
Sbjct: 170 EVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPI 229
Query: 270 QRLLGDM 276
              L +M
Sbjct: 230 DTFLMEM 236

>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 = 61.2 bits (147), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 45/76 (59%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           ++ GL +   VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF
Sbjct: 161 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 220
Query: 344 KETIGDIPIQRLLGDM 359
            + IGD PI   L +M
Sbjct: 221 FKLIGDTPIDTFLMEM 236

>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 =  109 bits (273), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 61/187 (32%), Positives = 99/187 (52%), Gaps = 2/187 (1%)
Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
           CQ    +L+ + V W + +  F  L   DQ++LL+  W EL +   +  SI     +L+ 
Sbjct: 33  CQAADKQLVTL-VEWAKRIPHFSDLPIDDQVILLRAGWNELLIAAFSHRSIDVKDGILLA 91
Query: 151 CEKARERLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
                 R       V     +++ E++A+ R +  D +E GC++A++LF P+  GL D  
Sbjct: 92  SGLHVHRSSAHQAGVGTIFDRVLTELVAKMRDMKMDKTELGCLRAIVLFNPDAKGLTDPS 151
Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
            VE L+++    L +Y + +Y  QP RF +LLL LP+LR++    +E LFF + IGD PI
Sbjct: 152 LVESLREKVYASLEEYCKQQYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPI 211
Query: 270 QRLLGDM 276
              L +M
Sbjct: 212 DTFLMEM 218

>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 = 61.6 bits (148), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 31/76 (40%), Positives = 45/76 (59%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           +  GL D   VE L+++    L +Y + +Y  QP RF +LLL LP+LR++    +E LFF
Sbjct: 143 DAKGLTDPSLVESLREKVYASLEEYCKQQYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 202
Query: 344 KETIGDIPIQRLLGDM 359
            + IGD PI   L +M
Sbjct: 203 FKLIGDTPIDTFLMEM 218

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

Iteration: 1
 Score =  109 bits (273), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 60/187 (32%), Positives = 98/187 (52%), Gaps = 2/187 (1%)
Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
           CQ    + LF  V W + +  F  L   DQ++LL+  W EL +   +  SI     +L+ 
Sbjct: 89  CQ-AADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLA 147
Query: 151 CEKARERLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
                 R       V     +++ E++++ R +  D +E GC++A++LF P++ GL +  
Sbjct: 148 TGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPA 207
Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
            VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF + IGD PI
Sbjct: 208 EVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPI 267
Query: 270 QRLLGDM 276
              L +M
Sbjct: 268 DTFLMEM 274

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

Iteration: 1
 Score = 60.8 bits (146), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 45/76 (59%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           ++ GL +   VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF
Sbjct: 199 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 258
Query: 344 KETIGDIPIQRLLGDM 359
            + IGD PI   L +M
Sbjct: 259 FKLIGDTPIDTFLMEM 274

>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 =  109 bits (272), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 60/187 (32%), Positives = 98/187 (52%), Gaps = 2/187 (1%)
Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
           CQ    +L F  V W + +  F  L   DQ++LL+  W EL +   +  SI     +L+ 
Sbjct: 49  CQAADKQL-FTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLA 107
Query: 151 CEKARERLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
                 R       V     +++ E++++ R +  D +E GC++A++LF P++ GL +  
Sbjct: 108 TGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPA 167
Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
            VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF + IGD PI
Sbjct: 168 EVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPI 227
Query: 270 QRLLGDM 276
              L +M
Sbjct: 228 DTFLMEM 234

>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 = 61.2 bits (147), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 45/76 (59%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           ++ GL +   VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF
Sbjct: 159 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 218
Query: 344 KETIGDIPIQRLLGDM 359
            + IGD PI   L +M
Sbjct: 219 FKLIGDTPIDTFLMEM 234

>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 =  109 bits (272), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 60/187 (32%), Positives = 98/187 (52%), Gaps = 2/187 (1%)
Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
           CQ    +L F  V W + +  F  L   DQ++LL+  W EL +   +  SI     +L+ 
Sbjct: 49  CQAADKQL-FTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLA 107
Query: 151 CEKARERLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
                 R       V     +++ E++++ R +  D +E GC++A++LF P++ GL +  
Sbjct: 108 TGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPA 167
Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
            VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF + IGD PI
Sbjct: 168 EVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPI 227
Query: 270 QRLLGDM 276
              L +M
Sbjct: 228 DTFLMEM 234

>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 = 61.2 bits (147), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 45/76 (59%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           ++ GL +   VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF
Sbjct: 159 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 218
Query: 344 KETIGDIPIQRLLGDM 359
            + IGD PI   L +M
Sbjct: 219 FKLIGDTPIDTFLMEM 234

>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 =  109 bits (272), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 60/187 (32%), Positives = 98/187 (52%), Gaps = 2/187 (1%)
Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
           CQ    +L F  V W + +  F  L   DQ++LL+  W EL +   +  SI     +L+ 
Sbjct: 45  CQAADKQL-FTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLA 103
Query: 151 CEKARERLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
                 R       V     +++ E++++ R +  D +E GC++A++LF P++ GL +  
Sbjct: 104 TGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPA 163
Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
            VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF + IGD PI
Sbjct: 164 EVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPI 223
Query: 270 QRLLGDM 276
              L +M
Sbjct: 224 DTFLMEM 230

>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 = 61.2 bits (147), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 45/76 (59%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           ++ GL +   VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF
Sbjct: 155 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 214
Query: 344 KETIGDIPIQRLLGDM 359
            + IGD PI   L +M
Sbjct: 215 FKLIGDTPIDTFLMEM 230

>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 =  109 bits (272), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 60/187 (32%), Positives = 98/187 (52%), Gaps = 2/187 (1%)
Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
           CQ    +L F  V W + +  F  L   DQ++LL+  W EL +   +  SI     +L+ 
Sbjct: 47  CQAADKQL-FTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLA 105
Query: 151 CEKARERLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
                 R       V     +++ E++++ R +  D +E GC++A++LF P++ GL +  
Sbjct: 106 TGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPA 165
Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
            VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF + IGD PI
Sbjct: 166 EVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPI 225
Query: 270 QRLLGDM 276
              L +M
Sbjct: 226 DTFLMEM 232

>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 = 61.2 bits (147), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 45/76 (59%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           ++ GL +   VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF
Sbjct: 157 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 216
Query: 344 KETIGDIPIQRLLGDM 359
            + IGD PI   L +M
Sbjct: 217 FKLIGDTPIDTFLMEM 232

>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 =  109 bits (272), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 60/187 (32%), Positives = 98/187 (52%), Gaps = 2/187 (1%)
Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
           CQ    +L F  V W + +  F  L   DQ++LL+  W EL +   +  SI     +L+ 
Sbjct: 45  CQAADKQL-FTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLA 103
Query: 151 CEKARERLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
                 R       V     +++ E++++ R +  D +E GC++A++LF P++ GL +  
Sbjct: 104 TGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPA 163
Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
            VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF + IGD PI
Sbjct: 164 EVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPI 223
Query: 270 QRLLGDM 276
              L +M
Sbjct: 224 DTFLMEM 230

>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 = 61.2 bits (147), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 45/76 (59%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           ++ GL +   VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF
Sbjct: 155 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 214
Query: 344 KETIGDIPIQRLLGDM 359
            + IGD PI   L +M
Sbjct: 215 FKLIGDTPIDTFLMEM 230

>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 =  109 bits (272), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 60/187 (32%), Positives = 98/187 (52%), Gaps = 2/187 (1%)
Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
           CQ    +L F  V W + +  F  L   DQ++LL+  W EL +   +  SI     +L+ 
Sbjct: 43  CQAADKQL-FTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLA 101
Query: 151 CEKARERLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
                 R       V     +++ E++++ R +  D +E GC++A++LF P++ GL +  
Sbjct: 102 TGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPA 161
Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
            VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF + IGD PI
Sbjct: 162 EVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPI 221
Query: 270 QRLLGDM 276
              L +M
Sbjct: 222 DTFLMEM 228

>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 = 61.2 bits (147), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 45/76 (59%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           ++ GL +   VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF
Sbjct: 153 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 212
Query: 344 KETIGDIPIQRLLGDM 359
            + IGD PI   L +M
Sbjct: 213 FKLIGDTPIDTFLMEM 228

>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 =  109 bits (272), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 60/187 (32%), Positives = 98/187 (52%), Gaps = 2/187 (1%)
Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
           CQ    +L F  V W + +  F  L   DQ++LL+  W EL +   +  SI     +L+ 
Sbjct: 47  CQAADKQL-FTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLA 105
Query: 151 CEKARERLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
                 R       V     +++ E++++ R +  D +E GC++A++LF P++ GL +  
Sbjct: 106 TGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPA 165
Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
            VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF + IGD PI
Sbjct: 166 EVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPI 225
Query: 270 QRLLGDM 276
              L +M
Sbjct: 226 DTFLMEM 232

>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 = 61.2 bits (147), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 45/76 (59%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           ++ GL +   VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF
Sbjct: 157 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 216
Query: 344 KETIGDIPIQRLLGDM 359
            + IGD PI   L +M
Sbjct: 217 FKLIGDTPIDTFLMEM 232

>pdb|1FBY|A Chain A, Crystal Structure Of The Human Rxr Alpha Ligand Binding Domain Bound To 9-Cis Retinoic Acid Length = 239

Iteration: 1
 Score =  109 bits (272), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 60/187 (32%), Positives = 98/187 (52%), Gaps = 2/187 (1%)
Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
           CQ    +L F  V W + +  F  L   DQ++LL+  W EL +   +  SI     +L+ 
Sbjct: 46  CQAADKQL-FTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLA 104
Query: 151 CEKARERLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
                 R       V     +++ E++++ R +  D +E GC++A++LF P++ GL +  
Sbjct: 105 TGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPA 164
Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
            VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF + IGD PI
Sbjct: 165 EVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPI 224
Query: 270 QRLLGDM 276
              L +M
Sbjct: 225 DTFLMEM 231

>pdb|1FBY|A Chain A, Crystal Structure Of The Human Rxr Alpha Ligand Binding Domain Bound To 9-Cis Retinoic Acid Length = 239

Iteration: 1
 Score = 61.2 bits (147), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 45/76 (59%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           ++ GL +   VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF
Sbjct: 156 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 215
Query: 344 KETIGDIPIQRLLGDM 359
            + IGD PI   L +M
Sbjct: 216 FKLIGDTPIDTFLMEM 231

>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 =  108 bits (271), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 60/187 (32%), Positives = 98/187 (52%), Gaps = 2/187 (1%)
Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
           CQ    +L F  V W + +  F  L   DQ++LL+  W EL +   +  SI     +L+ 
Sbjct: 41  CQAADKQL-FTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLA 99
Query: 151 CEKARERLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
                 R       V     +++ E++++ R +  D +E GC++A++LF P++ GL +  
Sbjct: 100 TGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPA 159
Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
            VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF + IGD PI
Sbjct: 160 EVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPI 219
Query: 270 QRLLGDM 276
              L +M
Sbjct: 220 DTFLMEM 226

>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 = 61.2 bits (147), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 45/76 (59%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           ++ GL +   VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF
Sbjct: 151 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 210
Query: 344 KETIGDIPIQRLLGDM 359
            + IGD PI   L +M
Sbjct: 211 FKLIGDTPIDTFLMEM 226

>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 =  108 bits (271), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 60/187 (32%), Positives = 98/187 (52%), Gaps = 2/187 (1%)
Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
           CQ    +L F  V W + +  F  L   DQ++LL+  W EL +   +  SI     +L+ 
Sbjct: 43  CQAADKQL-FTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLA 101
Query: 151 CEKARERLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
                 R       V     +++ E++++ R +  D +E GC++A++LF P++ GL +  
Sbjct: 102 TGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPA 161
Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
            VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF + IGD PI
Sbjct: 162 EVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPI 221
Query: 270 QRLLGDM 276
              L +M
Sbjct: 222 DTFLMEM 228

>pdb|1XLS|A Chain A, Crystal Structure Of The Mouse CarRXR LBD HETERODIMER Bound To Tcpobop And 9cra And A Tif2 Peptide Containg The Third Lxxll Motifs Length = 232

Iteration: 1
 Score = 61.2 bits (147), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 45/76 (59%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           ++ GL +   VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF
Sbjct: 153 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 212
Query: 344 KETIGDIPIQRLLGDM 359
            + IGD PI   L +M
Sbjct: 213 FKLIGDTPIDTFLMEM 228

>pdb|3OAP|A Chain A, Crystal Structure Of Human Retinoid X Receptor Alpha-Ligand Binding Domain Complex With 9-Cis Retinoic Acid And The Coactivator Peptide Grip-1 Length = 231

Iteration: 1
 Score =  108 bits (271), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 60/187 (32%), Positives = 98/187 (52%), Gaps = 2/187 (1%)
Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
           CQ    +L F  V W + +  F  L   DQ++LL+  W EL +   +  SI     +L+ 
Sbjct: 42  CQAADKQL-FTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLA 100
Query: 151 CEKARERLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
                 R       V     +++ E++++ R +  D +E GC++A++LF P++ GL +  
Sbjct: 101 TGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPA 160
Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
            VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF + IGD PI
Sbjct: 161 EVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPI 220
Query: 270 QRLLGDM 276
              L +M
Sbjct: 221 DTFLMEM 227

>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 = 61.2 bits (147), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 45/76 (59%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           ++ GL +   VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF
Sbjct: 152 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 211
Query: 344 KETIGDIPIQRLLGDM 359
            + IGD PI   L +M
Sbjct: 212 FKLIGDTPIDTFLMEM 227

>pdb|3H0A|A Chain A, Crystal Structure Of Peroxisome Proliferator-Activated Receptor Gamma (Pparg) And Retinoic Acid Receptor Alpha (Rxra) In Complex With 9-Cis Retinoic Acid, Co-Activator Peptide, And A Partial Agonist Length = 228

Iteration: 1
 Score =  108 bits (271), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 60/187 (32%), Positives = 98/187 (52%), Gaps = 2/187 (1%)
Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
           CQ    +L F  V W + +  F  L   DQ++LL+  W EL +   +  SI     +L+ 
Sbjct: 42  CQAADKQL-FTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLA 100
Query: 151 CEKARERLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
                 R       V     +++ E++++ R +  D +E GC++A++LF P++ GL +  
Sbjct: 101 TGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPA 160
Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
            VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF + IGD PI
Sbjct: 161 EVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPI 220
Query: 270 QRLLGDM 276
              L +M
Sbjct: 221 DTFLMEM 227

>pdb|3H0A|A Chain A, Crystal Structure Of Peroxisome Proliferator-Activated Receptor Gamma (Pparg) And Retinoic Acid Receptor Alpha (Rxra) In Complex With 9-Cis Retinoic Acid, Co-Activator Peptide, And A Partial Agonist Length = 228

Iteration: 1
 Score = 60.8 bits (146), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 45/76 (59%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           ++ GL +   VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF
Sbjct: 152 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 211
Query: 344 KETIGDIPIQRLLGDM 359
            + IGD PI   L +M
Sbjct: 212 FKLIGDTPIDTFLMEM 227

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

Iteration: 1
 Score =  108 bits (270), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 60/187 (32%), Positives = 98/187 (52%), Gaps = 2/187 (1%)
Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
           CQ    +L F  V W + +  F  L   DQ++LL+  W EL +   +  SI     +L+ 
Sbjct: 45  CQAADKQL-FTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASASHRSIAVKDGILLA 103
Query: 151 CEKARERLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
                 R       V     +++ E++++ R +  D +E GC++A++LF P++ GL +  
Sbjct: 104 TGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPA 163
Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
            VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF + IGD PI
Sbjct: 164 EVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPI 223
Query: 270 QRLLGDM 276
              L +M
Sbjct: 224 DTFLMEM 230

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

Iteration: 1
 Score = 61.2 bits (147), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 45/76 (59%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           ++ GL +   VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF
Sbjct: 155 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 214
Query: 344 KETIGDIPIQRLLGDM 359
            + IGD PI   L +M
Sbjct: 215 FKLIGDTPIDTFLMEM 230

>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 =  107 bits (268), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 59/192 (30%), Positives = 98/192 (51%), Gaps = 1/192 (0%)
Query: 93  ETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCE 152
           +   R L   V W + +  F +L   DQ++LL+  W EL +   +  SI    S+L+   
Sbjct: 65  KAADRQLVTLVEWAKRIPHFSSLPLEDQVILLRAGWNELLIASFSHRSIDVKDSILLASG 124
Query: 153 KARERLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPV 211
               R       V     +++ E++++ R +  D +E GC++AV+LF P+     D+  +
Sbjct: 125 LHVHRHSAHQAGVGPIFDRVLTELVSKMRDMMMDKTELGCLRAVVLFNPDVKNPSDSAHI 184
Query: 212 EMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQR 271
           E L+++    L  Y R +Y  QP RF +LLL LP+LR++    +E LFF + IGD PI +
Sbjct: 185 ESLREKVYASLEAYCRSKYPDQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDK 244
Query: 272 LLGDMYTMEKSY 283
            L +M      +
Sbjct: 245 FLMNMLETTSDF 256

>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 = 61.6 bits (148), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 29/77 (37%), Positives = 44/77 (57%)
Query: 290 DAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGD 349
           D+  +E L+++    L  Y R +Y  QP RF +LLL LP+LR++    +E LFF + IGD
Sbjct: 180 DSAHIESLREKVYASLEAYCRSKYPDQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGD 239
Query: 350 IPIQRLLGDMYTMEKSY 366
            PI + L +M      +
Sbjct: 240 TPIDKFLMNMLETTSDF 256

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

Iteration: 1
 Score =  105 bits (262), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 60/187 (32%), Positives = 98/187 (52%), Gaps = 2/187 (1%)
Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
           CQ    +L F  V W + +  F +L   DQ++LL+  W EL +   +  SI     +L+ 
Sbjct: 43  CQAADKQL-FTLVEWAKRIPHFSSLPLDDQVILLRAGWNELLIASFSHRSIDVRDGILLA 101
Query: 151 CEKARERLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
                 R       V     +++ E++++ R +  D +E GC++A+ILF P+  GL +  
Sbjct: 102 TGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMRMDKTELGCLRAIILFNPDAKGLSNPS 161
Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
            VE+L+++    L  Y + +Y  Q  RF +LLL LP+LR++    +E LFF + IGD PI
Sbjct: 162 EVEVLREKVYASLETYCKQKYPEQQGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPI 221
Query: 270 QRLLGDM 276
              L +M
Sbjct: 222 DTFLMEM 228

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

Iteration: 1
 Score = 57.8 bits (138), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 29/76 (38%), Positives = 44/76 (57%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           +  GL +   VE+L+++    L  Y + +Y  Q  RF +LLL LP+LR++    +E LFF
Sbjct: 153 DAKGLSNPSEVEVLREKVYASLETYCKQKYPEQQGRFAKLLLRLPALRSIGLKCLEHLFF 212
Query: 344 KETIGDIPIQRLLGDM 359
            + IGD PI   L +M
Sbjct: 213 FKLIGDTPIDTFLMEM 228

>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 =  103 bits (258), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 59/184 (32%), Positives = 96/184 (52%), Gaps = 2/184 (1%)
Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
           CQ    +L F  V W + +  F +L   DQ++LL+  W EL +   +  SI     +L+ 
Sbjct: 42  CQAADKQL-FTLVEWAKRIPHFSSLPLDDQVILLRAGWNELLIASFSHRSIDVRDGILLA 100
Query: 151 CEKARERLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
                 R       V     +++ E++++ R +  D +E GC++A+ILF P+  GL +  
Sbjct: 101 TGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMRMDKTELGCLRAIILFNPDAKGLSNPS 160
Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
            VE+L+++    L  Y + +Y  Q  RF +LLL LP+LR++    +E LFF + IGD PI
Sbjct: 161 EVEVLREKVYASLETYCKQKYPEQQGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPI 220
Query: 270 QRLL 273
              L
Sbjct: 221 DTFL 224

>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 = 55.8 bits (133), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 28/73 (38%), Positives = 42/73 (57%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           +  GL +   VE+L+++    L  Y + +Y  Q  RF +LLL LP+LR++    +E LFF
Sbjct: 152 DAKGLSNPSEVEVLREKVYASLETYCKQKYPEQQGRFAKLLLRLPALRSIGLKCLEHLFF 211
Query: 344 KETIGDIPIQRLL 356
            + IGD PI   L
Sbjct: 212 FKLIGDTPIDTFL 224

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

Iteration: 1
 Score =  102 bits (254), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 57/187 (30%), Positives = 96/187 (51%), Gaps = 2/187 (1%)
Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
           CQ    R L+  + W + +  F  L   DQ++LL+  W EL +   +  S+     +++ 
Sbjct: 70  CQ-AADRQLYQLIEWAKHIPHFTELPVEDQVILLKSGWNELLIAGFSHRSMSVKDGIMLA 128
Query: 151 CEKARERLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
                 R       V     +++ E++A+ R++  D +E GC+++++LF PE  GL   Q
Sbjct: 129 TGLVVHRNCAHQAGVGAIFDRVLTELVAKMREMKMDKTELGCLRSIVLFNPEAKGLKSTQ 188
Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
            VE L+++   IL +Y R  Y  Q  RF +LLL LP+LR++    +E LFF + +G+  I
Sbjct: 189 QVENLREKVYAILEEYCRQTYPDQSGRFAKLLLRLPALRSIGLKCLEHLFFFKLVGNTSI 248
Query: 270 QRLLGDM 276
              L  M
Sbjct: 249 DSFLLSM 255

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

Iteration: 1
 Score = 57.0 bits (136), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 42/76 (55%)
Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           E  GL   Q VE L+++   IL +Y R  Y  Q  RF +LLL LP+LR++    +E LFF
Sbjct: 180 EAKGLKSTQQVENLREKVYAILEEYCRQTYPDQSGRFAKLLLRLPALRSIGLKCLEHLFF 239
Query: 344 KETIGDIPIQRLLGDM 359
            + +G+  I   L  M
Sbjct: 240 FKLVGNTSIDSFLLSM 255

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

Iteration: 1
 Score =  102 bits (254), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 64/188 (34%), Positives = 93/188 (49%), Gaps = 15/188 (7%)
Query: 99  LFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLL--------HLAQWSIPWDLSLLIN 150
           LF  V W R    F+ L   DQ+ LLQ  W EL +L        H  + +I      L+ 
Sbjct: 60  LFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVAHGKEGTI-----FLVT 114
Query: 151 CEKARER--LPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDA 208
            E       +   +V  NN + L QE++ R R L  D  E  C+K ++LF+ +   L + 
Sbjct: 115 GEHVDYSTIISHTEVAFNNLLSLAQELVVRLRSLQFDQREFVCLKFLVLFSSDVKNLENL 174
Query: 209 QPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIP 268
           Q VE +Q+Q    L DY    Y +Q  +FG+LLL LP LRA+ +   + L++K   GD+P
Sbjct: 175 QLVEGVQEQVNAALLDYTVCNYPQQTEKFGQLLLRLPELRAISKQAEDYLYYKHVNGDVP 234
Query: 269 IQRLLGDM 276
              LL +M
Sbjct: 235 YNNLLIEM 242

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

Iteration: 1
 Score = 59.3 bits (142), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 30/78 (38%), Positives = 44/78 (56%)
Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
           S +   L + Q VE +Q+Q    L DY    Y +Q  +FG+LLL LP LRA+ +   + L
Sbjct: 165 SSDVKNLENLQLVEGVQEQVNAALLDYTVCNYPQQTEKFGQLLLRLPELRAISKQAEDYL 224
Query: 342 FFKETIGDIPIQRLLGDM 359
           ++K   GD+P   LL +M
Sbjct: 225 YYKHVNGDVPYNNLLIEM 242

>pdb|1ZH7|A Chain A, Structural And Biochemical Basis For Selective Repression Of The Orphan Nuclear Receptor Lrh-1 By Shp Length = 243

Iteration: 1
 Score =  101 bits (251), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 63/188 (33%), Positives = 93/188 (49%), Gaps = 15/188 (7%)
Query: 99  LFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLL--------HLAQWSIPWDLSLLIN 150
           LF  V W R    F+ L   DQ+ LLQ  W EL +L        H  + +I      L+ 
Sbjct: 55  LFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVAHGKEGTI-----FLVT 109
Query: 151 CEKARER--LPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDA 208
            E       +   +V  NN + L QE++ R R L  D  E  C+K ++LF+ +   L + 
Sbjct: 110 GEHVDYSTIISHTEVAFNNLLSLAQELVVRLRSLQFDQREFVCLKFLVLFSSDVKNLENL 169
Query: 209 QPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIP 268
           Q VE +Q+Q    L DY    Y +Q  +FG+LLL LP +RA+ +   + L++K   GD+P
Sbjct: 170 QLVEGVQEQVNAALLDYTVCNYPQQTEKFGQLLLRLPEIRAISKQAEDYLYYKHVNGDVP 229
Query: 269 IQRLLGDM 276
              LL +M
Sbjct: 230 YNNLLIEM 237

>pdb|1ZH7|A Chain A, Structural And Biochemical Basis For Selective Repression Of The Orphan Nuclear Receptor Lrh-1 By Shp Length = 243

Iteration: 1
 Score = 58.2 bits (139), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 29/78 (37%), Positives = 44/78 (56%)
Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
           S +   L + Q VE +Q+Q    L DY    Y +Q  +FG+LLL LP +RA+ +   + L
Sbjct: 160 SSDVKNLENLQLVEGVQEQVNAALLDYTVCNYPQQTEKFGQLLLRLPEIRAISKQAEDYL 219
Query: 342 FFKETIGDIPIQRLLGDM 359
           ++K   GD+P   LL +M
Sbjct: 220 YYKHVNGDVPYNNLLIEM 237

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

Iteration: 1
 Score = 99.0 bits (245), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 62/188 (32%), Positives = 92/188 (48%), Gaps = 15/188 (7%)
Query: 99  LFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLL--------HLAQWSIPWDLSLLIN 150
           LF  V W R    F+ L   DQ+ LLQ  W EL +L        H  + SI      L+ 
Sbjct: 164 LFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSI-----FLVT 218
Query: 151 CEKARERLPPDDV--RVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDA 208
            ++    +        +NN +   QE++A+ R L  D  E  C+K ++LF+ +   L + 
Sbjct: 219 GQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENF 278
Query: 209 QPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIP 268
           Q VE +Q+Q    L DY    Y +Q  +FG+LLL LP +RA+     E L++K   GD+P
Sbjct: 279 QLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVP 338
Query: 269 IQRLLGDM 276
              LL +M
Sbjct: 339 YNNLLIEM 346

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 30/78 (38%), Positives = 43/78 (55%)
Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
           S +   L + Q VE +Q+Q    L DY    Y +Q  +FG+LLL LP +RA+     E L
Sbjct: 269 SLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYL 328
Query: 342 FFKETIGDIPIQRLLGDM 359
           ++K   GD+P   LL +M
Sbjct: 329 YYKHLNGDVPYNNLLIEM 346

>pdb|1YUC|A Chain A, Human Nuclear Receptor Liver Receptor Homologue-1, Lrh-1, Bound To Phospholipid And A Fragment Of Human Shp Length = 255

Iteration: 1
 Score = 97.4 bits (241), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 62/188 (32%), Positives = 92/188 (48%), Gaps = 15/188 (7%)
Query: 99  LFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLL--------HLAQWSIPWDLSLLIN 150
           LF  V W R    F+ L   DQ+ LLQ  W EL +L        H  + SI      L+ 
Sbjct: 67  LFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSI-----FLVT 121
Query: 151 CEKARERLPPDDV--RVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDA 208
            ++    +        +NN +   QE++A+ R L  D  E  C+K ++LF+ +   L + 
Sbjct: 122 GQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENF 181
Query: 209 QPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIP 268
           Q VE +Q+Q    L DY    Y +Q  +FG+LLL LP +RA+     E L++K   GD+P
Sbjct: 182 QLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVP 241
Query: 269 IQRLLGDM 276
              LL +M
Sbjct: 242 YNNLLIEM 249

>pdb|1YUC|A Chain A, Human Nuclear Receptor Liver Receptor Homologue-1, Lrh-1, Bound To Phospholipid And A Fragment Of Human Shp Length = 255

Iteration: 1
 Score = 58.5 bits (140), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 30/78 (38%), Positives = 43/78 (55%)
Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
           S +   L + Q VE +Q+Q    L DY    Y +Q  +FG+LLL LP +RA+     E L
Sbjct: 172 SLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYL 231
Query: 342 FFKETIGDIPIQRLLGDM 359
           ++K   GD+P   LL +M
Sbjct: 232 YYKHLNGDVPYNNLLIEM 249

>pdb|4DOS|A Chain A, Human Nuclear Receptor Liver Receptor Homologue-1, Lrh-1, Bound To Dlpc And A Fragment Of Tif-2 Length = 242

Iteration: 1
 Score = 97.1 bits (240), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 62/188 (32%), Positives = 92/188 (48%), Gaps = 15/188 (7%)
Query: 99  LFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLL--------HLAQWSIPWDLSLLIN 150
           LF  V W R    F+ L   DQ+ LLQ  W EL +L        H  + SI      L+ 
Sbjct: 57  LFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSI-----FLVT 111
Query: 151 CEKARERLPPDDV--RVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDA 208
            ++    +        +NN +   QE++A+ R L  D  E  C+K ++LF+ +   L + 
Sbjct: 112 GQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENF 171
Query: 209 QPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIP 268
           Q VE +Q+Q    L DY    Y +Q  +FG+LLL LP +RA+     E L++K   GD+P
Sbjct: 172 QLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVP 231
Query: 269 IQRLLGDM 276
              LL +M
Sbjct: 232 YNNLLIEM 239

>pdb|4DOS|A Chain A, Human Nuclear Receptor Liver Receptor Homologue-1, Lrh-1, Bound To Dlpc And A Fragment Of Tif-2 Length = 242

Iteration: 1
 Score = 58.5 bits (140), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 30/78 (38%), Positives = 43/78 (55%)
Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
           S +   L + Q VE +Q+Q    L DY    Y +Q  +FG+LLL LP +RA+     E L
Sbjct: 162 SLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYL 221
Query: 342 FFKETIGDIPIQRLLGDM 359
           ++K   GD+P   LL +M
Sbjct: 222 YYKHLNGDVPYNNLLIEM 239

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

Iteration: 1
 Score = 97.1 bits (240), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 62/188 (32%), Positives = 92/188 (48%), Gaps = 15/188 (7%)
Query: 99  LFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLL--------HLAQWSIPWDLSLLIN 150
           LF  V W R    F+ L   DQ+ LLQ  W EL +L        H  + SI      L+ 
Sbjct: 57  LFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSI-----FLVT 111
Query: 151 CEKARERLPPDDV--RVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDA 208
            ++    +        +NN +   QE++A+ R L  D  E  C+K ++LF+ +   L + 
Sbjct: 112 GQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENF 171
Query: 209 QPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIP 268
           Q VE +Q+Q    L DY    Y +Q  +FG+LLL LP +RA+     E L++K   GD+P
Sbjct: 172 QLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVP 231
Query: 269 IQRLLGDM 276
              LL +M
Sbjct: 232 YNNLLIEM 239

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 30/78 (38%), Positives = 43/78 (55%)
Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
           S +   L + Q VE +Q+Q    L DY    Y +Q  +FG+LLL LP +RA+     E L
Sbjct: 162 SLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYL 221
Query: 342 FFKETIGDIPIQRLLGDM 359
           ++K   GD+P   LL +M
Sbjct: 222 YYKHLNGDVPYNNLLIEM 239

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

Iteration: 1
 Score = 96.7 bits (239), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 62/188 (32%), Positives = 92/188 (48%), Gaps = 15/188 (7%)
Query: 99  LFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLL--------HLAQWSIPWDLSLLIN 150
           LF  V W R    F+ L   DQ+ LLQ  W EL +L        H  + SI      L+ 
Sbjct: 69  LFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSI-----FLVT 123
Query: 151 CEKARERLPPDDV--RVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDA 208
            ++    +        +NN +   QE++A+ R L  D  E  C+K ++LF+ +   L + 
Sbjct: 124 GQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENF 183
Query: 209 QPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIP 268
           Q VE +Q+Q    L DY    Y +Q  +FG+LLL LP +RA+     E L++K   GD+P
Sbjct: 184 QLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVP 243
Query: 269 IQRLLGDM 276
              LL +M
Sbjct: 244 YNNLLIEM 251

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

Iteration: 1
 Score = 58.2 bits (139), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 30/78 (38%), Positives = 43/78 (55%)
Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
           S +   L + Q VE +Q+Q    L DY    Y +Q  +FG+LLL LP +RA+     E L
Sbjct: 174 SLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYL 233
Query: 342 FFKETIGDIPIQRLLGDM 359
           ++K   GD+P   LL +M
Sbjct: 234 YYKHLNGDVPYNNLLIEM 251

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

Iteration: 1
 Score = 96.7 bits (239), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 62/188 (32%), Positives = 92/188 (48%), Gaps = 15/188 (7%)
Query: 99  LFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLL--------HLAQWSIPWDLSLLIN 150
           LF  V W R    F+ L   DQ+ LLQ  W EL +L        H  + SI      L+ 
Sbjct: 68  LFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSI-----FLVT 122
Query: 151 CEKARERLPPDDV--RVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDA 208
            ++    +        +NN +   QE++A+ R L  D  E  C+K ++LF+ +   L + 
Sbjct: 123 GQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENF 182
Query: 209 QPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIP 268
           Q VE +Q+Q    L DY    Y +Q  +FG+LLL LP +RA+     E L++K   GD+P
Sbjct: 183 QLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVP 242
Query: 269 IQRLLGDM 276
              LL +M
Sbjct: 243 YNNLLIEM 250

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 30/78 (38%), Positives = 43/78 (55%)
Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
           S +   L + Q VE +Q+Q    L DY    Y +Q  +FG+LLL LP +RA+     E L
Sbjct: 173 SLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYL 232
Query: 342 FFKETIGDIPIQRLLGDM 359
           ++K   GD+P   LL +M
Sbjct: 233 YYKHLNGDVPYNNLLIEM 250

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

Iteration: 1
 Score = 82.0 bits (201), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 59/197 (29%), Positives = 100/197 (50%), Gaps = 2/197 (1%)
Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
           C+    +LL + V W + +  F  L   DQ+ LL+    E  LL   + S+ +   LL+ 
Sbjct: 47  CESMKEQLLVL-VEWAKYIPAFCELLLDDQVALLRAHAGEHLLLGATKRSMVFKDVLLLG 105
Query: 151 CEKARERLPPDDVRVNN-EIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
            +    R  P+   ++   I+++ E++  F++L  D +E  C+KA+I F P+  GL D  
Sbjct: 106 NDYIVPRHCPELAEMSRVSIRILDELVLPFQELQIDDNEYACLKAIIFFDPDAKGLSDPG 165
Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
            ++ L+ Q Q  L DY+  R      RFG LLL+LP+L+++    IE++ F +  G   I
Sbjct: 166 KIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFIKLFGMAKI 225
Query: 270 QRLLGDMYTMEKSYETP 286
             LL +M     + + P
Sbjct: 226 DNLLQEMLLGGSASDAP 242

>pdb|1PZL|A Chain A, Crystal Structure Of Hnf4a Lbd In Complex With The Ligand And The Coactivator Src-1 Peptide Length = 237

Iteration: 1
 Score = 77.0 bits (188), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 58/190 (30%), Positives = 98/190 (51%), Gaps = 2/190 (1%)
Query: 88  AEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSL 147
           A+ C+    +LL + V W + +  F  L   DQ+ LL+    E  LL   + S+ +   L
Sbjct: 44  ADVCESMKEQLLVL-VEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVL 102
Query: 148 LINCEKARERLPPDDVRVNN-EIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLV 206
           L+  +    R  P+   ++   I+++ E++  F++L  D +E   +KA+I F P+  GL 
Sbjct: 103 LLGNDYIVPRHCPELAEMSRVSIRILDELVLPFQELQIDDNEYAYLKAIIFFDPDAKGLS 162
Query: 207 DAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGD 266
           D   ++ L+ Q Q  L DY+  R      RFG LLL+LP+L+++    IE++ F +  G 
Sbjct: 163 DPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFIKLFGM 222
Query: 267 IPIQRLLGDM 276
             I  LL +M
Sbjct: 223 AKIDNLLQEM 232

>pdb|3FS1|A Chain A, Crystal Structure Of Hnf4a Lbd In Complex With The Ligand And The Coactivator Pgc-1a Fragment Length = 230

Iteration: 1
 Score = 77.0 bits (188), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 58/190 (30%), Positives = 98/190 (51%), Gaps = 2/190 (1%)
Query: 88  AEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSL 147
           A+ C+    +LL + V W + +  F  L   DQ+ LL+    E  LL   + S+ +   L
Sbjct: 38  ADVCESMKEQLLVL-VEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVL 96
Query: 148 LINCEKARERLPPDDVRVNN-EIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLV 206
           L+  +    R  P+   ++   I+++ E++  F++L  D +E   +KA+I F P+  GL 
Sbjct: 97  LLGNDYIVPRHCPELAEMSRVSIRILDELVLPFQELQIDDNEYAYLKAIIFFDPDAKGLS 156
Query: 207 DAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGD 266
           D   ++ L+ Q Q  L DY+  R      RFG LLL+LP+L+++    IE++ F +  G 
Sbjct: 157 DPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFIKLFGM 216
Query: 267 IPIQRLLGDM 276
             I  LL +M
Sbjct: 217 AKIDNLLQEM 226

>pdb|1VJB|A Chain A, Crystal Structure Of The Ligand-Binding Domain Of The Estrogen-Related Receptor Gamma In Complex With 4- Hydroxytamoxifen Length = 251

Iteration: 1
 Score = 75.5 bits (184), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 47/187 (25%), Positives = 93/187 (49%), Gaps = 14/187 (7%)
Query: 97  RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE 156
           R L + + W + +  F TLS  DQ+ LLQ +W E+ +L +   S+ ++  L+     A +
Sbjct: 67  RELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDELVY----ADD 122
Query: 157 RLPPDD-------VRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
            +  +D       + +NN I    +++ +++ +  +  E   +KA+ L   ++  + D +
Sbjct: 123 YIMDEDQSKLAGLLDLNNAI---LQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVE 179
Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
            V+ LQD     L DY  G++   P R G++L+ LP LR      ++  +  +  G +P+
Sbjct: 180 AVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPM 239
Query: 270 QRLLGDM 276
            +L  +M
Sbjct: 240 HKLFLEM 246

>pdb|1VJB|A Chain A, Crystal Structure Of The Ligand-Binding Domain Of The Estrogen-Related Receptor Gamma In Complex With 4- Hydroxytamoxifen Length = 251

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/70 (30%), Positives = 36/70 (51%)
Query: 290 DAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGD 349
           D + V+ LQD     L DY  G++   P R G++L+ LP LR      ++  +  +  G 
Sbjct: 177 DVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGK 236
Query: 350 IPIQRLLGDM 359
           +P+ +L  +M
Sbjct: 237 VPMHKLFLEM 246

>pdb|1S9Q|A Chain A, Crystal Structure Of The Ligand-Binding Domain Of The Estrogen-Related Receptor Gamma In Complex With 4-Hydroxytamoxifen Length = 251

Iteration: 1
 Score = 75.5 bits (184), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 47/187 (25%), Positives = 93/187 (49%), Gaps = 14/187 (7%)
Query: 97  RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE 156
           R L + + W + +  F TLS  DQ+ LLQ +W E+ +L +   S+ ++  L+     A +
Sbjct: 67  RELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDELVY----ADD 122
Query: 157 RLPPDD-------VRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
            +  +D       + +NN I    +++ +++ +  +  E   +KA+ L   ++  + D +
Sbjct: 123 YIMDEDQSKLAGLLDLNNAI---LQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVE 179
Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
            V+ LQD     L DY  G++   P R G++L+ LP LR      ++  +  +  G +P+
Sbjct: 180 AVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPM 239
Query: 270 QRLLGDM 276
            +L  +M
Sbjct: 240 HKLFLEM 246

>pdb|1S9Q|A Chain A, Crystal Structure Of The Ligand-Binding Domain Of The Estrogen-Related Receptor Gamma In Complex With 4-Hydroxytamoxifen Length = 251

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/70 (30%), Positives = 36/70 (51%)
Query: 290 DAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGD 349
           D + V+ LQD     L DY  G++   P R G++L+ LP LR      ++  +  +  G 
Sbjct: 177 DVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGK 236
Query: 350 IPIQRLLGDM 359
           +P+ +L  +M
Sbjct: 237 VPMHKLFLEM 246

>pdb|1KV6|A Chain A, X-Ray Structure Of The Orphan Nuclear Receptor Err3 Ligand- Binding Domain In The Constitutively Active Conformation Length = 230

Iteration: 1
 Score = 75.5 bits (184), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 47/187 (25%), Positives = 93/187 (49%), Gaps = 14/187 (7%)
Query: 97  RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE 156
           R L + + W + +  F TLS  DQ+ LLQ +W E+ +L +   S+ ++  L+     A +
Sbjct: 46  RELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDELVY----ADD 101
Query: 157 RLPPDD-------VRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
            +  +D       + +NN I    +++ +++ +  +  E   +KA+ L   ++  + D +
Sbjct: 102 YIMDEDQSKLAGLLDLNNAI---LQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVE 158
Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
            V+ LQD     L DY  G++   P R G++L+ LP LR      ++  +  +  G +P+
Sbjct: 159 AVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPM 218
Query: 270 QRLLGDM 276
            +L  +M
Sbjct: 219 HKLFLEM 225

>pdb|1KV6|A Chain A, X-Ray Structure Of The Orphan Nuclear Receptor Err3 Ligand- Binding Domain In The Constitutively Active Conformation Length = 230

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/70 (30%), Positives = 36/70 (51%)
Query: 290 DAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGD 349
           D + V+ LQD     L DY  G++   P R G++L+ LP LR      ++  +  +  G 
Sbjct: 156 DVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGK 215
Query: 350 IPIQRLLGDM 359
           +P+ +L  +M
Sbjct: 216 VPMHKLFLEM 225

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

Iteration: 1
 Score = 75.1 bits (183), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 57/191 (29%), Positives = 98/191 (51%), Gaps = 5/191 (2%)
Query: 88  AEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSL 147
            + C+    +LL + V W + +  F  L   DQ+ LL+    E  LL   + S+ +   L
Sbjct: 38  GDVCESMKQQLLVL-VEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMMYKDIL 96
Query: 148 LI--NCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGL 205
           L+  N    R     +  RV N  +++ E++  F+++  D +E  C+KA++ F P+  GL
Sbjct: 97  LLGNNYVIHRNSCEVEISRVAN--RVLDELVRPFQEIQIDDNEYACLKAIVFFDPDAKGL 154
Query: 206 VDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIG 265
            D   ++ ++ Q Q  L DY+  R      RFG LLL+LP+L+++    IE++ F +  G
Sbjct: 155 SDPVKIKNMRFQVQIGLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFVKLFG 214
Query: 266 DIPIQRLLGDM 276
            + I  LL +M
Sbjct: 215 MVKIDNLLQEM 225

>pdb|1S9P|A Chain A, Crystal Structure Of The Ligand-Binding Domain Of The Estrogen-Related Receptor Gamma In Complex With Diethylstilbestrol Length = 227

Iteration: 1
 Score = 75.1 bits (183), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 47/187 (25%), Positives = 93/187 (49%), Gaps = 14/187 (7%)
Query: 97  RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE 156
           R L + + W + +  F TLS  DQ+ LLQ +W E+ +L +   S+ ++  L+     A +
Sbjct: 43  RELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDELVY----ADD 98
Query: 157 RLPPDD-------VRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
            +  +D       + +NN I    +++ +++ +  +  E   +KA+ L   ++  + D +
Sbjct: 99  YIMDEDQSKLAGLLDLNNAI---LQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVE 155
Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
            V+ LQD     L DY  G++   P R G++L+ LP LR      ++  +  +  G +P+
Sbjct: 156 AVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPM 215
Query: 270 QRLLGDM 276
            +L  +M
Sbjct: 216 HKLFLEM 222

>pdb|1S9P|A Chain A, Crystal Structure Of The Ligand-Binding Domain Of The Estrogen-Related Receptor Gamma In Complex With Diethylstilbestrol Length = 227

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/70 (30%), Positives = 36/70 (51%)
Query: 290 DAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGD 349
           D + V+ LQD     L DY  G++   P R G++L+ LP LR      ++  +  +  G 
Sbjct: 153 DVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGK 212
Query: 350 IPIQRLLGDM 359
           +P+ +L  +M
Sbjct: 213 VPMHKLFLEM 222

>pdb|2EWP|A Chain A, Crystal Structure Of Estrogen Related Receptor-3 (Err-Gamma) Ligand Binding Domaind With Tamoxifen Analog Gsk5182 Length = 226

Iteration: 1
 Score = 75.1 bits (183), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 47/187 (25%), Positives = 93/187 (49%), Gaps = 14/187 (7%)
Query: 97  RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE 156
           R L + + W + +  F TLS  DQ+ LLQ +W E+ +L +   S+ ++  L+     A +
Sbjct: 42  RELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDELVY----ADD 97
Query: 157 RLPPDD-------VRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
            +  +D       + +NN I    +++ +++ +  +  E   +KA+ L   ++  + D +
Sbjct: 98  YIMDEDQSKLAGLLDLNNAI---LQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVE 154
Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
            V+ LQD     L DY  G++   P R G++L+ LP LR      ++  +  +  G +P+
Sbjct: 155 AVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPM 214
Query: 270 QRLLGDM 276
            +L  +M
Sbjct: 215 HKLFLEM 221

>pdb|2EWP|A Chain A, Crystal Structure Of Estrogen Related Receptor-3 (Err-Gamma) Ligand Binding Domaind With Tamoxifen Analog Gsk5182 Length = 226

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/70 (30%), Positives = 36/70 (51%)
Query: 290 DAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGD 349
           D + V+ LQD     L DY  G++   P R G++L+ LP LR      ++  +  +  G 
Sbjct: 152 DVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGK 211
Query: 350 IPIQRLLGDM 359
           +P+ +L  +M
Sbjct: 212 VPMHKLFLEM 221

>pdb|2E2R|A Chain A, Crystal Structure Of Human Estrogen-Related Receptor Gamma Ligand Binding Domain Complex With Bisphenol A Length = 244

Iteration: 1
 Score = 75.1 bits (183), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 47/187 (25%), Positives = 93/187 (49%), Gaps = 14/187 (7%)
Query: 97  RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE 156
           R L + + W + +  F TLS  DQ+ LLQ +W E+ +L +   S+ ++  L+     A +
Sbjct: 59  RELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDELVY----ADD 114
Query: 157 RLPPDD-------VRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
            +  +D       + +NN I    +++ +++ +  +  E   +KA+ L   ++  + D +
Sbjct: 115 YIMDEDQSKLAGLLDLNNAI---LQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVE 171
Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
            V+ LQD     L DY  G++   P R G++L+ LP LR      ++  +  +  G +P+
Sbjct: 172 AVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPM 231
Query: 270 QRLLGDM 276
            +L  +M
Sbjct: 232 HKLFLEM 238

>pdb|2E2R|A Chain A, Crystal Structure Of Human Estrogen-Related Receptor Gamma Ligand Binding Domain Complex With Bisphenol A Length = 244

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/70 (30%), Positives = 36/70 (51%)
Query: 290 DAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGD 349
           D + V+ LQD     L DY  G++   P R G++L+ LP LR      ++  +  +  G 
Sbjct: 169 DVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGK 228
Query: 350 IPIQRLLGDM 359
           +P+ +L  +M
Sbjct: 229 VPMHKLFLEM 238

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

Iteration: 1
 Score = 65.1 bits (157), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 50/206 (24%), Positives = 90/206 (43%), Gaps = 29/206 (14%)
Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSI--------- 141
           CQ    + LF  V + R +  F  +   DQ++LL+ +W EL + ++A  SI         
Sbjct: 53  CQ-VVNKQLFQMVEYARMMPHFAQVPLDDQVILLKAAWIELLIANVAWCSIVSLDDGGAG 111
Query: 142 --PWDLSLLINCEKARERLPPDDVRVNNEI-----------------KLIQEILARFRQL 182
                L    + E+    L P  + +N                    +++ E+  + ++L
Sbjct: 112 GGGGGLGHDGSFERRSPGLQPQQLFLNQSFSYHRNSAIKAGVSAIFDRILSELSVKMKRL 171
Query: 183 SPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLL 242
           + D  E  C+KA+IL+ P+  G+     +EM +++    L ++ R  +     RF +LLL
Sbjct: 172 NLDRRELSCLKAIILYNPDIRGIKSRAEIEMCREKVYACLDEHCRLEHPGDDGRFAQLLL 231
Query: 243 MLPSLRAVRQSTIERLFFKETIGDIP 268
            LP+LR++     + LF      D P
Sbjct: 232 RLPALRSISLKCQDHLFLFRITSDRP 257

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

Iteration: 1
 Score = 65.1 bits (157), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 52/181 (28%), Positives = 83/181 (45%), Gaps = 9/181 (4%)
Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPW---DLSLLINCEKARERLP 159
           V W R    F+ L   DQ+ LLQ SW EL +L      + +   D  LL+  ++    L 
Sbjct: 60  VDWARRCMVFKELEVADQMTLLQNSWSELLVLDHIYRQVQYGKEDSILLVTGQEVE--LS 117
Query: 160 PDDVRVNNEIKLI----QEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQ 215
              V+  + +  +    QE++ +   L  D  E  C+K +ILF+ +   L +   V+  Q
Sbjct: 118 TVAVQAGSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILFSLDVKFLNNHSLVKDAQ 177
Query: 216 DQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGD 275
           ++A   L DY    Y     +F +LLL L  +RA+     E L+ K    ++P   LL +
Sbjct: 178 EKANAALLDYTLSHYPHSGDKFQQLLLSLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIE 237
Query: 276 M 276
           M
Sbjct: 238 M 238

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

Iteration: 1
 Score = 64.7 bits (156), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 52/181 (28%), Positives = 83/181 (45%), Gaps = 9/181 (4%)
Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPW---DLSLLINCEKARERLP 159
           V W R    F+ L   DQ+ LLQ SW EL +L      + +   D  LL+  ++    L 
Sbjct: 62  VDWARRCMVFKELEVADQMTLLQNSWSELLVLDHIYRQVQYGKEDSILLVTGQEVE--LS 119
Query: 160 PDDVRVNNEIKLI----QEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQ 215
              V+  + +  +    QE++ +   L  D  E  C+K +ILF+ +   L +   V+  Q
Sbjct: 120 TVAVQAGSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILFSLDVKFLNNHSLVKDAQ 179
Query: 216 DQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGD 275
           ++A   L DY    Y     +F +LLL L  +RA+     E L+ K    ++P   LL +
Sbjct: 180 EKANAALLDYTLSHYPHSGDKFQQLLLSLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIE 239
Query: 276 M 276
           M
Sbjct: 240 M 240

>pdb|1R1K|A Chain A, Crystal Structure Of The Ligand-Binding Domains Of The Heterodimer EcrUSP BOUND TO PONASTERONE A Length = 263

Iteration: 1
 Score = 63.9 bits (154), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 57/204 (27%), Positives = 94/204 (46%), Gaps = 20/204 (9%)
Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
           CQ    ++  + V W R +  F  L   DQ+LL++ SW EL L  +A  S+ +       
Sbjct: 47  CQIGNKQIAALVV-WARDIPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLTEERDG 105
Query: 151 CEKARER----------LPPDDVRVNNEI---------KLIQEILARFRQLSPDGSECGC 191
            +    R          +P   +  N+ +         +++ E+  + R L  D +E   
Sbjct: 106 VDGTGNRTTSPPQLMCLMPGMTLHRNSALQAGVGQIFDRVLSELSLKMRTLRVDQAEYVA 165
Query: 192 MKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVR 251
           +KA+IL  P+  GL + Q VE+L+++    L +Y R   S +  RF  LLL LP+LR++ 
Sbjct: 166 LKAIILLNPDVKGLKNRQEVEVLREKMFLCLDEYCRRSRSSEEGRFAALLLRLPALRSIS 225
Query: 252 QSTIERLFFKETIGDIPIQRLLGD 275
             + E LFF   + D  I   + D
Sbjct: 226 LKSFEHLFFFHLVADTSIAGYIRD 249

>pdb|1G2N|A Chain A, Crystal Structure Of The Ligand Binding Domain Of The Ultraspiracle Protein Usp, The Ortholog Of Rxrs In Insects Length = 264

Iteration: 1
 Score = 63.9 bits (154), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 57/204 (27%), Positives = 94/204 (46%), Gaps = 20/204 (9%)
Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
           CQ    ++  + V W R +  F  L   DQ+LL++ SW EL L  +A  S+ +       
Sbjct: 48  CQIGNKQIAALVV-WARDIPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLTEERDG 106
Query: 151 CEKARER----------LPPDDVRVNNEI---------KLIQEILARFRQLSPDGSECGC 191
            +    R          +P   +  N+ +         +++ E+  + R L  D +E   
Sbjct: 107 VDGTGNRTTSPPQLMCLMPGMTLHRNSALQAGVGQIFDRVLSELSLKMRTLRVDQAEYVA 166
Query: 192 MKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVR 251
           +KA+IL  P+  GL + Q VE+L+++    L +Y R   S +  RF  LLL LP+LR++ 
Sbjct: 167 LKAIILLNPDVKGLKNRQEVEVLREKMFLCLDEYCRRSRSSEEGRFAALLLRLPALRSIS 226
Query: 252 QSTIERLFFKETIGDIPIQRLLGD 275
             + E LFF   + D  I   + D
Sbjct: 227 LKSFEHLFFFHLVADTSIAGYIRD 250

>pdb|2XHS|A Chain A, Crystal Structure Of The Ligand Binding Domain Of Fushi Tarazu Factor 1 Of Drosophila Melanogaster Length = 245

Iteration: 1
 Score = 60.1 bits (144), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 51/191 (26%), Positives = 73/191 (38%), Gaps = 30/191 (15%)
Query: 99  LFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERL 158
           LF  V W R    F+ L   DQ  LLQ SW +  +L      I   L             
Sbjct: 59  LFSQVDWARNTVFFKDLKVDDQXKLLQHSWSDXLVLDHLHHRIHNGL------------- 105
Query: 159 PPDDVRVNN-------EIKLI---------QEILARFRQLSPDGSECGCMKAVILFTPET 202
            PD+ ++NN        + L+          E+  + + L  D  +  C K +IL  P  
Sbjct: 106 -PDETQLNNGQVFNLXSLGLLGVPQLGDYFNELQNKLQDLKFDXGDYVCXKFLILLNPSV 164
Query: 203 PGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKE 262
            G+V+ + V    D  Q  L DY    Y     +F  L+ +LP + A      + L+ K 
Sbjct: 165 RGIVNRKTVSEGHDNVQAALLDYTLTCYPSVNDKFRGLVNILPEIHAXAVRGEDHLYTKH 224
Query: 263 TIGDIPIQRLL 273
             G  P Q LL
Sbjct: 225 CAGSAPTQTLL 235

>pdb|1YP0|A Chain A, Structure Of The Steroidogenic Factor-1 Ligand Binding Domain Bound To Phospholipid And A Shp Peptide Motif Length = 239

Iteration: 1
 Score = 59.7 bits (143), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 51/181 (28%), Positives = 82/181 (45%), Gaps = 9/181 (4%)
Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPW---DLSLLINCEKARERLP 159
           V W R    F+ L   DQ+ LLQ  W EL +L      + +   D  LL+  ++    L 
Sbjct: 56  VDWARRCMVFKELEVADQMTLLQNCWSELLVLDHIYRQVQYGKEDSILLVTGQEVE--LS 113
Query: 160 PDDVRVNNEIKLI----QEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQ 215
              V+  + +  +    QE++ +   L  D  E  C+K +ILF+ +   L +   V+  Q
Sbjct: 114 TVAVQAGSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILFSLDVKFLNNHSLVKDAQ 173
Query: 216 DQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGD 275
           ++A   L DY    Y     +F +LLL L  +RA+     E L+ K    ++P   LL +
Sbjct: 174 EKANAALLDYTLCHYPHCGDKFQQLLLCLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIE 233
Query: 276 M 276
           M
Sbjct: 234 M 234

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 51/212 (24%), Positives = 91/212 (42%), Gaps = 27/212 (12%)
Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
           C+  +A LL   +R+V+ L  FQ L    QL+L++  W  L +L LAQ  + +++  +  
Sbjct: 53  CEAASAGLL-KTLRFVKYLPCFQILPLDQQLVLVRSCWAPLLMLELAQDHLHFEMMEIPE 111
Query: 151 CEKARERLP----------PDDVRVNNE----------------IKLIQEILARFRQLSP 184
               +E L           P + +   +                ++ I+    +   L+ 
Sbjct: 112 TNTTQEMLTTRRQETEGPEPAEPQATEQPQMVSAEAGHLLPAAAVQAIKSFFFKCWSLNI 171
Query: 185 DGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLML 244
           D  E   +K  +LF P+ PGL   + +E LQ + Q IL +++R        R   L   L
Sbjct: 172 DTKEYAYLKGTVLFNPDLPGLQCVKYIEGLQWRTQQILTEHIRMMQREYQIRSAELNSAL 231
Query: 245 PSLRAVRQSTIERLFFKETIGDIPIQRLLGDM 276
             LR +    +  LFF+  IG + +  ++ +M
Sbjct: 232 FLLRFINSDVVTELFFRPIIGAVSMDDMMLEM 263

>pdb|1OVL|B Chain B, Crystal Structure Of Nurr1 Lbd Length = 271

Iteration: 1
 Score = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 51/160 (31%), Positives = 75/160 (46%), Gaps = 8/160 (5%)
Query: 105 WVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVR 164
           W   +  F  L K DQ LL + ++ ELF+L LA  S P +  L+        RL    VR
Sbjct: 93  WAEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIFCNGVVLHRLQC--VR 150
Query: 165 VNNE-IKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILG 223
              E I  I E  +  +  + D S   C+ A+   T E  GL + + VE LQ++    L 
Sbjct: 151 GFGEWIDSIVEFSSNLQNXNIDISAFSCIAALAXVT-ERHGLKEPKRVEELQNKIVNCLK 209
Query: 224 DYV---RGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 260
           D+V    G  +R P    +LL  LP LR +    ++R+F+
Sbjct: 210 DHVTFNNGGLNR-PNYLSKLLGKLPELRTLCTQGLQRIFY 248

>pdb|1OVL|A Chain A, Crystal Structure Of Nurr1 Lbd Length = 271

Iteration: 1
 Score = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 51/160 (31%), Positives = 75/160 (46%), Gaps = 8/160 (5%)
Query: 105 WVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVR 164
           W   +  F  L K DQ LL + ++ ELF+L LA  S P +  L+        RL    VR
Sbjct: 93  WAEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIFCNGVVLHRLQC--VR 150
Query: 165 VNNE-IKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILG 223
              E I  I E  +  +  + D S   C+ A+   T E  GL + + VE LQ++    L 
Sbjct: 151 GFGEWIDSIVEFSSNLQNXNIDISAFSCIAALAXVT-ERHGLKEPKRVEELQNKIVNCLK 209
Query: 224 DYV---RGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 260
           D+V    G  +R P    +LL  LP LR +    ++R+F+
Sbjct: 210 DHVTFNNGGLNR-PNYLSKLLGKLPELRTLCTQGLQRIFY 248

>pdb|2QW4|A Chain A, Human Nr4a1 Ligand-Binding Domain Length = 273

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 50/162 (30%), Positives = 73/162 (45%), Gaps = 10/162 (6%)
Query: 104 RWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDV 163
           +W   +  F  LS  DQ LLL+ ++ ELF+L LA  S P +  L+        RL     
Sbjct: 94  KWAEKIPGFAELSPADQDLLLESAFLELFILRLAYRSKPGEGKLIFCSGLVLHRLQ---- 149
Query: 164 RVNNEIKLIQEILARFRQLSP---DGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQC 220
                   I  ILA  R L     D     C+ A++L T +  GL + + VE LQ++   
Sbjct: 150 CARGFGDWIDSILAFSRSLHSLLVDVPAFACLSALVLIT-DRHGLQEPRRVEELQNRIAS 208
Query: 221 ILGDYVRGRYSR-QPTR-FGRLLLMLPSLRAVRQSTIERLFF 260
            L ++V       QP     RLL  LP LR +    ++R+F+
Sbjct: 209 CLKEHVAAVAGEPQPASCLSRLLGKLPELRTLCTQGLQRIFY 250

>pdb|3V3E|B Chain B, Crystal Structure Of The Human Nur77 Ligand-Binding Domain Length = 257

Iteration: 1
 Score = 49.7 bits (117), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 50/162 (30%), Positives = 73/162 (45%), Gaps = 10/162 (6%)
Query: 104 RWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDV 163
           +W   +  F  LS  DQ LLL+ ++ ELF+L LA  S P +  L+        RL     
Sbjct: 70  KWAEKIPGFAELSPADQDLLLESAFLELFILRLAYRSKPGEGKLIFCSGLVLHRLQC--- 126
Query: 164 RVNNEIKLIQEILARFRQLSP---DGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQC 220
                   I  ILA  R L     D     C+ A++L T +  GL + + VE LQ++   
Sbjct: 127 -ARGFGDWIDSILAFSRSLHSLLVDVPAFACLSALVLIT-DRHGLQEPRRVEELQNRIAS 184
Query: 221 ILGDYVRGRYSR-QPTR-FGRLLLMLPSLRAVRQSTIERLFF 260
            L ++V       QP     RLL  LP LR +    ++R+F+
Sbjct: 185 CLKEHVAAVAGEPQPASCLSRLLGKLPELRTLCTQGLQRIFY 226

>pdb|1YJE|A Chain A, Crystal Structure Of The Rngfi-B Ligand-Binding Domain Length = 264

Iteration: 1
 Score = 48.9 bits (115), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 50/161 (31%), Positives = 73/161 (45%), Gaps = 10/161 (6%)
Query: 104 RWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDV 163
           +W   +  F  LS  DQ LLL+ ++ ELF+L LA  S P +  L+        RL     
Sbjct: 85  KWAEKIPGFIELSPGDQDLLLESAFLELFILRLAYRSKPGEGKLIFCSGLVLHRLQC--- 141
Query: 164 RVNNEIKLIQEILARFRQLSPDGSEC---GCMKAVILFTPETPGLVDAQPVEMLQDQAQC 220
                   I  ILA  R L   G +     C+ A++L T +  GL D + VE LQ++   
Sbjct: 142 -ARGFGDWIDNILAFSRSLHSLGVDVPAFACLSALVLIT-DRHGLQDPRRVEELQNRIAS 199
Query: 221 ILGDYVRGRYSR-QPTR-FGRLLLMLPSLRAVRQSTIERLF 259
            L +++       QP     RLL  LP LR +    ++R+F
Sbjct: 200 CLKEHMAAVAGDPQPASCLSRLLGKLPELRTLCTQGLQRIF 240

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 44/159 (27%), Positives = 72/159 (45%), Gaps = 3/159 (1%)
Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD--LSLLINCEKARERLPP 160
           V + + L  F  LS+ DQ+ LL+ S  E+ LL  ++   P    ++ L +    RE    
Sbjct: 88  VDFAKQLPGFLQLSREDQIALLKTSAIEVMLLETSRRYNPGSESITFLKDFSYNREDFAK 147
Query: 161 DDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQC 220
             ++V   I  I E      +L  + +E   + A+ +F+ + P + D   VE LQ     
Sbjct: 148 AGLQVEF-INPIFEFSRAMNELQLNDAEFALLIAISIFSADRPNVQDQLQVERLQHTYVE 206
Query: 221 ILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLF 259
            L  YV   +   P  F R+L+ L SLR +     E++F
Sbjct: 207 ALHAYVSINHPHDPLMFPRMLMKLVSLRTLSSVHSEQVF 245

>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 = 48.5 bits (114), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 38/159 (23%), Positives = 80/159 (50%), Gaps = 12/159 (7%)
Query: 102 AVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPD 161
            + + + +  F+ L+  DQ++LL+ S  E+ +L   Q     D+S   +C     +    
Sbjct: 85  VIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMSW--DCGSQDYKYDVT 142
Query: 162 DV-RVNNEIKLIQEIL---ARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQ 217
           DV +  + ++LI+ ++      ++L+    E   + A+ + +P+ PG+ DA+ VE +QD+
Sbjct: 143 DVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAKLVEAIQDR 202
Query: 218 AQCILGDYVRGRY----SRQPTRFGRLLLMLPSLRAVRQ 252
               L  Y+R R+    S Q   + +++  L  LR++ +
Sbjct: 203 LSNTLQTYIRCRHPPPGSHQ--LYAKMIQKLADLRSLNE 239

>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 = 48.1 bits (113), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 38/159 (23%), Positives = 80/159 (50%), Gaps = 12/159 (7%)
Query: 102 AVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPD 161
            + + + +  F+ L+  DQ++LL+ S  E+ +L   Q     D+S   +C     +    
Sbjct: 79  VIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMSW--DCGSQDYKYDVT 136
Query: 162 DV-RVNNEIKLIQEIL---ARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQ 217
           DV +  + ++LI+ ++      ++L+    E   + A+ + +P+ PG+ DA+ VE +QD+
Sbjct: 137 DVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAKLVEAIQDR 196
Query: 218 AQCILGDYVRGRY----SRQPTRFGRLLLMLPSLRAVRQ 252
               L  Y+R R+    S Q   + +++  L  LR++ +
Sbjct: 197 LSNTLQTYIRCRHPPPGSHQ--LYAKMIQKLADLRSLNE 233

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 44/159 (27%), Positives = 72/159 (45%), Gaps = 3/159 (1%)
Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD--LSLLINCEKARERLPP 160
           V + + L  F  LS+ DQ+ LL+ S  E+ LL  ++   P    ++ L +    RE    
Sbjct: 66  VDFAKQLPGFLQLSREDQIALLKTSAIEVMLLETSRRYNPGSESITFLKDFSYNREDFAK 125
Query: 161 DDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQC 220
             ++V   I  I E      +L  + +E   + A+ +F+ + P + D   VE LQ     
Sbjct: 126 AGLQVEF-INPIFEFSRAMNELQLNDAEFALLIAISIFSADRPNVQDQLQVERLQHTYVE 184
Query: 221 ILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLF 259
            L  YV   +   P  F R+L+ L SLR +     E++F
Sbjct: 185 ALHAYVSINHPHDPLMFPRMLMKLVSLRTLSSVHSEQVF 223

>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 = 48.1 bits (113), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 38/159 (23%), Positives = 80/159 (50%), Gaps = 12/159 (7%)
Query: 102 AVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPD 161
            + + + +  F+ L+  DQ++LL+ S  E+ +L   Q     D+S   +C     +    
Sbjct: 75  VIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMSW--DCGSQDYKYDVT 132
Query: 162 DV-RVNNEIKLIQEIL---ARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQ 217
           DV +  + ++LI+ ++      ++L+    E   + A+ + +P+ PG+ DA+ VE +QD+
Sbjct: 133 DVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAKLVEAIQDR 192
Query: 218 AQCILGDYVRGRY----SRQPTRFGRLLLMLPSLRAVRQ 252
               L  Y+R R+    S Q   + +++  L  LR++ +
Sbjct: 193 LSNTLQTYIRCRHPPPGSHQ--LYAKMIQKLADLRSLNE 229

>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 = 47.8 bits (112), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 33/156 (21%), Positives = 78/156 (50%), Gaps = 6/156 (3%)
Query: 102 AVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPD 161
            + + + +  F+ L+  DQ++LL+ S  E+ +L   +     D+S     +  + R+  D
Sbjct: 94  VIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVS-D 152
Query: 162 DVRVNNEIKLIQEIL---ARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQA 218
             +  + ++LI+ ++      ++L+    E   + A+ + +P+ PG+ DA  +E +QD+ 
Sbjct: 153 VTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRL 212
Query: 219 QCILGDYVRGRYSRQPTR--FGRLLLMLPSLRAVRQ 252
              L  Y+R R+    +   + +++  L  LR++ +
Sbjct: 213 SNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNE 248

>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 = 47.8 bits (112), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 38/171 (22%), Positives = 72/171 (42%)
Query: 89  EKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLL 148
           +K  E + + +   V + + L  F TL+  DQ+ LL+ +  ++ +L +     P   ++ 
Sbjct: 71  DKFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMT 130
Query: 149 INCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDA 208
            +      R    +        L+     +   L  D +E G + A+ L   +   L   
Sbjct: 131 FSDGLTLNRTQMHNAGFGPLTDLVFAFANQLLPLEMDDAETGLLSAICLICGDRQDLEQP 190
Query: 209 QPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLF 259
             V+MLQ+     L  YVR R   +P  F ++L+ +  LR++     ER+ 
Sbjct: 191 DRVDMLQEPLLEALKVYVRKRRPSRPHMFPKMLMKITDLRSISAKGAERVI 241

>pdb|2FSZ|A Chain A, A Second Binding Site For Hydroxytamoxifen Within The Coactivator-Binding Groove Of Estrogen Receptor Beta Length = 246

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 48/194 (24%), Positives = 79/194 (40%), Gaps = 29/194 (14%)
Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDD 162
           + W + +  F  LS  DQ+ LL+ SW E+ ++ L   SI             +    PD 
Sbjct: 54  ISWAKKIPGFVELSLFDQVRLLESSWMEVLMMGLMWRSID---------HPGKLIFAPDL 104
Query: 163 VRVNNEIKLIQEIL----------ARFRQLSPDGSECGCMKAVILFTPETPGLVDA---- 208
           V   +E K ++ IL          +RFR+L     E  C+KA+IL       LV A    
Sbjct: 105 VLDRDEGKSVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDA 164
Query: 209 ----QPVEMLQDQAQCILGDYVRGRYS--RQPTRFGRLLLMLPSLRAVRQSTIERLFFKE 262
               +   +L      ++    +   S  +Q  R   LL++L  +R      +E L   +
Sbjct: 165 DSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMK 224
Query: 263 TIGDIPIQRLLGDM 276
           +   +P+  LL +M
Sbjct: 225 SKNVVPVYDLLLEM 238

>pdb|1XV9|B Chain B, Crystal Structure Of CarRXR HETERODIMER BOUND WITH SRC1 Peptide, Fatty Acid, And 5b-Pregnane-3,20-Dione. Length = 246

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 44/183 (24%), Positives = 85/183 (46%), Gaps = 10/183 (5%)
Query: 77  PHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHL 136
           P P L  +L       +    ++   +++ + L  F++L   DQ+ LL+ +  E+  + L
Sbjct: 45  PLPTLAPVLPLVTHFADINTFMVLQVIKFTKDLPVFRSLPIEDQISLLKGAAVEICHIVL 104
Query: 137 AQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARF----RQLSPDGSECGCM 192
                    + L  C   R  +  D  RV  +++ + E+L  F    R+L     E   +
Sbjct: 105 NTTFCLQTQNFL--CGPLRYTIE-DGARVGFQVEFL-ELLFHFHGTLRKLQLQEPEYVLL 160
Query: 193 KAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRF--GRLLLMLPSLRAV 250
            A+ LF+P+ PG+     ++ LQ++    L  Y++G+  R   RF   +LL +L  LR++
Sbjct: 161 AAMALFSPDRPGVTQRDEIDQLQEEMALTLQSYIKGQQRRPRDRFLYAKLLGLLAELRSI 220
Query: 251 RQS 253
            ++
Sbjct: 221 NEA 223

>pdb|1S0Z|A Chain A, Crystal Structure Of The Vdr Lbd Complexed To Seocalcitol. Length = 263

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 33/156 (21%), Positives = 78/156 (50%), Gaps = 6/156 (3%)
Query: 102 AVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPD 161
            + + + +  F+ L+  DQ++LL+ S  E+ +L   +     D+S     +  + R+  D
Sbjct: 77  VIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVS-D 135
Query: 162 DVRVNNEIKLIQEIL---ARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQA 218
             +  + ++LI+ ++      ++L+    E   + A+ + +P+ PG+ DA  +E +QD+ 
Sbjct: 136 VTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRL 195
Query: 219 QCILGDYVRGRYSRQPTR--FGRLLLMLPSLRAVRQ 252
              L  Y+R R+    +   + +++  L  LR++ +
Sbjct: 196 SNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNE 231

>pdb|3B0T|A Chain A, Human Vdr Ligand Binding Domain In Complex With Maxacalcitol Length = 254

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 33/156 (21%), Positives = 78/156 (50%), Gaps = 6/156 (3%)
Query: 102 AVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPD 161
            + + + +  F+ L+  DQ++LL+ S  E+ +L   +     D+S     +  + R+  D
Sbjct: 72  VIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVS-D 130
Query: 162 DVRVNNEIKLIQEIL---ARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQA 218
             +  + ++LI+ ++      ++L+    E   + A+ + +P+ PG+ DA  +E +QD+ 
Sbjct: 131 VTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRL 190
Query: 219 QCILGDYVRGRYSRQPTR--FGRLLLMLPSLRAVRQ 252
              L  Y+R R+    +   + +++  L  LR++ +
Sbjct: 191 SNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNE 226

>pdb|1DB1|A Chain A, Crystal Structure Of The Nuclear Receptor For Vitamin D Complexed To Vitamin D Length = 259

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 33/156 (21%), Positives = 78/156 (50%), Gaps = 6/156 (3%)
Query: 102 AVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPD 161
            + + + +  F+ L+  DQ++LL+ S  E+ +L   +     D+S     +  + R+  D
Sbjct: 73  VIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVS-D 131
Query: 162 DVRVNNEIKLIQEIL---ARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQA 218
             +  + ++LI+ ++      ++L+    E   + A+ + +P+ PG+ DA  +E +QD+ 
Sbjct: 132 VTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRL 191
Query: 219 QCILGDYVRGRYSRQPTR--FGRLLLMLPSLRAVRQ 252
              L  Y+R R+    +   + +++  L  LR++ +
Sbjct: 192 SNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNE 227

>pdb|3AZ1|A Chain A, Crystal Structure Analysis Of Vitamin D Receptor Length = 253

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 33/156 (21%), Positives = 78/156 (50%), Gaps = 6/156 (3%)
Query: 102 AVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPD 161
            + + + +  F+ L+  DQ++LL+ S  E+ +L   +     D+S     +  + R+  D
Sbjct: 71  VIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVS-D 129
Query: 162 DVRVNNEIKLIQEIL---ARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQA 218
             +  + ++LI+ ++      ++L+    E   + A+ + +P+ PG+ DA  +E +QD+ 
Sbjct: 130 VTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRL 189
Query: 219 QCILGDYVRGRYSRQPTR--FGRLLLMLPSLRAVRQ 252
              L  Y+R R+    +   + +++  L  LR++ +
Sbjct: 190 SNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNE 225

>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 = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 38/171 (22%), Positives = 72/171 (42%)
Query: 89  EKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLL 148
           +K  E + + +   V + + L  F TL+  DQ+ LL+ +  ++ +L +     P   ++ 
Sbjct: 45  DKFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMT 104
Query: 149 INCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDA 208
            +      R    +        L+     +   L  D +E G + A+ L   +   L   
Sbjct: 105 FSDGLTLNRTQMHNAGFGPLTDLVFAFANQLLPLEMDDAETGLLSAICLICGDRQDLEQP 164
Query: 209 QPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLF 259
             V+MLQ+     L  YVR R   +P  F ++L+ +  LR++     ER+ 
Sbjct: 165 DRVDMLQEPLLEALKVYVRKRRPSRPHMFPKMLMKITDLRSISAKGAERVI 215

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 38/171 (22%), Positives = 72/171 (42%)
Query: 89  EKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLL 148
           +K  E + + +   V + + L  F TL+  DQ+ LL+ +  ++ +L +     P   ++ 
Sbjct: 45  DKFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMT 104
Query: 149 INCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDA 208
            +      R    +        L+     +   L  D +E G + A+ L   +   L   
Sbjct: 105 FSDGLTLNRTQMHNAGFGPLTDLVFAFANQLLPLEMDDAETGLLSAICLICGDRQDLEQP 164
Query: 209 QPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLF 259
             V+MLQ+     L  YVR R   +P  F ++L+ +  LR++     ER+ 
Sbjct: 165 DRVDMLQEPLLEALKVYVRKRRPSRPHMFPKMLMKITDLRSISAKGAERVI 215

>pdb|3M7R|A Chain A, Crystal Structure Of Vdr H305q Mutant Length = 253

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 33/156 (21%), Positives = 77/156 (49%), Gaps = 6/156 (3%)
Query: 102 AVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPD 161
            + + + +  F+ L+  DQ++LL+ S  E+ +L   +     D+S     +  + R+  D
Sbjct: 71  VIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVS-D 129
Query: 162 DVRVNNEIKLIQEIL---ARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQA 218
             +    ++LI+ ++      ++L+    E   + A+ + +P+ PG+ DA  +E +QD+ 
Sbjct: 130 VTKAGQSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRL 189
Query: 219 QCILGDYVRGRYSRQPTR--FGRLLLMLPSLRAVRQ 252
              L  Y+R R+    +   + +++  L  LR++ +
Sbjct: 190 SNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNE 225

>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 = 46.2 bits (108), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 38/171 (22%), Positives = 72/171 (42%)
Query: 89  EKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLL 148
           +K  E + + +   V + + L  F TL+  DQ+ LL+ +  ++ +L +     P   ++ 
Sbjct: 74  DKFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMT 133
Query: 149 INCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDA 208
            +      R    +        L+     +   L  D +E G + A+ L   +   L   
Sbjct: 134 FSDGLTLNRTQMHNAGFGPLTDLVFAFANQLLPLEMDDAETGLLSAICLICGDRQDLEQP 193
Query: 209 QPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLF 259
             V+MLQ+     L  YVR R   +P  F ++L+ +  LR++     ER+ 
Sbjct: 194 DRVDMLQEPLLEALKVYVRKRRPSRPHMFPKMLMKITDLRSISAKGAERVI 244

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

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 50/179 (27%), Positives = 79/179 (44%), Gaps = 5/179 (2%)
Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLL-HL---AQWSIPWDLSLLINCEKARERL 158
           V W R    F+ L   DQ+ LLQ  W EL +  H+    Q      + L+   E     +
Sbjct: 57  VDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQHGKEGSILLVTGQEVELTTV 116
Query: 159 PPDDVRVNNEIKL-IQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQ 217
                 + + + L  QE++ +   L  D  E  C+K +ILF+ +   L +   V+  Q++
Sbjct: 117 ATQAGSLLHSLVLRAQELVLQLLALQLDRQEFVCLKFIILFSLDLKFLNNHILVKDAQEK 176
Query: 218 AQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDM 276
           A   L DY    Y     +F +LLL L  +RA+     E L+ K    ++P   LL +M
Sbjct: 177 ANAALLDYTLCHYPHSGDKFQQLLLCLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIEM 235

>pdb|3D24|A Chain A, Crystal Structure Of Ligand-Binding Domain Of Estrogen- Related Receptor Alpha (Erralpha) In Complex With The Peroxisome Proliferators-Activated Receptor Coactivator- 1alpha Box3 Peptide (Pgc-1alpha) Length = 253

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 44/184 (23%), Positives = 82/184 (44%), Gaps = 4/184 (2%)
Query: 97  RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE 156
           R + + + W + +  F +LS  DQ+ +LQ  W E+ +L +AQ S+P    L    +   +
Sbjct: 64  REIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQDELAFAEDLVLD 123
Query: 157 RLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQD 216
                   +      + +++ R + L  +  E   +KA+ L   ++  + DA+ VE L++
Sbjct: 124 EEGARAAGLGELGAALLQLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQLRE 183
Query: 217 QAQCILGDY----VRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRL 272
                L +Y           +  R GRLLL LP LR      +   +  +  G +P+ +L
Sbjct: 184 ALHEALLEYEAGRAGPGGGAERRRAGRLLLTLPLLRQTAGKVLAHFYGVKLEGKVPMHKL 243
Query: 273 LGDM 276
             +M
Sbjct: 244 FLEM 247

>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 = 45.8 bits (107), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 33/156 (21%), Positives = 77/156 (49%), Gaps = 6/156 (3%)
Query: 102 AVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPD 161
            + + + +  F+ L+  DQ++LL+ S  E+ +L   +     D+S     +  + R+  D
Sbjct: 77  VIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVS-D 135
Query: 162 DVRVNNEIKLIQEIL---ARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQA 218
             +    ++LI+ ++      ++L+    E   + A+ + +P+ PG+ DA  +E +QD+ 
Sbjct: 136 VTKAGFSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRL 195
Query: 219 QCILGDYVRGRYSRQPTR--FGRLLLMLPSLRAVRQ 252
              L  Y+R R+    +   + +++  L  LR++ +
Sbjct: 196 SNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNE 231

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

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 48/162 (29%), Positives = 71/162 (43%), Gaps = 4/162 (2%)
Query: 119 DQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILAR 178
           DQ LL Q +  ELF+L LA +    D + LI C                 +  I E    
Sbjct: 80  DQELLFQSASLELFVLRLA-YRARIDDTKLIFCNGTVLHRTQCLRSFGEWLNDIMEFSRS 138
Query: 179 FRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTR-- 236
              L  D S   C+ A+ L T E  GL + + VE LQ +    L D+V      Q  +  
Sbjct: 139 LHNLEIDISAFACLCALTLIT-ERHGLREPKKVEQLQMKIIGSLRDHVTYNAEAQKKQHY 197
Query: 237 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT 278
           F RLL  LP LR++    ++R+F+ +    +P   L+ +M+ 
Sbjct: 198 FSRLLGKLPELRSLSVQGLQRIFYLKLEDLVPAPALIENMFV 239

>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 = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 33/156 (21%), Positives = 77/156 (49%), Gaps = 6/156 (3%)
Query: 102 AVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPD 161
            + + + +  F+ L+  DQ++LL+ S  E+ +L   +     D+S     +  + R+  D
Sbjct: 77  VIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVS-D 135
Query: 162 DVRVNNEIKLIQEIL---ARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQA 218
             +    ++LI+ ++      ++L+    E   + A+ + +P+ PG+ DA  +E +QD+ 
Sbjct: 136 VTKAGFSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRL 195
Query: 219 QCILGDYVRGRYSRQPTR--FGRLLLMLPSLRAVRQ 252
              L  Y+R R+    +   + +++  L  LR++ +
Sbjct: 196 SNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNE 231

>pdb|1L2J|A Chain A, Human Estrogen Receptor Beta Ligand-Binding Domain In Complex With (R, R)-5,11-Cis-Diethyl-5,6,11,12-Tetrahydrochrysene-2, 8-Diol Length = 271

Iteration: 1
 Score = 45.4 bits (106), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 47/196 (23%), Positives = 77/196 (39%), Gaps = 29/196 (14%)
Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDD 162
           + W + +  F  LS  DQ+ LL+  W E+ ++ L   SI             +    PD 
Sbjct: 76  ISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSID---------HPGKLIFAPDL 126
Query: 163 VRVNNEIKLIQEIL----------ARFRQLSPDGSECGCMKAVILFTPETPGLVDA---- 208
           V   +E K ++ IL          +RFR+L     E  C+KA+IL       LV A    
Sbjct: 127 VLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDA 186
Query: 209 ----QPVEMLQDQAQCILGDYVRGRYS--RQPTRFGRLLLMLPSLRAVRQSTIERLFFKE 262
               +   +L      ++    +   S  +Q  R   LL++L  +R      +E L   +
Sbjct: 187 DSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMK 246
Query: 263 TIGDIPIQRLLGDMYT 278
               +P+  LL +M  
Sbjct: 247 CKNVVPVYDLLLEMLN 262

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 43/159 (27%), Positives = 71/159 (44%), Gaps = 3/159 (1%)
Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD--LSLLINCEKARERLPP 160
           V + + L  F  LS+ DQ+ LL+ S  E+ LL  ++   P    ++ L +    RE    
Sbjct: 105 VDFAKQLPGFLQLSREDQIALLKTSAIEVMLLETSRRYNPGSESITFLKDFSYNREDFAK 164
Query: 161 DDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQC 220
             ++V   I  I E      +L  + +E   + A+ +F+ + P + D   VE LQ     
Sbjct: 165 AGLQVEF-INPIFEFSRAMNELQLNDAEFALLIAISIFSADRPNVQDQLQVERLQHTYVE 223
Query: 221 ILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLF 259
            L  YV   +      F R+L+ L SLR +     E++F
Sbjct: 224 ALHAYVSIHHPHDRLMFPRMLMKLVSLRTLSSVHSEQVF 262

>pdb|2YLY|A Chain A, Sulfonamides As Selective Estrogen Receptor Beta Agonists. Length = 240

Iteration: 1
 Score = 45.4 bits (106), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 47/193 (24%), Positives = 77/193 (39%), Gaps = 28/193 (14%)
Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDD 162
           + W + +  F  LS  DQ+ LL+  W E+ ++ L   SI             +    PD 
Sbjct: 51  ISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSID---------HPGKLIFAPDL 101
Query: 163 VRVNNEIKLIQEIL----------ARFRQLSPDGSECGCMKAVILFTPETPGLVDA---- 208
           V   +E K ++ IL          +RFR+L     E  C+KA+IL       LV A    
Sbjct: 102 VLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDD 161
Query: 209 ---QPVEMLQDQAQCILGDYVRGRYS--RQPTRFGRLLLMLPSLRAVRQSTIERLFFKET 263
              +   +L      ++    +   S  +Q  R   LL++L  +R      +E L   + 
Sbjct: 162 SSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKC 221
Query: 264 IGDIPIQRLLGDM 276
              +P+  LL +M
Sbjct: 222 KNVVPVYDLLLEM 234

>pdb|2PJL|A Chain A, Crystal Structure Of Human Estrogen-Related Receptor Alpha In Complex With A Synthetic Inverse Agonist Reveals Its Novel Molecular Mechanism Length = 247

Iteration: 1
 Score = 45.4 bits (106), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 47/190 (24%), Positives = 87/190 (45%), Gaps = 16/190 (8%)
Query: 97  RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIP------WDLSLLIN 150
           R + + + W + +  F +LS  DQ+ +LQ  W E+ +L +AQ S+P      +   L+++
Sbjct: 58  REIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQDELAFAEDLVLD 117
Query: 151 CEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQP 210
            E AR         +      + +++ R + L  +  E   +KA+ L   ++  + DA+ 
Sbjct: 118 EEGARA------AGLGELGAALLQLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEA 171
Query: 211 VEMLQDQAQCILGDY----VRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGD 266
           VE L++     L +Y           +  R GRLLL LP LR      +   +  +  G 
Sbjct: 172 VEQLREALHEALLEYEAGRAGPGGGAERRRAGRLLLTLPLLRQTAGKVLAHFYGVKLEGK 231
Query: 267 IPIQRLLGDM 276
           +P+ +L  +M
Sbjct: 232 VPMHKLFLEM 241

>pdb|1XLS|E Chain E, Crystal Structure Of The Mouse CarRXR LBD HETERODIMER Bound To Tcpobop And 9cra And A Tif2 Peptide Containg The Third Lxxll Motifs Length = 242

Iteration: 1
 Score = 45.4 bits (106), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 36/158 (22%), Positives = 73/158 (46%), Gaps = 12/158 (7%)
Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN--CEKARERLPP 160
           +++ + L  F++L+  DQ+ LL+ +  E+  + L         +      C K       
Sbjct: 67  IKFTKDLPLFRSLTMEDQISLLKGAAVEILHISLNTTFCLQTENFFCGPLCYKME----- 121
Query: 161 DDVRVNNEIKLIQEIL---ARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQ 217
           D V    + + ++ IL      + L     E   M A  LF+P+ PG+   + ++ LQ++
Sbjct: 122 DAVHAGFQYEFLESILHFHKNLKGLHLQEPEYVLMAATALFSPDRPGVTQREEIDQLQEE 181
Query: 218 AQCILGDYVRGRYSRQPTRF--GRLLLMLPSLRAVRQS 253
              IL +++  + SR  +RF   +L+ +L  LR++  +
Sbjct: 182 MALILNNHIMEQQSRLQSRFLYAKLMGLLADLRSINNA 219

>pdb|1XNX|A Chain A, Crystal Structure Of Constitutive Androstane Receptor Length = 256

Iteration: 1
 Score = 45.4 bits (106), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 36/158 (22%), Positives = 73/158 (46%), Gaps = 12/158 (7%)
Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN--CEKARERLPP 160
           +++ + L  F++L+  DQ+ LL+ +  E+  + L         +      C K       
Sbjct: 81  IKFTKDLPLFRSLTMEDQISLLKGAAVEILHISLNTTFCLQTENFFCGPLCYKME----- 135
Query: 161 DDVRVNNEIKLIQEIL---ARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQ 217
           D V    + + ++ IL      + L     E   M A  LF+P+ PG+   + ++ LQ++
Sbjct: 136 DAVHAGFQYEFLESILHFHKNLKGLHLQEPEYVLMAATALFSPDRPGVTQREEIDQLQEE 195
Query: 218 AQCILGDYVRGRYSRQPTRF--GRLLLMLPSLRAVRQS 253
              IL +++  + SR  +RF   +L+ +L  LR++  +
Sbjct: 196 MALILNNHIMEQQSRLQSRFLYAKLMGLLADLRSINNA 233

>pdb|3ET0|A Chain A, Structure Of Ppargamma With 3-(5-Methoxy-1h-Indol-3-Yl)- Propionic Acid Length = 292

Iteration: 1
 Score = 45.4 bits (106), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 104 SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 153
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 154 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 213
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 214 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 273
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 274 TETDMSLHPLLQEIY 288

>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 = 45.4 bits (106), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 108 SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 157
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 158 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 217
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 218 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 277
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 278 TETDMSLHPLLQEIY 292

>pdb|3K6P|A Chain A, Estrogen Related Receptor Alpha In Complex With An Ether Based Ligand Length = 248

Iteration: 1
 Score = 45.4 bits (106), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 44/184 (23%), Positives = 82/184 (44%), Gaps = 4/184 (2%)
Query: 97  RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE 156
           R + + + W + +  F +LS  DQ+ +LQ  W E+ +L +AQ S+P    L    +   +
Sbjct: 59  REIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQDELAFAEDLVLD 118
Query: 157 RLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQD 216
                   +      + +++ R + L  +  E   +KA+ L   ++  + DA+ VE L++
Sbjct: 119 EEGARAAGLGELGAALLQLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQLRE 178
Query: 217 QAQCILGDY----VRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRL 272
                L +Y           +  R GRLLL LP LR      +   +  +  G +P+ +L
Sbjct: 179 ALHEALLEYEAGRAGPGGGAERRRAGRLLLTLPLLRQTAGKVLAHFYGVKLEGKVPMHKL 238
Query: 273 LGDM 276
             +M
Sbjct: 239 FLEM 242

>pdb|2NV7|A Chain A, Crystal Structure Of Estrogen Receptor Beta Complexed With Way-555 Length = 238

Iteration: 1
 Score = 45.1 bits (105), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 47/194 (24%), Positives = 77/194 (39%), Gaps = 29/194 (14%)
Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDD 162
           + W + +  F  LS  DQ+ LL+  W E+ ++ L   SI             +    PD 
Sbjct: 48  ISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSID---------HPGKLIFAPDL 98
Query: 163 VRVNNEIKLIQEIL----------ARFRQLSPDGSECGCMKAVILFTPETPGLVDA---- 208
           V   +E K ++ IL          +RFR+L     E  C+KA+IL       LV A    
Sbjct: 99  VLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDA 158
Query: 209 ----QPVEMLQDQAQCILGDYVRGRYS--RQPTRFGRLLLMLPSLRAVRQSTIERLFFKE 262
               +   +L      ++    +   S  +Q  R   LL++L  +R      +E L   +
Sbjct: 159 DSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMK 218
Query: 263 TIGDIPIQRLLGDM 276
               +P+  LL +M
Sbjct: 219 CKNVVPVYDLLLEM 232

>pdb|3OLL|A Chain A, Crystal Structure Of Phosphorylated Estrogen Receptor Beta Ligand Binding Domain Length = 240

Iteration: 1
 Score = 45.1 bits (105), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 47/196 (23%), Positives = 77/196 (39%), Gaps = 29/196 (14%)
Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDD 162
           + W + +  F  LS  DQ+ LL+  W E+ ++ L   SI             +    PD 
Sbjct: 50  ISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSID---------HPGKLIFAPDL 100
Query: 163 VRVNNEIKLIQEIL----------ARFRQLSPDGSECGCMKAVILFTPETPGLVDA---- 208
           V   +E K ++ IL          +RFR+L     E  C+KA+IL       LV A    
Sbjct: 101 VLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDA 160
Query: 209 ----QPVEMLQDQAQCILGDYVRGRYS--RQPTRFGRLLLMLPSLRAVRQSTIERLFFKE 262
               +   +L      ++    +   S  +Q  R   LL++L  +R      +E L   +
Sbjct: 161 DSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMK 220
Query: 263 TIGDIPIQRLLGDMYT 278
               +P+  LL +M  
Sbjct: 221 CKNVVPVXDLLLEMLN 236

>pdb|1XB7|A Chain A, X-Ray Structure Of Erralpha Lbd In Complex With A Pgc- 1alpha Peptide At 2.5a Resolution Length = 247

Iteration: 1
 Score = 45.1 bits (105), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 44/184 (23%), Positives = 82/184 (44%), Gaps = 4/184 (2%)
Query: 97  RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE 156
           R + + + W + +  F +LS  DQ+ +LQ  W E+ +L +AQ S+P    L    +   +
Sbjct: 58  REIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQDELAFAEDLVLD 117
Query: 157 RLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQD 216
                   +      + +++ R + L  +  E   +KA+ L   ++  + DA+ VE L++
Sbjct: 118 EEGARAAGLGELGAALLQLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQLRE 177
Query: 217 QAQCILGDY----VRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRL 272
                L +Y           +  R GRLLL LP LR      +   +  +  G +P+ +L
Sbjct: 178 ALHEALLEYEAGRAGPGGGAERRRAGRLLLTLPLLRQTAGKVLAHFYGVKLEGKVPMHKL 237
Query: 273 LGDM 276
             +M
Sbjct: 238 FLEM 241

>pdb|1X76|A Chain A, Crystal Structure Of Estrogen Receptor Beta Complexed With Way-697 Length = 240

Iteration: 1
 Score = 45.1 bits (105), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 47/194 (24%), Positives = 77/194 (39%), Gaps = 29/194 (14%)
Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDD 162
           + W + +  F  LS  DQ+ LL+  W E+ ++ L   SI             +    PD 
Sbjct: 50  ISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSID---------HPGKLIFAPDL 100
Query: 163 VRVNNEIKLIQEIL----------ARFRQLSPDGSECGCMKAVILFTPETPGLVDA---- 208
           V   +E K ++ IL          +RFR+L     E  C+KA+IL       LV A    
Sbjct: 101 VLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDA 160
Query: 209 ----QPVEMLQDQAQCILGDYVRGRYS--RQPTRFGRLLLMLPSLRAVRQSTIERLFFKE 262
               +   +L      ++    +   S  +Q  R   LL++L  +R      +E L   +
Sbjct: 161 DSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMK 220
Query: 263 TIGDIPIQRLLGDM 276
               +P+  LL +M
Sbjct: 221 CKNVVPVYDLLLEM 234

>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 = 45.1 bits (105), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 35/156 (22%), Positives = 68/156 (43%)
Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDD 162
           V + + +  F+ LS+ DQ+ LL+    E+ ++  A      D +++              
Sbjct: 82  VEFAKHIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFNVKDQTVMFLSRTTYSLQELGA 141
Query: 163 VRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCIL 222
           + + + +  + +   +   L+    E G   AV+L + +  G+ ++  VE LQ+     L
Sbjct: 142 MGMGDLLSAMFDFSEKLNSLALTEEELGLFTAVVLVSADRSGMENSASVEQLQETLLRAL 201
Query: 223 GDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 258
              V      + +RF +LLL LP LR +     E+L
Sbjct: 202 RALVLKNRPLETSRFTKLLLKLPDLRTLNNMHSEKL 237

>pdb|1YY4|A Chain A, Crystal Structure Of Estrogen Receptor Beta Complexed With 1-Chloro-6-(4-Hydroxy-Phenyl)-Naphthalen-2-Ol Length = 268

Iteration: 1
 Score = 45.1 bits (105), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 48/194 (24%), Positives = 78/194 (40%), Gaps = 29/194 (14%)
Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDD 162
           + W + +  F  LS  DQ+ LL+  W E+ ++ L   SI     L+           PD 
Sbjct: 48  ISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLI---------FAPDL 98
Query: 163 VRVNNEIKLIQEIL----------ARFRQLSPDGSECGCMKAVILFTPETPGLVDA---- 208
           V   +E K ++ IL          +RFR+L     E  C+KA+IL       LV A    
Sbjct: 99  VLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDA 158
Query: 209 ----QPVEMLQDQAQCILGDYVRGRYS--RQPTRFGRLLLMLPSLRAVRQSTIERLFFKE 262
               +   +L      ++    +   S  +Q  R   LL++L  +R      +E L   +
Sbjct: 159 DSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMK 218
Query: 263 TIGDIPIQRLLGDM 276
               +P+  LL +M
Sbjct: 219 CKNVVPVYDLLLEM 232

>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 = 6e-05,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 104 SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 153
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 154 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 213
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 214 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 273
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 274 TETDMSLHPLLQEIY 288

>pdb|1ZAF|A Chain A, Crystal Structure Of Estrogen Receptor Beta Complexed With 3-Bromo-6-Hydroxy-2-(4-Hydroxy-Phenyl)-Inden-1-One Length = 238

Iteration: 1
 Score = 45.1 bits (105), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 47/194 (24%), Positives = 77/194 (39%), Gaps = 29/194 (14%)
Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDD 162
           + W + +  F  LS  DQ+ LL+  W E+ ++ L   SI             +    PD 
Sbjct: 48  ISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSID---------HPGKLIFAPDL 98
Query: 163 VRVNNEIKLIQEIL----------ARFRQLSPDGSECGCMKAVILFTPETPGLVDA---- 208
           V   +E K ++ IL          +RFR+L     E  C+KA+IL       LV A    
Sbjct: 99  VLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSAMYPLVTATQDA 158
Query: 209 ----QPVEMLQDQAQCILGDYVRGRYS--RQPTRFGRLLLMLPSLRAVRQSTIERLFFKE 262
               +   +L      ++    +   S  +Q  R   LL++L  +R      +E L   +
Sbjct: 159 DSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMK 218
Query: 263 TIGDIPIQRLLGDM 276
               +P+  LL +M
Sbjct: 219 CKNVVPVYDLLLEM 232

>pdb|2GIU|A Chain A, Human Estrogen Receptor Beta Ligand-Binding Domain In Complex With Compound 45 Length = 241

Iteration: 1
 Score = 45.1 bits (105), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 47/194 (24%), Positives = 77/194 (39%), Gaps = 29/194 (14%)
Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDD 162
           + W + +  F  LS  DQ+ LL+  W E+ ++ L   SI             +    PD 
Sbjct: 51  ISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSID---------HPGKLIFAPDL 101
Query: 163 VRVNNEIKLIQEIL----------ARFRQLSPDGSECGCMKAVILFTPETPGLVDA---- 208
           V   +E K ++ IL          +RFR+L     E  C+KA+IL       LV A    
Sbjct: 102 VLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDA 161
Query: 209 ----QPVEMLQDQAQCILGDYVRGRYS--RQPTRFGRLLLMLPSLRAVRQSTIERLFFKE 262
               +   +L      ++    +   S  +Q  R   LL++L  +R      +E L   +
Sbjct: 162 DSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMK 221
Query: 263 TIGDIPIQRLLGDM 276
               +P+  LL +M
Sbjct: 222 CKNVVPVYDLLLEM 235

>pdb|1U9E|A Chain A, Crystal Structure Of Estrogen Receptor Beta Complexed With Way-397 Length = 241

Iteration: 1
 Score = 45.1 bits (105), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 47/194 (24%), Positives = 77/194 (39%), Gaps = 29/194 (14%)
Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDD 162
           + W + +  F  LS  DQ+ LL+  W E+ ++ L   SI             +    PD 
Sbjct: 50  ISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSID---------HPGKLIFAPDL 100
Query: 163 VRVNNEIKLIQEIL----------ARFRQLSPDGSECGCMKAVILFTPETPGLVDA---- 208
           V   +E K ++ IL          +RFR+L     E  C+KA+IL       LV A    
Sbjct: 101 VLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDA 160
Query: 209 ----QPVEMLQDQAQCILGDYVRGRYS--RQPTRFGRLLLMLPSLRAVRQSTIERLFFKE 262
               +   +L      ++    +   S  +Q  R   LL++L  +R      +E L   +
Sbjct: 161 DSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMK 220
Query: 263 TIGDIPIQRLLGDM 276
               +P+  LL +M
Sbjct: 221 CKNVVPVYDLLLEM 234

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 90  SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 139
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 140 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 199
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 200 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 259
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 260 TETDMSLHPLLQEIY 274

>pdb|1QKM|A Chain A, Human Oestrogen Receptor Beta Ligand-Binding Domain In Complex With Partial Agonist Genistein Length = 255

Iteration: 1
 Score = 45.1 bits (105), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 47/194 (24%), Positives = 77/194 (39%), Gaps = 29/194 (14%)
Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDD 162
           + W + +  F  LS  DQ+ LL+  W E+ ++ L   SI             +    PD 
Sbjct: 56  ISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSID---------HPGKLIFAPDL 106
Query: 163 VRVNNEIKLIQEIL----------ARFRQLSPDGSECGCMKAVILFTPETPGLVDA---- 208
           V   +E K ++ IL          +RFR+L     E  C+KA+IL       LV A    
Sbjct: 107 VLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDA 166
Query: 209 ----QPVEMLQDQAQCILGDYVRGRYS--RQPTRFGRLLLMLPSLRAVRQSTIERLFFKE 262
               +   +L      ++    +   S  +Q  R   LL++L  +R      +E L   +
Sbjct: 167 DSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMK 226
Query: 263 TIGDIPIQRLLGDM 276
               +P+  LL +M
Sbjct: 227 CKNVVPVYDLLLEM 240

>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 = 7e-05,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 95  SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 144
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 145 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 204
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 205 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 264
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 265 TETDMSLHPLLQEIY 279

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 43/159 (27%), Positives = 71/159 (44%), Gaps = 3/159 (1%)
Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD--LSLLINCEKARERLPP 160
           V + + L  F  LS+ DQ+ LL+ S  E+ LL  ++   P    ++ L +    RE    
Sbjct: 64  VDFAKQLPGFLQLSREDQIALLKTSAIEVMLLETSRRYNPGSESITFLKDFSYNREDFAK 123
Query: 161 DDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQC 220
             ++V   I  I E      +L  + +E   + A+ +F+ + P + D   VE LQ     
Sbjct: 124 AGLQVEF-INPIFEFSRAMNELQLNDAEFALLIAISIFSADRPNVQDQLQVERLQHTYVE 182
Query: 221 ILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLF 259
            L  YV   +      F R+L+ L SLR +     E++F
Sbjct: 183 ALHAYVSIHHPHDRLMFPRMLMKLVSLRTLSSVHSEQVF 221

>pdb|2I0G|A Chain A, Benzopyrans Are Selective Estrogen Receptor Beta Agonists (Serbas) With Novel Activity In Models Of Benign Prostatic Hyperplasia Length = 257

Iteration: 1
 Score = 44.7 bits (104), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 47/194 (24%), Positives = 77/194 (39%), Gaps = 29/194 (14%)
Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDD 162
           + W + +  F  LS  DQ+ LL+  W E+ ++ L   SI             +    PD 
Sbjct: 62  ISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSID---------HPGKLIFAPDL 112
Query: 163 VRVNNEIKLIQEIL----------ARFRQLSPDGSECGCMKAVILFTPETPGLVDA---- 208
           V   +E K ++ IL          +RFR+L     E  C+KA+IL       LV A    
Sbjct: 113 VLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDA 172
Query: 209 ----QPVEMLQDQAQCILGDYVRGRYS--RQPTRFGRLLLMLPSLRAVRQSTIERLFFKE 262
               +   +L      ++    +   S  +Q  R   LL++L  +R      +E L   +
Sbjct: 173 DSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMK 232
Query: 263 TIGDIPIQRLLGDM 276
               +P+  LL +M
Sbjct: 233 CKNVVPVYDLLLEM 246

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 50/179 (27%), Positives = 79/179 (44%), Gaps = 5/179 (2%)
Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLL-HL---AQWSIPWDLSLLINCEKARERL 158
           V W R    F+ L   DQ+ LLQ  W EL +  H+    Q      + L+   E     +
Sbjct: 58  VDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQHGKEGSILLVTGQEVELTTV 117
Query: 159 PPDDVRVNNEIKL-IQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQ 217
                 + + + L  QE++ +   L  D  E  C+K +ILF+ +   L +   V+  Q++
Sbjct: 118 ATQAGSLLHSLVLRAQELVLQLLALQLDRQEFVCLKFIILFSLDLKFLNNHILVKDAQEK 177
Query: 218 AQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDM 276
           A   L DY    Y     +F +LLL L  +RA+     E L+ K    ++P   LL +M
Sbjct: 178 ANAALLDYTLCHYPHCGDKFQQLLLCLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIEM 236

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 90  SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 139
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 140 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 199
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 200 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 259
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 260 TETDMSLHPLLQEIY 274

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 96  SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 145
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 146 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 205
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 206 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 265
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 266 TETDMSLHPLLQEIY 280

>pdb|2Q59|A Chain A, Crystal Structure Of Ppargamma Lbd Bound To Full Agonist Mrl20 Length = 274

Iteration: 1
 Score = 44.7 bits (104), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 86  SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 135
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 136 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 195
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 196 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 255
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 256 TETDMSLHPLLQEIY 270

>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 = 44.7 bits (104), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 104 SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 153
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 154 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 213
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 214 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 273
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 274 TETDMSLHPLLQEIY 288

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 87  SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 136
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 137 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 196
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 197 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 256
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 257 TETDMSLHPLLQEIY 271

>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 = 8e-05,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 88  SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 137
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 138 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 197
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 198 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 257
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 258 TETDMSLHPLLQEIY 272

>pdb|2Q59|B Chain B, Crystal Structure Of Ppargamma Lbd Bound To Full Agonist Mrl20 Length = 274

Iteration: 1
 Score = 44.7 bits (104), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 86  SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 135
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 136 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 195
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 196 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 255
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 256 TETDMSLHPLLQEIY 270

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 97  SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 146
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 147 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 206
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 207 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 266
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 267 TETDMSLHPLLQEIY 281

>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 = 8e-05,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 95  SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 144
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 145 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 204
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 205 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 264
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 265 TETDMSLHPLLQEIY 279

>pdb|2VV4|B Chain B, Hppargamma Ligand Binding Domain In Complex With 6-Oxoote Length = 276

Iteration: 1
 Score = 44.7 bits (104), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 88  SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 137
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 138 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 197
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 198 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 257
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 258 TETDMSLHPLLQEIY 272

>pdb|1NDE|A Chain A, Estrogen Receptor Beta With Selective Triazine Modulator Length = 255

Iteration: 1
 Score = 44.7 bits (104), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 47/194 (24%), Positives = 77/194 (39%), Gaps = 29/194 (14%)
Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDD 162
           + W + +  F  LS  DQ+ LL+  W E+ ++ L   SI             +    PD 
Sbjct: 64  ISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSID---------HPGKLIFAPDL 114
Query: 163 VRVNNEIKLIQEIL----------ARFRQLSPDGSECGCMKAVILFTPETPGLVDA---- 208
           V   +E K ++ IL          +RFR+L     E  C+KA+IL       LV A    
Sbjct: 115 VLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDA 174
Query: 209 ----QPVEMLQDQAQCILGDYVRGRYS--RQPTRFGRLLLMLPSLRAVRQSTIERLFFKE 262
               +   +L      ++    +   S  +Q  R   LL++L  +R      +E L   +
Sbjct: 175 DSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMK 234
Query: 263 TIGDIPIQRLLGDM 276
               +P+  LL +M
Sbjct: 235 CKNVVPVYDLLLEM 248

>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 = 8e-05,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 98  SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 147
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 148 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 207
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 208 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 267
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 268 TETDMSLHPLLQEIY 282

>pdb|3ADS|A Chain A, Human Ppargamma Ligand-Binding Domain In Complex With Indomethacin Length = 287

Iteration: 1
 Score = 44.7 bits (104), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 99  SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 148
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 149 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 208
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 209 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 268
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 269 TETDMSLHPLLQEIY 283

>pdb|2ZVT|A Chain A, Cys285ser Mutant Ppargamma Ligand-Binding Domain Complexed With 15-Deoxy-Delta12,14-Prostaglandin J2 Length = 286

Iteration: 1
 Score = 44.7 bits (104), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 99  SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 148
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 149 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 208
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 209 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 268
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 269 TETDMSLHPLLQEIY 283

>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 = 44.7 bits (104), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 86  SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 135
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 136 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 195
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 196 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 255
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 256 TETDMSLHPLLQEIY 270

>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 = 9e-05,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 94  SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 143
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 144 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 203
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 204 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 263
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 264 TETDMSLHPLLQEIY 278

>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 = 9e-05,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 98  SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 147
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 148 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 207
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 208 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 267
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 268 TETDMSLHPLLQEIY 282

>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 = 9e-05,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 96  SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 145
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 146 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 205
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 206 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 265
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 266 TETDMSLHPLLQEIY 280

>pdb|2VSR|A Chain A, Hppargamma Ligand Binding Domain In Complex With 9-(S)-Hode Length = 276

Iteration: 1
 Score = 44.7 bits (104), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 88  SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 137
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 138 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 197
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 198 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 257
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 258 TETDMSLHPLLQEIY 272

>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 = 9e-05,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 88  SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 137
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 138 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 197
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 198 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 257
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 258 TETDMSLHPLLQEIY 272

>pdb|2VV1|B Chain B, Hppargamma Ligand Binding Domain In Complex With 4-Hdha Length = 276

Iteration: 1
 Score = 44.7 bits (104), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 88  SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 137
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 138 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 197
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 198 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 257
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 258 TETDMSLHPLLQEIY 272

>pdb|2I4J|A Chain A, Crystal Structure Of The Complex Between Ppargamma And The Agonist Lt160 (Ureidofibrate Derivative) Length = 286

Iteration: 1
 Score = 44.7 bits (104), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 99  SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 148
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 149 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 208
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 209 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 268
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 269 TETDMSLHPLLQEIY 283

>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 = 44.7 bits (104), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 89  SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 138
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 139 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 198
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 199 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 258
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 259 TETDMSLHPLLQEIY 273

>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 = 9e-05,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 84  SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 133
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 134 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 193
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 194 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 253
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 254 TETDMSLHPLLQEIY 268

>pdb|1QKN|A Chain A, Rat Oestrogen Receptor Beta Ligand-Binding Domain In Complex With Antagonist Raloxifene Length = 255

Iteration: 1
 Score = 44.7 bits (104), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 46/194 (23%), Positives = 76/194 (39%), Gaps = 29/194 (14%)
Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDD 162
           + W + +  F  LS  DQ+ LL+  W E+ ++ L   SI             +    PD 
Sbjct: 56  IGWAKKIPGFVELSLLDQVRLLESCWMEVLMVGLMWRSID---------HPGKLIFAPDL 106
Query: 163 VRVNNEIKLIQEIL----------ARFRQLSPDGSECGCMKAVILFTPETPGLVDAQP-- 210
           V   +E K ++ IL          +RFR+L     E  C+KA+IL       L  A    
Sbjct: 107 VLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLASANQEA 166
Query: 211 ------VEMLQDQAQCILGDYVRGRYS--RQPTRFGRLLLMLPSLRAVRQSTIERLFFKE 262
                   +L      ++    +   S  +Q  R   LL++L  +R +    +E L   +
Sbjct: 167 ESSRKLTHLLNAVTDALVWVIAKSGISSQQQSVRLANLLMLLSHVRHISNKGMEHLLSMK 226
Query: 263 TIGDIPIQRLLGDM 276
               +P+  LL +M
Sbjct: 227 CKNVVPVYDLLLEM 240

>pdb|2J7X|A Chain A, Structure Of Estradiol-bound Estrogen Receptor Beta Lbd In Complex With Lxxll Motif From Ncoa5 Length = 255

Iteration: 1
 Score = 44.7 bits (104), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 46/194 (23%), Positives = 76/194 (39%), Gaps = 29/194 (14%)
Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDD 162
           + W + +  F  LS  DQ+ LL+  W E+ ++ L   SI             +    PD 
Sbjct: 56  IGWAKKIPGFVELSLLDQVRLLESCWMEVLMVGLMWRSID---------HPGKLIFAPDL 106
Query: 163 VRVNNEIKLIQEIL----------ARFRQLSPDGSECGCMKAVILFTPETPGLVDAQP-- 210
           V   +E K ++ IL          +RFR+L     E  C+KA+IL       L  A    
Sbjct: 107 VLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLASANQEA 166
Query: 211 ------VEMLQDQAQCILGDYVRGRYS--RQPTRFGRLLLMLPSLRAVRQSTIERLFFKE 262
                   +L      ++    +   S  +Q  R   LL++L  +R +    +E L   +
Sbjct: 167 ESSRKLTHLLNAVTDALVWVIAKSGISSQQQSVRLANLLMLLSHVRHISNKGMEHLLSMK 226
Query: 263 TIGDIPIQRLLGDM 276
               +P+  LL +M
Sbjct: 227 CKNVVPVYDLLLEM 240

>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 = 1e-04,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 94  SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 143
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 144 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 203
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 204 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 263
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 264 TETDMSLHPLLQEIY 278

>pdb|1WM0|X Chain X, Ppargamma In Complex With A 2-Baba Compound Length = 292

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 104 SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 153
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 154 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 213
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 214 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 273
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 274 TETDMSLHPLLQEIY 288

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 28/105 (26%), Positives = 51/105 (48%), Gaps = 1/105 (0%)
Query: 174 EILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQ 233
           E   +F  L  D S+     AVI+ + + PGL++ +P+E +QD     L   ++  +   
Sbjct: 162 EFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPES 221
Query: 234 PTRFGRLLLMLPSLRAVRQSTIERL-FFKETIGDIPIQRLLGDMY 277
              F +LL  +  LR +    ++ L   K+T  D+ +  LL ++Y
Sbjct: 222 SQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIY 266

>pdb|4PRG|A Chain A, 0072 Partial Agonist Ppar Gamma Cocrystal Length = 270

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 28/105 (26%), Positives = 51/105 (48%), Gaps = 1/105 (0%)
Query: 174 EILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQ 233
           E   +F  L  D S+     AVI+ + + PGL++ +P+E +QD     L   ++  +   
Sbjct: 163 EFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPES 222
Query: 234 PTRFGRLLLMLPSLRAVRQSTIERL-FFKETIGDIPIQRLLGDMY 277
              F +LL  +  LR +    ++ L   K+T  D+ +  LL ++Y
Sbjct: 223 SQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIY 267

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 82  SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 131
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 132 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 191
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 192 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 251
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 252 TETDMSLHPLLQEIY 266

>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 = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 87  SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS 146
           S E  QE T         + + +  F  L   DQ+ LL+    E+    LA  S+     
Sbjct: 96  SVEAVQEIT--------EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDG 145
Query: 147 LLINCEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
           +LI+  +    RE L        + ++   E   +F  L  D S+     AVI+ + + P
Sbjct: 146 VLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP 205
Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKE 262
           GL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+
Sbjct: 206 GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKK 265
Query: 263 TIGDIPIQRLLGDMY 277
           T  D+ +  LL ++Y
Sbjct: 266 TETDMSLHPLLQEIY 280

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 28/105 (26%), Positives = 51/105 (48%), Gaps = 1/105 (0%)
Query: 174 EILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQ 233
           E   +F  L  D S+     AVI+ + + PGL++ +P+E +QD     L   ++  +   
Sbjct: 163 EFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPES 222
Query: 234 PTRFGRLLLMLPSLRAVRQSTIERL-FFKETIGDIPIQRLLGDMY 277
              F +LL  +  LR +    ++ L   K+T  D+ +  LL ++Y
Sbjct: 223 SQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIY 267

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 44/192 (22%), Positives = 82/192 (42%), Gaps = 12/192 (6%)
Query: 97  RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE 156
           R L   + W + +  F  L+  DQ+ LL+ +W E+ ++ L   S+     LL       +
Sbjct: 53  RELVHMINWAKRVPGFVDLTLHDQVHLLESAWLEILMIGLVWRSMEHPGKLLFAPNLLLD 112
Query: 157 RLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILF--------TPETPGLVD 207
           R     V    EI  ++    +RFR ++  G E  C+K++IL         +     L +
Sbjct: 113 RNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEE 172
Query: 208 AQPVEMLQDQAQCILGDYVRG---RYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETI 264
              +  + D+    L   +        +Q  R  +LLL+L  +R +    +E L+  ++ 
Sbjct: 173 KDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKSK 232
Query: 265 GDIPIQRLLGDM 276
             +P+  LL +M
Sbjct: 233 NVVPLYDLLLEM 244

>pdb|1NUO|A Chain A, Two Rth Mutants With Impaired Hormone Binding Length = 261

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 37/158 (23%), Positives = 64/158 (40%)
Query: 102 AVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPD 161
            V + + L  F  L   DQ++LL+    E+  LH A    P   +L +N E A  R    
Sbjct: 83  VVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLHAAVRYDPESETLTLNGEMAVTRGQLK 142
Query: 162 DVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCI 221
           +  +      I ++       + D +E   ++AV+L + + PGL   + +E  QD     
Sbjct: 143 NGGLGVVSDAIFDLGMSLSSFNLDDTEVALLQAVLLMSSDRPGLACVERIEKYQDSFLLA 202
Query: 222 LGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLF 259
              Y+  R       + +LL+ +  LR +      R  
Sbjct: 203 FEHYINYRKHHVTHFWPKLLMKVTDLRMIGACHASRFL 240

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 44/192 (22%), Positives = 82/192 (42%), Gaps = 12/192 (6%)
Query: 97  RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE 156
           R L   + W + +  F  L+  DQ+ LL+ +W E+ ++ L   S+     LL       +
Sbjct: 49  RELVHMINWAKRVPGFVDLTLHDQVHLLESAWLEILMIGLVWRSMEHPGKLLFAPNLLLD 108
Query: 157 RLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILF--------TPETPGLVD 207
           R     V    EI  ++    +RFR ++  G E  C+K++IL         +     L +
Sbjct: 109 RNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEE 168
Query: 208 AQPVEMLQDQAQCILGDYVRG---RYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETI 264
              +  + D+    L   +        +Q  R  +LLL+L  +R +    +E L+  ++ 
Sbjct: 169 KDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKSK 228
Query: 265 GDIPIQRLLGDM 276
             +P+  LL +M
Sbjct: 229 NVVPLYDLLLEM 240

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 44/192 (22%), Positives = 82/192 (42%), Gaps = 12/192 (6%)
Query: 97  RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE 156
           R L   + W + +  F  L+  DQ+ LL+ +W E+ ++ L   S+     LL       +
Sbjct: 53  RELVHMINWAKRVPGFVDLTLHDQVHLLESAWLEILMIGLVWRSMEHPGKLLFAPNLLLD 112
Query: 157 RLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILF--------TPETPGLVD 207
           R     V    EI  ++    +RFR ++  G E  C+K++IL         +     L +
Sbjct: 113 RNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEE 172
Query: 208 AQPVEMLQDQAQCILGDYVRG---RYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETI 264
              +  + D+    L   +        +Q  R  +LLL+L  +R +    +E L+  ++ 
Sbjct: 173 KDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKSK 232
Query: 265 GDIPIQRLLGDM 276
             +P+  LL +M
Sbjct: 233 NVVPLYDLLLEM 244

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 44/192 (22%), Positives = 82/192 (42%), Gaps = 12/192 (6%)
Query: 97  RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE 156
           R L   + W + +  F  L+  DQ+ LL+ +W E+ ++ L   S+     LL       +
Sbjct: 49  RELVHMINWAKRVPGFVDLTLHDQVHLLESAWLEILMIGLVWRSMEHPGKLLFAPNLLLD 108
Query: 157 RLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILF--------TPETPGLVD 207
           R     V    EI  ++    +RFR ++  G E  C+K++IL         +     L +
Sbjct: 109 RNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEE 168
Query: 208 AQPVEMLQDQAQCILGDYVRG---RYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETI 264
              +  + D+    L   +        +Q  R  +LLL+L  +R +    +E L+  ++ 
Sbjct: 169 KDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKSK 228
Query: 265 GDIPIQRLLGDM 276
             +P+  LL +M
Sbjct: 229 NVVPLYDLLLEM 240

>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 = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 44/192 (22%), Positives = 81/192 (42%), Gaps = 12/192 (6%)
Query: 97  RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE 156
           R L   + W + +  F  L+  DQ+ LL+ +W E+ ++ L   S+     LL       +
Sbjct: 55  RELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFAPNLLLD 114
Query: 157 RLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILF--------TPETPGLVD 207
           R     V    EI  ++    +RFR ++  G E  C+K++IL         +     L +
Sbjct: 115 RNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEE 174
Query: 208 AQPVEMLQDQAQCILGDYVRG---RYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETI 264
              +  + D+    L   +        +Q  R  +LLL+L  +R +    +E L+  +  
Sbjct: 175 KDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCK 234
Query: 265 GDIPIQRLLGDM 276
             +P+  LL +M
Sbjct: 235 NVVPLSDLLLEM 246

>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 = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 45/191 (23%), Positives = 83/191 (43%), Gaps = 6/191 (3%)
Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
           CQ  +   +     + + +  F  L   DQ+ LL+    E+    LA  S+     +LI+
Sbjct: 227 CQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLIS 284
Query: 151 CEKA---RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVD 207
             +    RE L        + ++   E   +F  L  D S+     AVI+ + + PGL++
Sbjct: 285 EGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLN 344
Query: 208 AQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL-FFKETIGD 266
            +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L   K+T  D
Sbjct: 345 VKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETD 404
Query: 267 IPIQRLLGDMY 277
           + +  LL ++Y
Sbjct: 405 MSLHPLLQEIY 415

>pdb|3JZC|A Chain A, Crystal Structure Of Tr-Beta Bound To The Selective Thyromimetic Triac Length = 263

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 36/157 (22%), Positives = 63/157 (40%)
Query: 102 AVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPD 161
            V + + L  F  L   DQ++LL+    E+  L  A    P   +L +N E A  R    
Sbjct: 85  VVDFAKKLPMFXELPXEDQIILLKGCCMEIMSLRAAVRYDPESETLTLNGEMAVTRGQLK 144
Query: 162 DVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCI 221
           +  +      I ++       + D +E   ++AV+L + + PGL   + +E  QD     
Sbjct: 145 NGGLGVVSDAIFDLGMSLSSFNLDDTEVALLQAVLLMSSDRPGLAXVERIEKYQDSFLLA 204
Query: 222 LGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 258
              Y+  R       + +LL+ +  LR +      R 
Sbjct: 205 FEHYINYRKHHVTHFWPKLLMKVTDLRMIGAXHASRF 241

>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 = 43.1 bits (100), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 44/192 (22%), Positives = 81/192 (42%), Gaps = 12/192 (6%)
Query: 97  RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE 156
           R L   + W + +  F  L+  DQ+ LL+ +W E+ ++ L   S+     LL       +
Sbjct: 55  RELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFAPNLLLD 114
Query: 157 RLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILF--------TPETPGLVD 207
           R     V    EI  ++    +RFR ++  G E  C+K++IL         +     L +
Sbjct: 115 RNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEE 174
Query: 208 AQPVEMLQDQAQCILGDYVRG---RYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETI 264
              +  + D+    L   +        +Q  R  +LLL+L  +R +    +E L+  +  
Sbjct: 175 KDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKXK 234
Query: 265 GDIPIQRLLGDM 276
             +P+  LL +M
Sbjct: 235 NVVPLSDLLLEM 246

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 35/171 (20%), Positives = 70/171 (40%)
Query: 89  EKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLL 148
           +K  E   + +   V + + L  F  L+  DQ+ LL+ +  ++ +L +     P   ++ 
Sbjct: 72  DKFSELATKCIIKIVEFAKRLPGFTGLTIADQITLLKAACLDILILRICTRYTPEQDTMT 131
Query: 149 INCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDA 208
            +      R    +        L+     +   L  D +E G + A+ L   +   L + 
Sbjct: 132 FSDGLTLNRTQMHNAGFGPLTDLVFTFANQLLPLEMDDTETGLLSAICLICGDRQDLEEP 191
Query: 209 QPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLF 259
             V+ LQ+     L  Y+R R   +P  F ++L+ +  LR++     ER+ 
Sbjct: 192 TKVDKLQEPLLEALKIYIRKRRPSKPHMFPKILMKITDLRSISAKGAERVI 242

>pdb|3UU7|B Chain B, Crystal Structure Of Hera-Lbd (Y537s) In Complex With Bisphenol-A Length = 251

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 44/192 (22%), Positives = 81/192 (42%), Gaps = 12/192 (6%)
Query: 97  RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE 156
           R L   + W + +  F  L+  DQ+ LL+ +W E+ ++ L   S+     LL       +
Sbjct: 51  RELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFAPNLLLD 110
Query: 157 RLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILF--------TPETPGLVD 207
           R     V    EI  ++    +RFR ++  G E  C+K++IL         +     L +
Sbjct: 111 RNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEE 170
Query: 208 AQPVEMLQDQAQCILGDYVRG---RYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETI 264
              +  + D+    L   +        +Q  R  +LLL+L  +R +    +E L+  +  
Sbjct: 171 KDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKXK 230
Query: 265 GDIPIQRLLGDM 276
             +P+  LL +M
Sbjct: 231 NVVPLSDLLLEM 242

>pdb|3Q97|A Chain A, Crystal Structure Of Human Estrogen Receptor Alpha Lbd In Complex With Grip Peptide And Two Isomers Of Ethoxy Triphenylethylene Length = 260

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 44/192 (22%), Positives = 81/192 (42%), Gaps = 12/192 (6%)
Query: 97  RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE 156
           R L   + W + +  F  L+  DQ+ LL+ +W E+ ++ L   S+     LL       +
Sbjct: 58  RELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFAPNLLLD 117
Query: 157 RLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILF--------TPETPGLVD 207
           R     V    EI  ++    +RFR ++  G E  C+K++IL         +     L +
Sbjct: 118 RNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEE 177
Query: 208 AQPVEMLQDQAQCILGDYVRG---RYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETI 264
              +  + D+    L   +        +Q  R  +LLL+L  +R +    +E L+  +  
Sbjct: 178 KDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKXK 237
Query: 265 GDIPIQRLLGDM 276
             +P+  LL +M
Sbjct: 238 NVVPLSDLLLEM 249

>pdb|3UU7|A Chain A, Crystal Structure Of Hera-Lbd (Y537s) In Complex With Bisphenol-A Length = 251

Iteration: 1
 Score = 42.7 bits (99), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 44/192 (22%), Positives = 81/192 (42%), Gaps = 12/192 (6%)
Query: 97  RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE 156
           R L   + W + +  F  L+  DQ+ LL+ +W E+ ++ L   S+     LL       +
Sbjct: 51  RELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFAPNLLLD 110
Query: 157 RLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILF--------TPETPGLVD 207
           R     V    EI  ++    +RFR ++  G E  C+K++IL         +     L +
Sbjct: 111 RNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEE 170
Query: 208 AQPVEMLQDQAQCILGDYVRG---RYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETI 264
              +  + D+    L   +        +Q  R  +LLL+L  +R +    +E L+  +  
Sbjct: 171 KDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCK 230
Query: 265 GDIPIQRLLGDM 276
             +P+  LL +M
Sbjct: 231 NVVPLSDLLLEM 242

>pdb|3Q95|B Chain B, Crystal Structure Of Human Estrogen Receptor Alpha Lbd In Complex With Grip Peptide And Estriol Length = 260

Iteration: 1
 Score = 42.7 bits (99), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 44/192 (22%), Positives = 81/192 (42%), Gaps = 12/192 (6%)
Query: 97  RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE 156
           R L   + W + +  F  L+  DQ+ LL+ +W E+ ++ L   S+     LL       +
Sbjct: 58  RELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFAPNLLLD 117
Query: 157 RLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILF--------TPETPGLVD 207
           R     V    EI  ++    +RFR ++  G E  C+K++IL         +     L +
Sbjct: 118 RNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEE 177
Query: 208 AQPVEMLQDQAQCILGDYVRG---RYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETI 264
              +  + D+    L   +        +Q  R  +LLL+L  +R +    +E L+  +  
Sbjct: 178 KDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCK 237
Query: 265 GDIPIQRLLGDM 276
             +P+  LL +M
Sbjct: 238 NVVPLSDLLLEM 249

>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 = 42.7 bits (99), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 36/155 (23%), Positives = 72/155 (46%), Gaps = 6/155 (3%)
Query: 102 AVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPD 161
            + + + +  F+ L+  DQ+ LL+ S  E+ +L   Q     D+S   +C     +   +
Sbjct: 118 VIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLRSNQSFSLEDMSW--SCGGPDFKYCIN 175
Query: 162 DVRVNNEIKLIQEILARF----RQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQ 217
           DV        + E L +F    ++L     E   + A+ L +P+ PG+ D   +E LQD+
Sbjct: 176 DVTKAGHTLELLEPLVKFQVGLKKLKLHEEEHVLLMAICLLSPDRPGVQDHVRIEALQDR 235
Query: 218 AQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQ 252
              +L  Y+R ++      + +++  L  LR++ +
Sbjct: 236 LCDVLQAYIRIQHPGGRLLYAKMIQKLADLRSLNE 270

>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 = 42.4 bits (98), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 36/155 (23%), Positives = 72/155 (46%), Gaps = 6/155 (3%)
Query: 102 AVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPD 161
            + + + +  F+ L+  DQ+ LL+ S  E+ +L   Q     D+S   +C     +   +
Sbjct: 116 VIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLRSNQSFSLEDMSW--SCGGPDFKYCIN 173
Query: 162 DVRVNNEIKLIQEILARF----RQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQ 217
           DV        + E L +F    ++L     E   + A+ L +P+ PG+ D   +E LQD+
Sbjct: 174 DVTKAGHTLELLEPLVKFQVGLKKLKLHEEEHVLLMAICLLSPDRPGVQDHVRIEALQDR 233
Query: 218 AQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQ 252
              +L  Y+R ++      + +++  L  LR++ +
Sbjct: 234 LCDVLQAYIRIQHPGGRLLYAKMIQKLADLRSLNE 268

>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 = 42.4 bits (98), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 44/192 (22%), Positives = 81/192 (42%), Gaps = 12/192 (6%)
Query: 97  RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE 156
           R L   + W + +  F  L+  DQ+ LL+ +W E+ ++ L   S+     LL       +
Sbjct: 55  RELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFAPNLLLD 114
Query: 157 RLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILF--------TPETPGLVD 207
           R     V    EI  ++    +RFR ++  G E  C+K++IL         +     L +
Sbjct: 115 RNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEE 174
Query: 208 AQPVEMLQDQAQCILGDYVRG---RYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETI 264
              +  + D+    L   +        +Q  R  +LLL+L  +R +    +E L+  +  
Sbjct: 175 KDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKXK 234
Query: 265 GDIPIQRLLGDM 276
             +P+  LL +M
Sbjct: 235 NVVPLSDLLLEM 246

>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 = 42.4 bits (98), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 35/171 (20%), Positives = 70/171 (40%)
Query: 89  EKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLL 148
           +K  E   + +   V + + L  F  L+  DQ+ LL+ +  ++ +L +     P   ++ 
Sbjct: 74  DKFSELATKCIIKIVEFAKRLPGFTGLTIADQITLLKAACLDILILRICTRYTPEQDTMT 133
Query: 149 INCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDA 208
            +      R    +        L+     +   L  D +E G + A+ L   +   L + 
Sbjct: 134 FSDGLTLNRTQMHNAGFGPLTDLVFTFANQLLPLEMDDTETGLLSAICLICGDRQDLEEP 193
Query: 209 QPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLF 259
             V+ LQ+     L  Y+R R   +P  F ++L+ +  LR++     ER+ 
Sbjct: 194 TKVDKLQEPLLEALKIYIRKRRPSKPHMFPKILMKITDLRSISAKGAERVI 244

>pdb|3IMY|A Chain A, Structure Of Tr-Beta Bound To Selective Thyromimetic Gc-1 Length = 261

Iteration: 1
 Score = 42.0 bits (97), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 36/157 (22%), Positives = 63/157 (40%)
Query: 102 AVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPD 161
            V + + L  F  L   DQ++LL+    E+  L  A    P   +L +N E A  R    
Sbjct: 83  VVDFAKKLPMFXELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLNGEMAVTRGQLK 142
Query: 162 DVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCI 221
           +  +      I ++       + D +E   ++AV+L + + PGL   + +E  QD     
Sbjct: 143 NGGLGVVSDAIFDLGMSLSSFNLDDTEVALLQAVLLMSSDRPGLAXVERIEKYQDSFLLA 202
Query: 222 LGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 258
              Y+  R       + +LL+ +  LR +      R 
Sbjct: 203 FEHYINYRKHHVTHFWPKLLMKVTDLRMIGAXHASRF 239

>pdb|3GWS|X Chain X, Crystal Structure Of T3-Bound Thyroid Hormone Receptor Length = 259

Iteration: 1
 Score = 42.0 bits (97), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 36/157 (22%), Positives = 63/157 (40%)
Query: 102 AVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPD 161
            V + + L  F  L   DQ++LL+    E+  L  A    P   +L +N E A  R    
Sbjct: 82  VVDFAKKLPMFXELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLNGEMAVTRGQLK 141
Query: 162 DVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCI 221
           +  +      I ++       + D +E   ++AV+L + + PGL   + +E  QD     
Sbjct: 142 NGGLGVVSDAIFDLGMSLSSFNLDDTEVALLQAVLLMSSDRPGLAXVERIEKYQDSFLLA 201
Query: 222 LGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 258
              Y+  R       + +LL+ +  LR +      R 
Sbjct: 202 FEHYINYRKHHVTHFWPKLLMKVTDLRMIGAXHASRF 238

>pdb|3UUA|B Chain B, Crystal Structure Of Hera-Lbd (Y537s) In Complex With Bisphenol-Af Length = 251

Iteration: 1
 Score = 42.0 bits (97), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 44/192 (22%), Positives = 81/192 (42%), Gaps = 12/192 (6%)
Query: 97  RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE 156
           R L   + W + +  F  L+  DQ+ LL+ +W E+ ++ L   S+     LL       +
Sbjct: 51  RELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFAPNLLLD 110
Query: 157 RLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILF--------TPETPGLVD 207
           R     V    EI  ++    +RFR ++  G E  C+K++IL         +     L +
Sbjct: 111 RNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEE 170
Query: 208 AQPVEMLQDQAQCILGDYVRG---RYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETI 264
              +  + D+    L   +        +Q  R  +LLL+L  +R +    +E L+  +  
Sbjct: 171 KDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKXK 230
Query: 265 GDIPIQRLLGDM 276
             +P+  LL +M
Sbjct: 231 NVVPLSDLLLEM 242

>pdb|2QZO|B Chain B, Crystal Structure Of The Estrogen Receptor Alpha Ligand Binding Domain Complexed With Way-169916 Length = 258

Iteration: 1
 Score = 42.0 bits (97), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 44/192 (22%), Positives = 81/192 (42%), Gaps = 12/192 (6%)
Query: 97  RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE 156
           R L   + W + +  F  L+  DQ+ LL+ +W E+ ++ L   S+     LL       +
Sbjct: 56  RELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFAPNLLLD 115
Query: 157 RLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILF--------TPETPGLVD 207
           R     V    EI  ++    +RFR ++  G E  C+K++IL         +     L +
Sbjct: 116 RNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEE 175
Query: 208 AQPVEMLQDQAQCILGDYVRG---RYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETI 264
              +  + D+    L   +        +Q  R  +LLL+L  +R +    +E L+  +  
Sbjct: 176 KDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKXK 235
Query: 265 GDIPIQRLLGDM 276
             +P+  LL +M
Sbjct: 236 NVVPLSDLLLEM 247

>pdb|3H52|A Chain A, Crystal Structure Of The Antagonist Form Of Human Glucocorticoid Receptor Length = 254

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 46/199 (23%), Positives = 85/199 (42%), Gaps = 24/199 (12%)
Query: 96  ARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWS--------IPWDLSL 147
            R +  AV+W + +  F+ L   DQ+ LLQ SW  L    L   S        + +   L
Sbjct: 45  GRQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMSLMAFALGWRSYRQSSANLLCFAPDL 104
Query: 148 LINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTP------E 201
           +IN  + R  LP     + ++ K +  + +   +L     E  CMK ++L +       +
Sbjct: 105 IIN--EQRMTLPD----MYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSSVPKDGLK 158
Query: 202 TPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLF-- 259
           +  L DA  +  +++  + I+     G  S+   RF +L  +L S+  V ++ +   F  
Sbjct: 159 SQALFDAIRMTYIKELGKAIVKR--EGNSSQNSQRFYQLTKLLDSMHEVVENLLNYCFQT 216
Query: 260 FKETIGDIPIQRLLGDMYT 278
           F +    I    +L ++ T
Sbjct: 217 FLDKTMSIEFPEMLAEIIT 235

>pdb|3UUA|A Chain A, Crystal Structure Of Hera-Lbd (Y537s) In Complex With Bisphenol-Af Length = 251

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 44/192 (22%), Positives = 81/192 (42%), Gaps = 12/192 (6%)
Query: 97  RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE 156
           R L   + W + +  F  L+  DQ+ LL+ +W E+ ++ L   S+     LL       +
Sbjct: 51  RELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFAPNLLLD 110
Query: 157 RLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILF--------TPETPGLVD 207
           R     V    EI  ++    +RFR ++  G E  C+K++IL         +     L +
Sbjct: 111 RNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEE 170
Query: 208 AQPVEMLQDQAQCILGDYVRG---RYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETI 264
              +  + D+    L   +        +Q  R  +LLL+L  +R +    +E L+  +  
Sbjct: 171 KDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCK 230
Query: 265 GDIPIQRLLGDM 276
             +P+  LL +M
Sbjct: 231 NVVPLSDLLLEM 242

>pdb|2H79|A Chain A, Crystal Structure Of Human Tr Alpha Bound T3 In Orthorhombic Space Group Length = 269

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 38/151 (25%), Positives = 67/151 (44%), Gaps = 4/151 (2%)
Query: 102 AVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKA--RERLP 159
            V + + L  F  L   DQ++LL+    E+  L  A    P   +L ++ E A  RE+L 
Sbjct: 88  VVDFAKKLPMFSELPXEDQIILLKGCCMEIMSLRAAVRYDPESDTLTLSGEMAVKREQLK 147
Query: 160 PDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQ 219
              + V ++   I E+       + D +E   ++AV+L + +  GL+    +E  Q+   
Sbjct: 148 NGGLGVVSDA--IFELGKSLSAFNLDDTEVALLQAVLLMSTDRSGLLXVDKIEKSQEAYL 205
Query: 220 CILGDYVRGRYSRQPTRFGRLLLMLPSLRAV 250
                YV  R    P  + +LL+ +  LR +
Sbjct: 206 LAFEHYVNHRKHNIPHFWPKLLMKVTDLRMI 236

>pdb|3JZB|A Chain A, Crystal Structure Of Tr-Alfa Bound To The Selective Thyromimetic Triac Length = 267

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 38/151 (25%), Positives = 67/151 (44%), Gaps = 4/151 (2%)
Query: 102 AVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKA--RERLP 159
            V + + L  F  L   DQ++LL+    E+  L  A    P   +L ++ E A  RE+L 
Sbjct: 86  VVDFAKKLPMFSELPXEDQIILLKGCCMEIMSLRAAVRYDPESDTLTLSGEMAVKREQLK 145
Query: 160 PDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQ 219
              + V ++   I E+       + D +E   ++AV+L + +  GL+    +E  Q+   
Sbjct: 146 NGGLGVVSDA--IFELGKSLSAFNLDDTEVALLQAVLLMSTDRSGLLXVDKIEKSQEAYL 203
Query: 220 CILGDYVRGRYSRQPTRFGRLLLMLPSLRAV 250
                YV  R    P  + +LL+ +  LR +
Sbjct: 204 LAFEHYVNHRKHNIPHFWPKLLMKVTDLRMI 234

>pdb|3HZF|A Chain A, Structure Of Tr-alfa Bound To Selective Thyromimetic Gc-1 In C2 Space Group Length = 269

Iteration: 1
 Score = 41.6 bits (96), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 38/151 (25%), Positives = 67/151 (44%), Gaps = 4/151 (2%)
Query: 102 AVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKA--RERLP 159
            V + + L  F  L   DQ++LL+    E+  L  A    P   +L ++ E A  RE+L 
Sbjct: 88  VVDFAKKLPMFSELPXEDQIILLKGCCMEIMSLRAAVRYDPESDTLTLSGEMAVKREQLK 147
Query: 160 PDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQ 219
              + V ++   I E+       + D +E   ++AV+L + +  GL+    +E  Q+   
Sbjct: 148 NGGLGVVSDA--IFELGKSLSAFNLDDTEVALLQAVLLMSTDRSGLLXVDKIEKSQEAYL 205
Query: 220 CILGDYVRGRYSRQPTRFGRLLLMLPSLRAV 250
                YV  R    P  + +LL+ +  LR +
Sbjct: 206 LAFEHYVNHRKHNIPHFWPKLLMKVTDLRMI 236

>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 = 41.6 bits (96), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 44/192 (22%), Positives = 81/192 (42%), Gaps = 12/192 (6%)
Query: 97  RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE 156
           R L   + W + +  F  L+  DQ+ LL+ +W E+ ++ L   S+     LL       +
Sbjct: 56  RELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFAPNLLLD 115
Query: 157 RLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILF--------TPETPGLVD 207
           R     V    EI  ++    +RFR ++  G E  C+K++IL         +     L +
Sbjct: 116 RNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEE 175
Query: 208 AQPVEMLQDQAQCILGDYVRG---RYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETI 264
              +  + D+    L   +        +Q  R  +LLL+L  +R +    +E L+  +  
Sbjct: 176 KDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCK 235
Query: 265 GDIPIQRLLGDM 276
             +P+  LL +M
Sbjct: 236 NVVPLSDLLLEM 247

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 41/162 (25%), Positives = 74/162 (45%), Gaps = 9/162 (5%)
Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQW--SIPWDLSLLINCEKARERLPP 160
           V + + +  F  L + DQ+ LL+ S  E+ LL  A+        ++ L +   +++    
Sbjct: 75  VDFAKQVPGFLQLGREDQIALLKASTIEIMLLETARRYNHETESITFLKDFTYSKD---- 130
Query: 161 DDVRVNNEIKLIQEILARFRQLSP---DGSECGCMKAVILFTPETPGLVDAQPVEMLQDQ 217
           D  R   +++ I  I    R +S    D +E   + A+ +F+ + P + +   VE LQ  
Sbjct: 131 DFHRAGLQVEFINPIFEFSRAMSSLGLDDAEYALLIAINIFSADRPNVQEPGRVEALQQP 190
Query: 218 AQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLF 259
               L  Y R +  +   RF R+L+ L SLR +     E++F
Sbjct: 191 YVEALLSYTRIKRPQDQLRFPRMLMKLVSLRTLSSVHSEQVF 232

>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 = 41.6 bits (96), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 44/192 (22%), Positives = 81/192 (42%), Gaps = 12/192 (6%)
Query: 97  RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE 156
           R L   + W + +  F  L+  DQ+ LL+ +W E+ ++ L   S+     LL       +
Sbjct: 58  RELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFAPNLLLD 117
Query: 157 RLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILF--------TPETPGLVD 207
           R     V    EI  ++    +RFR ++  G E  C+K++IL         +     L +
Sbjct: 118 RNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEE 177
Query: 208 AQPVEMLQDQAQCILGDYVRG---RYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETI 264
              +  + D+    L   +        +Q  R  +LLL+L  +R +    +E L+  +  
Sbjct: 178 KDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCK 237
Query: 265 GDIPIQRLLGDM 276
             +P+  LL +M
Sbjct: 238 NVVPLSDLLLEM 249

>pdb|1ERR|A Chain A, Human Estrogen Receptor Ligand-Binding Domain In Complex With Raloxifene Length = 253

Iteration: 1
 Score = 41.2 bits (95), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 44/192 (22%), Positives = 81/192 (42%), Gaps = 12/192 (6%)
Query: 97  RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE 156
           R L   + W + +  F  L+  DQ+ LL+ +W E+ ++ L   S+     LL       +
Sbjct: 52  RELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFAPNLLLD 111
Query: 157 RLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILF--------TPETPGLVD 207
           R     V    EI  ++    +RFR ++  G E  C+K++IL         +     L +
Sbjct: 112 RNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEE 171
Query: 208 AQPVEMLQDQAQCILGDYVRG---RYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETI 264
              +  + D+    L   +        +Q  R  +LLL+L  +R +    +E L+  +  
Sbjct: 172 KDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCK 231
Query: 265 GDIPIQRLLGDM 276
             +P+  LL +M
Sbjct: 232 NVVPLYDLLLEM 243

>pdb|1X7E|A Chain A, Crystal Structure Of Estrogen Receptor Alpha Complexed With Way-244 Length = 245

Iteration: 1
 Score = 41.2 bits (95), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 44/192 (22%), Positives = 82/192 (42%), Gaps = 12/192 (6%)
Query: 97  RLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE 156
           R L   + W + +  F  L+  DQ+ LL+ +W E+ ++ L   S+   + LL       +
Sbjct: 48  RELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPVKLLFAPNLLLD 107
Query: 157 RLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILF--------TPETPGLVD 207
           R     V    EI  ++    +RFR ++  G E  C+K++IL         +     L +
Sbjct: 108 RNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEE 167
Query: 208 AQPVEMLQDQAQCILGDYVRG---RYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETI 264
              +  + D+    L   +        +Q  R  +LLL+L  +R +    +E L+  +  
Sbjct: 168 KDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCK 227
Query: 265 GDIPIQRLLGDM 276
             +P+  LL +M
Sbjct: 228 NVVPLYDLLLEM 239

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	367
1pzl_A	237	Hepatocyte nuclear factor 4-alpha; transcription;	7e-69
1pzl_A	237	Hepatocyte nuclear factor 4-alpha; transcription;	2e-25
1ymt_A	246	Steroidogenic factor 1; SF-1, ligand-binding domai	2e-68
1ymt_A	246	Steroidogenic factor 1; SF-1, ligand-binding domai	8e-27
2nxx_A	235	Ultraspiracle (USP, NR2B4); hormone receptor, APO	1e-67
2nxx_A	235	Ultraspiracle (USP, NR2B4); hormone receptor, APO	1e-25
3plz_A	257	FTZ-F1 related protein; alpha helical sandwhich, f	4e-66
3plz_A	257	FTZ-F1 related protein; alpha helical sandwhich, f	1e-25
3cjw_A	244	COUP transcription factor 2; COUP-TFII, nuclear re	3e-65
3cjw_A	244	COUP transcription factor 2; COUP-TFII, nuclear re	9e-25
2e2r_A	244	Estrogen-related receptor gamma; ERR gamma, BPA, n	5e-65
2e2r_A	244	Estrogen-related receptor gamma; ERR gamma, BPA, n	2e-23
1lbd_A	282	RXR_LBD, retinoid X receptor; transcription factor	5e-65
1lbd_A	282	RXR_LBD, retinoid X receptor; transcription factor	1e-23
3p0u_A	249	Nuclear receptor subfamily 2 group C member 2; lig	1e-64
3p0u_A	249	Nuclear receptor subfamily 2 group C member 2; lig	9e-24
2p1t_A	240	Retinoic acid receptor RXR-alpha; protein-ligand c	3e-64
2p1t_A	240	Retinoic acid receptor RXR-alpha; protein-ligand c	4e-24
1g2n_A	264	Ultraspiracle protein; antiparallel alpha-helical	3e-64
1g2n_A	264	Ultraspiracle protein; antiparallel alpha-helical	5e-25
3k6p_A	248	Steroid hormone receptor ERR1; estrogen related re	6e-64
3k6p_A	248	Steroid hormone receptor ERR1; estrogen related re	5e-21
3tx7_B	352	Nuclear receptor subfamily 5 group A member 2; LRH	1e-63
3tx7_B	352	Nuclear receptor subfamily 5 group A member 2; LRH	4e-24
2iz2_A	243	FTZ-F1 alpha, nuclear hormone receptor FTZ-F1; nuc	4e-63
2iz2_A	243	FTZ-F1 alpha, nuclear hormone receptor FTZ-F1; nuc	4e-24
1hg4_A	279	Ultraspiracle; nuclear hormone receptor, transcrip	8e-59
3ltx_A	243	Estrogen receptor; constitutive, nuclear receptor,	3e-58
3ltx_A	243	Estrogen receptor; constitutive, nuclear receptor,	8e-22
3u9q_A	269	Peroxisome proliferator-activated receptor gamma;	5e-56
3u9q_A	269	Peroxisome proliferator-activated receptor gamma;	2e-20
1ovl_A	271	Orphan nuclear receptor NURR1 (MSe 414, 496, 511);	3e-55
1ovl_A	271	Orphan nuclear receptor NURR1 (MSe 414, 496, 511);	1e-20
3f5c_B	268	Nuclear receptor subfamily 0 group B member 1; tra	1e-53
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	5e-53
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	8e-19
2ocf_A	298	Estrogen receptor; estrogen receptor, LBD, monobod	2e-51
2ocf_A	298	Estrogen receptor; estrogen receptor, LBD, monobod	5e-17
3oll_A	240	Estrogen receptor beta; steroid binding, phosphory	4e-50
3oll_A	240	Estrogen receptor beta; steroid binding, phosphory	3e-13
1xpc_A	248	Estrogen receptor; nuclear receptor, transcription	8e-50
1xpc_A	248	Estrogen receptor; nuclear receptor, transcription	6e-17
1yje_A	264	Orphan nuclear receptor NR4A1; NGFI-B, NUR77, liga	1e-49
1yje_A	264	Orphan nuclear receptor NR4A1; NGFI-B, NUR77, liga	2e-19
1t7r_A	269	Androgen receptor; nuclear receptor, transcription	2e-46
1t7r_A	269	Androgen receptor; nuclear receptor, transcription	4e-15
3ipq_A	283	Oxysterols receptor LXR-alpha; LXR homodimer, LXR	7e-46
3ipq_A	283	Oxysterols receptor LXR-alpha; LXR homodimer, LXR	3e-15
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	1e-45
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	3e-16
3n00_A	245	REV-ERBA-alpha; reverba ncorid1, anti-parallel B-s	2e-45
3n00_A	245	REV-ERBA-alpha; reverba ncorid1, anti-parallel B-s	8e-13
1xvp_B	246	Orphan nuclear receptor NR1I3; CAR, RXR, citco, SR	2e-45
1xvp_B	246	Orphan nuclear receptor NR1I3; CAR, RXR, citco, SR	2e-14
1fcy_A	236	RAR-gamma-1, retinoic acid receptor gamma-1; isoty	2e-45
1fcy_A	236	RAR-gamma-1, retinoic acid receptor gamma-1; isoty	2e-16
3kmr_A	266	Retinoic acid receptor alpha; nuclear receptor tra	3e-44
3kmr_A	266	Retinoic acid receptor alpha; nuclear receptor tra	2e-15
1yye_A	268	ER-beta, estrogen receptor beta; ER-beta, nuclear	5e-44
1yye_A	268	ER-beta, estrogen receptor beta; ER-beta, nuclear	9e-12
3cqv_A	199	Nuclear receptor subfamily 1 group D member 2; rev	7e-44
3cqv_A	199	Nuclear receptor subfamily 1 group D member 2; rev	3e-13
1l2j_A	271	Estrogen receptor beta; nuclear receptor, transcri	1e-43
1l2j_A	271	Estrogen receptor beta; nuclear receptor, transcri	1e-11
1pdu_A	244	DHR38, nuclear hormone receptor HR38; nuclear rece	2e-43
1pdu_A	244	DHR38, nuclear hormone receptor HR38; nuclear rece	3e-17
2hc4_A	302	Vitamin D receptor; alpha helical sandwich, gene r	3e-43
2hc4_A	302	Vitamin D receptor; alpha helical sandwich, gene r	4e-15
1xdk_B	303	RAR-beta, retinoic acid receptor, beta; nuclear re	4e-42
1xdk_B	303	RAR-beta, retinoic acid receptor, beta; nuclear re	5e-15
3mnp_A	261	Glucocorticoid receptor; protein-ligand complex, s	6e-40
3mnp_A	261	Glucocorticoid receptor; protein-ligand complex, s	4e-13
3ilz_A	267	Thyroid hormone receptor, alpha isoform 1 variant;	2e-39
3ilz_A	267	Thyroid hormone receptor, alpha isoform 1 variant;	1e-11
1osh_A	232	BIle acid receptor; nuclear receptor, ligand bindi	3e-39
1osh_A	232	BIle acid receptor; nuclear receptor, ligand bindi	1e-14
2p54_A	267	PPAR-alpha, peroxisome proliferator-activated rece	7e-39
2p54_A	267	PPAR-alpha, peroxisome proliferator-activated rece	8e-13
1nrl_A	316	Orphan nuclear receptor PXR; PXR, xenobiotic, SRC-	9e-39
1nrl_A	316	Orphan nuclear receptor PXR; PXR, xenobiotic, SRC-	6e-11
2o4j_A	292	Vitamin D3 receptor; nuclear receptor-ligand compl	2e-37
2o4j_A	292	Vitamin D3 receptor; nuclear receptor-ligand compl	2e-10
1sqn_A	261	PR, progesterone receptor; nuclear receptor, stero	1e-36
1sqn_A	261	PR, progesterone receptor; nuclear receptor, stero	2e-09
1nq7_A	244	Nuclear receptor ROR-beta; ligand-binding domain,	4e-35
1nq7_A	244	Nuclear receptor ROR-beta; ligand-binding domain,	7e-10
3b0t_A	254	Vitamin D3 receptor; nuclear receptor, transcripti	6e-33
3b0t_A	254	Vitamin D3 receptor; nuclear receptor, transcripti	2e-09
3vhu_A	294	Mineralocorticoid receptor; nuclear receptor, tran	9e-33
3vhu_A	294	Mineralocorticoid receptor; nuclear receptor, tran	3e-09
3vhv_A	260	Mineralocorticoid receptor; nuclear receptor, tran	3e-32
3vhv_A	260	Mineralocorticoid receptor; nuclear receptor, tran	1e-09
1n83_A	270	Nuclear receptor ROR-alpha; three-layered alpha he	1e-31
1n83_A	270	Nuclear receptor ROR-alpha; three-layered alpha he	5e-09
2r40_D	266	Ecdysone receptor, 20-hydroxy-ecdysone receptor; n	1e-30
2r40_D	266	Ecdysone receptor, 20-hydroxy-ecdysone receptor; n	3e-09
2nxx_E	248	Ecdysone receptor (ECR, NRH1); hormone receptor, A	2e-30
2nxx_E	248	Ecdysone receptor (ECR, NRH1); hormone receptor, A	1e-09
3up3_A	243	Acedaf-12; ligand binding domain, nematode, steroi	2e-30
3up3_A	243	Acedaf-12; ligand binding domain, nematode, steroi	6e-11
3l0l_A	248	Nuclear receptor ROR-gamma; nuclear receptor, rorg	4e-30
3l0l_A	248	Nuclear receptor ROR-gamma; nuclear receptor, rorg	4e-08
1z5x_E	310	Ecdysone receptor ligand binding domain; ponastero	2e-29
1z5x_E	310	Ecdysone receptor ligand binding domain; ponastero	2e-10
3gyt_A	244	Nuclear hormone receptor of the steroid/thyroid ho	1e-27
3gyt_A	244	Nuclear hormone receptor of the steroid/thyroid ho	6e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-07

>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 =  215 bits (549), Expect = 7e-69
 Identities = 57/194 (29%), Positives = 96/194 (49%), Gaps = 1/194 (0%)

Query: 85  LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD 144
           + S     E+    L + V W + +  F  L   DQ+ LL+    E  LL   + S+ + 
Sbjct: 40  IASIADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFK 99

Query: 145 LSLLINCEKARERLPPDDVRVNNE-IKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
             LL+  +    R  P+   ++   I+++ E++  F++L  D +E   +KA+I F P+  
Sbjct: 100 DVLLLGNDYIVPRHCPELAEMSRVSIRILDELVLPFQELQIDDNEYAYLKAIIFFDPDAK 159

Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKET 263
           GL D   ++ L+ Q Q  L DY+  R      RFG LLL+LP+L+++    IE++ F + 
Sbjct: 160 GLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFIKL 219

Query: 264 IGDIPIQRLLGDMY 277
            G   I  LL +M 
Sbjct: 220 FGMAKIDNLLQEML 233

>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 =  102 bits (255), Expect = 2e-25
 Identities = 27/77 (35%), Positives = 41/77 (53%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           +  GL D   ++ L+ Q Q  L DY+  R      RFG LLL+LP+L+++    IE++ F
Sbjct: 157 DAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQF 216

Query: 344 KETIGDIPIQRLLGDMY 360
            +  G   I  LL +M 
Sbjct: 217 IKLFGMAKIDNLLQEML 233

>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 =  214 bits (547), Expect = 2e-68
 Identities = 51/227 (22%), Positives = 86/227 (37%), Gaps = 5/227 (2%)

Query: 61  PSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQ 120
           P        +      P                   +     V W R    F+ L   DQ
Sbjct: 20  PEEDQVRARIVGCLQEPAKSRSDQPAPFSLLCRMADQTFISIVDWARRCMVFKELEVADQ 79

Query: 121 LLLLQESWKELFLLHLAQWSIPWD----LSLLINCEKARERLPPDDVRVNNE-IKLIQEI 175
           + LLQ SW EL +L      + +     + L+   E     +      + +  +   QE+
Sbjct: 80  MTLLQNSWSELLVLDHIYRQVQYGKEDSILLVTGQEVELSTVAVQAGSLLHSLVLRAQEL 139

Query: 176 LARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPT 235
           + +   L  D  E  C+K +ILF+ +   L +   V+  Q++A   L DY    Y     
Sbjct: 140 VLQLHALQLDRQEFVCLKFLILFSLDVKFLNNHSLVKDAQEKANAALLDYTLSHYPHSGD 199

Query: 236 RFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKS 282
           +F +LLL L  +RA+     E L+ K    ++P   LL +M   +++
Sbjct: 200 KFQQLLLSLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIEMLQAKQT 246

>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 =  106 bits (265), Expect = 8e-27
 Identities = 22/82 (26%), Positives = 38/82 (46%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           +   L +   V+  Q++A   L DY    Y     +F +LLL L  +RA+     E L+ 
Sbjct: 165 DVKFLNNHSLVKDAQEKANAALLDYTLSHYPHSGDKFQQLLLSLVEVRALSMQAKEYLYH 224

Query: 344 KETIGDIPIQRLLGDMYTMEKS 365
           K    ++P   LL +M   +++
Sbjct: 225 KHLGNEMPRNNLLIEMLQAKQT 246

>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 =  212 bits (541), Expect = 1e-67
 Identities = 58/210 (27%), Positives = 108/210 (51%), Gaps = 1/210 (0%)

Query: 74  QPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFL 133
            P     + +   +     + T + LF  V+W + +  F +L   DQ+ LL+  W EL +
Sbjct: 25  DPLVALVVNENNTTVNNICQATHKQLFQLVQWAKLVPHFTSLPLTDQVQLLRAGWNELLI 84

Query: 134 LHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNE-IKLIQEILARFRQLSPDGSECGCM 192
              +  S+    ++++       +     V V N   +++ E++ + +++  D +E GC+
Sbjct: 85  AAFSHRSMQAQDAIVLATGLTVNKSTAHAVGVGNIYDRVLSELVNKMKEMKMDKTELGCL 144

Query: 193 KAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQ 252
           +A+IL+ P+  G+   Q VEML+++   +L +Y R  +  +P RF +LLL LP+LR++  
Sbjct: 145 RAIILYNPDVRGIKSVQEVEMLREKIYGVLEEYTRTTHPNEPGRFAKLLLRLPALRSIGL 204

Query: 253 STIERLFFKETIGDIPIQRLLGDMYTMEKS 282
             +E LFF + IGD+PI   L +M      
Sbjct: 205 KCLEHLFFFKLIGDVPIDTFLMEMLEGTTD 234

>2nxx_A Ultraspiracle (USP, NR2B4); hormone receptor, APO and holo ligand binding pocket, hormone/growth factor complex; HET: P1A; 2.75A {Tribolium castaneum} Length = 235

 Score =  102 bits (256), Expect = 1e-25
 Identities = 30/82 (36%), Positives = 47/82 (57%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           +  G+   Q VEML+++   +L +Y R  +  +P RF +LLL LP+LR++    +E LFF
Sbjct: 153 DVRGIKSVQEVEMLREKIYGVLEEYTRTTHPNEPGRFAKLLLRLPALRSIGLKCLEHLFF 212

Query: 344 KETIGDIPIQRLLGDMYTMEKS 365
            + IGD+PI   L +M      
Sbjct: 213 FKLIGDVPIDTFLMEMLEGTTD 234

>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 =  208 bits (532), Expect = 4e-66
 Identities = 64/233 (27%), Positives = 103/233 (44%), Gaps = 5/233 (2%)

Query: 55  LKSPPPPSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQT 114
           LK  P        +     Q   +    + L +     +   + LF  V W R    F+ 
Sbjct: 25  LKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLFSIVEWARSSIFFRE 84

Query: 115 LSKRDQLLLLQESWKELFLLHLAQWSIPWDLS---LLINCEKARERLPPDDVR--VNNEI 169
           L   DQ+ LLQ  W EL +L      +         L+  ++    +        +NN +
Sbjct: 85  LKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQAGATLNNLM 144

Query: 170 KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGR 229
              QE++A+ R L  D  E  C+K ++LF+ +   L + Q VE +Q+Q    L DY    
Sbjct: 145 SHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCN 204

Query: 230 YSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKS 282
           Y +Q  +FG+LLL LP +RA+     E L++K   GD+P   LL +M   +++
Sbjct: 205 YPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHAKRA 257

>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 =  102 bits (256), Expect = 1e-25
 Identities = 29/82 (35%), Positives = 45/82 (54%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           +   L + Q VE +Q+Q    L DY    Y +Q  +FG+LLL LP +RA+     E L++
Sbjct: 176 DVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYY 235

Query: 344 KETIGDIPIQRLLGDMYTMEKS 365
           K   GD+P   LL +M   +++
Sbjct: 236 KHLNGDVPYNNLLIEMLHAKRA 257

>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 =  206 bits (525), Expect = 3e-65
 Identities = 89/234 (38%), Positives = 128/234 (54%), Gaps = 12/234 (5%)

Query: 55  LKSPPPPSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQT 114
           L++ P P+    S         P+      +M  E   E  AR+LF AV W R +  F  
Sbjct: 16  LRAEPYPTSRFGS-----QCMQPNN-----IMGIENICELAARMLFSAVEWARNIPFFPD 65

Query: 115 LSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINC-EKARERLPPDDVRVNNE-IKLI 172
           L   DQ+ LL+ +W ELF+L+ AQ S+P  ++ L+         +  D V    + I++ 
Sbjct: 66  LQITDQVALLRLTWSELFVLNAAQCSMPLHVAPLLAAAGLHASPMSADRVVAFMDHIRIF 125

Query: 173 QEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSR 232
           QE + + + L  D +E  C+KA++LFT +  GL D   VE LQ+++QC L +YVR +Y  
Sbjct: 126 QEQVEKLKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVESLQEKSQCALEEYVRSQYPN 185

Query: 233 QPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETP 286
           QPTRFG+LLL LPSLR V  S IE+LFF   +G  PI+ L+ DM     S+  P
Sbjct: 186 QPTRFGKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDMLLSGSSFNWP 239

>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 =  100 bits (250), Expect = 9e-25
 Identities = 42/85 (49%), Positives = 55/85 (64%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
           + +  GL D   VE LQ+++QC L +YVR +Y  QPTRFG+LLL LPSLR V  S IE+L
Sbjct: 152 TSDACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQL 211

Query: 342 FFKETIGDIPIQRLLGDMYTMEKSY 366
           FF   +G  PI+ L+ DM     S+
Sbjct: 212 FFVRLVGKTPIETLIRDMLLSGSSF 236

>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 =  205 bits (524), Expect = 5e-65
 Identities = 55/251 (21%), Positives = 107/251 (42%), Gaps = 11/251 (4%)

Query: 30  SPDLLPPNGISSVKIPPTVLYPPSGLKSPPPPSHHHPSMFLATHQPPPHPGLLQILMSAE 89
           SP+ L P  +   K P   +     L + P   +  P        P      L  L    
Sbjct: 3   SPEFLNPQLVQPAKKPYNKIVS-HLLVAEPEKIYAMPDP----TVPDSDIKALTTL---- 53

Query: 90  KCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLI 149
              +   R L + + W + +  F TLS  DQ+ LLQ +W E+ +L +   S+ ++  L+ 
Sbjct: 54  --CDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDELVY 111

Query: 150 NCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
             +   +        + +    I +++ +++ +  +  E   +KA+ L   ++  + D +
Sbjct: 112 ADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVE 171

Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
            V+ LQD     L DY  G++   P R G++L+ LP LR      ++  +  +  G +P+
Sbjct: 172 AVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPM 231

Query: 270 QRLLGDMYTME 280
            +L  +M   +
Sbjct: 232 HKLFLEMLEAK 242

>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 = 96.7 bits (241), Expect = 2e-23
 Identities = 21/80 (26%), Positives = 40/80 (50%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           ++  + D + V+ LQD     L DY  G++   P R G++L+ LP LR      ++  + 
Sbjct: 163 DSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYN 222

Query: 344 KETIGDIPIQRLLGDMYTME 363
            +  G +P+ +L  +M   +
Sbjct: 223 IKLEGKVPMHKLFLEMLEAK 242

>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 =  206 bits (527), Expect = 5e-65
 Identities = 71/278 (25%), Positives = 116/278 (41%), Gaps = 28/278 (10%)

Query: 1   VQHERGPRKPKIHNAHHQDSKLEPHNPHHSPDLLPPNGISSVKIPPTVLYPPSGLKSPPP 60
           VQ ER   K +  N     S      P     +L          P T  Y  + +   P 
Sbjct: 25  VQEERQRGKDRNENEVESTSSANEDMPVER--ILEAELAVE---PKTETYVEANMGLNPS 79

Query: 61  PSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQ 120
             +   +                         +   + LF  V W + +  F  L   DQ
Sbjct: 80  SPNDPVTNI----------------------CQAADKQLFTLVEWAKRIPHFSELPLDDQ 117

Query: 121 LLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNN-EIKLIQEILARF 179
           ++LL+  W EL +   +  SI     +L+       R       V     +++ E++++ 
Sbjct: 118 VILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKM 177

Query: 180 RQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGR 239
           R +  D +E GC++A++LF P++ GL +   VE L+++    L  Y + +Y  QP RF +
Sbjct: 178 RDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAK 237

Query: 240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMY 277
           LLL LP+LR++    +E LFF + IGD PI   L +M 
Sbjct: 238 LLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEML 275

>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 = 97.9 bits (244), Expect = 1e-23
 Identities = 30/77 (38%), Positives = 45/77 (58%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           ++ GL +   VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF
Sbjct: 199 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 258

Query: 344 KETIGDIPIQRLLGDMY 360
            + IGD PI   L +M 
Sbjct: 259 FKLIGDTPIDTFLMEML 275

>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 =  204 bits (521), Expect = 1e-64
 Identities = 66/238 (27%), Positives = 106/238 (44%), Gaps = 10/238 (4%)

Query: 57  SPPPPSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLS 116
                        +      P P  +   ++     E+ +RLLF+++ W R +  FQ L 
Sbjct: 7   IIEVEGPLLSDTHVTFKLTMPSP--MPEYLNVHYICESASRLLFLSMHWARSIPAFQALG 64

Query: 117 KRDQLLLLQESWKELFLLHLAQWSIPWDLSLLI--------NCEKARERLPPDDVRVNNE 168
           +     L++  W ELF L LAQ +    LS ++        N  +  +       +V   
Sbjct: 65  QDCNTSLVRACWNELFTLGLAQCAQVMSLSTILAAIVNHLQNSIQEDKLSGDRIKQVMEH 124

Query: 169 IKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRG 228
           I  +QE      +L  DG E   +KA++LF+P+ PGL     +E  Q+ AQ  L DYV+ 
Sbjct: 125 IWKLQEFCNSMAKLDIDGYEYAYLKAIVLFSPDHPGLTSTSQIEKFQEAAQMELQDYVQA 184

Query: 229 RYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETP 286
            YS    R  R+L+ LP+LR +  +  E LFF   IG++ I  ++  +  ME +    
Sbjct: 185 TYSEDTYRLARILVRLPALRLMSSNITEELFFTGLIGNVSIDSIIPYILKMETAEYNG 242

>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 = 97.7 bits (243), Expect = 9e-24
 Identities = 30/84 (35%), Positives = 45/84 (53%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
           S + PGL     +E  Q+ AQ  L DYV+  YS    R  R+L+ LP+LR +  +  E L
Sbjct: 155 SPDHPGLTSTSQIEKFQEAAQMELQDYVQATYSEDTYRLARILVRLPALRLMSSNITEEL 214

Query: 342 FFKETIGDIPIQRLLGDMYTMEKS 365
           FF   IG++ I  ++  +  ME +
Sbjct: 215 FFTGLIGNVSIDSIIPYILKMETA 238

>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 =  203 bits (518), Expect = 3e-64
 Identities = 61/221 (27%), Positives = 105/221 (47%), Gaps = 10/221 (4%)

Query: 58  PPPPSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSK 117
           P   ++   +M      P      +  +       +   + LF  V W + +  F  L  
Sbjct: 22  PKTETYVEANM---GLNPSSPNDPVTNI------CQAADKQLFTLVEWAKRIPHFSELPL 72

Query: 118 RDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEI-KLIQEIL 176
            DQ++LL+  W EL +   +  SI     +L+       R       V     +++ E++
Sbjct: 73  DDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELV 132

Query: 177 ARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTR 236
           ++ R +  D +E GC++A++LF P++ GL +   VE L+++    L  Y + +Y  QP R
Sbjct: 133 SKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGR 192

Query: 237 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMY 277
           F +LLL LP+LR++    +E LFF + IGD PI   L +M 
Sbjct: 193 FAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEML 233

>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 = 98.3 bits (245), Expect = 4e-24
 Identities = 30/77 (38%), Positives = 45/77 (58%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           ++ GL +   VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF
Sbjct: 157 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 216

Query: 344 KETIGDIPIQRLLGDMY 360
            + IGD PI   L +M 
Sbjct: 217 FKLIGDTPIDTFLMEML 233

>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 =  204 bits (520), Expect = 3e-64
 Identities = 59/265 (22%), Positives = 103/265 (38%), Gaps = 25/265 (9%)

Query: 44  IPPTVLYPPSGLKSPPPPSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAV 103
           +    L     L + P        +   ++ PP     +  L       +   + +   V
Sbjct: 6   LSIERLLEMESLVADPSEEFQFLRVGPDSNVPPKFRAPVSSLC------QIGNKQIAALV 59

Query: 104 RWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPP--- 160
            W R +  F  L   DQ+LL++ SW EL L  +A  S+ +        +    R      
Sbjct: 60  VWARDIPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLTEERDGVDGTGNRTTSPPQ 119

Query: 161 -----DDVRVNNE-----------IKLIQEILARFRQLSPDGSECGCMKAVILFTPETPG 204
                  + ++              +++ E+  + R L  D +E   +KA+IL  P+  G
Sbjct: 120 LMCLMPGMTLHRNSALQAGVGQIFDRVLSELSLKMRTLRVDQAEYVALKAIILLNPDVKG 179

Query: 205 LVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETI 264
           L + Q VE+L+++    L +Y R   S +  RF  LLL LP+LR++   + E LFF   +
Sbjct: 180 LKNRQEVEVLREKMFLCLDEYCRRSRSSEEGRFAALLLRLPALRSISLKSFEHLFFFHLV 239

Query: 265 GDIPIQRLLGDMYTMEKSYETPGLV 289
            D  I   + D            ++
Sbjct: 240 ADTSIAGYIRDALRNHAPPIDTNMM 264

>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 =  101 bits (253), Expect = 5e-25
 Identities = 26/80 (32%), Positives = 40/80 (50%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           +  GL + Q VE+L+++    L +Y R   S +  RF  LLL LP+LR++   + E LFF
Sbjct: 176 DVKGLKNRQEVEVLREKMFLCLDEYCRRSRSSEEGRFAALLLRLPALRSISLKSFEHLFF 235

Query: 344 KETIGDIPIQRLLGDMYTME 363
              + D  I   + D     
Sbjct: 236 FHLVADTSIAGYIRDALRNH 255

>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 =  203 bits (517), Expect = 6e-64
 Identities = 55/243 (22%), Positives = 96/243 (39%), Gaps = 26/243 (10%)

Query: 60  PPSHHHPSMFLATHQPPPHPGLLQILMSAE---------------------KCQETTARL 98
             SHHH        Q P    L+  L+  E                        +   R 
Sbjct: 2   GSSHHHHHHLEVLFQGPV-NALVSHLLVVEPEKLYAMPDPAGPDGHLPAVATLCDLFDRE 60

Query: 99  LFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERL 158
           + + + W + +  F +LS  DQ+ +LQ  W E+ +L +AQ S+P    L    +   +  
Sbjct: 61  IVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQDELAFAEDLVLDEE 120

Query: 159 PPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQA 218
                 +      + +++ R + L  +  E   +KA+ L   ++  + DA+ VE L++  
Sbjct: 121 GARAAGLGELGAALLQLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQLREAL 180

Query: 219 QCILGDYVRGRY----SRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLG 274
              L +Y  GR       +  R GRLLL LP LR      +   +  +  G +P+ +L  
Sbjct: 181 HEALLEYEAGRAGPGGGAERRRAGRLLLTLPLLRQTAGKVLAHFYGVKLEGKVPMHKLFL 240

Query: 275 DMY 277
           +M 
Sbjct: 241 EML 243

>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 = 89.8 bits (223), Expect = 5e-21
 Identities = 23/81 (28%), Positives = 38/81 (46%), Gaps = 4/81 (4%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRY----SRQPTRFGRLLLMLPSLRAVRQSTIE 339
           ++  + DA+ VE L++     L +Y  GR       +  R GRLLL LP LR      + 
Sbjct: 163 DSVHIEDAEAVEQLREALHEALLEYEAGRAGPGGGAERRRAGRLLLTLPLLRQTAGKVLA 222

Query: 340 RLFFKETIGDIPIQRLLGDMY 360
             +  +  G +P+ +L  +M 
Sbjct: 223 HFYGVKLEGKVPMHKLFLEML 243

>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 =  205 bits (523), Expect = 1e-63
 Identities = 72/299 (24%), Positives = 111/299 (37%), Gaps = 36/299 (12%)

Query: 20  SKLEPHNPHHSPDLLPPNGISSVKIPPTVLYPPSGLKSPPPPSHHHPSMFLATHQPPPHP 79
           S +    P H                    YP     SP     +       T  P   P
Sbjct: 54  SPISMTMPPHGSLQGYQTYGHFPSRAIKSEYPDPYTSSPESIMGYSYMDSYQTSSPASIP 113

Query: 80  GLLQILMSAE-------------------------------KCQETTARLLFMAVRWVRC 108
            L+  L+  E                                  +   + LF  V W R 
Sbjct: 114 HLILELLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLFSIVEWARS 173

Query: 109 LAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD----LSLLINCEKARERLPPDDVR 164
              F+ L   DQ+ LLQ  W EL +L      +       + L+   +     +      
Sbjct: 174 SIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQAGA 233

Query: 165 -VNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILG 223
            +NN +   QE++A+ R L  D  E  C+K ++LF+ +   L + Q VE +Q+Q    L 
Sbjct: 234 TLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALL 293

Query: 224 DYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKS 282
           DY    Y +Q  +FG+LLL LP +RA+     E L++K   GD+P   LL +M   +++
Sbjct: 294 DYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHAKRA 352

>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 =  100 bits (250), Expect = 4e-24
 Identities = 29/82 (35%), Positives = 45/82 (54%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           +   L + Q VE +Q+Q    L DY    Y +Q  +FG+LLL LP +RA+     E L++
Sbjct: 271 DVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYY 330

Query: 344 KETIGDIPIQRLLGDMYTMEKS 365
           K   GD+P   LL +M   +++
Sbjct: 331 KHLNGDVPYNNLLIEMLHAKRA 352

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

 Score =  190 bits (485), Expect = 8e-59
 Identities = 46/254 (18%), Positives = 91/254 (35%), Gaps = 31/254 (12%)

Query: 55  LKSPPPPSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQT 114
            ++         +           P     +       +   + LF  V + R +  F  
Sbjct: 19  QRAETQCGDRALTFLRVGPYSTVQPDYKGAV---SALCQVVNKQLFQMVEYARMMPHFAQ 75

Query: 115 LSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNE------ 168
           +   DQ++LL+ +W EL + ++A  SI                      R +        
Sbjct: 76  VPLDDQVILLKAAWIELLIANVAWCSIVSLDDGGAGGGGGGLGHDGSFERRSPGLQPQQL 135

Query: 169 ----------------------IKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLV 206
                                  +++ E+  + ++L+ D  E  C+KA+IL+ P+  G+ 
Sbjct: 136 FLNQSFSYHRNSAIKAGVSAIFDRILSELSVKMKRLNLDRRELSCLKAIILYNPDIRGIK 195

Query: 207 DAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGD 266
               +EM +++    L ++ R  +     RF +LLL LP+LR++     + LF      D
Sbjct: 196 SRAEIEMCREKVYACLDEHCRLEHPGDDGRFAQLLLRLPALRSISLKCQDHLFLFRITSD 255

Query: 267 IPIQRLLGDMYTME 280
            P++ L  +     
Sbjct: 256 RPLEELFLEQLEAP 269

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

 Score =  187 bits (478), Expect = 3e-58
 Identities = 36/185 (19%), Positives = 69/185 (37%), Gaps = 1/185 (0%)

Query: 93  ETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINC- 151
           +   R L   + W + +  +  LS  DQ+ L++  W EL LL+ A  SI      L    
Sbjct: 43  KLAERELVHLINWAKNVPGYTDLSLSDQVHLIECCWMELLLLNCAFRSIEHGGKSLAFAP 102

Query: 152 EKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPV 211
           +   +R     V +    + +  +  +  Q      E   ++A++L   E   L     +
Sbjct: 103 DLVLDRSSWSTVEMTEIFEQVAAVSEQMMQNHLHKDELLLLQAMVLVNAEVRRLASYNQI 162

Query: 212 EMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQR 271
             +Q      + D  +  +         +LL+L  +R   +  I      ++ G +    
Sbjct: 163 FNMQQSLLDAIVDTAQKYHPDNVRHVPAVLLLLTHIRQAGERGIAFFQRLKSEGVVTFCD 222

Query: 272 LLGDM 276
           LL +M
Sbjct: 223 LLKEM 227

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

 Score = 92.1 bits (229), Expect = 8e-22
 Identities = 13/76 (17%), Positives = 26/76 (34%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           E   L     +  +Q      + D  +  +         +LL+L  +R   +  I     
Sbjct: 152 EVRRLASYNQIFNMQQSLLDAIVDTAQKYHPDNVRHVPAVLLLLTHIRQAGERGIAFFQR 211

Query: 344 KETIGDIPIQRLLGDM 359
            ++ G +    LL +M
Sbjct: 212 LKSEGVVTFCDLLKEM 227

>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 =  183 bits (466), Expect = 5e-56
 Identities = 49/269 (18%), Positives = 95/269 (35%), Gaps = 14/269 (5%)

Query: 11  KIHNAHHQDSKLEPHNPHHSPDLLPPNGISSVKIPPTVLYPPSGLKSPPPPSHHHPSMFL 70
            +++++ +   L                  +    P V+Y  + L              L
Sbjct: 10  HLYDSYIKSFPLTKAKARAILTG------KTTDKSPFVIYDMNSLMMGEDKIKFKHITPL 63

Query: 71  ATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKE 130
                     + Q       CQ  +   +     + + +  F  L   DQ+ LL+    E
Sbjct: 64  QEQSKEVAIRIFQG------CQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHE 117

Query: 131 LFLLHLAQWSIPWDLSLLIN-CEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSEC 189
           +    LA       + +        RE L        + ++   E   +F  L  D S+ 
Sbjct: 118 IIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDL 177

Query: 190 GCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRA 249
               AVI+ + + PGL++ +P+E +QD     L   ++  +      F +LL  +  LR 
Sbjct: 178 AIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQ 237

Query: 250 VRQSTIERLF-FKETIGDIPIQRLLGDMY 277
           +    ++ L   K+T  D+ +  LL ++Y
Sbjct: 238 IVTEHVQLLQVIKKTETDMSLHPLLQEIY 266

>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 = 89.1 bits (221), Expect = 2e-20
 Identities = 20/78 (25%), Positives = 39/78 (50%), Gaps = 1/78 (1%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLF- 342
           + PGL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L  
Sbjct: 189 DRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQV 248

Query: 343 FKETIGDIPIQRLLGDMY 360
            K+T  D+ +  LL ++Y
Sbjct: 249 IKKTETDMSLHPLLQEIY 266

>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 =  181 bits (461), Expect = 3e-55
 Identities = 47/206 (22%), Positives = 85/206 (41%), Gaps = 4/206 (1%)

Query: 74  QPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFL 133
             P +          ++  +     + +   W   +  F  L K DQ LL + ++ ELF+
Sbjct: 62  ANPDYQMSGDDTQHIQQFYDLLTGSMEIIRGWAEKIPGFADLPKADQDLLFESAFLELFV 121

Query: 134 LHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMK 193
           L LA  S P +  L+        RL          I  I E  +  + ++ D S   C+ 
Sbjct: 122 LRLAYRSNPVEGKLIFCNGVVLHRLQCVRG-FGEWIDSIVEFSSNLQNMNIDISAFSCIA 180

Query: 194 AVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRY--SRQPTRFGRLLLMLPSLRAVR 251
           A+ +   E  GL + + VE LQ++    L D+V        +P    +LL  LP LR + 
Sbjct: 181 ALAMV-TERHGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLGKLPELRTLC 239

Query: 252 QSTIERLFFKETIGDIPIQRLLGDMY 277
              ++R+F+ +    +P   ++  ++
Sbjct: 240 TQGLQRIFYLKLEDLVPPPAIIDKLF 265

>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 = 89.0 bits (221), Expect = 1e-20
 Identities = 20/79 (25%), Positives = 38/79 (48%), Gaps = 2/79 (2%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRY--SRQPTRFGRLLLMLPSLRAVRQSTIERL 341
           E  GL + + VE LQ++    L D+V        +P    +LL  LP LR +    ++R+
Sbjct: 187 ERHGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLGKLPELRTLCTQGLQRI 246

Query: 342 FFKETIGDIPIQRLLGDMY 360
           F+ +    +P   ++  ++
Sbjct: 247 FYLKLEDLVPPPAIIDKLF 265

>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 =  177 bits (449), Expect = 1e-53
 Identities = 54/253 (21%), Positives = 95/253 (37%), Gaps = 28/253 (11%)

Query: 52  PSGLKSPPPPSHHHPSMFLATHQPPPHPGLLQI--LMSAEKCQETTARLLFMAVRWVRCL 109
            SG       +   P            PG+ ++  L   +   E  +  L   +R+V+ L
Sbjct: 11  ASGTPVSADQTPATPQEQPRAPWWDASPGVQRLITLKDPQVVCEAASAGLLKTLRFVKYL 70

Query: 110 APFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNN-- 167
             FQ L    QL+L++  W  L +L LAQ  + +++  +      +E L           
Sbjct: 71  PCFQILPLDQQLVLVRSCWAPLLMLELAQDHLHFEMMEIPETNTTQEMLTTRRQETEGPE 130

Query: 168 ------------------------EIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP 203
                                    ++ I+    +   L+ D  E   +K  +LF P+ P
Sbjct: 131 PAEPQATEQPQMVSAEAGHLLPAAAVQAIKSFFFKCWSLNIDTKEYAYLKGTVLFNPDLP 190

Query: 204 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKET 263
           GL   + +E LQ + Q IL +++R        R   L   L  LR +    +  LFF+  
Sbjct: 191 GLQCVKYIEGLQWRTQQILTEHIRMMQREYQIRSAELNSALFLLRFINSDVVTELFFRPI 250

Query: 264 IGDIPIQRLLGDM 276
           IG + +  ++ +M
Sbjct: 251 IGAVSMDDMMLEM 263

>3dzy_D Peroxisome proliferator-activated receptor gamma; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_D* 3e00_D* 2env_A Length = 419

 Score =  179 bits (456), Expect = 5e-53
 Identities = 52/295 (17%), Positives = 101/295 (34%), Gaps = 19/295 (6%)

Query: 1   VQHERGPRKPKIHNAHHQDSKLEPHNPHHSPDLLPPNGISSVKIPPTVLYPPSGLKSPPP 60
           ++  R P+  K        S ++  NP  S DL             +     +  ++   
Sbjct: 122 IRFGRMPQAEKEKLLAEISSDIDQLNPE-SADLRALAKHLYDSYIKSFPLTKAKARAILT 180

Query: 61  PSHHHPSMFLATHQPPPHPGLLQILMSA----------------EKCQETTARLLFMAVR 104
                 S F+         G  +I                    + CQ  +   +     
Sbjct: 181 GKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITE 240

Query: 105 WVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVR 164
           + + +  F  L   DQ+ LL+    E+    LA       + +                +
Sbjct: 241 YAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRK 300

Query: 165 VNNE-IKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILG 223
              + ++   E   +F  L  D S+     AVI+ + + PGL++ +P+E +QD     L 
Sbjct: 301 PFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALE 360

Query: 224 DYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLF-FKETIGDIPIQRLLGDMY 277
             ++  +      F +LL  +  LR +    ++ L   K+T  D+ +  LL ++Y
Sbjct: 361 LQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIY 415

>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 = 86.3 bits (213), Expect = 8e-19
 Identities = 20/78 (25%), Positives = 39/78 (50%), Gaps = 1/78 (1%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLF- 342
           + PGL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L  
Sbjct: 338 DRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQV 397

Query: 343 FKETIGDIPIQRLLGDMY 360
            K+T  D+ +  LL ++Y
Sbjct: 398 IKKTETDMSLHPLLQEIY 415

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

 Score =  172 bits (437), Expect = 2e-51
 Identities = 49/240 (20%), Positives = 91/240 (37%), Gaps = 18/240 (7%)

Query: 74  QPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFL 133
           +P     ++ +L           R L   + W + +  F  L+  DQ+ LL+ +W E+ +
Sbjct: 38  RPFSEASMMGLLT------NLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILM 91

Query: 134 LHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCM 192
           + L   S+     LL       +R     V    EI  ++    +RFR ++  G E  C+
Sbjct: 92  IGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCL 151

Query: 193 KAVILFTP--------ETPGLVDAQPVEMLQDQAQCILGDYV---RGRYSRQPTRFGRLL 241
           K++IL               L +   +  + D+    L   +        +Q  R  +LL
Sbjct: 152 KSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLL 211

Query: 242 LMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQA 301
           L+L  +R +    +E L+  +    +P+  LL +M    + +       A   E  Q   
Sbjct: 212 LILSHIRHMSNKGMEHLYSMKCKNVVPLSDLLLEMLDAHRLHAPTSRGGASVEETDQSHL 271

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

 Score = 79.5 bits (196), Expect = 5e-17
 Identities = 17/81 (20%), Positives = 33/81 (40%), Gaps = 3/81 (3%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYV---RGRYSRQPTRFGRLLLMLPSLRAVRQSTI 338
           S     L +   +  + D+    L   +        +Q  R  +LLL+L  +R +    +
Sbjct: 166 SSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGM 225

Query: 339 ERLFFKETIGDIPIQRLLGDM 359
           E L+  +    +P+  LL +M
Sbjct: 226 EHLYSMKCKNVVPLSDLLLEM 246

>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 =  167 bits (424), Expect = 4e-50
 Identities = 45/195 (23%), Positives = 75/195 (38%), Gaps = 11/195 (5%)

Query: 93  ETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCE 152
           +   + L   + W + +  F  LS  DQ+ LL+  W E+ ++ L   SI     L+   +
Sbjct: 40  KLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPD 99

Query: 153 KARERLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPV 211
              +R     V    EI  ++    +RFR+L     E  C+KA+IL       LV A   
Sbjct: 100 LVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQD 159

Query: 212 EMLQDQAQCILGDYV----------RGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFK 261
                +   +L                   +Q  R   LL++L  +R      +E L   
Sbjct: 160 ADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNM 219

Query: 262 ETIGDIPIQRLLGDM 276
           +    +P+  LL +M
Sbjct: 220 KCKNVVPVYDLLLEM 234

>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 = 67.9 bits (166), Expect = 3e-13
 Identities = 16/86 (18%), Positives = 27/86 (31%), Gaps = 10/86 (11%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYV----------RGRYSRQPTRFGRLLLMLPSLRAV 333
               LV A        +   +L                   +Q  R   LL++L  +R  
Sbjct: 149 SMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHA 208

Query: 334 RQSTIERLFFKETIGDIPIQRLLGDM 359
               +E L   +    +P+  LL +M
Sbjct: 209 SNKGMEHLLNMKCKNVVPVYDLLLEM 234

>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 =  166 bits (422), Expect = 8e-50
 Identities = 45/215 (20%), Positives = 85/215 (39%), Gaps = 18/215 (8%)

Query: 74  QPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFL 133
           +P     ++ +L           R L   + W + +  F  L+  DQ+ LL+ +W E+ +
Sbjct: 29  RPFSEASMMGLLT------NLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILM 82

Query: 134 LHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNE-IKLIQEILARFRQLSPDGSECGCM 192
           + L   S+     LL       +R     V    E   ++    +RFR ++  G E  C+
Sbjct: 83  IGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCL 142

Query: 193 KAVILFTP--------ETPGLVDAQPVEMLQDQAQCILGDYV---RGRYSRQPTRFGRLL 241
           K++IL               L +   +  + D+    L   +        +Q  R  +LL
Sbjct: 143 KSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLL 202

Query: 242 LMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDM 276
           L+L  +R +    +E L+  +    +P+  LL +M
Sbjct: 203 LILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEM 237

>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 = 78.3 bits (193), Expect = 6e-17
 Identities = 19/91 (20%), Positives = 35/91 (38%), Gaps = 3/91 (3%)

Query: 272 LLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYV---RGRYSRQPTRFGRLLLMLP 328
           LL        S     L +   +  + D+    L   +        +Q  R  +LLL+L 
Sbjct: 147 LLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILS 206

Query: 329 SLRAVRQSTIERLFFKETIGDIPIQRLLGDM 359
            +R +    +E L+  +    +P+  LL +M
Sbjct: 207 HIRHMSNKGMEHLYSMKCKNVVPLYDLLLEM 237

>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 =  166 bits (422), Expect = 1e-49
 Identities = 61/275 (22%), Positives = 108/275 (39%), Gaps = 18/275 (6%)

Query: 13  HNAHHQDSKLEPHNPH-HSPDLLPPNGISSVKIPPTVLYPPSGLKSPPPPSHHHPSMFLA 71
           H+ HH  S L P   H   PD  P N ++S+            +++      +   +  +
Sbjct: 4   HHHHHHSSGLVPRGSHMQPPDASPTNLLTSL------------IRAHLDSGPNTAKLDYS 51

Query: 72  THQPPPHPGLLQI-LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKE 130
             Q    P   +      ++  +  +  L +  +W   +  F  LS  DQ LLL+ ++ E
Sbjct: 52  KFQELVLPRFGKEDAGDVQQFYDLLSGSLDVIRKWAEKIPGFIELSPGDQDLLLESAFLE 111

Query: 131 LFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECG 190
           LF+L LA  S P +  L+        RL        + I  I         L  D     
Sbjct: 112 LFILRLAYRSKPGEGKLIFCSGLVLHRLQCAR-GFGDWIDNILAFSRSLHSLGVDVPAFA 170

Query: 191 CMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSR--QPTRFGRLLLMLPSLR 248
           C+ A++L   +  GL D + VE LQ++    L +++          +   RLL  LP LR
Sbjct: 171 CLSALVLI-TDRHGLQDPRRVEELQNRIASCLKEHMAAVAGDPQPASCLSRLLGKLPELR 229

Query: 249 AVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSY 283
            +    ++R+F  +    +P   ++  ++    S+
Sbjct: 230 TLCTQGLQRIFCLKLEDLVPPPPIVDKIFMDTLSF 264

>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 = 85.6 bits (212), Expect = 2e-19
 Identities = 19/85 (22%), Positives = 38/85 (44%), Gaps = 2/85 (2%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSR--QPTRFGRLLLMLPSLRAVRQSTIERL 341
           +  GL D + VE LQ++    L +++          +   RLL  LP LR +    ++R+
Sbjct: 180 DRHGLQDPRRVEELQNRIASCLKEHMAAVAGDPQPASCLSRLLGKLPELRTLCTQGLQRI 239

Query: 342 FFKETIGDIPIQRLLGDMYTMEKSY 366
           F  +    +P   ++  ++    S+
Sbjct: 240 FCLKLEDLVPPPPIVDKIFMDTLSF 264

>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 =  158 bits (401), Expect = 2e-46
 Identities = 44/251 (17%), Positives = 85/251 (33%), Gaps = 31/251 (12%)

Query: 51  PPSGLKSPPPPSHHHPSMFLATH----------------QPPPHPGLLQILMSAEKCQET 94
             SG         +                         QP     LL  L       E 
Sbjct: 4   GISGGGGGSHIEGYECQPIFLNVLEAIEPGVVCAGHDNNQPDSFAALLSSLN------EL 57

Query: 95  TARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN--CE 152
             R L   V+W + L  F+ L   DQ+ ++Q SW  L +  +   S     S ++    +
Sbjct: 58  GERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPD 117

Query: 153 KARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFT-PETPGLVDAQPV 211
                      R+ ++   ++ +   F  L     E  CMKA++LF+     GL + +  
Sbjct: 118 LVFNEYRMHKSRMYSQCVRMRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFF 177

Query: 212 EMLQDQAQCILGDYVRGRY---SRQPTRFGRLLLMLPSLRAVRQSTIERLF---FKETIG 265
           + L+      L   +  +    +    RF +L  +L S++ + +   +  F    K  + 
Sbjct: 178 DELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPIARELHQFTFDLLIKSHMV 237

Query: 266 DIPIQRLLGDM 276
            +    ++ ++
Sbjct: 238 SVDFPEMMAEI 248

>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 = 73.8 bits (181), Expect = 4e-15
 Identities = 11/84 (13%), Positives = 31/84 (36%), Gaps = 6/84 (7%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRY---SRQPTRFGRLLLMLPSLRAVRQSTI 338
                GL + +  + L+      L   +  +    +    RF +L  +L S++ + +   
Sbjct: 165 IIPVDGLKNQKFFDELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPIARELH 224

Query: 339 ERLF---FKETIGDIPIQRLLGDM 359
           +  F    K  +  +    ++ ++
Sbjct: 225 QFTFDLLIKSHMVSVDFPEMMAEI 248

>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 =  157 bits (399), Expect = 7e-46
 Identities = 56/257 (21%), Positives = 95/257 (36%), Gaps = 20/257 (7%)

Query: 40  SSVKIPPTVLYPPSGLKSPPPPSHHHPSMFLATHQ--------------PPPHPGLLQIL 85
            +  +PP    PP  L    P         +A  Q              P P        
Sbjct: 24  HATSLPPRASSPPQILPQLSPEQLGMIEKLVAAQQQCNRRSFSDRLRVTPWPMAPDPHSR 83

Query: 86  MSAEK----CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSI 141
            + ++      E     +   V + + L  F  LS+ DQ+ LL+ S  E+ LL  ++   
Sbjct: 84  EARQQRFAHFTELAIVSVQEIVDFAKQLPGFLQLSREDQIALLKTSAIEVMLLETSRRYN 143

Query: 142 PWDLSLLINCEKARERLPPDDVRVNNE-IKLIQEILARFRQLSPDGSECGCMKAVILFTP 200
           P   S+    + +  R       +  E I  I E      +L  + +E   + A+ +F+ 
Sbjct: 144 PGSESITFLKDFSYNREDFAKAGLQVEFINPIFEFSRAMNELQLNDAEFALLIAISIFSA 203

Query: 201 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 260
           + P + D   VE LQ      L  YV   +      F R+L+ L SLR +     E++F 
Sbjct: 204 DRPNVQDQLQVERLQHTYVEALHAYVSIHHPHDRLMFPRMLMKLVSLRTLSSVHSEQVFA 263

Query: 261 KETIGDIPIQRLLGDMY 277
              + D  +  LL +++
Sbjct: 264 L-RLQDKKLPPLLSEIW 279

>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 = 74.4 bits (183), Expect = 3e-15
 Identities = 22/79 (27%), Positives = 35/79 (44%), Gaps = 1/79 (1%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
           S + P + D   VE LQ      L  YV   +      F R+L+ L SLR +     E++
Sbjct: 202 SADRPNVQDQLQVERLQHTYVEALHAYVSIHHPHDRLMFPRMLMKLVSLRTLSSVHSEQV 261

Query: 342 FFKETIGDIPIQRLLGDMY 360
           F    + D  +  LL +++
Sbjct: 262 FAL-RLQDKKLPPLLSEIW 279

>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 =  161 bits (409), Expect = 1e-45
 Identities = 69/278 (24%), Positives = 122/278 (43%), Gaps = 28/278 (10%)

Query: 1   VQHERGPRKPKIHNAHHQDSKLEPHNPHHSPDLLPPNGISSVKIPPTVLYPPSGLKSPPP 60
           VQ ER   K +        ++ E  +   + + +P   I                 +  P
Sbjct: 210 VQEERQRGKDR--------NENEVESTSSANEDMPVERI------------LEAELAVEP 249

Query: 61  PSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQ 120
            +  +    +  +   P+  +  I        +   + LF  V W + +  F  L   DQ
Sbjct: 250 KTETYVEANMGLNPSSPNDPVTNI-------CQAADKQLFTLVEWAKRIPHFSELPLDDQ 302

Query: 121 LLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNE-IKLIQEILARF 179
           ++LL+  W EL +   +  SI     +L+       R       V     +++ E++++ 
Sbjct: 303 VILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKM 362

Query: 180 RQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGR 239
           R +  D +E GC++A++LF P++ GL +   VE L+++    L  Y + +Y  QP RF +
Sbjct: 363 RDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAK 422

Query: 240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMY 277
           LLL LP+LR++    +E LFF + IGD PI   L +M 
Sbjct: 423 LLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEML 460

>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 = 78.6 bits (193), Expect = 3e-16
 Identities = 30/77 (38%), Positives = 45/77 (58%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           ++ GL +   VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF
Sbjct: 384 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 443

Query: 344 KETIGDIPIQRLLGDMY 360
            + IGD PI   L +M 
Sbjct: 444 FKLIGDTPIDTFLMEML 460

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

 Score =  155 bits (393), Expect = 2e-45
 Identities = 48/238 (20%), Positives = 91/238 (38%), Gaps = 5/238 (2%)

Query: 25  HNPHHSPDLLPPNGISSVKI--PPTVLYPPSGLKSPPPPSHHHPSMFLATHQPPPHPGLL 82
           H+ HH P+    + IS V         Y    L S P   + + +             + 
Sbjct: 5   HHHHHGPEPTVEDVISQVARAHREIFTYAHDKLGSSPGNFNANHASGSPYPHGRSGRTVQ 64

Query: 83  QILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIP 142
           +I    E    +    +   V + + +  F+ LS+ DQ+ LL+    E+ ++  A     
Sbjct: 65  EIW---EDFSMSFTPAVREVVEFAKHIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFNV 121

Query: 143 WDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPET 202
            D +++              + + + +  + +   +   L+    E G   AV+L + + 
Sbjct: 122 KDQTVMFLSRTTYSLQELGAMGMGDLLSAMFDFSEKLNSLALTEEELGLFTAVVLVSADR 181

Query: 203 PGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 260
            G+ ++  VE LQ+     L   V      + +RF +LLL LP LR +     E+L  
Sbjct: 182 SGMENSASVEQLQETLLRALRALVLKNRPLETSRFTKLLLKLPDLRTLNNMHSEKLLS 239

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

 Score = 66.4 bits (162), Expect = 8e-13
 Identities = 19/62 (30%), Positives = 29/62 (46%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
           S +  G+ ++  VE LQ+     L   V      + +RF +LLL LP LR +     E+L
Sbjct: 178 SADRSGMENSASVEQLQETLLRALRALVLKNRPLETSRFTKLLLKLPDLRTLNNMHSEKL 237

Query: 342 FF 343
             
Sbjct: 238 LS 239

>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 =  155 bits (393), Expect = 2e-45
 Identities = 40/215 (18%), Positives = 88/215 (40%), Gaps = 6/215 (2%)

Query: 66  PSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQ 125
           P+     HQP P      +L       +    ++   +++ + L  F++L   DQ+ LL+
Sbjct: 36  PAHLFIHHQPLPTLA--PVLPLVTHFADINTFMVLQVIKFTKDLPVFRSLPIEDQISLLK 93

Query: 126 ESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPD 185
            +  E+  + L         + L    +               ++L+       R+L   
Sbjct: 94  GAAVEICHIVLNTTFCLQTQNFLCGPLRYTIEDGARVGFQVEFLELLFHFHGTLRKLQLQ 153

Query: 186 GSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRY--SRQPTRFGRLLLM 243
             E   + A+ LF+P+ PG+     ++ LQ++    L  Y++G+    R    + +LL +
Sbjct: 154 EPEYVLLAAMALFSPDRPGVTQRDEIDQLQEEMALTLQSYIKGQQRRPRDRFLYAKLLGL 213

Query: 244 LPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT 278
           L  LR++ ++   ++   +  G   +  LL ++ +
Sbjct: 214 LAELRSINEAYGYQIQHIQ--GLSAMMPLLQEICS 246

>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 = 70.8 bits (174), Expect = 2e-14
 Identities = 16/80 (20%), Positives = 39/80 (48%), Gaps = 4/80 (5%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRY--SRQPTRFGRLLLMLPSLRAVRQSTIERL 341
           + PG+     ++ LQ++    L  Y++G+    R    + +LL +L  LR++ ++   ++
Sbjct: 169 DRPGVTQRDEIDQLQEEMALTLQSYIKGQQRRPRDRFLYAKLLGLLAELRSINEAYGYQI 228

Query: 342 FFKETIGDIPIQRLLGDMYT 361
              +  G   +  LL ++ +
Sbjct: 229 QHIQ--GLSAMMPLLQEICS 246

>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 =  154 bits (392), Expect = 2e-45
 Identities = 43/223 (19%), Positives = 81/223 (36%), Gaps = 4/223 (1%)

Query: 55  LKSPPPPSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQT 114
            ++ P           ++        L       +K  E   + +   V + + L  F  
Sbjct: 17  QETFPSLCQLGKYTTNSSADHRVQLDLGLW----DKFSELATKCIIKIVEFAKRLPGFTG 72

Query: 115 LSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQE 174
           LS  DQ+ LL+ +  ++ +L +     P   ++  +      R    +        L+  
Sbjct: 73  LSIADQITLLKAACLDILMLRICTRYTPEQDTMTFSDGLTLNRTQMHNAGFGPLTDLVFA 132

Query: 175 ILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP 234
              +   L  D +E G + A+ L   +   L + + V+ LQ+     L  Y R R   QP
Sbjct: 133 FAGQLLPLEMDDTETGLLSAICLICGDRMDLEEPEKVDKLQEPLLEALRLYARRRRPSQP 192

Query: 235 TRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMY 277
             F R+L+ +  LR +     ER    +     P+  L+ +M 
Sbjct: 193 YMFPRMLMKITDLRGISTKGAERAITLKMEIPGPMPPLIREML 235

>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 = 76.6 bits (189), Expect = 2e-16
 Identities = 20/79 (25%), Positives = 33/79 (41%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
             +   L + + V+ LQ+     L  Y R R   QP  F R+L+ +  LR +     ER 
Sbjct: 157 CGDRMDLEEPEKVDKLQEPLLEALRLYARRRRPSQPYMFPRMLMKITDLRGISTKGAERA 216

Query: 342 FFKETIGDIPIQRLLGDMY 360
              +     P+  L+ +M 
Sbjct: 217 ITLKMEIPGPMPPLIREML 235

>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 =  152 bits (386), Expect = 3e-44
 Identities = 51/265 (19%), Positives = 99/265 (37%), Gaps = 9/265 (3%)

Query: 25  HNPHHSPDLLPPNGISSVKIPPTVLYPPSGL-----KSPPPPSHHHPSMFLATHQPPPHP 79
           H+ HHS  L+P     S  + P V      +     ++ P            T       
Sbjct: 6   HHHHHSSGLVPRGSHESYTLTPEVGELIEKVRKAHQETFPALCQLGKY----TTNNSSEQ 61

Query: 80  GLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQW 139
            +   +   +K  E + + +   V + + L  F TL+  DQ+ LL+ +  ++ +L +   
Sbjct: 62  RVSLDIDLWDKFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTR 121

Query: 140 SIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFT 199
             P   ++  +      R    +        L+     +   L  D +E G + A+ L  
Sbjct: 122 YTPEQDTMTFSDGLTLNRTQMHNAGFGPLTDLVFAFANQLLPLEMDDAETGLLSAICLIC 181

Query: 200 PETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLF 259
            +   L     V+MLQ+     L  YVR R   +P  F ++L+ +  LR++     ER+ 
Sbjct: 182 GDRQDLEQPDRVDMLQEPLLEALKVYVRKRRPSRPHMFPKMLMKITDLRSISAKGAERVI 241

Query: 260 FKETIGDIPIQRLLGDMYTMEKSYE 284
             +      +  L+ +M    +  +
Sbjct: 242 TLKMEIPGSMPPLIQEMLENSEGLD 266

>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 = 74.4 bits (183), Expect = 2e-15
 Identities = 19/77 (24%), Positives = 34/77 (44%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           +   L     V+MLQ+     L  YVR R   +P  F ++L+ +  LR++     ER+  
Sbjct: 183 DRQDLEQPDRVDMLQEPLLEALKVYVRKRRPSRPHMFPKMLMKITDLRSISAKGAERVIT 242

Query: 344 KETIGDIPIQRLLGDMY 360
            +      +  L+ +M 
Sbjct: 243 LKMEIPGSMPPLIQEML 259

>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 =  152 bits (385), Expect = 5e-44
 Identities = 45/206 (21%), Positives = 75/206 (36%), Gaps = 11/206 (5%)

Query: 93  ETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCE 152
           +   + L   + W + +  F  LS  DQ+ LL+  W E+ ++ L   SI     L+   +
Sbjct: 38  KLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPD 97

Query: 153 KARERLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPV 211
              +R     V    EI  ++    +RFR+L     E  C+KA+IL       LV A   
Sbjct: 98  LVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQD 157

Query: 212 EMLQDQAQCILGDYV----------RGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFK 261
                +   +L                   +Q  R   LL++L  +R      +E L   
Sbjct: 158 ADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNM 217

Query: 262 ETIGDIPIQRLLGDMYTMEKSYETPG 287
           +    +P+  LL +M           
Sbjct: 218 KCKNVVPVYDLLLEMLNAHVLRGCKS 243

>1yye_A ER-beta, estrogen receptor beta; ER-beta, nuclear receptor, transcription factor, agonist; HET: 196; 2.03A {Homo sapiens} SCOP: a.123.1.1 PDB: 1yy4_A* Length = 268

 Score = 63.8 bits (155), Expect = 9e-12
 Identities = 16/88 (18%), Positives = 28/88 (31%), Gaps = 10/88 (11%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYV----------RGRYSRQPTRFGRLLLMLPSLR 331
           +     LV A        +   +L                   +Q  R   LL++L  +R
Sbjct: 145 NSSMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVR 204

Query: 332 AVRQSTIERLFFKETIGDIPIQRLLGDM 359
                 +E L   +    +P+  LL +M
Sbjct: 205 HASNKGMEHLLNMKCKNVVPVYDLLLEM 232

>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 =  149 bits (378), Expect = 7e-44
 Identities = 34/172 (19%), Positives = 68/172 (39%)

Query: 89  EKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLL 148
           E+   +    +   V + + +  F+ LS+ DQ+ LL+    E+ ++  A      + ++ 
Sbjct: 23  EEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLFDAKERTVT 82

Query: 149 INCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDA 208
               K         +   + +  + E   +   L     E     AV+L + +  G+ + 
Sbjct: 83  FLSGKKYSVDDLHSMGAGDLLNSMFEFSEKLNALQLSDEEMSLFTAVVLVSADRSGIENV 142

Query: 209 QPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 260
             VE LQ+     L   +   +  + + F +LLL LP LR++     E L  
Sbjct: 143 NSVEALQETLIRALRTLIMKNHPNEASIFTKLLLKLPDLRSLNNMHSEELLA 194

>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 = 66.6 bits (163), Expect = 3e-13
 Identities = 17/62 (27%), Positives = 28/62 (45%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
           S +  G+ +   VE LQ+     L   +   +  + + F +LLL LP LR++     E L
Sbjct: 133 SADRSGIENVNSVEALQETLIRALRTLIMKNHPNEASIFTKLLLKLPDLRSLNNMHSEEL 192

Query: 342 FF 343
             
Sbjct: 193 LA 194

>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 =  151 bits (382), Expect = 1e-43
 Identities = 58/269 (21%), Positives = 95/269 (35%), Gaps = 28/269 (10%)

Query: 25  HNPHHSPDLLPPNGISSVKIPPTVLYPPSGLKS-----PPPPSHHHPSMFLATHQPPPHP 79
           H+ HH    L P G    ++    L P   + +     PP      PS       P    
Sbjct: 5   HHHHHHSSGLVPRGSHMRELLLDALSPEQLVLTLLEAEPPHVLISRPSA------PFTEA 58

Query: 80  GLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQW 139
            ++  L       +   + L   + W + +  F  LS  DQ+ LL+  W E+ ++ L   
Sbjct: 59  SMMMSLT------KLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWR 112

Query: 140 SIPWDLSLLINCEKARERLPPDDVRVNNE-IKLIQEILARFRQLSPDGSECGCMKAVILF 198
           SI     L+   +   +R     V    E   ++    +RFR+L     E  C+KA+IL 
Sbjct: 113 SIDHPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILL 172

Query: 199 TPETPGLVDAQPVEMLQDQAQCIL----------GDYVRGRYSRQPTRFGRLLLMLPSLR 248
                 LV A        +   +L                   +Q  R   LL++L  +R
Sbjct: 173 NSSMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVR 232

Query: 249 AVRQSTIERLFFKETIGDIPIQRLLGDMY 277
                 +E L   +    +P+  LL +M 
Sbjct: 233 HASNKGMEHLLNMKCKNVVPVYDLLLEML 261

>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 = 63.1 bits (153), Expect = 1e-11
 Identities = 16/89 (17%), Positives = 28/89 (31%), Gaps = 10/89 (11%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCIL----------GDYVRGRYSRQPTRFGRLLLMLPSLR 331
           +     LV A        +   +L                   +Q  R   LL++L  +R
Sbjct: 173 NSSMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVR 232

Query: 332 AVRQSTIERLFFKETIGDIPIQRLLGDMY 360
                 +E L   +    +P+  LL +M 
Sbjct: 233 HASNKGMEHLLNMKCKNVVPVYDLLLEML 261

>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 =  149 bits (379), Expect = 2e-43
 Identities = 56/236 (23%), Positives = 88/236 (37%), Gaps = 20/236 (8%)

Query: 60  PPSHHHPSMFLATH------QPPPHPGLLQILMSAEK----------CQETTARLLFMAV 103
              HHH ++ L T          P P  L      E+            +     + +  
Sbjct: 5   HHHHHHGAISLITALVRSHVDTTPDPSCLDYSHYEEQSMSEADKVQQFYQLLTSSVDVIK 64

Query: 104 RWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDV 163
           ++   +  +  L   DQ LL Q +  ELF+L LA  +   D  L+        R      
Sbjct: 65  QFAEKIPGYFDLLPEDQELLFQSASLELFVLRLAYRARIDDTKLIFCNGTVLHR-TQCLR 123

Query: 164 RVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILG 223
                +  I E       L  D S   C+ A+ L   E  GL + + VE LQ +    L 
Sbjct: 124 SFGEWLNDIMEFSRSLHNLEIDISAFACLCALTLI-TERHGLREPKKVEQLQMKIIGSLR 182

Query: 224 DYVRGRYSRQP--TRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMY 277
           D+V      Q     F RLL  LP LR++    ++R+F+ +    +P   L+ +M+
Sbjct: 183 DHVTYNAEAQKKQHYFSRLLGKLPELRSLSVQGLQRIFYLKLEDLVPAPALIENMF 238

>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 = 79.3 bits (196), Expect = 3e-17
 Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 2/79 (2%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP--TRFGRLLLMLPSLRAVRQSTIERL 341
           E  GL + + VE LQ +    L D+V      Q     F RLL  LP LR++    ++R+
Sbjct: 160 ERHGLREPKKVEQLQMKIIGSLRDHVTYNAEAQKKQHYFSRLLGKLPELRSLSVQGLQRI 219

Query: 342 FFKETIGDIPIQRLLGDMY 360
           F+ +    +P   L+ +M+
Sbjct: 220 FYLKLEDLVPAPALIENMF 238

>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 =  151 bits (382), Expect = 3e-43
 Identities = 39/248 (15%), Positives = 97/248 (39%), Gaps = 6/248 (2%)

Query: 40  SSVKIPPTVLYPPSGLKSPPPPSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLL 99
            S     +  + P  + +    S+       +             L       +  +  +
Sbjct: 56  LSDASSDSFNHSPESVDTKLNFSNLLMMYQDSGSPDSSEEDQQSRLSMLPHLADLVSYSI 115

Query: 100 FMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLP 159
              + + + +  F+ L+  DQ+ LL+ S  E+ +L   Q     D+S        +    
Sbjct: 116 QKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLRSNQSFSLEDMSWSCGGPDFK-YCI 174

Query: 160 PDDVRVNNEIKLIQEILA---RFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQD 216
            D  +  + ++L++ ++      ++L     E   + A+ L +P+ PG+ D   +E LQD
Sbjct: 175 NDVTKAGHTLELLEPLVKFQVGLKKLKLHEEEHVLLMAICLLSPDRPGVQDHVRIEALQD 234

Query: 217 QAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF--KETIGDIPIQRLLG 274
           +   +L  Y+R ++      + +++  L  LR++ +   ++      +    + +  L+ 
Sbjct: 235 RLCDVLQAYIRIQHPGGRLLYAKMIQKLADLRSLNEEHSKQYRSLSFQPEHSMQLTPLVL 294

Query: 275 DMYTMEKS 282
           +++  E S
Sbjct: 295 EVFGSEVS 302

>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 = 74.1 bits (182), Expect = 4e-15
 Identities = 16/84 (19%), Positives = 40/84 (47%), Gaps = 2/84 (2%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           + PG+ D   +E LQD+   +L  Y+R ++      + +++  L  LR++ +   ++   
Sbjct: 219 DRPGVQDHVRIEALQDRLCDVLQAYIRIQHPGGRLLYAKMIQKLADLRSLNEEHSKQYRS 278

Query: 344 --KETIGDIPIQRLLGDMYTMEKS 365
              +    + +  L+ +++  E S
Sbjct: 279 LSFQPEHSMQLTPLVLEVFGSEVS 302

>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 =  148 bits (374), Expect = 4e-42
 Identities = 40/214 (18%), Positives = 82/214 (38%)

Query: 72  THQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKEL 131
           T        +   L   +K  E   + +   V + + L  F  L+  DQ+ LL+ +  ++
Sbjct: 57  TTNSSADHRVRLDLGLWDKFSELATKCIIKIVEFAKRLPGFTGLTIADQITLLKAACLDI 116

Query: 132 FLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGC 191
            +L +     P   ++  +      R    +        L+     +   L  D +E G 
Sbjct: 117 LILRICTRYTPEQDTMTFSDGLTLNRTQMHNAGFGPLTDLVFTFANQLLPLEMDDTETGL 176

Query: 192 MKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVR 251
           + A+ L   +   L +   V+ LQ+     L  Y+R R   +P  F ++L+ +  LR++ 
Sbjct: 177 LSAICLICGDRQDLEEPTKVDKLQEPLLEALKIYIRKRRPSKPHMFPKILMKITDLRSIS 236

Query: 252 QSTIERLFFKETIGDIPIQRLLGDMYTMEKSYET 285
               ER+   +      +  L+ +M    + +E 
Sbjct: 237 AKGAERVITLKMEIPGSMPPLIQEMLENSEGHEP 270

>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 = 74.1 bits (182), Expect = 5e-15
 Identities = 17/79 (21%), Positives = 34/79 (43%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
             +   L +   V+ LQ+     L  Y+R R   +P  F ++L+ +  LR++     ER+
Sbjct: 184 CGDRQDLEEPTKVDKLQEPLLEALKIYIRKRRPSKPHMFPKILMKITDLRSISAKGAERV 243

Query: 342 FFKETIGDIPIQRLLGDMY 360
              +      +  L+ +M 
Sbjct: 244 ITLKMEIPGSMPPLIQEML 262

>3mnp_A Glucocorticoid receptor; protein-ligand complex, steroid nuclear receptor, mouse GR, hormone receptor; HET: DEX; 1.50A {Mus musculus} PDB: 3mno_A* 3mne_A* 1m2z_A* 3k22_A* 3cld_A* 3k23_A* 3e7c_A* 1nhz_A* 1p93_A* 3bqd_A* 3h52_A* 3gn8_A* 4e2j_A* Length = 261

 Score =  141 bits (356), Expect = 6e-40
 Identities = 49/267 (18%), Positives = 98/267 (36%), Gaps = 23/267 (8%)

Query: 31  PDLLPPNGISSVKIPPTVLYPPSGLKSPPPPSHHHPSMFLATHQPPPHPGLLQILMSAEK 90
             ++P    +  ++ PT++     ++     + +  S       P     ++  L     
Sbjct: 2   SHMVPA---ALPQLTPTLVSLLEVIEPEVLYAGYDSS------VPDSAWRIMTTLN---- 48

Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
                 R +  AV+W + +  F+ L   DQ+ LLQ SW  L +  L   S       L+ 
Sbjct: 49  --MLGGRQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMVFALGWRSYRQASGNLLC 106

Query: 151 CEK--ARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPET-PGLVD 207
                           + ++ K +  I    ++L     E  CMK ++L +     GL  
Sbjct: 107 FAPDLIINEQRMTLPCMYDQCKHMLFISTELQRLQVSYEEYLCMKTLLLLSSVPKEGLKS 166

Query: 208 AQPVEMLQDQAQCILGDYVRGR---YSRQPTRFGRLLLMLPSLRAVRQSTIERLF--FKE 262
            +  + ++      LG  +  R    S+   RF +L  +L S+  V ++ +   F  F +
Sbjct: 167 QELFDEIRMTYIKELGKAIAKRGGNSSQNWQRFYQLTKLLDSMHDVVENLLSYCFQTFLD 226

Query: 263 TIGDIPIQRLLGDMYTMEKSYETPGLV 289
               I    +L ++ T +    + G +
Sbjct: 227 KSMSIEFPEMLAEIITNQIPKYSNGNI 253

>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 = 67.6 bits (165), Expect = 4e-13
 Identities = 16/79 (20%), Positives = 32/79 (40%), Gaps = 5/79 (6%)

Query: 286 PGLVDAQPVEMLQDQAQCILGDYVRGR---YSRQPTRFGRLLLMLPSLRAVRQSTIERLF 342
            GL   +  + ++      LG  +  R    S+   RF +L  +L S+  V ++ +   F
Sbjct: 162 EGLKSQELFDEIRMTYIKELGKAIAKRGGNSSQNWQRFYQLTKLLDSMHDVVENLLSYCF 221

Query: 343 --FKETIGDIPIQRLLGDM 359
             F +    I    +L ++
Sbjct: 222 QTFLDKSMSIEFPEMLAEI 240

>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 =  140 bits (354), Expect = 2e-39
 Identities = 41/217 (18%), Positives = 79/217 (36%), Gaps = 1/217 (0%)

Query: 66  PSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQ 125
           P     +       G    L +  +  +     +   V + + L  F  L   DQ++LL+
Sbjct: 50  PDDIGQSPIVSMPDGDKVDLEAFSEFTKIITPAITRVVDFAKKLPMFSELPXEDQIILLK 109

Query: 126 ESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPD 185
               E+  L  A    P   +L ++ E A +R    +  +      I E+       + D
Sbjct: 110 GCCMEIMSLRAAVRYDPESDTLTLSGEMAVKREQLKNGGLGVVSDAIFELGKSLSAFNLD 169

Query: 186 GSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLP 245
            +E   ++AV+L + +  GL+    +E  Q+        YV  R    P  + +LL+ + 
Sbjct: 170 DTEVALLQAVLLMSTDRSGLLXVDKIEKSQEAYLLAFEHYVNHRKHNIPHFWPKLLMKVT 229

Query: 246 SLRAVRQSTIERLF-FKETIGDIPIQRLLGDMYTMEK 281
            LR +      R    K          L  +++  ++
Sbjct: 230 DLRMIGAXHASRFLHMKVEXPTELFPPLFLEVFEDQE 266

>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 = 63.7 bits (155), Expect = 1e-11
 Identities = 15/82 (18%), Positives = 29/82 (35%), Gaps = 1/82 (1%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLF- 342
           +  GL+    +E  Q+        YV  R    P  + +LL+ +  LR +      R   
Sbjct: 185 DRSGLLXVDKIEKSQEAYLLAFEHYVNHRKHNIPHFWPKLLMKVTDLRMIGAXHASRFLH 244

Query: 343 FKETIGDIPIQRLLGDMYTMEK 364
            K          L  +++  ++
Sbjct: 245 MKVEXPTELFPPLFLEVFEDQE 266

>1osh_A BIle acid receptor; nuclear receptor, ligand binding domain, transcription; HET: FEX; 1.80A {Homo sapiens} SCOP: a.123.1.1 PDB: 3l1b_A* 3bej_A* 3fli_A* 3hc5_A* 3rvf_A* 3dct_A* 3dcu_A* 3ruu_A* 3rut_A* 3olf_A* 3okh_A* 3fxv_A* 3oki_A* 3omk_A* 3omm_A* 3oof_A* 3ook_A* 3hc6_A* 3p89_A* 3p88_A* ... Length = 232

 Score =  138 bits (350), Expect = 3e-39
 Identities = 42/193 (21%), Positives = 75/193 (38%), Gaps = 6/193 (3%)

Query: 89  EKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLL 148
               E     + + V + + L  FQTL   DQ+ LL+ S  E   L  A+  I       
Sbjct: 45  LILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAE--IFNKKLPS 102

Query: 149 INCEKARERLPPDDVRVNNE-IKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVD 207
            + +   ER+   +  +++E I  +        +L     E   + A+++ +P+   + D
Sbjct: 103 GHSDLLEERIR--NSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKD 160

Query: 208 AQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDI 267
            + VE LQ+    +L    +      P  F  LL  L  LR       E L     + D 
Sbjct: 161 REAVEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAEMLMSW-RVNDH 219

Query: 268 PIQRLLGDMYTME 280
               LL +++ ++
Sbjct: 220 KFTPLLCEIWDVQ 232

>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 = 71.6 bits (176), Expect = 1e-14
 Identities = 18/80 (22%), Positives = 30/80 (37%), Gaps = 1/80 (1%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           +   + D + VE LQ+    +L    +      P  F  LL  L  LR       E L  
Sbjct: 154 DRQYIKDREAVEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAEMLMS 213

Query: 344 KETIGDIPIQRLLGDMYTME 363
              + D     LL +++ ++
Sbjct: 214 W-RVNDHKFTPLLCEIWDVQ 232

>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 =  138 bits (349), Expect = 7e-39
 Identities = 38/236 (16%), Positives = 81/236 (34%), Gaps = 9/236 (3%)

Query: 51  PPSGLKSPPPPSHHHPSMFLATHQPPPHPGLLQILMSAEK-------CQETTARLLFMAV 103
                 + PP   H         +      +   + + E        CQ T+   +    
Sbjct: 28  LSGKASNNPPFVIHDMETLCMAEKTLVAKLVANGIQNKEAEVRIFHCCQCTSVETVTELT 87

Query: 104 RWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDV 163
            + + +  F  L   DQ+ LL+    E     L+       + +                
Sbjct: 88  EFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGMLVAYGNGFITREFLKSLR 147

Query: 164 RVNNE-IKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCIL 222
           +   + ++   +   +F  L  D S+     A I+   + PGL++   +E +Q+    +L
Sbjct: 148 KPFCDIMEPKFDFAMKFNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKMQEGIVHVL 207

Query: 223 GDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLF-FKETIGDIPIQRLLGDMY 277
             +++  +      F +LL  +  LR +     + +   K+T  D  +  LL ++Y
Sbjct: 208 RLHLQSNHPDDIFLFPKLLQKMADLRQLVTEHAQLVQIIKKTESDAALHPLLQEIY 263

>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 = 66.9 bits (163), Expect = 8e-13
 Identities = 17/80 (21%), Positives = 37/80 (46%), Gaps = 1/80 (1%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
             + PGL++   +E +Q+    +L  +++  +      F +LL  +  LR +     + +
Sbjct: 184 CGDRPGLLNVGHIEKMQEGIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQLVTEHAQLV 243

Query: 342 F-FKETIGDIPIQRLLGDMY 360
              K+T  D  +  LL ++Y
Sbjct: 244 QIIKKTESDAALHPLLQEIY 263

>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 =  139 bits (352), Expect = 9e-39
 Identities = 47/287 (16%), Positives = 103/287 (35%), Gaps = 22/287 (7%)

Query: 12  IHNAHHQDSKLE-PHNPHHSPDLLPPNGISSVKIPPTVLYPPSGLKSPPPPSHHHPSMFL 70
           + +A  +       H  +     +  +G    +         +   S          + L
Sbjct: 36  LMDAQMKTFDTTFSHFKNFRLPGVLSSGCELPESLQAPSREEAAKWSQVRKDLCSLKVSL 95

Query: 71  ---------ATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQL 121
                      ++PP   G  +I        + +  +    + + + ++ F+ L   DQ+
Sbjct: 96  QLRGEDGSVWNYKPPADSGGKEIFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQI 155

Query: 122 LLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILA---R 178
            LL+ +  EL  L           +        R     +D     +  L++ +L     
Sbjct: 156 SLLKGAAFELCQLRFNTVFNAETGTWECG----RLSYCLEDTAGGFQQLLLEPMLKFHYM 211

Query: 179 FRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTR-- 236
            ++L     E   M+A+ LF+P+ PG++  + V+ LQ+Q    L  Y+     +   R  
Sbjct: 212 LKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFL 271

Query: 237 FGRLLLMLPSLRAVRQSTIERLF-FKETIGDIPIQRLLGDMYTMEKS 282
           F +++ ML  LR++     +RL   ++         L+ +++ +  S
Sbjct: 272 FLKIMAMLTELRSINAQHTQRLLRIQDIHPFAT--PLMQELFGITGS 316

>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 = 61.8 bits (150), Expect = 6e-11
 Identities = 18/85 (21%), Positives = 39/85 (45%), Gaps = 5/85 (5%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTR--FGRLLLMLPSLRAVRQSTIERL 341
           + PG++  + V+ LQ+Q    L  Y+     +   R  F +++ ML  LR++     +RL
Sbjct: 234 DRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLKIMAMLTELRSINAQHTQRL 293

Query: 342 F-FKETIGDIPIQRLLGDMYTMEKS 365
              ++         L+ +++ +  S
Sbjct: 294 LRIQDIHPFAT--PLMQELFGITGS 316

>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 =  135 bits (341), Expect = 2e-37
 Identities = 43/245 (17%), Positives = 94/245 (38%), Gaps = 13/245 (5%)

Query: 60  PPSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRD 119
           PP     S    T    P   L           +  +  +   + + + +  F+ L+  D
Sbjct: 40  PPVRMDGSTGSVTLDLSPLSMLPH-------LADLVSYSIQKVIGFAKMIPGFRDLTSDD 92

Query: 120 QLLLLQESWKELFLLHLAQWSIPWDLSLLIN-CEKARERLPPDDVRVNNE-IKLIQEILA 177
           Q++LL+ S  E+ +L   Q     D+S      +   +           E I+ + +   
Sbjct: 93  QIVLLKSSAIEVIMLRSNQSFTMDDMSWDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQV 152

Query: 178 RFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSR--QPT 235
             ++L+    E   + A+ + +P+ PG+ DA+ VE +QD+    L  Y+R R+       
Sbjct: 153 GLKKLNLHEEEHVLLMAICIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQ 212

Query: 236 RFGRLLLMLPSLRAVRQSTIERLFF--KETIGDIPIQRLLGDMYTMEKSYETPGLVDAQP 293
            + +++  L  LR++ +   ++      +    + +  L+ +++  E S    G +    
Sbjct: 213 LYAKMIQKLADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFGNEISLVPRGSMAISD 272

Query: 294 VEMLQ 298
                
Sbjct: 273 PNSSS 277

>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 = 60.2 bits (146), Expect = 2e-10
 Identities = 18/87 (20%), Positives = 41/87 (47%), Gaps = 4/87 (4%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSR--QPTRFGRLLLMLPSLRAVRQSTIERL 341
           + PG+ DA+ VE +QD+    L  Y+R R+        + +++  L  LR++ +   ++ 
Sbjct: 176 DRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQKLADLRSLNEEHSKQY 235

Query: 342 FF--KETIGDIPIQRLLGDMYTMEKSY 366
                +    + +  L+ +++  E S 
Sbjct: 236 RSLSFQPENSMKLTPLVLEVFGNEISL 262

>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 =  132 bits (334), Expect = 1e-36
 Identities = 42/235 (17%), Positives = 73/235 (31%), Gaps = 30/235 (12%)

Query: 72  THQPPPHPGLLQILMSAEKCQ---------------------ETTARLLFMAVRWVRCLA 110
                  P L+ +LMS E                        +   R L   V+W + L 
Sbjct: 6   GQDIQLIPPLINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLP 65

Query: 111 PFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS--LLINCEKARERLPPDDVRVNNE 168
            F+ L   DQ+ L+Q SW  L +  L   S        L    +         +    + 
Sbjct: 66  GFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSFYSL 125

Query: 169 IKLIQEILARFRQLSPDGSECGCMKAVILFTP-ETPGLVDAQPVEMLQDQAQCILGDYVR 227
              + +I   F +L     E  CMK ++L       GL      E ++      L   + 
Sbjct: 126 CLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELIKAIG 185

Query: 228 GRY---SRQPTRFGRLLLMLPSLRAVRQSTIER---LFFKETIGDIPIQRLLGDM 276
            R         RF +L  +L +L  + +         F +     +    ++ ++
Sbjct: 186 LRQKGVVSSSQRFYQLTKLLDNLHDLVKQLHLYCLNTFIQSRALSVEFPEMMSEV 240

>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 = 56.4 bits (136), Expect = 2e-09
 Identities = 11/85 (12%), Positives = 26/85 (30%), Gaps = 6/85 (7%)

Query: 281 KSYETPGLVDAQPVEMLQDQAQCILGDYVRGRY---SRQPTRFGRLLLMLPSLRAVRQST 337
            +    GL      E ++      L   +  R         RF +L  +L +L  + +  
Sbjct: 156 NTIPLEGLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDLVKQL 215

Query: 338 IER---LFFKETIGDIPIQRLLGDM 359
                  F +     +    ++ ++
Sbjct: 216 HLYCLNTFIQSRALSVEFPEMMSEV 240

>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 =  128 bits (322), Expect = 4e-35
 Identities = 32/220 (14%), Positives = 81/220 (36%), Gaps = 2/220 (0%)

Query: 58  PPPPSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSK 117
                 H  +    T++              ++C       +   V + + +  F  L +
Sbjct: 22  YTMEELHQLAWQTHTYEEIKAYQSKSREALWQQCAIQITHAIQYVVEFAKRITGFMELCQ 81

Query: 118 RDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILA 177
            DQ+LLL+    E+ L+ + +   P + ++L   +    ++    +  ++ +    +   
Sbjct: 82  NDQILLLKSGCLEVVLVRMCRAFNPLNNTVLFEGKYGGMQMF-KALGSDDLVNEAFDFAK 140

Query: 178 RFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRF 237
               L     E     + +L +P+   L++ + V+ LQ++    L   ++  +       
Sbjct: 141 NLCSLQLTEEEIALFSSAVLISPDRAWLLEPRKVQKLQEKIYFALQHVIQKNH-LDDETL 199

Query: 238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMY 277
            +L+  +P++ AV     E+L   +      +  L   +Y
Sbjct: 200 AKLIAKIPTITAVCNLHGEKLQVFKQSHPDIVNTLFPPLY 239

>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 = 57.9 bits (140), Expect = 7e-10
 Identities = 14/79 (17%), Positives = 33/79 (41%), Gaps = 1/79 (1%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
           S +   L++ + V+ LQ++    L   ++  +        +L+  +P++ AV     E+L
Sbjct: 162 SPDRAWLLEPRKVQKLQEKIYFALQHVIQKNH-LDDETLAKLIAKIPTITAVCNLHGEKL 220

Query: 342 FFKETIGDIPIQRLLGDMY 360
              +      +  L   +Y
Sbjct: 221 QVFKQSHPDIVNTLFPPLY 239

>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 =  122 bits (308), Expect = 6e-33
 Identities = 39/237 (16%), Positives = 91/237 (38%), Gaps = 13/237 (5%)

Query: 47  TVLYPPSGLKSPPPPSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWV 106
           T     S      PP   +      T +      L           +  +  +   + + 
Sbjct: 24  TYDPTYSDFCQFRPPVRVNDGGGSVTLELSQLSMLPH-------LADLVSYSIQKVIGFA 76

Query: 107 RCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLI--NCEKARERLPPDDVR 164
           + +  F+ L+  DQ++LL+ S  E+ +L   +     D+S        K R         
Sbjct: 77  KMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVSDVTKAGH 136

Query: 165 VNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGD 224
               I+ + +     ++L+    E   + A+ + +P+ PG+ DA  +E +QD+    L  
Sbjct: 137 SLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRLSNTLQT 196

Query: 225 YVRGRYSRQPTR--FGRLLLMLPSLRAVRQSTIERLFF--KETIGDIPIQRLLGDMY 277
           Y+R R+    +   + +++  L  LR++ +   ++      +    + +  L+ +++
Sbjct: 197 YIRCRHPPPGSHLLYAKMIQKLADLRSLNEEHSKQYRCLSFQPECSMKLTPLVLEVF 253

>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 = 56.4 bits (136), Expect = 2e-09
 Identities = 16/83 (19%), Positives = 40/83 (48%), Gaps = 4/83 (4%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTR--FGRLLLMLPSLRAVRQSTIE 339
           S + PG+ DA  +E +QD+    L  Y+R R+    +   + +++  L  LR++ +   +
Sbjct: 171 SPDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNEEHSK 230

Query: 340 RLFF--KETIGDIPIQRLLGDMY 360
           +      +    + +  L+ +++
Sbjct: 231 QYRCLSFQPECSMKLTPLVLEVF 253

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

 Score =  123 bits (309), Expect = 9e-33
 Identities = 46/282 (16%), Positives = 91/282 (32%), Gaps = 21/282 (7%)

Query: 4   ERGPRKPKIHNAHHQDSKLEPHNPHHSPDLLPPNGISSVKIPPTVLYPPSGLKSPPPPSH 63
           ++       H   +         P  +  L+P     S  + P+ +     ++     + 
Sbjct: 4   DKIIHHHHHHENLYFQGSAPAKEPSVNTALVPQLSTISRALTPSPVMVLENIEPEIVYAG 63

Query: 64  HHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLL 123
           +  S      +P     LL  L           + +   V+W + L  F+ L   DQ+ L
Sbjct: 64  YDSS------KPDTAENLLSTLN------RLAGKQMIQVVKWAKVLPGFKNLPLEDQITL 111

Query: 124 LQESWKELFLLHLAQWSIPWDLSLLINC--EKARERLPPDDVRVNNEIKLIQEILARFRQ 181
           +Q SW  L    L+  S     S  +    +            +    + + +I  +F +
Sbjct: 112 IQYSWMSLLSFALSWRSYKHTNSQFLYFAPDLVFNEEKMHQSAMYELCQGMHQISLQFVR 171

Query: 182 LSPDGSECGCMKAVILFTPET-PGLVDAQPVEMLQDQAQCILGDYVRGR---YSRQPTRF 237
           L     E   MK ++L +     GL      E ++      L   V        +   RF
Sbjct: 172 LQLTFEEYTIMKVLLLLSTIPKDGLKSQAAFEEMRTNYIKELRKMVTKCPNNSGQSWQRF 231

Query: 238 GRLLLMLPSLRAVRQSTIERLFFKETIGD---IPIQRLLGDM 276
            +L  +L S+  +    +E  F+         +    +L ++
Sbjct: 232 YQLTKLLDSMHDLVSDLLEFCFYTFRESHALKVEFPAMLVEI 273

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

 Score = 56.9 bits (137), Expect = 3e-09
 Identities = 13/80 (16%), Positives = 26/80 (32%), Gaps = 6/80 (7%)

Query: 286 PGLVDAQPVEMLQDQAQCILGDYVRGR---YSRQPTRFGRLLLMLPSLRAVRQSTIERLF 342
            GL      E ++      L   V        +   RF +L  +L S+  +    +E  F
Sbjct: 194 DGLKSQAAFEEMRTNYIKELRKMVTKCPNNSGQSWQRFYQLTKLLDSMHDLVSDLLEFCF 253

Query: 343 FKETIGD---IPIQRLLGDM 359
           +         +    +L ++
Sbjct: 254 YTFRESHALKVEFPAMLVEI 273

>3vhv_A Mineralocorticoid receptor; nuclear receptor, transcription factor, activating mutation, hypertension, non-steroidal antagonist; HET: LD1 LD2; 1.35A {Homo sapiens} PDB: 2aax_A* 2aa6_A* 2ab2_A* 2aa2_A* 2aa5_A* 2aa7_A* 2a3i_A* 1y9r_A* 1ya3_A* 2oax_A* 2abi_A* 2q1h_A* 2q1v_A* 2q3y_A* 3ry9_A* Length = 260

 Score =  120 bits (303), Expect = 3e-32
 Identities = 43/243 (17%), Positives = 77/243 (31%), Gaps = 29/243 (11%)

Query: 74  QPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFL 133
           +P     LL  L           + +   V+W + L  F+ L   DQ+ L+Q SW  L  
Sbjct: 34  KPDTAENLLSTLN------RLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQYSWMSLLS 87

Query: 134 LHLAQWSIPWDLSLLINC--EKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGC 191
             L+  S     S  +    +            +    + + +I  +F +L     E   
Sbjct: 88  FALSWRSYKHTNSQFLYFAPDLVFNEEKMHQSAMYELCQGMHQISLQFVRLQLTFEEYTI 147

Query: 192 MKAVILFTPET-PGLVDAQPVEMLQDQAQCILGDYVRGR---YSRQPTRFGRLLLMLPSL 247
           MK ++L +     GL      E ++      L   V        +   RF +L  +L S+
Sbjct: 148 MKVLLLLSTIPKDGLKSQAAFEEMRTNYIKELRKMVTKCPNNSGQSWQRFYQLTKLLDSM 207

Query: 248 RAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGD 307
             +    +E  F+               +                 VE++ DQ   +   
Sbjct: 208 HDLVSDLLEFCFYTFRESHALKVEFPAML-----------------VEIISDQLPKVESG 250

Query: 308 YVR 310
            V+
Sbjct: 251 NVK 253

>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 = 57.2 bits (138), Expect = 1e-09
 Identities = 13/80 (16%), Positives = 26/80 (32%), Gaps = 6/80 (7%)

Query: 286 PGLVDAQPVEMLQDQAQCILGDYVRGR---YSRQPTRFGRLLLMLPSLRAVRQSTIERLF 342
            GL      E ++      L   V        +   RF +L  +L S+  +    +E  F
Sbjct: 160 DGLKSQAAFEEMRTNYIKELRKMVTKCPNNSGQSWQRFYQLTKLLDSMHDLVSDLLEFCF 219

Query: 343 FKETIGD---IPIQRLLGDM 359
           +         +    +L ++
Sbjct: 220 YTFRESHALKVEFPAMLVEI 239

>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 =  119 bits (299), Expect = 1e-31
 Identities = 35/238 (14%), Positives = 81/238 (34%), Gaps = 20/238 (8%)

Query: 47  TVLYPPSGLKSPPPPSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWV 106
           T  Y    L+     +     +    +Q      + Q+      C       +   V + 
Sbjct: 34  TCQYLREELQQITWQTFLQEEI--ENYQNKQREVMWQL------CAIKITEAIQYVVEFA 85

Query: 107 RCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVN 166
           + +  F  L + DQ++LL+    E+  + + +     + ++  +     +   PD  +  
Sbjct: 86  KRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQNNTVYFD----GKYASPDVFKSL 141

Query: 167 NEIKLIQEILA---RFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILG 223
                I  +         +     E     A +L + +   L +   +E LQ + Q  L 
Sbjct: 142 GCEDFISFVFEFGKSLCSMHLTEDEIALFSAFVLMSADRSWLQEKVKIEKLQQKIQLALQ 201

Query: 224 DYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF----KETIGDIPIQRLLGDMY 277
             ++  + R+     +L+  + +LRA+     E+L         I  +    L  +++
Sbjct: 202 HVLQKNH-REDGILTKLICKVSTLRALCGRHTEKLMAFKAIYPDIVRLHFPPLYKELF 258

>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 = 55.6 bits (134), Expect = 5e-09
 Identities = 16/83 (19%), Positives = 34/83 (40%), Gaps = 5/83 (6%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
           S +   L +   +E LQ + Q  L   ++  + R+     +L+  + +LRA+     E+L
Sbjct: 177 SADRSWLQEKVKIEKLQQKIQLALQHVLQKNH-REDGILTKLICKVSTLRALCGRHTEKL 235

Query: 342 FF----KETIGDIPIQRLLGDMY 360
                    I  +    L  +++
Sbjct: 236 MAFKAIYPDIVRLHFPPLYKELF 258

>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 =  116 bits (292), Expect = 1e-30
 Identities = 38/192 (19%), Positives = 71/192 (36%), Gaps = 4/192 (2%)

Query: 72  THQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKEL 131
           T             M   +  E T   + + V + + L  F  +S+ DQ+ LL+    E+
Sbjct: 54  TQTWQSDEDDEDSDMPFRQITEMTILTVQLIVEFAKGLPGFAKISQSDQITLLKACSSEV 113

Query: 132 FLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGC 191
            +L +A+       S+L    +A  R       +   I+ +         +  D      
Sbjct: 114 MMLRVARRYDAATDSVLFANNQAYTRDNYRKAGMAYVIEDLLHFCRCMYSMMMDNVHYAL 173

Query: 192 MKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP---TRFGRLLLMLPSLR 248
           + A+++F+ + PGL     VE +Q      L  Y+  + S  P     FG++L +L  +R
Sbjct: 174 LTAIVIFS-DRPGLEQPLLVEEIQRYYLNTLRVYILNQNSASPRCAVIFGKILGILTEIR 232

Query: 249 AVRQSTIERLFF 260
            +          
Sbjct: 233 TLGMQNSNMCIS 244

>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 = 56.3 bits (136), Expect = 3e-09
 Identities = 15/63 (23%), Positives = 24/63 (38%), Gaps = 3/63 (4%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP---TRFGRLLLMLPSLRAVRQSTIER 340
           + PGL     VE +Q      L  Y+  + S  P     FG++L +L  +R +       
Sbjct: 182 DRPGLEQPLLVEEIQRYYLNTLRVYILNQNSASPRCAVIFGKILGILTEIRTLGMQNSNM 241

Query: 341 LFF 343
              
Sbjct: 242 CIS 244

>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 =  115 bits (291), Expect = 2e-30
 Identities = 43/224 (19%), Positives = 87/224 (38%), Gaps = 7/224 (3%)

Query: 60  PPSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRD 119
            PS       +           ++         E T   + + V + + L  F  L + D
Sbjct: 30  HPSEEDVKRIINQPMDGEDQCDVRF----RHITEITILTVQLIVEFAKRLPGFDKLLRED 85

Query: 120 QLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARF 179
           Q+ LL+    E+ +  +A+       S+L    +   R   +   +   I+ +       
Sbjct: 86  QIALLKACSSEVMMFRMARRYDVQTDSILFVNNQPYSRDSYNLAGMGETIEDLLHFCRTM 145

Query: 180 RQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP-TRFG 238
             +  D +E   + A+++F+ E P L++   VE +Q+     L  YV  R   +P T F 
Sbjct: 146 YSMRVDNAEYALLTAIVIFS-ERPALIEGWKVEKIQEIYLEALRAYVDNRRKPKPGTIFA 204

Query: 239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKS 282
           +LL +L  LR +     E  F  + + +  +   L +++ ++  
Sbjct: 205 KLLSVLTELRTLGNQNSEMCFSLK-LKNKKLPPFLAEIWDVDLK 247

>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 = 57.4 bits (139), Expect = 1e-09
 Identities = 20/81 (24%), Positives = 37/81 (45%), Gaps = 2/81 (2%)

Query: 286 PGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP-TRFGRLLLMLPSLRAVRQSTIERLFFK 344
           P L++   VE +Q+     L  YV  R   +P T F +LL +L  LR +     E  F  
Sbjct: 168 PALIEGWKVEKIQEIYLEALRAYVDNRRKPKPGTIFAKLLSVLTELRTLGNQNSEMCFSL 227

Query: 345 ETIGDIPIQRLLGDMYTMEKS 365
           + + +  +   L +++ ++  
Sbjct: 228 K-LKNKKLPPFLAEIWDVDLK 247

>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 =  115 bits (290), Expect = 2e-30
 Identities = 32/229 (13%), Positives = 69/229 (30%), Gaps = 16/229 (6%)

Query: 64  HHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLL 123
               M     Q       L+   S           +   V+  + L  F  LS+  +  L
Sbjct: 19  AFKGMNDPMEQGRQATSFLKNEKSPADIMNIMDVTMRRFVKMAKRLPAFNDLSQDGKFAL 78

Query: 124 LQESWKELFLLHLAQWSIP-----WDLSLLINCEKARERLPPDDVRVNNEIKLIQEILAR 178
           L+    E+  +   +            +L  + E +      D +  +   +     L  
Sbjct: 79  LKGGMIEMLTVRGVRRFDSSSGSWTTPTLGESSEVSINMF--DQLNADVRSEQKMRFLQF 136

Query: 179 FR----QLSPDGSECGCMKAVILFTPETPG--LVDAQPVEMLQDQAQCILGDYVRGRYSR 232
           F+     +  +      +  ++LF+P        D + +    +Q   +L  Y+   Y  
Sbjct: 137 FKIFHEDIRSNDLVISMIMLIVLFSPRDSITDPEDRRIIARHHEQFSALLNRYLESLYGD 196

Query: 233 QPTR-FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME 280
              +   +L   L  LR +  S+         +     + L  + + +E
Sbjct: 197 DAHQLNEQLPTALRMLREISASSGMLFLGT--VNTSEAEPLPREFFKVE 243

>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 = 61.0 bits (148), Expect = 6e-11
 Identities = 12/78 (15%), Positives = 26/78 (33%), Gaps = 3/78 (3%)

Query: 287 GLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTR-FGRLLLMLPSLRAVRQSTIERLFFKE 345
              D + +    +Q   +L  Y+   Y     +   +L   L  LR +  S+        
Sbjct: 168 DPEDRRIIARHHEQFSALLNRYLESLYGDDAHQLNEQLPTALRMLREISASSGMLFLGT- 226

Query: 346 TIGDIPIQRLLGDMYTME 363
            +     + L  + + +E
Sbjct: 227 -VNTSEAEPLPREFFKVE 243

>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 =  115 bits (288), Expect = 4e-30
 Identities = 36/223 (16%), Positives = 73/223 (32%), Gaps = 10/223 (4%)

Query: 58  PPPPSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSK 117
                       + + +         +    E+C       +   V + + L+ F  L +
Sbjct: 28  LRLEDLLRQRSNIFSREEVTGYQRKSMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQ 87

Query: 118 RDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILA 177
            DQ++LL+    E+ L+ + +     + ++    +        +  R     +LI  I  
Sbjct: 88  NDQIVLLKAGAMEVVLVRMCRAYNADNRTVFFEGKY----GGMELFRALGCSELISSIFD 143

Query: 178 ---RFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP 234
                  L     E     A++L     PGL + + VE LQ   +     ++        
Sbjct: 144 FSHSLSALHFSEDEIALYTALVLINAHRPGLQEKRKVEQLQYNLELAFHHHLC---KTHR 200

Query: 235 TRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMY 277
                 L     LR++    +ERL   + +  I +Q     +Y
Sbjct: 201 QSILAKLPPKGKLRSLCSQHVERLQIFQHLHPIVVQAAFPPLY 243

>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 = 52.6 bits (126), Expect = 4e-08
 Identities = 16/79 (20%), Positives = 29/79 (36%), Gaps = 3/79 (3%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
           +   PGL + + VE LQ   +     ++              L     LR++    +ERL
Sbjct: 168 NAHRPGLQEKRKVEQLQYNLELAFHHHLC---KTHRQSILAKLPPKGKLRSLCSQHVERL 224

Query: 342 FFKETIGDIPIQRLLGDMY 360
              + +  I +Q     +Y
Sbjct: 225 QIFQHLHPIVVQAAFPPLY 243

>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 =  114 bits (287), Expect = 2e-29
 Identities = 39/205 (19%), Positives = 77/205 (37%), Gaps = 3/205 (1%)

Query: 74  QPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFL 133
                              E T   + + V + + L  F  L + DQ+ LL+    E+ +
Sbjct: 104 VNAAPEEENVAEERFRHITEITILTVQLIVEFSKRLPGFDKLIREDQIALLKACSSEVMM 163

Query: 134 LHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMK 193
             +A+       S+L    +   R       + + ++ +         +  D +E   + 
Sbjct: 164 FRMARRYDAETDSILFATNQPYTRESYTVAGMGDTVEDLLRFCRHMCAMKVDNAEYALLT 223

Query: 194 AVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYS-RQPTRFGRLLLMLPSLRAVRQ 252
           A+++F+ E P L +   VE +Q+     L  YV  R      T F +LL +L  LR +  
Sbjct: 224 AIVIFS-ERPSLSEGWKVEKIQEIYIEALKAYVENRRKPYATTIFAKLLSVLTELRTLGN 282

Query: 253 STIERLFFKETIGDIPIQRLLGDMY 277
              E  F  + + +  +   L +++
Sbjct: 283 MNSETCFSLK-LKNRKVPSFLEEIW 306

>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 = 59.8 bits (145), Expect = 2e-10
 Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 2/76 (2%)

Query: 286 PGLVDAQPVEMLQDQAQCILGDYVRGRYS-RQPTRFGRLLLMLPSLRAVRQSTIERLFFK 344
           P L +   VE +Q+     L  YV  R      T F +LL +L  LR +     E  F  
Sbjct: 232 PSLSEGWKVEKIQEIYIEALKAYVENRRKPYATTIFAKLLSVLTELRTLGNMNSETCFSL 291

Query: 345 ETIGDIPIQRLLGDMY 360
           + + +  +   L +++
Sbjct: 292 K-LKNRKVPSFLEEIW 306

>3gyt_A Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily; nuclear receptor, ligand binding domain, dafachronic acid, nematode, DNA-binding, metal-binding, nucleus, receptor; HET: DL4; 2.40A {Strongyloides stercoralis} PDB: 3gyu_A* Length = 244

 Score =  108 bits (270), Expect = 1e-27
 Identities = 32/226 (14%), Positives = 70/226 (30%), Gaps = 16/226 (7%)

Query: 69  FLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVR----WVRCLAPFQTLSKRDQLLLL 124
           F   ++P  +      L   E        ++ + +R      + L  F  +S+  +  LL
Sbjct: 20  FQCMNEPLDNDQQASTLAKKEHNPTDILNVMDITMRRLVKMAKRLGAFNEISEAGKFSLL 79

Query: 125 QESWKELFLLHLAQWSIP----WDLSLLINCEKARERLPPDDVRVNNE-IKLIQEILARF 179
           +    E+  +            W   +  + + +          + +   K         
Sbjct: 80  KGGMIEMLTIRGVTVFNADKGVWQTPVDGHSQISFNMFDKLRPDIKDTQKKGFLHFFNLL 139

Query: 180 RQ-LSPDGSECGCMKAVILFTPETPGLV---DAQPVEMLQDQAQCILGDYVRGRY-SRQP 234
              +  +      +  ++LF  +  GLV   D + VE L    + +L  Y+   +     
Sbjct: 140 HSDVRKNDLAIDIIVLMVLFDSKREGLVSQQDKETVEKLHRNYESLLHRYLYSIHKEEAE 199

Query: 235 TRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME 280
            RF  +   L +LR V ++ +    F           L  + +   
Sbjct: 200 QRFASIPKALVALRKVAENAVTL--FLGAGNTTEAASLPKEFFATN 243

>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 = 52.3 bits (125), Expect = 6e-08
 Identities = 14/75 (18%), Positives = 26/75 (34%), Gaps = 3/75 (4%)

Query: 290 DAQPVEMLQDQAQCILGDYVRGRY-SRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIG 348
           D + VE L    + +L  Y+   +      RF  +   L +LR V ++ +    F     
Sbjct: 171 DKETVEKLHRNYESLLHRYLYSIHKEEAEQRFASIPKALVALRKVAENAVTL--FLGAGN 228

Query: 349 DIPIQRLLGDMYTME 363
                 L  + +   
Sbjct: 229 TTEAASLPKEFFATN 243

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 52.2 bits (124), Expect = 2e-07
 Identities = 61/414 (14%), Positives = 124/414 (29%), Gaps = 102/414 (24%)

Query: 11  KIHNAHHQDSK-----LEPHNP-HHSPDLLPPNGISSVKIPPTVLYPPSGLKSPPPPSHH 64
            I     Q S      +E  +  ++   +       +V      L     L         
Sbjct: 97  PIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKY---NVSRLQPYLKLRQALLE------L 147

Query: 65  HPSMFLATHQPPPHPGLL----QILMSAEKCQETTARLLF-MAVRWV---RCLAPFQTLS 116
            P+  +         G+L      + + + C     +      + W+    C +P     
Sbjct: 148 RPAKNVLID------GVLGSGKTWV-ALDVCLSYKVQCKMDFKIFWLNLKNCNSP----- 195

Query: 117 KRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARER----LPP--------DDVR 164
               L +LQ+   ++     ++     ++ L I+  +A  R      P         +V+
Sbjct: 196 -ETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQ 254

Query: 165 VNNEIKL--IQ-EILA--RFRQLSPDGSECGCMKAVIL------FTP-ETPGL------V 206
                    +  +IL   RF+Q++ D         + L       TP E   L       
Sbjct: 255 NAKAWNAFNLSCKILLTTRFKQVT-DFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDC 313

Query: 207 DAQ--PVEMLQD--QAQCILGDYVRGRYSRQPTRFGRLL-LMLPSLRAVRQSTIE----- 256
             Q  P E+L    +   I+ + +R         +     +    L  + +S++      
Sbjct: 314 RPQDLPREVLTTNPRRLSIIAESIRDG----LATWDNWKHVNCDKLTTIIESSLNVLEPA 369

Query: 257 ---RLF-----FKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDY 308
              ++F     F  +   IP   L   +   +       +V    V  L   +  +    
Sbjct: 370 EYRKMFDRLSVFPPSA-HIPTILL--SLIWFDVIKSDVMVV----VNKLHKYS-LVEKQP 421

Query: 309 VRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETI--GDIPIQRLLGDMY 360
                S  P+ +  L + L +  A+ +S ++     +T    D+    L  D Y
Sbjct: 422 KESTIS-IPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYL--DQY 472

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	367
2e2r_A	244	Estrogen-related receptor gamma; ERR gamma, BPA, n	100.0
3k6p_A	248	Steroid hormone receptor ERR1; estrogen related re	100.0
3ltx_A	243	Estrogen receptor; constitutive, nuclear receptor,	100.0
3v3e_B	257	Nuclear receptor subfamily 4 group A member 1; orp	100.0
1g2n_A	264	Ultraspiracle protein; antiparallel alpha-helical	100.0
1fcy_A	236	RAR-gamma-1, retinoic acid receptor gamma-1; isoty	100.0
2iz2_A	243	FTZ-F1 alpha, nuclear hormone receptor FTZ-F1; nuc	100.0
1xpc_A	248	Estrogen receptor; nuclear receptor, transcription	100.0
3ilz_A	267	Thyroid hormone receptor, alpha isoform 1 variant;	100.0
3oll_A	240	Estrogen receptor beta; steroid binding, phosphory	100.0
3p0u_A	249	Nuclear receptor subfamily 2 group C member 2; lig	100.0
3f5c_B	268	Nuclear receptor subfamily 0 group B member 1; tra	100.0
3plz_A	257	FTZ-F1 related protein; alpha helical sandwhich, f	100.0
3cjw_A	244	COUP transcription factor 2; COUP-TFII, nuclear re	100.0
3kmr_A	266	Retinoic acid receptor alpha; nuclear receptor tra	100.0
1yye_A	268	ER-beta, estrogen receptor beta; ER-beta, nuclear	100.0
2nxx_A	235	Ultraspiracle (USP, NR2B4); hormone receptor, APO	100.0
3ipq_A	283	Oxysterols receptor LXR-alpha; LXR homodimer, LXR	100.0
3vi8_A	273	Peroxisome proliferator-activated receptor alpha;	100.0
1ymt_A	246	Steroidogenic factor 1; SF-1, ligand-binding domai	100.0
2ocf_A	298	Estrogen receptor; estrogen receptor, LBD, monobod	100.0
1nq7_A	244	Nuclear receptor ROR-beta; ligand-binding domain,	100.0
1xdk_B	303	RAR-beta, retinoic acid receptor, beta; nuclear re	100.0
3b0t_A	254	Vitamin D3 receptor; nuclear receptor, transcripti	100.0
2r40_D	266	Ecdysone receptor, 20-hydroxy-ecdysone receptor; n	100.0
3vhv_A	260	Mineralocorticoid receptor; nuclear receptor, tran	100.0
3mnp_A	261	Glucocorticoid receptor; protein-ligand complex, s	100.0
1hg4_A	279	Ultraspiracle; nuclear hormone receptor, transcrip	100.0
1l2j_A	271	Estrogen receptor beta; nuclear receptor, transcri	100.0
1n83_A	270	Nuclear receptor ROR-alpha; three-layered alpha he	100.0
1xvp_B	246	Orphan nuclear receptor NR1I3; CAR, RXR, citco, SR	100.0
1nrl_A	316	Orphan nuclear receptor PXR; PXR, xenobiotic, SRC-	100.0
2hc4_A	302	Vitamin D receptor; alpha helical sandwich, gene r	100.0
2o4j_A	292	Vitamin D3 receptor; nuclear receptor-ligand compl	100.0
3tx7_B	352	Nuclear receptor subfamily 5 group A member 2; LRH	100.0
1sqn_A	261	PR, progesterone receptor; nuclear receptor, stero	100.0
3n00_A	245	REV-ERBA-alpha; reverba ncorid1, anti-parallel B-s	100.0
1pdu_A	244	DHR38, nuclear hormone receptor HR38; nuclear rece	100.0
3vhu_A	294	Mineralocorticoid receptor; nuclear receptor, tran	100.0
3cqv_A	199	Nuclear receptor subfamily 1 group D member 2; rev	100.0
1t7r_A	269	Androgen receptor; nuclear receptor, transcription	100.0
2p1t_A	240	Retinoic acid receptor RXR-alpha; protein-ligand c	100.0
2nxx_E	248	Ecdysone receptor (ECR, NRH1); hormone receptor, A	100.0
1z5x_E	310	Ecdysone receptor ligand binding domain; ponastero	100.0
3l0l_A	248	Nuclear receptor ROR-gamma; nuclear receptor, rorg	100.0
1lbd_A	282	RXR_LBD, retinoid X receptor; transcription factor	100.0
1osh_A	232	BIle acid receptor; nuclear receptor, ligand bindi	100.0
1ovl_A	271	Orphan nuclear receptor NURR1 (MSe 414, 496, 511);	100.0
3u9q_A	269	Peroxisome proliferator-activated receptor gamma;	100.0
1pzl_A	237	Hepatocyte nuclear factor 4-alpha; transcription;	100.0
3up3_A	243	Acedaf-12; ligand binding domain, nematode, steroi	100.0
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	100.0
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	100.0
3gyt_A	244	Nuclear hormone receptor of the steroid/thyroid ho	99.98
3f5c_B	268	Nuclear receptor subfamily 0 group B member 1; tra	99.72
3plz_A	257	FTZ-F1 related protein; alpha helical sandwhich, f	99.71
3ltx_A	243	Estrogen receptor; constitutive, nuclear receptor,	99.7
3p0u_A	249	Nuclear receptor subfamily 2 group C member 2; lig	99.69
3tx7_B	352	Nuclear receptor subfamily 5 group A member 2; LRH	99.67
2iz2_A	243	FTZ-F1 alpha, nuclear hormone receptor FTZ-F1; nuc	99.67
3k6p_A	248	Steroid hormone receptor ERR1; estrogen related re	99.67
2e2r_A	244	Estrogen-related receptor gamma; ERR gamma, BPA, n	99.67
1fcy_A	236	RAR-gamma-1, retinoic acid receptor gamma-1; isoty	99.67
3vi8_A	273	Peroxisome proliferator-activated receptor alpha;	99.66
1ymt_A	246	Steroidogenic factor 1; SF-1, ligand-binding domai	99.65
3v3e_B	257	Nuclear receptor subfamily 4 group A member 1; orp	99.65
3kmr_A	266	Retinoic acid receptor alpha; nuclear receptor tra	99.65
3cjw_A	244	COUP transcription factor 2; COUP-TFII, nuclear re	99.64
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	99.62
1g2n_A	264	Ultraspiracle protein; antiparallel alpha-helical	99.62
1hg4_A	279	Ultraspiracle; nuclear hormone receptor, transcrip	99.62
3ilz_A	267	Thyroid hormone receptor, alpha isoform 1 variant;	99.61
1xdk_B	303	RAR-beta, retinoic acid receptor, beta; nuclear re	99.61
2nxx_A	235	Ultraspiracle (USP, NR2B4); hormone receptor, APO	99.61
1osh_A	232	BIle acid receptor; nuclear receptor, ligand bindi	99.6
3u9q_A	269	Peroxisome proliferator-activated receptor gamma;	99.6
2p1t_A	240	Retinoic acid receptor RXR-alpha; protein-ligand c	99.6
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	99.6
3oll_A	240	Estrogen receptor beta; steroid binding, phosphory	99.58
3ipq_A	283	Oxysterols receptor LXR-alpha; LXR homodimer, LXR	99.58
3b0t_A	254	Vitamin D3 receptor; nuclear receptor, transcripti	99.57
1pdu_A	244	DHR38, nuclear hormone receptor HR38; nuclear rece	99.57
2hc4_A	302	Vitamin D receptor; alpha helical sandwich, gene r	99.56
1nrl_A	316	Orphan nuclear receptor PXR; PXR, xenobiotic, SRC-	99.55
1lbd_A	282	RXR_LBD, retinoid X receptor; transcription factor	99.55
1nq7_A	244	Nuclear receptor ROR-beta; ligand-binding domain,	99.55
2o4j_A	292	Vitamin D3 receptor; nuclear receptor-ligand compl	99.54
2ocf_A	298	Estrogen receptor; estrogen receptor, LBD, monobod	99.54
2r40_D	266	Ecdysone receptor, 20-hydroxy-ecdysone receptor; n	99.54
1xpc_A	248	Estrogen receptor; nuclear receptor, transcription	99.53
1xvp_B	246	Orphan nuclear receptor NR1I3; CAR, RXR, citco, SR	99.53
1yye_A	268	ER-beta, estrogen receptor beta; ER-beta, nuclear	99.53
1n83_A	270	Nuclear receptor ROR-alpha; three-layered alpha he	99.52
1l2j_A	271	Estrogen receptor beta; nuclear receptor, transcri	99.5
1ovl_A	271	Orphan nuclear receptor NURR1 (MSe 414, 496, 511);	99.47
2nxx_E	248	Ecdysone receptor (ECR, NRH1); hormone receptor, A	99.47
1pzl_A	237	Hepatocyte nuclear factor 4-alpha; transcription;	99.46
3l0l_A	248	Nuclear receptor ROR-gamma; nuclear receptor, rorg	99.46
1z5x_E	310	Ecdysone receptor ligand binding domain; ponastero	99.45
3vhv_A	260	Mineralocorticoid receptor; nuclear receptor, tran	99.43
3up3_A	243	Acedaf-12; ligand binding domain, nematode, steroi	99.43
3gyt_A	244	Nuclear hormone receptor of the steroid/thyroid ho	99.38
3vhu_A	294	Mineralocorticoid receptor; nuclear receptor, tran	99.35
3cqv_A	199	Nuclear receptor subfamily 1 group D member 2; rev	99.35
1t7r_A	269	Androgen receptor; nuclear receptor, transcription	99.32
3mnp_A	261	Glucocorticoid receptor; protein-ligand complex, s	99.32
3n00_A	245	REV-ERBA-alpha; reverba ncorid1, anti-parallel B-s	99.3
1sqn_A	261	PR, progesterone receptor; nuclear receptor, stero	99.3

>2e2r_A Estrogen-related receptor gamma; ERR gamma, BPA, nuclear receptor, transcription; HET: 2OH; 1.60A {Homo sapiens} SCOP: a.123.1.1 PDB: 2zas_A* 2zbs_A 2zkc_A* 2p7g_A* 1vjb_A* 1tfc_A 2p7a_A* 2p7z_A* 2gpu_A* 1kv6_A 2gp7_A 2gpp_A* 2gpo_A* 2gpv_A* 1s9q_A* 1s9p_A* 2ewp_A*

Probab=100.00  E-value=5.7e-39  Score=292.75  Aligned_cols=213  Identities=22%  Similarity=0.386  Sum_probs=188.6

Q ss_pred             CCcccccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCC
Q psy6602          65 HPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD  144 (367)
Q Consensus        65 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~  144 (367)
                      +|..+++.+++..|++..   ..++++++++.+.++.+|+|||++|||.+|+.+||++|||++|+|+++++.|||++..+
T Consensus        30 ep~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~a~rs~~~~  106 (244)
T 2e2r_A           30 EPEKIYAMPDPTVPDSDI---KALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFE  106 (244)
T ss_dssp             CCCCCCCCCCTTSCCCHH---HHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTSS
T ss_pred             CCCcccCCCCCCCCcchh---HHHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHhHHHHHHHHHHHHhcccC
Confidence            445566666666665443   45889999999999999999999999999999999999999999999999999999887


Q ss_pred             CceEecCCccccCCCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHH
Q psy6602         145 LSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGD  224 (367)
Q Consensus       145 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~  224 (367)
                      +..++.++..+.+......+..+.++.+.+++.+|++|++|++||+|||||+||+||++|+++..+|+++|++|..+|.+
T Consensus       107 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~v~~lq~~~~~aL~~  186 (244)
T 2e2r_A          107 DELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQD  186 (244)
T ss_dssp             SCEEEETTEEECHHHHHHTTCHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHTCCCTTCSCHHHHHHHHHHHHHHHHH
T ss_pred             CeEEecCCEeecHHHhhhccHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhccCCCCCcCHHHHHHHHHHHHHHHHH
Confidence            77777666554433222234567778899999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhCCCcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHccc
Q psy6602         225 YVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  280 (367)
Q Consensus       225 y~~~~~~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~  280 (367)
                      ||..+|++++.||++|+++++.||+++..+.|.+++.+.++..++++++.||++..
T Consensus       187 y~~~~~~~~~~Rf~~LL~~L~~Lr~~~~~~~e~l~~~~~~~~~~~~~Ll~Eml~~~  242 (244)
T 2e2r_A          187 YEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPMHKLFLEMLEAK  242 (244)
T ss_dssp             HHHHHCTTCTTHHHHHHTTHHHHHHHHHHHHHHHHHHHHHCCSCCCHHHHHHHTSC
T ss_pred             HHHhcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCChHHHHHHHHhCc
Confidence            99999999999999999999999999999999999999999999999999999864

>3k6p_A Steroid hormone receptor ERR1; estrogen related receptor alpha, DNA-binding, isopeptide BON binding, nucleus, phosphoprotein, transcription; HET: 5FB; 2.00A {Homo sapiens} SCOP: a.123.1.1 PDB: 1xb7_A 2pjl_A* 3d24_A

Probab=100.00  E-value=5.5e-39  Score=293.52  Aligned_cols=212  Identities=24%  Similarity=0.387  Sum_probs=177.6

Q ss_pred             CCcccccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCC
Q psy6602          65 HPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD  144 (367)
Q Consensus        65 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~  144 (367)
                      +|..+++++++..|++.   ...++++++++++.++.+|+|||++|+|.+|+.+||++|||++|+|+++++.||+++..+
T Consensus        30 ep~~~~~~~~~~~~~~~---~~~~~~l~e~a~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~lL~~a~~s~~~~  106 (248)
T 3k6p_A           30 EPEKLYAMPDPAGPDGH---LPAVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQ  106 (248)
T ss_dssp             SCCCCCCCC-------C---CCHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTSS
T ss_pred             CCcccccCCCCCCCCch---hhHHHHHHHHHHHHHHHHHHHHhcCcccccCCHHHHHHHHHHHHHHHHHHHHHHHccCCC
Confidence            45556666665555433   455889999999999999999999999999999999999999999999999999999877


Q ss_pred             CceEecCCccccCCCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHH
Q psy6602         145 LSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGD  224 (367)
Q Consensus       145 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~  224 (367)
                      +..++.++....+......+..+.++.+.+++.+|++|++|++||+|||||+||+||++|+++..+|+++|++|..+|.+
T Consensus       107 ~~l~~~~g~~~~~~~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkAivL~npd~~gL~~~~~ve~lq~~~~~aL~~  186 (248)
T 3k6p_A          107 DELAFAEDLVLDEEGARAAGLGELGAALLQLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQLREALHEALLE  186 (248)
T ss_dssp             SCEEEETTEEECHHHHHHTTTTTHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTCCCTTCSCHHHHHHHHHHHHHHHHH
T ss_pred             CeEEeCCCcccChhhhhhccHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHH
Confidence            55555554333322211123445678899999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhCC----CcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcc
Q psy6602         225 YVRGRYS----RQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM  279 (367)
Q Consensus       225 y~~~~~~----~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~  279 (367)
                      ||..+|+    +++.||++|+++++.||+++..+.|.+++.+.++..++++++.||++.
T Consensus       187 y~~~~~~~~~~~~~~Rf~~LL~~Lp~Lr~l~~~~~e~l~~~k~~g~~~i~~Ll~Eml~~  245 (248)
T 3k6p_A          187 YEAGRAGPGGGAERRRAGRLLLTLPLLRQTAGKVLAHFYGVKLEGKVPMHKLFLEMLEA  245 (248)
T ss_dssp             HHHTC----CCCCCH-HHHHHTTHHHHHHHHHHHHHHHHCC-CCCSSCHHHHHHHHHHH
T ss_pred             HHHHhCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCHHHHHHHHHhc
Confidence            9999998    899999999999999999999999999999999999999999999975

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

Probab=100.00  E-value=1.7e-38  Score=289.43  Aligned_cols=211  Identities=18%  Similarity=0.200  Sum_probs=182.7

Q ss_pred             cccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceE
Q psy6602          69 FLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLL  148 (367)
Q Consensus        69 ~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l  148 (367)
                      ++.++++..+++   ....++++++++++.++.+|+|||++|+|.+|+.+||++|||++|+|+++|+.||+++..+...+
T Consensus        22 ~~~~~~~~~~~~---~~~~~~~~~~~a~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~~~l   98 (243)
T 3ltx_A           22 LESHHNHGQPPT---KVHLLNSLVKLAERELVHLINWAKNVPGYTDLSLSDQVHLIECCWMELLLLNCAFRSIEHGGKSL   98 (243)
T ss_dssp             CCCCCCTTSCCC---HHHHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTTTTSEE
T ss_pred             hhccccCCCCcc---HHHHHHHHHHHHHHHHHHHHHHHHcCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCCeE
Confidence            334444334443   34458899999999999999999999999999999999999999999999999999988777656


Q ss_pred             ecCCcc-ccCCCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHH
Q psy6602         149 INCEKA-RERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVR  227 (367)
Q Consensus       149 ~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~  227 (367)
                      +++++. +........+..+.++.+.+++.+|++|++|++||+|||||+||+||++|+++..+|+++|++|..+|.+||.
T Consensus        99 ~~~~g~~~~~~~~~~~~~~~~~~~i~~~~~~l~~L~ld~~E~~lLkaivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~  178 (243)
T 3ltx_A           99 AFAPDLVLDRSSWSTVEMTEIFEQVAAVSEQMMQNHLHKDELLLLQAMVLVNAEVRRLASYNQIFNMQQSLLDAIVDTAQ  178 (243)
T ss_dssp             EEETTEEEEHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTSCCSCCTTHHHHHHHHHHHHHHHHHHHH
T ss_pred             EecCCcccchhhhcccCHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            555543 2222111224567778889999999999999999999999999999999999999999999999999999999


Q ss_pred             hhCCCcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCC
Q psy6602         228 GRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKS  282 (367)
Q Consensus       228 ~~~~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s  282 (367)
                      .+|++++.||++||++++.||+++..+.|++++.+.++..++++++.|||+....
T Consensus       179 ~~~p~~~~Rf~~LL~~Lp~Lr~l~~~~~e~l~~~~~~g~~~~~~Ll~Eml~~~~~  233 (243)
T 3ltx_A          179 KYHPDNVRHVPAVLLLLTHIRQAGERGIAFFQRLKSEGVVTFCDLLKEMLDAQDF  233 (243)
T ss_dssp             HHSTTCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHHHHHC--
T ss_pred             HhCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHhCccc
Confidence            9999999999999999999999999999999999999999999999999997664

>3v3e_B Nuclear receptor subfamily 4 group A member 1; orphan nuclear receptor, transcription; 2.06A {Homo sapiens} PDB: 3v3q_A* 2qw4_A 1yje_A

Probab=100.00  E-value=2.5e-39  Score=296.74  Aligned_cols=190  Identities=25%  Similarity=0.365  Sum_probs=172.8

Q ss_pred             CHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccchH
Q psy6602          87 SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVN  166 (367)
Q Consensus        87 ~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  166 (367)
                      .+..+++++++.++.+|+|||++|||.+|+.+||++|||+||+|++++++||++++..+..++.++....+... ..+..
T Consensus        53 ~~~~~~~l~~~~i~~iV~wAK~iP~F~~L~~~DQi~LLk~~w~ElllL~~a~~~~~~~~~l~~~~~~~~~~~~~-~~~~~  131 (257)
T 3v3e_B           53 DVQQFYDLLSGSLEVIRKWAEKIPGFAELSPADQDLLLESAFLELFILRLAYRSKPGEGKLIFCSGLVLHRLQC-ARGFG  131 (257)
T ss_dssp             HHHHHHHHHHHTHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHSBGGGTEEECTTSBEEEHHHH-HHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhccCCCCeeEeCCCccccHHHH-HhhhH
Confidence            47889999999999999999999999999999999999999999999999999998777777777665554332 23455


Q ss_pred             HHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhh--CCCcchHHHHHHHhh
Q psy6602         167 NEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGR--YSRQPTRFGRLLLML  244 (367)
Q Consensus       167 ~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~--~~~~~~Rf~~LL~~l  244 (367)
                      +.++.+.+|+.+|++|++|++||+|||||+||+ |++|+.+..+|+++|+++..+|++|+..+  +++++.||++||++|
T Consensus       132 ~~~~~l~~~~~~l~~L~ld~~E~a~LkAivLfs-d~~gL~~~~~Ve~lqe~~~~aL~~yi~~~~~~p~~~~rf~kLL~~L  210 (257)
T 3v3e_B          132 DWIDSILAFSRSLHSLLVDVPAFACLSALVLIT-DRHGLQEPRRVEELQNRIASCLKEHVAAVAGEPQPASCLSRLLGKL  210 (257)
T ss_dssp             THHHHHHHHHHHHHHTTCCHHHHHHHHHHHHSS-CCTTCSSHHHHHHHHHHHHHHHHHHHHHHHCSCC-CHHHHHHHTHH
T ss_pred             HHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHhC-CCCCCCCHHHHHHHHHHHHHHHHHHHHHhcCCCcHhhHHHHHHHHH
Confidence            677899999999999999999999999999998 99999999999999999999999999754  578999999999999


Q ss_pred             hHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHc
Q psy6602         245 PSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT  278 (367)
Q Consensus       245 ~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~  278 (367)
                      +.||+++..+.|.+++.+..+..++++|+.|||.
T Consensus       211 p~LR~l~~~~~e~l~~~k~~~~~~~~~Ll~Emf~  244 (257)
T 3v3e_B          211 PELRTLCTQGLQRIFYLKLEDLVPPPPIIDKIFM  244 (257)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhhcCCCCCccHHHHHHHH
Confidence            9999999999999999999999999999999995

>1g2n_A Ultraspiracle protein; antiparallel alpha-helical sandwich, structural proteomics in europe, spine, structural genomics, gene regulation; HET: EPH; 1.65A {Heliothis virescens} SCOP: a.123.1.1 PDB: 2r40_A* 1r20_A* 1r1k_A* 3ixp_A*

Probab=100.00  E-value=3.9e-38  Score=290.61  Aligned_cols=217  Identities=26%  Similarity=0.402  Sum_probs=182.2

Q ss_pred             cccccCCCCCCCCChh-hhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccC--
Q psy6602          67 SMFLATHQPPPHPGLL-QILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPW--  143 (367)
Q Consensus        67 ~~~~~~~~~~~~~~~~-~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~--  143 (367)
                      ..+++++++..+++.. .....++++++++.+.++.+|+|||++|+|.+|+.+||++|||++|+|+++|+.||+++..  
T Consensus        22 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~w~el~lL~~a~~s~~~~~  101 (264)
T 1g2n_A           22 SEEFQFLRVGPDSNVPPKFRAPVSSLCQIGNKQIAALVVWARDIPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLT  101 (264)
T ss_dssp             CCCCCSBCCCTTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHGGGSC
T ss_pred             CccccccccCCCcccchhhhhHHHHHHHHHHHHHHHHHHHHHcCCChhcCCHHHHHHHHHHhhHHHHHHHHHHHcccccc
Confidence            3445555555555443 2235689999999999999999999999999999999999999999999999999999876  


Q ss_pred             --CCc--------------eEecCCccccCCCCCccchHHHH-HHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCC
Q psy6602         144 --DLS--------------LLINCEKARERLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLV  206 (367)
Q Consensus       144 --~~~--------------~l~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~  206 (367)
                        .+.              .++.++..+.+......+..+.+ +.+.+++.+|++|++|++||+|||||+||+||++|++
T Consensus       102 ~~~~~~~~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~ld~~E~~lLkAivL~npd~~gL~  181 (264)
T 1g2n_A          102 EERDGVDGTGNRTTSPPQLMCLMPGMTLHRNSALQAGVGQIFDRVLSELSLKMRTLRVDQAEYVALKAIILLNPDVKGLK  181 (264)
T ss_dssp             CC----------CCCCCCEEEEETTEEEEHHHHHHHTCHHHHHHHHHHTHHHHHHTTCCHHHHHHHHHHHHSCTTCTTCS
T ss_pred             ccccccccccccccccccceeecCCcccCchhhhhccHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCc
Confidence              443              33333333332222222445555 6788999999999999999999999999999999999


Q ss_pred             ChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCC
Q psy6602         207 DAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSY  283 (367)
Q Consensus       207 ~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~  283 (367)
                      +...|+++|++|..+|.+||..+|++++.||++|+++++.||+++..+.|.+++.+.++..++++++.||++....+
T Consensus       182 ~~~~ve~lq~~~~~aL~~y~~~~~~~~~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~Eml~~~~~~  258 (264)
T 1g2n_A          182 NRQEVEVLREKMFLCLDEYCRRSRSSEEGRFAALLLRLPALRSISLKSFEHLFFFHLVADTSIAGYIRDALRNHAPP  258 (264)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSTTCTTHHHHHHTHHHHHHHHHHHHHHHHHHTTCBCTTTHHHHHHHHHTCCC--
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHhCCCHhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCChHHHHHHHHhCCCCc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999876643

>1fcy_A RAR-gamma-1, retinoic acid receptor gamma-1; isotype selectivity, retinoid ligand complexes, drug design, antiparallel alpha-helical sandwich fold; HET: 564 LMU; 1.30A {Homo sapiens} SCOP: a.123.1.1 PDB: 1fcz_A* 1fcx_A* 1fd0_A* 1exa_A* 1exx_A* 1dkf_B*

Probab=100.00  E-value=2.1e-38  Score=287.69  Aligned_cols=193  Identities=21%  Similarity=0.283  Sum_probs=172.7

Q ss_pred             cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccch
Q psy6602          86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRV  165 (367)
Q Consensus        86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~  165 (367)
                      ..++++++++++.++.+|+|||++|||.+|+.+||++|||++|+|+++++.||+++..++..++.++..+.+......|.
T Consensus        44 ~~~~~~~~~~~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~l~~a~~~~~~~~~l~~~~g~~~~~~~~~~~g~  123 (236)
T 1fcy_A           44 GLWDKFSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMTFSDGLTLNRTQMHNAGF  123 (236)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETTTTEEECTTCBEEEHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhccCCCeEEeCCCceecHHHHHHcCc
Confidence            34889999999999999999999999999999999999999999999999999999865554444443333322112234


Q ss_pred             HHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhhh
Q psy6602         166 NNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLP  245 (367)
Q Consensus       166 ~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~  245 (367)
                      .+.++.+.+++.+|++|++|++||+|||||+||+||++|+++...|+++|++|..+|.+||..+||+++.||++|+++++
T Consensus       124 ~~~~~~i~~~~~~l~~L~ld~~E~~lLkaivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL~~L~  203 (236)
T 1fcy_A          124 GPLTDLVFAFAGQLLPLEMDDTETGLLSAICLICGDRMDLEEPEKVDKLQEPLLEALRLYARRRRPSQPYMFPRMLMKIT  203 (236)
T ss_dssp             GGGHHHHHHHHHHHGGGCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCchhHHHHHHHHhH
Confidence            45667888999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhHhhhhhHHHHHHhhhccCCchhHhHHHHHHc
Q psy6602         246 SLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT  278 (367)
Q Consensus       246 ~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~  278 (367)
                      .||+++..+.|.+++.+..+..++++++.||++
T Consensus       204 ~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~Eml~  236 (236)
T 1fcy_A          204 DLRGISTKGAERAITLKMEIPGPMPPLIREMLE  236 (236)
T ss_dssp             HHHHHHHHHHHHHHHHHTTSSSCCCHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHccCCCCccHHHHHHhC
Confidence            999999999999999999999999999999985

>1xpc_A Estrogen receptor; nuclear receptor, transcription factor, ER-alpha, antagonist hormone-growth factor receptor complex; HET: AIT; 1.60A {Homo sapiens} SCOP: a.123.1.1 PDB: 1sj0_A* 1xp1_A* 1xp9_A* 1xp6_A* 1yim_A* 1yin_A* 3ert_A* 1r5k_A* 3erd_A* 1l2i_A* 2iok_A* 1a52_A* 2ouz_A* 1ere_A* 1err_A* 2qxs_A* 3q95_A* 3q97_A* 2b1z_A* 1zky_A* ...

Probab=100.00  E-value=1.6e-37  Score=283.98  Aligned_cols=213  Identities=20%  Similarity=0.307  Sum_probs=181.4

Q ss_pred             CcccccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCC
Q psy6602          66 PSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDL  145 (367)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~  145 (367)
                      |..+++++++..|++..   ..++.+++++++.++.+|+|||++|||.+|+.+||++|||++|+|+++|+.||+++...+
T Consensus        18 p~~~~~~~~~~~~~~~~---~~~~~l~~~a~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~   94 (248)
T 1xpc_A           18 PPILYSEYDPTRPFSEA---SMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPG   94 (248)
T ss_dssp             CCCCCCCSCTTSCSTTS---CHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTSTT
T ss_pred             CCccccCCCCCCCCchh---HHHHHHHHHHHHHHHHHHHHHHcCCccccCCHHHHHHHHHHHhHHHHHHHHHHHhccccC
Confidence            34455666655555432   347889999999999999999999999999999999999999999999999999998765


Q ss_pred             ceEecCCccccCCC-CCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCC--------CCChhHHHHHHH
Q psy6602         146 SLLINCEKARERLP-PDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPG--------LVDAQPVEMLQD  216 (367)
Q Consensus       146 ~~l~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~--------L~~~~~v~~~q~  216 (367)
                      ..++.++..+.+.. ....+..+.++.+.+++.+|++|++|++||+|||||+||+||++|        +.++..|+++|+
T Consensus        95 ~l~~~~g~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~~ls~~~~~gl~~~~~v~~lq~  174 (248)
T 1xpc_A           95 KLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLD  174 (248)
T ss_dssp             EEEEETTEEEEHHHHTTSTTHHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTTTCCCCCCHHHHHHHHHHHHHHH
T ss_pred             ceeecCCceeCccchhhhccHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHcCCcccccccccccccccHHHHHHHHH
Confidence            55555554444322 122346677788999999999999999999999999999999954        555789999999


Q ss_pred             HHHHHHHHHHHhhC---CCcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccC
Q psy6602         217 QAQCILGDYVRGRY---SRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEK  281 (367)
Q Consensus       217 ~~~~~L~~y~~~~~---~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~  281 (367)
                      +|..+|.+||..++   ++++.||++|+++++.||+++..+.|.+++.+.++..++++++.||++...
T Consensus       175 ~~~~aL~~y~~~~~~~~~~~~~Rf~~LL~~L~~Lr~~~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~  242 (248)
T 1xpc_A          175 KITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDAHR  242 (248)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCCSSCHHHHHHHHHSCCS
T ss_pred             HHHHHHHHHHHccCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHhCCc
Confidence            99999999999875   477899999999999999999999999999999999999999999998654

>3ilz_A Thyroid hormone receptor, alpha isoform 1 variant; nuclear receptor, signaling protein; HET: B72; 1.85A {Homo sapiens} SCOP: a.123.1.1 PDB: 3jzb_A* 3hzf_A* 2h79_A* 2h77_A* 1nav_A* 3uvv_A* 1xzx_X* 1y0x_X* 1nq1_A* 3jzc_A* 1nuo_A* 3imy_A* 1nq0_A* 1bsx_A* 1r6g_A* 1nq2_A* 3gws_X* 1n46_A* 2h6w_X* 2j4a_A* ...

Probab=100.00  E-value=1.4e-37  Score=287.11  Aligned_cols=201  Identities=19%  Similarity=0.248  Sum_probs=176.7

Q ss_pred             ChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCC
Q psy6602          80 GLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLP  159 (367)
Q Consensus        80 ~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~  159 (367)
                      ........|.++++++++.++.+|+|||++|+|.+|+.+||++|||++|+|+++|+.||+++..++..++.++..+.+..
T Consensus        64 ~~~~~~~~~~~~~~~~~~~l~~~VewaK~lP~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~l~~~~g~~~~~~~  143 (267)
T 3ilz_A           64 GDKVDLEAFSEFTKIITPAITRVVDFAKKLPMFSELPXEDQIILLKGCCMEIMSLRAAVRYDPESDTLTLSGEMAVKREQ  143 (267)
T ss_dssp             SCCBCHHHHHHHHHHHHHHHHHHHHHHHTSHHHHTSCHHHHHHHHHHHHHHHHHHHHHTTCBTTTTBEEETTTEEECHHH
T ss_pred             cchhhHHHHHHHHHHHHHHHHHHHHHHhcCcchhhCCHhHHHHHHHHHHHHHHHHHHHHHhcCCCCEEEecCCeeecHHH
Confidence            33344556899999999999999999999999999999999999999999999999999998766655555544333322


Q ss_pred             CCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHH
Q psy6602         160 PDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGR  239 (367)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~  239 (367)
                      ....+....++.+.+++.+|++|++|++||+|||||+||+||++|+++..+|+++|++|..+|.+||..+|++++.||++
T Consensus       144 ~~~~~~~~~~~~i~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~Rf~~  223 (267)
T 3ilz_A          144 LKNGGLGVVSDAIFELGKSLSAFNLDDTEVALLQAVLLMSTDRSGLLXVDKIEKSQEAYLLAFEHYVNHRKHNIPHFWPK  223 (267)
T ss_dssp             HHHTTTTHHHHHHHHHHHHHGGGCCCHHHHHHHHHHHHSCCCSSSCSCHHHHHHHHHHHHHHHHHHHHHHTCSSTTHHHH
T ss_pred             HhccCHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCchHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHH
Confidence            11223456678889999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhHhHhhhhhHHHHHHhhhccCCchh-HhHHHHHHccc
Q psy6602         240 LLLMLPSLRAVRQSTIERLFFKETIGDIPI-QRLLGDMYTME  280 (367)
Q Consensus       240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~-~~Ll~eml~~~  280 (367)
                      ||++++.||+++..+.|.+++.+..+..++ ++|+.|||+..
T Consensus       224 LL~~Lp~Lr~l~~~~~e~l~~~k~~~~~~~~~~Ll~Em~~~~  265 (267)
T 3ilz_A          224 LLMKVTDLRMIGAXHASRFLHMKVEXPTELFPPLFLEVFEDQ  265 (267)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHC-CCSSCGGGSCHHHHHHTCCS
T ss_pred             HHHHhHHHHHHHHHHHHHHHHHHhcCCccCCCcHHHHHhcCC
Confidence            999999999999999999999999998887 99999999853

>3oll_A Estrogen receptor beta; steroid binding, phosphorylation, hormone receptor-activator; HET: PTR EST; 1.50A {Homo sapiens} SCOP: a.123.1.1 PDB: 1u3s_A* 1u3q_A* 1x78_A* 1x7b_A* 1x7j_A* 1x76_A* 2yjd_A* 3ols_A* 3omo_A* 3omp_A* 3omq_A* 1u3r_A* 1u9e_A* 1qkm_A* 2giu_A* 1nde_A* 2jj3_A* 2i0g_A* 2qtu_A* 2z4b_A* ...

Probab=100.00  E-value=5e-37  Score=279.36  Aligned_cols=204  Identities=21%  Similarity=0.282  Sum_probs=177.1

Q ss_pred             CCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCc
Q psy6602          74 QPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEK  153 (367)
Q Consensus        74 ~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~  153 (367)
                      ++..|++...   .+.++++++++.++.+|+|||++|+|.+|+.+||++|||++|+|+++|+.||+++..++..++.++.
T Consensus        24 ~~~~~~~~~~---~~~~~~~~a~~~l~~~vewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~~l~~~~g~  100 (240)
T 3oll_A           24 RPSAPFTEAS---MMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDL  100 (240)
T ss_dssp             CCSSCCCHHH---HHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTSTTEEEEETBE
T ss_pred             CCCCCCchHH---HHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHccCCCCeeEecCCc
Confidence            4455665443   3788999999999999999999999999999999999999999999999999999876555555544


Q ss_pred             cccCCCCC-ccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCC-------hhHHHHHHHHHHHHHHHH
Q psy6602         154 ARERLPPD-DVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVD-------AQPVEMLQDQAQCILGDY  225 (367)
Q Consensus       154 ~~~~~~~~-~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~-------~~~v~~~q~~~~~~L~~y  225 (367)
                      ...+.... ..+..+.++.+.+++.+|++|++|++||+|||||+||+||++|+++       +.+|+.+|++|.++|.+|
T Consensus       101 ~~~~~~~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~gLs~~~~~~~~~~~v~~~q~~~~~aL~~y  180 (240)
T 3oll_A          101 VLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNAVTDALVWV  180 (240)
T ss_dssp             EEEGGGGGGSTTHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHCSCCCCCCCCC--CHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccchhhHHHHhhHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHcCCCCCCcccccchhhHHHHHHHHHHHHHHHHHHH
Confidence            44433221 2346677788999999999999999999999999999999999865       568899999999999999


Q ss_pred             HHhhC---CCcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHccc
Q psy6602         226 VRGRY---SRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  280 (367)
Q Consensus       226 ~~~~~---~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~  280 (367)
                      |..++   ++++.||++|+++++.||+++..+.|.+++.+.++..++++++.|||+..
T Consensus       181 ~~~~~~~~~~~~~Rf~~LL~~Lp~Lr~l~~~~~e~l~~~~~~g~~~~~~Ll~eml~~~  238 (240)
T 3oll_A          181 IAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEMLNAH  238 (240)
T ss_dssp             HHTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSCCCHHHHHHHHHC
T ss_pred             HhccCCCCcchhhHHHHHHHHhHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHhcc
Confidence            98764   57899999999999999999999999999999999999999999999854

>3p0u_A Nuclear receptor subfamily 2 group C member 2; ligand binding domain, orphan nuclear receptor, testicular R 4, signaling protein; 3.00A {Homo sapiens}

Probab=100.00  E-value=1.8e-37  Score=283.65  Aligned_cols=196  Identities=32%  Similarity=0.552  Sum_probs=172.6

Q ss_pred             CHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccc-----cCCC--
Q psy6602          87 SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKAR-----ERLP--  159 (367)
Q Consensus        87 ~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~-----~~~~--  159 (367)
                      +++++|+++.+.++.+|+|||++|+|.+|+.+||++|||++|+|+++|+.||++...+...++.+++..     .+..  
T Consensus        35 ~~~~~~e~a~~~L~~~VewaK~iP~F~~L~~~DQ~~LLk~~w~el~~L~~a~~s~~~~~~~~l~~~~~~~~~~~~~~~~~  114 (249)
T 3p0u_A           35 NVHYICESASRLLFLSMHWARSIPAFQALGQDCNTSLVRACWNELFTLGLAQCAQVMSLSTILAAIVNHLQNSIQEDKLS  114 (249)
T ss_dssp             CSSCHHHHHHHHHHHHHHHHHTCTTTGGGCHHHHHHHHHTTHHHHHHHHHHHTTTSCCCCCCCCC-CC---CC-------
T ss_pred             CHHHHHHHHHHHHHHHHHHHHcCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHcccCCcchhhcccccccccccccccch
Confidence            466699999999999999999999999999999999999999999999999999877766666554322     1111  


Q ss_pred             -CCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHH
Q psy6602         160 -PDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFG  238 (367)
Q Consensus       160 -~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~  238 (367)
                       ....+..+.++.+.+++.+|++|++|++||+|||||+||+||++|+++..+|+++|++|..+|.+||..+|++++.||+
T Consensus       115 ~~~~~~~~~~i~~l~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~Rf~  194 (249)
T 3p0u_A          115 GDRIKQVMEHIWKLQEFCNSMAKLDIDGYEYAYLKAIVLFSPDHPGLTSTSQIEKFQEAAQMELQDYVQATYSEDTYRLA  194 (249)
T ss_dssp             --CCCCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHTCSCSTTCCCSHHHHHHHHHHHHHHHHHHHHHTTTCSTHHH
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCChHHHHH
Confidence             1122345667788999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCC
Q psy6602         239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKS  282 (367)
Q Consensus       239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s  282 (367)
                      +|+++++.||+++..+.|.+++.+.+|..++++++.+||++...
T Consensus       195 ~LL~~L~~Lr~i~~~~~e~l~f~~~~g~~~i~~Ll~eml~~~~~  238 (249)
T 3p0u_A          195 RILVRLPALRLMSSNITEELFFTGLIGNVSIDSIIPYILKMETA  238 (249)
T ss_dssp             HHHTTHHHHHTSCHHHHHHHHCCSSHHHHCHHHHHHHHTTC---
T ss_pred             HHHHHHHHHHHHHHHHHHHeeeecccCCCCHHHHHHHHHhCCcc
Confidence            99999999999999999999999999999999999999997664

>3f5c_B Nuclear receptor subfamily 0 group B member 1; transcriptional corepressor, regulatory complex, DNA-binding, lipid-binding, metal-binding; 3.00A {Mus musculus}

Probab=100.00  E-value=2.4e-37  Score=285.17  Aligned_cols=197  Identities=25%  Similarity=0.372  Sum_probs=169.5

Q ss_pred             hhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecC----CccccCC
Q psy6602          83 QILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINC----EKARERL  158 (367)
Q Consensus        83 ~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~----~~~~~~~  158 (367)
                      ..+.+++++++++++.++.+|+|||++|||.+|+.+||++|||++|+|+++|++||+++..+...+..+    +...+..
T Consensus        44 v~l~~~~~l~e~a~~~L~~~V~wAK~iP~F~~L~~~DQv~LLk~~w~ElllL~~A~rs~~~~~~~~~~~~~~~~il~~~~  123 (268)
T 3f5c_B           44 ITLKDPQVVCEAASAGLLKTLRFVKYLPCFQILPLDQQLVLVRSCWAPLLMLELAQDHLHFEMMEIPETNTTQEMLTTRR  123 (268)
T ss_dssp             ---CCHHHHHHHHHHHHHHHHHHHHTCHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTTCCCCCCCC--------------
T ss_pred             cccCCHHHHHHHHHHHHHHHHHHHccCCCcccCCHHHHHHHHHHHhHHHHHHHHHHHhccccccccchhhhhhhhhcccc
Confidence            345678999999999999999999999999999999999999999999999999999987665432211    1111110


Q ss_pred             C----------------------CCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHH
Q psy6602         159 P----------------------PDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQD  216 (367)
Q Consensus       159 ~----------------------~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~  216 (367)
                      .                      .......+.++.+.+++.+|++|++|++||+|||||+||+||++|+++..+|+++|+
T Consensus       124 ~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~i~~l~~~~~~l~~L~ld~~E~~lLkAivL~npd~~gL~~~~~ve~lq~  203 (268)
T 3f5c_B          124 QETEGPEPAEPQATEQPQMVSAEAGHLLPAAAVQAIKSFFFKCWSLNIDTKEYAYLKGTVLFNPDLPGLQCVKYIEGLQW  203 (268)
T ss_dssp             -------------------------CCCCSSHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHH
T ss_pred             cccccccccccccccccccccchhccccHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCCCCchHHHHHHHHH
Confidence            0                      000112356788999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhCCCcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcc
Q psy6602         217 QAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM  279 (367)
Q Consensus       217 ~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~  279 (367)
                      +|..+|.+||..+|++++.||++|+++++.||+++..+.|.+++.+.++..++++++.||++.
T Consensus       204 ~~~~aL~~y~~~~~p~~~~Rf~~LL~~Lp~LR~i~~~~~e~l~~~k~~g~~~i~~Ll~Eml~a  266 (268)
T 3f5c_B          204 RTQQILTEHIRMMQREYQIRSAELNSALFLLRFINSDVVTELFFRPIIGAVSMDDMMLEMLCA  266 (268)
T ss_dssp             HHHHHHHHHHHHHSSCSSHHHHHHHHHHHHHTTSCSSHHHHHHTHHHHCSCCHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHHHCCChHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCchHHHHHHHhC
Confidence            999999999999999999999999999999999999999999999999999999999999975

>3plz_A FTZ-F1 related protein; alpha helical sandwhich, family five, TRAN factor, transcription-receptor-agonist comple; HET: 470; 1.75A {Homo sapiens} SCOP: a.123.1.1 PDB: 1yok_A* 1yuc_A* 4dor_A* 1zdu_A* 4dos_A* 1zh7_A 1pk5_A 3f5c_A

Probab=100.00  E-value=2.6e-37  Score=283.75  Aligned_cols=200  Identities=30%  Similarity=0.435  Sum_probs=174.5

Q ss_pred             hhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCC-CceEecCCcc-ccCC
Q psy6602          81 LLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD-LSLLINCEKA-RERL  158 (367)
Q Consensus        81 ~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~-~~~l~~~~~~-~~~~  158 (367)
                      ...+..++..+++++++.++.+|+|||++|+|.+|+.+||++|||++|+|+++|+.||++.... .+.+++.++. +...
T Consensus        51 ~~~~~~~~~~l~~~a~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~lL~~a~rs~~~~~~~~l~~~~g~~~~~~  130 (257)
T 3plz_A           51 KHEKLSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYS  130 (257)
T ss_dssp             ---CCCHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCBTTEEECTTSCEEEHH
T ss_pred             CccccchHHHHHHHHHHHHHHHHHHHHcCcChhcCCHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCeEEecCCCccChH
Confidence            3455677999999999999999999999999999999999999999999999999999987543 3444444443 2221


Q ss_pred             CC-Cccch--HHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcch
Q psy6602         159 PP-DDVRV--NNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPT  235 (367)
Q Consensus       159 ~~-~~~~~--~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~  235 (367)
                      .. ...+.  .+.++.+.+++.+|++|++|++||+|||||+||+||++|+++..+|+++|++|..+|.+||..+|++++.
T Consensus       131 ~~~~~~g~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkAivL~npd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~  210 (257)
T 3plz_A          131 IIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTE  210 (257)
T ss_dssp             HHHTTSCHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHSCTTCCSCTTHHHHHHHHHHHHHHHHHHHHHHCTTSTT
T ss_pred             HHhhhcCCcHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCchh
Confidence            10 01122  5667889999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHccc
Q psy6602         236 RFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  280 (367)
Q Consensus       236 Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~  280 (367)
                      ||++|+++++.||+++..+.|.+++.+.++..++++++.||++..
T Consensus       211 Rf~~LL~~Lp~Lr~l~~~~~e~l~~~~~~g~~~i~~Ll~Eml~~k  255 (257)
T 3plz_A          211 KFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHAK  255 (257)
T ss_dssp             HHHHHHTHHHHHHHHHHHHHHHHHHHHHTTCSCCCSHHHHHHTC-
T ss_pred             HHHHHHHHhHHHHHHHHHHHHHHhhhhhcCCCCHHHHHHHHHhcc
Confidence            999999999999999999999999999999999999999999864

>3cjw_A COUP transcription factor 2; COUP-TFII, nuclear receptor, ligand binding domain, orphan receptor, three-layered helical sandwich, DNA-binding; 1.48A {Homo sapiens}

Probab=100.00  E-value=4.1e-37  Score=280.58  Aligned_cols=199  Identities=41%  Similarity=0.713  Sum_probs=171.4

Q ss_pred             cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccC-C-CCCcc
Q psy6602          86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARER-L-PPDDV  163 (367)
Q Consensus        86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~-~-~~~~~  163 (367)
                      .+++++++++.+.++.+|+|||++|||.+|+.+||++|||++|+|+++|+.||+++..+...++.+++.... . .....
T Consensus        37 ~~~~~l~e~a~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~~~~l~~~g~~~~~~~~~~~~  116 (244)
T 3cjw_A           37 MGIENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHVAPLLAAAGLHASPMSADRVV  116 (244)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHHHSSSGGGSCHHHHHHHHHHHHHHHHHHHHHHHTCCCSCCC-----------------C
T ss_pred             ccHHHHHHHHHHHHHHHHhHHHhCCChhcCCHHHHHHHHHHHHHHHHHHHHHHHhccccccccccccccccCccchhhhH
Confidence            346679999999999999999999999999999999999999999999999999998777766666554321 1 11112


Q ss_pred             chHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHh
Q psy6602         164 RVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLM  243 (367)
Q Consensus       164 ~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~  243 (367)
                      ++.+.++.+.+++.+|++|++|++||+|||||+||+||++|+++...|+++|++|..+|.+||..+|++++.||++||++
T Consensus       117 ~~~~~~~~~~~~~~~~~~L~ld~~E~~lLkaivL~~pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~Rf~~LLl~  196 (244)
T 3cjw_A          117 AFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLR  196 (244)
T ss_dssp             CCSHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHH
Confidence            23455678889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCC
Q psy6602         244 LPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYE  284 (367)
Q Consensus       244 l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d  284 (367)
                      |+.||+++..+.|.+++.+.++..++++++.||++...+.+
T Consensus       197 L~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~~~~  237 (244)
T 3cjw_A          197 LPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDMLLSGSSFN  237 (244)
T ss_dssp             HHHHHHSCHHHHHHHHTHHHHTTCCGGGTHHHHHTCCCCCC
T ss_pred             hHHHHhhhHHHHHHHHhhcccCCCcHHHHHHHHHhCCCCCC
Confidence            99999999999999999999999999999999999766543

>3kmr_A Retinoic acid receptor alpha; nuclear receptor transcription factor ligand binding domain, binding, metal-binding, nucleus, phosphoprotein; HET: EQN; 1.80A {Homo sapiens} PDB: 3kmz_B* 3a9e_B* 4dm6_A* 1xap_A* 4dm8_A* 2lbd_A* 3lbd_A* 4lbd_A*

Probab=100.00  E-value=2.1e-37  Score=285.60  Aligned_cols=195  Identities=21%  Similarity=0.297  Sum_probs=172.2

Q ss_pred             CHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccchH
Q psy6602          87 SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVN  166 (367)
Q Consensus        87 ~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  166 (367)
                      .|.++++++++.++.+|+|||++|+|.+|+.+||++|||++|+|+++|+.||+++..++..++.++..+.+......+..
T Consensus        69 ~~~~~~e~~~~~l~~~VewaK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~~s~~~~~~l~~~~g~~~~~~~~~~~g~~  148 (266)
T 3kmr_A           69 LWDKFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMHNAGFG  148 (266)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETTTTEEECTTSBEEEHHHHHHHTTG
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCcChhhCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCeEEecCCcccchHHHhhcchH
Confidence            48899999999999999999999999999999999999999999999999999987655444444433332221112344


Q ss_pred             HHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhhhH
Q psy6602         167 NEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPS  246 (367)
Q Consensus       167 ~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~~  246 (367)
                      +..+.+.+++.+|++|++|++||+|||||+||+||++|+++..+|+++|++|..+|.+||..+|++++.||++||.+++.
T Consensus       149 ~~~~~i~~~~~~l~~L~ld~~E~~lLkAIvL~~pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL~~Lp~  228 (266)
T 3kmr_A          149 PLTDLVFAFANQLLPLEMDDAETGLLSAICLICGDRQDLEQPDRVDMLQEPLLEALKVYVRKRRPSRPHMFPKMLMKITD  228 (266)
T ss_dssp             GGHHHHHHHHHHHGGGCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHhHH
Confidence            55677889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccC
Q psy6602         247 LRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEK  281 (367)
Q Consensus       247 Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~  281 (367)
                      ||+++..+.|.+++.+.++..++++++.|||+...
T Consensus       229 Lr~i~~~~~e~l~~~k~~~~~~~~~Ll~Eml~~~~  263 (266)
T 3kmr_A          229 LRSISAKGAERVITLKMEIPGSMPPLIQEMLENSE  263 (266)
T ss_dssp             HHHHHHHHHHHHHHHHHHSSSCCCHHHHHHHC---
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCcchHHHHHhcCCC
Confidence            99999999999999999999999999999998643

>1yye_A ER-beta, estrogen receptor beta; ER-beta, nuclear receptor, transcription factor, agonist; HET: 196; 2.03A {Homo sapiens} SCOP: a.123.1.1 PDB: 1yy4_A*

Probab=100.00  E-value=5.2e-37  Score=283.39  Aligned_cols=209  Identities=21%  Similarity=0.272  Sum_probs=177.3

Q ss_pred             cCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEec
Q psy6602          71 ATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN  150 (367)
Q Consensus        71 ~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~  150 (367)
                      +++++..|++....   +.++++++++.++.+|+|||++|+|.+|+.+||++|||++|+|+++|+.|||++...+..++.
T Consensus        19 ~~~~~~~~~~~~~~---~~~l~e~a~~~l~~~VewAK~lp~F~~L~~~DQi~LLk~~w~el~lL~~a~rs~~~~~~l~~~   95 (268)
T 1yye_A           19 LISRPSAPFTEASM---MMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFA   95 (268)
T ss_dssp             CCCCCSCCCCHHHH---HHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTSTTEEEEE
T ss_pred             ccCCCCCCCchhHH---HHHHHHHHHHHHHHHHHHHhcCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCceEec
Confidence            44555566654332   778999999999999999999999999999999999999999999999999999877555555


Q ss_pred             CCccccCCCCC-ccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCC-------hhHHHHHHHHHHHHH
Q psy6602         151 CEKARERLPPD-DVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVD-------AQPVEMLQDQAQCIL  222 (367)
Q Consensus       151 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~-------~~~v~~~q~~~~~~L  222 (367)
                      ++..+.+.... ..+..+.++.+.+++.+|++|++|.+||+|||||+||+||++|+++       +.+|+++|++|..+|
T Consensus        96 ~g~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkAIvLfnpd~~gLs~~~~~~~~~~~v~~~q~~~~~aL  175 (268)
T 1yye_A           96 PDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNAVTDAL  175 (268)
T ss_dssp             TTEEEEGGGGGGSTTHHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHTCCC----------CCHHHHHHHHHHHHHHH
T ss_pred             CCcccChhhHhhhccHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHcCCCCCCcccchhhHHHHHHHHHHHHHHHHHH
Confidence            55444443211 2346677788999999999999999999999999999999999864       789999999999999


Q ss_pred             HHHHHhhC---CCcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCC
Q psy6602         223 GDYVRGRY---SRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKS  282 (367)
Q Consensus       223 ~~y~~~~~---~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s  282 (367)
                      .+||..++   ++++.||++||++++.||+++..+.|.+++.+.++..++++++.|||+....
T Consensus       176 ~~y~~~~~~~~~~~~~Rf~~LLl~Lp~Lr~i~~~~~e~l~~~~~~g~~~~~~Ll~Eml~~~~~  238 (268)
T 1yye_A          176 VWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEMLNAHVL  238 (268)
T ss_dssp             HHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSCCCHHHHHHHHHHHC
T ss_pred             HHHHHhcCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCHHHHHHHHHhCccc
Confidence            99999874   5788999999999999999999999999999999999999999999987664

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

Probab=100.00  E-value=4.6e-37  Score=278.74  Aligned_cols=196  Identities=29%  Similarity=0.586  Sum_probs=173.8

Q ss_pred             cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccch
Q psy6602          86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRV  165 (367)
Q Consensus        86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~  165 (367)
                      ..+.++++++.+.++.+|+|||++|||.+|+.+||++|||++|+|+++++.|||++...+..++.++..+.+......+.
T Consensus        37 ~~~~~~~~~~~~~l~~~vewaK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~a~rs~~~~~~~~~~~g~~~~~~~~~~~~~  116 (235)
T 2nxx_A           37 TTVNNICQATHKQLFQLVQWAKLVPHFTSLPLTDQVQLLRAGWNELLIAAFSHRSMQAQDAIVLATGLTVNKSTAHAVGV  116 (235)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHHSTTSTTSCHHHHHHHHHHHHHHHHHHHHHHTTSSSSSSEECSSSCEECSSSCSSSSC
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHhHHHHHHHHHHHhcccCCCceEecCCcccccchhhhhch
Confidence            45889999999999999999999999999999999999999999999999999999876665555554444443222223


Q ss_pred             HHHH-HHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhh
Q psy6602         166 NNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLML  244 (367)
Q Consensus       166 ~~~~-~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l  244 (367)
                      .+.+ +.+.+++.+|++|++|++||+|||||+||+||++|++++..|+++|++|..+|.+||..+|++++.||++|+.++
T Consensus       117 ~~~~~~~~~~~~~~l~~L~ld~~E~~lLkaivL~~pd~~gL~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LL~~L  196 (235)
T 2nxx_A          117 GNIYDRVLSELVNKMKEMKMDKTELGCLRAIILYNPDVRGIKSVQEVEMLREKIYGVLEEYTRTTHPNEPGRFAKLLLRL  196 (235)
T ss_dssp             SSSHHHHHHHTHHHHHHHTCCHHHHHHHHHHHHCCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTHH
T ss_pred             HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHh
Confidence            3333 346789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccC
Q psy6602         245 PSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEK  281 (367)
Q Consensus       245 ~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~  281 (367)
                      +.||+++..+.|.+++.+.++..++++++.||++...
T Consensus       197 ~~Lr~~~~~~~e~l~~~~~~g~~~~~~Ll~eml~~~~  233 (235)
T 2nxx_A          197 PALRSIGLKCLEHLFFFKLIGDVPIDTFLMEMLEGTT  233 (235)
T ss_dssp             HHHHHHHHTCCSCTTTTSSSSCCCHHHHHHHHTTC--
T ss_pred             HHHHHHHHHHHHHHHhhcccCCCcHHHHHHHHHhCCC
Confidence            9999999999999999999999999999999998654

>3ipq_A Oxysterols receptor LXR-alpha; LXR homodimer, LXR signaling, alternative DNA-binding, metal-binding, nucleus, polymorphism, receptor transcription; HET: 965; 2.00A {Homo sapiens} PDB: 3ips_A* 3ipu_A* 3fc6_B* 3fal_B* 1uhl_B* 2acl_B* 1upv_A* 1upw_A* 1p8d_A* 1pq9_A* 1pq6_A* 1pqc_A* 3kfc_A* 4dk7_A* 4dk8_A* 3l0e_A*

Probab=100.00  E-value=3e-37  Score=287.26  Aligned_cols=201  Identities=22%  Similarity=0.226  Sum_probs=174.2

Q ss_pred             CChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCC
Q psy6602          79 PGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERL  158 (367)
Q Consensus        79 ~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~  158 (367)
                      +........+.++++++.+.++.+|+|||+||||.+|+.+||++|||++|+|+++|+.|+++....+...+.++..+.+.
T Consensus        81 ~~~~~~~~~~~~l~e~~~~~l~~~VewaK~lP~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~~~~~g~~~~~~  160 (283)
T 3ipq_A           81 HSREARQQRFAHFTELAIVSVQEIVDFAKQLPGFLQLSREDQIALLKTSAIEVMLLETSRRYNPGSESITFLKDFSYNRE  160 (283)
T ss_dssp             ---CCHHHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETTTTEEEETTTEEECHH
T ss_pred             ccchhHHHHHHHHHHHHHHHHHHHHHHHhcCcChhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEeCCCceecHH
Confidence            33444566789999999999999999999999999999999999999999999999999998765555555554444332


Q ss_pred             CCCccch-HHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHH
Q psy6602         159 PPDDVRV-NNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRF  237 (367)
Q Consensus       159 ~~~~~~~-~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf  237 (367)
                      .....+. .+.++.+.+++.+|++|++|++||+|||||+||+||++|+++...|+++|++|..+|.+||..+|++++.||
T Consensus       161 ~~~~~g~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkAIvL~npd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~Rf  240 (283)
T 3ipq_A          161 DFAKAGLQVEFINPIFEFSRAMNELQLNDAEFALLIAISIFSADRPNVQDQLQVERLQHTYVEALHAYVSIHHPHDRLMF  240 (283)
T ss_dssp             HHHHTTCCHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHSTTCTTHH
T ss_pred             HHHHcCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCCCcHHHHHHHHHHHHHHHHHHHHHhCCChhhHH
Confidence            2111122 356788899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHccc
Q psy6602         238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  280 (367)
Q Consensus       238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~  280 (367)
                      ++||++|+.||+++..+.|.+++.+..+ .++++|+.|||+..
T Consensus       241 ~~LL~~Lp~Lr~l~~~~~e~l~~~k~~~-~~~~~Ll~Em~~~~  282 (283)
T 3ipq_A          241 PRMLMKLVSLRTLSSVHSEQVFALRLQD-KKLPPLLSEIWDVH  282 (283)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTT-CCCCHHHHHHHCC-
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhcCCC-CCCChHHHHHhcCC
Confidence            9999999999999999999999999886 48999999999864

>3vi8_A Peroxisome proliferator-activated receptor alpha; nuclear receptor, protein-ligand complex, PPAR, transcriptio; HET: 13M; 1.75A {Homo sapiens} PDB: 2znn_A* 3et1_A* 3kdu_A* 3kdt_A* 2rew_A* 1i7g_A* 3g8i_A* 1kkq_A* 1k7l_A* 3sp6_A* 2npa_A* 2p54_A* 3fei_A* 3tkm_A* 2znq_A* 2znp_A* 3sp9_A* 3gwx_A* 3dy6_A* 1gwx_A* ...

Probab=100.00  E-value=5.1e-37  Score=283.73  Aligned_cols=191  Identities=19%  Similarity=0.210  Sum_probs=168.6

Q ss_pred             CHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCC--CCCccc
Q psy6602          87 SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERL--PPDDVR  164 (367)
Q Consensus        87 ~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~--~~~~~~  164 (367)
                      -|.++...++..++.+|+|||++|||.+|+.+||++|||++|+|++++++|++++.. +..+.++++.....  .....+
T Consensus        77 ~~~~~~~~~~~~v~~iVewAK~iPgF~~L~~~DQi~LLk~~w~ElllL~~a~~~~~~-~~~~~~~~~~~~~~~~~~~~~~  155 (273)
T 3vi8_A           77 IFHCCQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKD-GMLVAYGNGFITREFLKSLRKP  155 (273)
T ss_dssp             HHHHHHHHHHHHHHHHHHHGGGSTTTTTSCHHHHHHHHHHHHHHHHHHHHGGGEETT-EEEETTTTEEEEHHHHHHSCTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHccCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCC-CCeeeeCCCccchHHHHHhhhh
Confidence            388999999999999999999999999999999999999999999999999988753 33344443332211  112234


Q ss_pred             hHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhh
Q psy6602         165 VNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLML  244 (367)
Q Consensus       165 ~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l  244 (367)
                      ..+.++.+.+|+.+|++|++|++||+|||||+||+||++|+.++..|+++|++|..+|.+|+..+||+++.||++|+.+|
T Consensus       156 ~~~~~~~l~~~~~~~~~L~ld~~E~alLkAivLf~pd~~gL~~~~~Ve~lqe~~~~aL~~yi~~~~p~~~~rF~kLL~~L  235 (273)
T 3vi8_A          156 FCDIMEPKFDFAMKFNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKMQEGIVHVLRLHLQSNHPDDIFLFPKLLQKM  235 (273)
T ss_dssp             THHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHH
Confidence            56778999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHhHhhhhhHHHHHHh-hhccCCchhHhHHHHHHc
Q psy6602         245 PSLRAVRQSTIERLFF-KETIGDIPIQRLLGDMYT  278 (367)
Q Consensus       245 ~~Lr~l~~~~~e~l~~-~~~~~~~~~~~Ll~eml~  278 (367)
                      +.||+++..+.|.++. +...+..++++|+.|||.
T Consensus       236 p~LR~l~~~~~e~l~~~k~~~~~~~~~~Ll~Emf~  270 (273)
T 3vi8_A          236 ADLRQLVTEHAQLVQIIKKTESDAALHPLLQEIYR  270 (273)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHccCCCCCccHHHHHHHH
Confidence            9999999999999985 445788999999999996

>1ymt_A Steroidogenic factor 1; SF-1, ligand-binding domain, ligand, phosphatidyl glycerol, CO-repressor peptide, transcription; HET: DR9; 1.20A {Mus musculus} PDB: 3f7d_A* 1yp0_A* 1yow_A* 1zdt_A*

Probab=100.00  E-value=7.9e-37  Score=279.03  Aligned_cols=196  Identities=24%  Similarity=0.342  Sum_probs=172.4

Q ss_pred             ccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccC-CCceEecCCc-cccCCC---
Q psy6602          85 LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPW-DLSLLINCEK-ARERLP---  159 (367)
Q Consensus        85 ~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~-~~~~l~~~~~-~~~~~~---  159 (367)
                      ..+++++++++.+.++.+|+|||++|||.+|+.+||++|||++|+|+++|+.|||++.. ..+.++..++ .+....   
T Consensus        44 ~~~~~~l~~~a~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~rs~~~~~~~~~~~~~g~~~~~~~~~~  123 (246)
T 1ymt_A           44 PAPFSLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNSWSELLVLDHIYRQVQYGKEDSILLVTGQEVELSTVAV  123 (246)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCTTEEECTTSCEEEHHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHHHHHHhChhHHhCCHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCeeEecCCCccchhhhhh
Confidence            35689999999999999999999999999999999999999999999999999999865 2344444333 332211   


Q ss_pred             CCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHH
Q psy6602         160 PDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGR  239 (367)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~  239 (367)
                      .......+.++.+.+++.+|++|++|++||+|||||+||+||++|+++...|+++|++|..+|.+||..+|++++.||++
T Consensus       124 ~~~~~~~~~~~~~~~~~~~~~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~Rf~~  203 (246)
T 1ymt_A          124 QAGSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILFSLDVKFLNNHSLVKDAQEKANAALLDYTLSHYPHSGDKFQQ  203 (246)
T ss_dssp             HCCHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHTCSCGGGSSCHHHHHHHHHHHHHHHHHHHHHHCTTSTTHHHH
T ss_pred             hcchhHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHhcCCcccccccHHHHHHHHHHHHHHHHHHHHhcCCchhhHHHH
Confidence            01111235668889999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHccc
Q psy6602         240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  280 (367)
Q Consensus       240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~  280 (367)
                      |+++++.||+++..+.|.+++.+.++..++++++.|||+..
T Consensus       204 LL~~L~~Lr~~~~~~~e~l~~~~~~~~~~~~~Ll~Eml~~~  244 (246)
T 1ymt_A          204 LLLSLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIEMLQAK  244 (246)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTCSCTTCHHHHHHHC-
T ss_pred             HHHHhHHHHHHHHHHHHHHHhhcccCCCcHHHHHHHHHhCc
Confidence            99999999999999999999999999999999999999854

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

Probab=100.00  E-value=8e-37  Score=285.69  Aligned_cols=213  Identities=20%  Similarity=0.318  Sum_probs=179.5

Q ss_pred             CcccccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCC
Q psy6602          66 PSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDL  145 (367)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~  145 (367)
                      |..++.++++..+++...   .+..+++++.+.++.+|+|||++|+|.+|+.+||++|||++|+|+++|+.||+++...+
T Consensus        27 p~~~~~~~~~~~~~~~~~---~~~~l~e~a~~~L~~~VewAK~lP~F~~L~~~DQi~LLk~~w~el~lL~~a~rs~~~~~  103 (298)
T 2ocf_A           27 PPILYSEYDPTRPFSEAS---MMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPG  103 (298)
T ss_dssp             CCCBCCCCCSSSCCCHHH---HHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTSTT
T ss_pred             CCcccccCCCCCCCchHH---HHHHHHHHHHHHHHHHHHHHHhCcchhcCCHHHHHHHHHHhhHHHHHHHHHHHhcccCC
Confidence            344566666656655433   36789999999999999999999999999999999999999999999999999998765


Q ss_pred             ceEecCCccccCCC-CCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCC--------CCCCChhHHHHHHH
Q psy6602         146 SLLINCEKARERLP-PDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPET--------PGLVDAQPVEMLQD  216 (367)
Q Consensus       146 ~~l~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~--------~~L~~~~~v~~~q~  216 (367)
                      ..++.++..+.+.. ....++.+.++.+.+++.+|++|++|.+||+|||||+||+||+        +|+.++.+|+++|+
T Consensus       104 ~l~~~~g~~~~~~~~~~~~g~~~~~~~l~~~~~~l~~L~ld~~Ey~lLkAIvLfnpd~~~LS~~~~~gL~~~~~ve~lqe  183 (298)
T 2ocf_A          104 KLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLD  183 (298)
T ss_dssp             EEEEETTEEEEHHHHTTSTTHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCSCCC-----------CHHHHHHHH
T ss_pred             ceeecCCceechhhhhhhhhHHHHHHHHHHHHHhHhhhCcCHHHHHHHHHHHHcCCCccccccccccccccHHHHHHHHH
Confidence            55555554443322 1223466777888999999999999999999999999999999        77888999999999


Q ss_pred             HHHHHHHHHHHhhC---CCcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccC
Q psy6602         217 QAQCILGDYVRGRY---SRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEK  281 (367)
Q Consensus       217 ~~~~~L~~y~~~~~---~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~  281 (367)
                      +|..+|.+||..++   ++++.||++||++++.||+++..+.|.+++.+.++..++++|+.|||+...
T Consensus       184 ~~~~aL~~y~~~~~~~~~~~~~RF~~LLl~Lp~Lr~i~~~~~e~l~~~kl~g~~~i~~Ll~Eml~~~~  251 (298)
T 2ocf_A          184 KITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLSDLLLEMLDAHR  251 (298)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSSCCCHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHcCCC
Confidence            99999999999874   477899999999999999999999999999999999999999999999765

>1nq7_A Nuclear receptor ROR-beta; ligand-binding domain, retinoids, retinoic acid, synthetic ligand, antagonist, transcription; HET: ARL; 1.50A {Rattus norvegicus} SCOP: a.123.1.1 PDB: 1k4w_A* 1n4h_A*

Probab=100.00  E-value=7.8e-37  Score=278.62  Aligned_cols=192  Identities=16%  Similarity=0.226  Sum_probs=173.0

Q ss_pred             ccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccc
Q psy6602          85 LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVR  164 (367)
Q Consensus        85 ~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~  164 (367)
                      ...+.++++.+++.++.+|+|||++|||.+|+.+||++|||++|+|+++++.||+++..++..++ ++..+.+......+
T Consensus        49 ~~~~~~~~~~~~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~l~~a~~~~~~~~~~~~-~g~~~~~~~~~~~~  127 (244)
T 1nq7_A           49 EALWQQCAIQITHAIQYVVEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPLNNTVLF-EGKYGGMQMFKALG  127 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCHHHHTSCHHHHHHHHHHHHHHHHHHHHGGGEETTTTEEEE-TTEEEEGGGGGGGS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcCCCCEEeE-CCEEecHHHHhhcC
Confidence            34488899999999999999999999999999999999999999999999999999876666666 55444444333345


Q ss_pred             hHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhh
Q psy6602         165 VNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLML  244 (367)
Q Consensus       165 ~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l  244 (367)
                      ..+.++.+.+++.+|++|++|++||+|||||+||+||++|+++...|+++|++|..+|.+||..+|++++ ||++|++++
T Consensus       128 ~~~~~~~i~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~-Rf~~LL~~L  206 (244)
T 1nq7_A          128 SDDLVNEAFDFAKNLCSLQLTEEEIALFSSAVLISPDRAWLLEPRKVQKLQEKIYFALQHVIQKNHLDDE-TLAKLIAKI  206 (244)
T ss_dssp             CHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCSCTT-HHHHHHHTH
T ss_pred             hHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcc-HHHHHHHHH
Confidence            6778889999999999999999999999999999999999999999999999999999999999999888 999999999


Q ss_pred             hHhHhhhhhHHHHHHhhhccCCc----hhHhHHHHHHc
Q psy6602         245 PSLRAVRQSTIERLFFKETIGDI----PIQRLLGDMYT  278 (367)
Q Consensus       245 ~~Lr~l~~~~~e~l~~~~~~~~~----~~~~Ll~eml~  278 (367)
                      +.||+++..+.|.+++.+..+..    ++++|+.|||+
T Consensus       207 ~~Lr~l~~~~~e~l~~~~~~~~~~~~~~~~~Ll~Em~~  244 (244)
T 1nq7_A          207 PTITAVCNLHGEKLQVFKQSHPDIVNTLFPPLYKELFN  244 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCHHHHHHTSCHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHhhCcccccCCCChHHHHhhC
Confidence            99999999999999999988765    78999999984

>1xdk_B RAR-beta, retinoic acid receptor, beta; nuclear receptor, coactivator, ligand, hormone/growth factor receptor complex; HET: REA; 2.90A {Mus musculus} SCOP: a.123.1.1

Probab=100.00  E-value=7e-37  Score=287.40  Aligned_cols=196  Identities=19%  Similarity=0.278  Sum_probs=174.9

Q ss_pred             CHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccchH
Q psy6602          87 SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVN  166 (367)
Q Consensus        87 ~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  166 (367)
                      .++++++++.+.++.+|+|||+||+|.+|+.+||++|||++|+|+++|+.||+++...+..++.++..+.+......++.
T Consensus        72 ~~~~~~~~~~~~l~~~VewaK~iP~F~~L~~~DQi~LLk~~~~el~lL~~a~~s~~~~~~l~~~~g~~~~~~~~~~~g~~  151 (303)
T 1xdk_B           72 LWDKFSELATKCIIKIVEFAKRLPGFTGLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMHNAGFG  151 (303)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTSTTTSSSCHHHHHHHHHHHHHHHHHHHHHTTEETTTTEEECTTCBEEEHHHHHHTTTG
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCcccccCCHHHHHHHHHhhHHHHHHHHHHHHhcccCCeEEecCCceecHHHHhhcCcH
Confidence            47899999999999999999999999999999999999999999999999999998655444444433332221112344


Q ss_pred             HHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhhhH
Q psy6602         167 NEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPS  246 (367)
Q Consensus       167 ~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~~  246 (367)
                      +.++.+.+|+.+|++|++|++||+|||||+||+||++|+++...|+++|++|..+|.+||..+|++++.||++||++|+.
T Consensus       152 ~~~~~i~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL~~L~~  231 (303)
T 1xdk_B          152 PLTDLVFTFANQLLPLEMDDTETGLLSAICLICGDRQDLEEPTKVDKLQEPLLEALKIYIRKRRPSKPHMFPKILMKITD  231 (303)
T ss_dssp             GGHHHHHHHHHHHGGGCCCHHHHHHHHHHHHSCSCSSSCSSHHHHHHHTHHHHHHHHHHHHHHCTTCTTHHHHHHTHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHH
Confidence            56678889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCC
Q psy6602         247 LRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKS  282 (367)
Q Consensus       247 Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s  282 (367)
                      ||+++..+.|.+++.+..+..++++|+.|||+....
T Consensus       232 Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~Eml~~~~~  267 (303)
T 1xdk_B          232 LRSISAKGAERVITLKMEIPGSMPPLIQEMLENSEG  267 (303)
T ss_dssp             HHHHHHHHHHHHHHHTTTCSSCCCHHHHHHHCCCCC
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCccHHHHHHHcCCCC
Confidence            999999999999999999999999999999987663

>3b0t_A Vitamin D3 receptor; nuclear receptor, transcription, gene regulation; HET: MCZ; 1.30A {Homo sapiens} PDB: 3a40_X* 1s0z_A* 1s19_A* 2ham_A* 2har_A* 2has_A* 1txi_A* 2hb8_A* 2hb7_A* 3a3z_X* 3a78_A* 3auq_A* 3aur_A* 3ax8_A* 3cs4_A* 3cs6_A* 1ie9_A* 1db1_A* 1ie8_A* 3kpz_A* ...

Probab=100.00  E-value=6.6e-37  Score=280.86  Aligned_cols=196  Identities=16%  Similarity=0.238  Sum_probs=171.3

Q ss_pred             hhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCc-cccCCCCC
Q psy6602          83 QILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEK-ARERLPPD  161 (367)
Q Consensus        83 ~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~-~~~~~~~~  161 (367)
                      .....+.++++++++.++.+|+|||++|||.+|+.+||++|||++|+|+++|+.||++...++..++.+++ .+......
T Consensus        53 ~~~~~~~~~~~~~~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~  132 (254)
T 3b0t_A           53 SQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVSDVT  132 (254)
T ss_dssp             HHCTTHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHGGGTEETTTTEEECSSGGGEECHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHhhCCCCcccCCHHHHHHHHHHhhHHHHHHHHHHHhccCCCeEEecCCCeeeeHHHHH
Confidence            34556999999999999999999999999999999999999999999999999999987755554444323 23322111


Q ss_pred             ccchH-HHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCC--CcchHHH
Q psy6602         162 DVRVN-NEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYS--RQPTRFG  238 (367)
Q Consensus       162 ~~~~~-~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~--~~~~Rf~  238 (367)
                      ..++. +.++.+.+++.+|++|++|++||+|||||+||+||++|+++...|+++|++|..+|.+||..+|+  +++.||+
T Consensus       133 ~~~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~~Rf~  212 (254)
T 3b0t_A          133 KAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLLYA  212 (254)
T ss_dssp             TTTCCHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHSCSCSTTCSCHHHHHHHHHHHHHHHHHHHHHHCCTTTTTTHHH
T ss_pred             HcCCcHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCccCCcCHHHHHHHHHHHHHHHHHHHHHhCCCCCchhHHH
Confidence            12333 67788999999999999999999999999999999999999999999999999999999999998  8899999


Q ss_pred             HHHHhhhHhHhhhhhHHHHHHhhhc--cCCchhHhHHHHHHc
Q psy6602         239 RLLLMLPSLRAVRQSTIERLFFKET--IGDIPIQRLLGDMYT  278 (367)
Q Consensus       239 ~LL~~l~~Lr~l~~~~~e~l~~~~~--~~~~~~~~Ll~eml~  278 (367)
                      +|+++++.||+++..+.|.+++.+.  .+..++++|+.|||+
T Consensus       213 ~LL~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~~~Ll~Em~~  254 (254)
T 3b0t_A          213 KMIQKLADLRSLNEEHSKQYRCLSFQPECSMKLTPLVLEVFG  254 (254)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSTTHHHHSCHHHHHHHC
T ss_pred             HHHHHhHHHHHHHHHHHHHHHHHhccccCCCCCChHHHHhcC
Confidence            9999999999999999999999998  556778999999985

>2r40_D Ecdysone receptor, 20-hydroxy-ecdysone receptor; nuclear receptor ligand-binding domain, anti-parallel alpha- sandwich, ecdysone receptor, ECR, gene regulation; HET: FLC 20E EPH; 2.40A {Heliothis virescens} SCOP: a.123.1.1 PDB: 1r1k_D* 3ixp_D* 1r20_D*

Probab=100.00  E-value=7.7e-37  Score=282.03  Aligned_cols=195  Identities=19%  Similarity=0.241  Sum_probs=173.0

Q ss_pred             hccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCcc
Q psy6602          84 ILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDV  163 (367)
Q Consensus        84 ~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~  163 (367)
                      ....++++++++.+.++.+|+|||++|||.+|+.+||++|||++|+|+++|+.||+++..++..++.++..+.+......
T Consensus        66 ~~~~~~~l~~~~~~~l~~~VewaK~lp~F~~L~~~DQi~LLk~~~~el~~L~~a~~~~~~~~~l~~~~g~~~~~~~~~~~  145 (266)
T 2r40_D           66 SDMPFRQITEMTILTVQLIVEFAKGLPGFAKISQSDQITLLKACSSEVMMLRVARRYDAATDSVLFANNQAYTRDNYRKA  145 (266)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEETTTTEEECTTSCEECHHHHHHT
T ss_pred             hhccHHHHHHHHHHHHHHHHHHHhcCcccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEecCCceecHHHHhhc
Confidence            34568999999999999999999999999999999999999999999999999999887665555544444433222223


Q ss_pred             chHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhC---CCcchHHHHH
Q psy6602         164 RVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRY---SRQPTRFGRL  240 (367)
Q Consensus       164 ~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~---~~~~~Rf~~L  240 (367)
                      +..+.++.+.+++.+|++|++|++||+|||||+||+ |++|+++...|+++|++|..+|.+||..+|   ++++.||++|
T Consensus       146 g~~~~~~~l~~~~~~l~~L~ld~~E~~lLkAivL~n-d~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~~~Rf~~L  224 (266)
T 2r40_D          146 GMAYVIEDLLHFCRCMYSMMMDNVHYALLTAIVIFS-DRPGLEQPLLVEEIQRYYLNTLRVYILNQNSASPRCAVIFGKI  224 (266)
T ss_dssp             TCHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHTS-CCTTCSCHHHHHHHHHHHHHHHHHHHHHHTTTCTTHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHhcccCCHHHHHHHhhheeec-CCCCCcCHHHHHHHHHHHHHHHHHHHHHhCCCCCchhhHHHHH
Confidence            456778889999999999999999999999999999 999999999999999999999999999998   7889999999


Q ss_pred             HHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHccc
Q psy6602         241 LLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  280 (367)
Q Consensus       241 L~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~  280 (367)
                      +++++.||+++..+.|.+++.+..+ .++++|+.|||+..
T Consensus       225 L~~L~~Lr~l~~~~~e~l~~~~~~~-~~~~~Ll~Em~~~~  263 (266)
T 2r40_D          225 LGILTEIRTLGMQNSNMCISLKLKN-RKLPPFLEEIWDVA  263 (266)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTT-CCCCHHHHHHTTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcC-CCccHHHHHHhCCC
Confidence            9999999999999999999999887 58999999999854

>3vhv_A Mineralocorticoid receptor; nuclear receptor, transcription factor, activating mutation, hypertension, non-steroidal antagonist; HET: LD1 LD2; 1.35A {Homo sapiens} SCOP: a.123.1.1 PDB: 2aax_A* 2aa6_A* 2ab2_A* 2aa2_A* 2aa5_A* 2aa7_A* 2a3i_A* 1y9r_A* 1ya3_A* 2oax_A* 2abi_A* 2q1h_A* 2q1v_A* 2q3y_A* 3ry9_A* 4fne_A* 4fn9_A*

Probab=100.00  E-value=7.9e-37  Score=280.96  Aligned_cols=215  Identities=17%  Similarity=0.208  Sum_probs=179.7

Q ss_pred             CCCcccccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccC
Q psy6602          64 HHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPW  143 (367)
Q Consensus        64 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~  143 (367)
                      .+|..+++++++..|++....   ++++++++++.++.+|+|||++|+|.+|+.+||++|||++|+|+++|+.||+++..
T Consensus        21 ~ep~~~~~~~~~~~~~~~~~~---~~~l~e~a~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~rs~~~   97 (260)
T 3vhv_A           21 IEPEIVYAGYDSSKPDTAENL---LSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQYSWMSLLSFALSWRSYKH   97 (260)
T ss_dssp             HCCCCCCCCCCTTSCCCHHHH---HHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCcccccCCCCCCCCchHHH---HHHHHHHHHHHHHHHHHHHHhChHHhcCCHHHHHHHHHHhHHHHHHHHHHHHhhcc
Confidence            467778888888888776544   78899999999999999999999999999999999999999999999999998765


Q ss_pred             CC--ceEecCCccccCCCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCC-CCCCCCChhHHHHHHHHHHH
Q psy6602         144 DL--SLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTP-ETPGLVDAQPVEMLQDQAQC  220 (367)
Q Consensus       144 ~~--~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~p-d~~~L~~~~~v~~~q~~~~~  220 (367)
                      ..  ..++.++..+.+......+..+.++.+.+++.+|++|++|++||+|||||+||+| |++|+++...|+++|++|..
T Consensus        98 ~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkAIvLfnp~d~~gL~~~~~ve~lqe~~~~  177 (260)
T 3vhv_A           98 TNSQFLYFAPDLVFNEEKMHQSAMYELCQGMHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKDGLKSQAAFEEMRTNYIK  177 (260)
T ss_dssp             HTTSSEEEETTEEECHHHHHHTTCHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHTSEEETTCCTTHHHHHHHHHHHHH
T ss_pred             CCCCeEEecCCccccHHHhhcccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCcCCCCCcCHHHHHHHHHHHHH
Confidence            33  3344444433332222234567788899999999999999999999999999999 99999999999999999999


Q ss_pred             HHHHHHHhhCCCc---chHHHHHHHhhhHhHhhhhhHHHHHHhhhc---cCCchhHhHHHHHHcccC
Q psy6602         221 ILGDYVRGRYSRQ---PTRFGRLLLMLPSLRAVRQSTIERLFFKET---IGDIPIQRLLGDMYTMEK  281 (367)
Q Consensus       221 ~L~~y~~~~~~~~---~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~---~~~~~~~~Ll~eml~~~~  281 (367)
                      +|.+||..++++.   +.||++|+.+++.||+++..+.|.+++...   .....+++++.|||+...
T Consensus       178 aL~~y~~~~~~~~~~~~~RF~~LL~~Lp~Lr~l~~~~~e~lff~~~~~~~~~~~~p~Ll~Ei~~~~~  244 (260)
T 3vhv_A          178 ELRKMVTKCPNNSGQSWQRFYQLTKLLDSMHDLVSDLLEFCFYTFRESHALKVEFPAMLVEIISDQL  244 (260)
T ss_dssp             HHHHHHHC-----CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTCCCCHHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCCCcHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCcHHHHHHHhccC
Confidence            9999999998755   799999999999999999999999986543   345679999999998653

>3mnp_A Glucocorticoid receptor; protein-ligand complex, steroid nuclear receptor, mouse GR, hormone receptor; HET: DEX; 1.50A {Mus musculus} SCOP: a.123.1.1 PDB: 3mno_A* 3mne_A* 1m2z_A* 3k22_A* 3cld_A* 3k23_A* 3e7c_A* 1nhz_A* 1p93_A* 3bqd_A* 3h52_A* 3gn8_A* 4e2j_A*

Probab=100.00  E-value=1.5e-36  Score=279.08  Aligned_cols=214  Identities=21%  Similarity=0.241  Sum_probs=184.3

Q ss_pred             CCCcccccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccC
Q psy6602          64 HHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPW  143 (367)
Q Consensus        64 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~  143 (367)
                      .+|..+++++++..|++....   +.++++++.+.++.+|+|||++|+|.+|+.+||++|||++|+|+++|+.|||++..
T Consensus        23 ~ep~~~~~~~~~~~~~~~~~~---~~~l~~~a~~~l~~~VewaK~iP~F~~L~~~DQ~~LLk~~~~el~iL~~a~rs~~~   99 (261)
T 3mnp_A           23 IEPEVLYAGYDSSVPDSAWRI---MTTLNMLGGRQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMVFALGWRSYRQ   99 (261)
T ss_dssp             HSCCCCCCCCCTTSCCCHHHH---HHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCccccccCCCCCCCchHHH---HHHHHHHHHHHHHHHHHHHHhCcChhcCCHHHHHHHHHHHHHHHHHHHHHHHcccC
Confidence            577788899888888876544   67899999999999999999999999999999999999999999999999998765


Q ss_pred             CCc-eE-ecCCccccCCCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCC-CCCCCCChhHHHHHHHHHHH
Q psy6602         144 DLS-LL-INCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTP-ETPGLVDAQPVEMLQDQAQC  220 (367)
Q Consensus       144 ~~~-~l-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~p-d~~~L~~~~~v~~~q~~~~~  220 (367)
                      .++ .+ +.++....+......++.+.++.+.+++.+|++|++|++||+|||||+||+| |++|+++..+|+++|++|..
T Consensus       100 ~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkAIvL~np~d~~gL~~~~~ve~lq~~~~~  179 (261)
T 3mnp_A          100 ASGNLLCFAPDLIINEQRMTLPCMYDQCKHMLFISTELQRLQVSYEEYLCMKTLLLLSSVPKEGLKSQELFDEIRMTYIK  179 (261)
T ss_dssp             HTTSSEEEETTEEECHHHHTSTTTHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHTSEEETTCCTTHHHHHHHHHHHHH
T ss_pred             CCCCEEEecCCcccchhhhhhhhHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHcCCCCcCCCccHHHHHHHHHHHHH
Confidence            443 34 4444334333323345667788899999999999999999999999999999 99999999999999999999


Q ss_pred             HHHHHHHhhCCC---cchHHHHHHHhhhHhHhhhhhHHHHHHhhhcc--CCchhHhHHHHHHccc
Q psy6602         221 ILGDYVRGRYSR---QPTRFGRLLLMLPSLRAVRQSTIERLFFKETI--GDIPIQRLLGDMYTME  280 (367)
Q Consensus       221 ~L~~y~~~~~~~---~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~--~~~~~~~Ll~eml~~~  280 (367)
                      +|.+||..++++   ++.||++|+.+++.||+++..+.|.+++....  ....+++++.|+|+..
T Consensus       180 aL~~y~~~~~~~~~~~~~Rf~~LL~lL~~Lr~l~~~~~e~~f~~~~~~~~~~~~p~Ll~Ei~~~~  244 (261)
T 3mnp_A          180 ELGKAIAKRGGNSSQNWQRFYQLTKLLDSMHDVVENLLSYCFQTFLDKSMSIEFPEMLAEIITNQ  244 (261)
T ss_dssp             HHHHHHHTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGGGCCCCCHHHHHHHHHH
T ss_pred             HHHHHHHhhCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCcHHHHHHHhcc
Confidence            999999999884   58999999999999999999999998776554  4567899999999854

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

Probab=100.00  E-value=4.1e-36  Score=279.32  Aligned_cols=199  Identities=23%  Similarity=0.381  Sum_probs=168.2

Q ss_pred             ccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCce-------EecCCccc--
Q psy6602          85 LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSL-------LINCEKAR--  155 (367)
Q Consensus        85 ~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~-------l~~~~~~~--  155 (367)
                      .++++++++++.+.++.+|+|||++|+|.+|+.+||++|||++|+|+++|+.|||++...+..       +..+||.+  
T Consensus        46 ~~~~~~l~~~~~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~rs~~~~~~~~~~~~~~~~~~dGs~~~  125 (279)
T 1hg4_A           46 KGAVSALCQVVNKQLFQMVEYARMMPHFAQVPLDDQVILLKAAWIELLIANVAWCSIVSLDDGGAGGGGGGLGHDGSFER  125 (279)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTTC--------------------
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHhcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhccCcccccccccccccCccccc
Confidence            346899999999999999999999999999999999999999999999999999988654431       23333321  


Q ss_pred             ------------------cCCCCCccchHHHH-HHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHH
Q psy6602         156 ------------------ERLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQD  216 (367)
Q Consensus       156 ------------------~~~~~~~~~~~~~~-~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~  216 (367)
                                        .+......+..... +.+.+++.+|++|++|++||+|||||+||+||++|++++..|+++|+
T Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~ld~~E~~lLkAivL~npd~~gL~~~~~v~~lq~  205 (279)
T 1hg4_A          126 RSPGLQPQQLFLNQSFSYHRNSAIKAGVSAIFDRILSELSVKMKRLNLDRRELSCLKAIILYNPDIRGIKSRAEIEMCRE  205 (279)
T ss_dssp             -----CCCEEESSSSCEEEHHHHHHHTCHHHHHHHHHHTHHHHHHHTCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHH
T ss_pred             cccccccceeeecCCcccchhhHhhcchHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHH
Confidence                              11100011233343 34568999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhCCCcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCC
Q psy6602         217 QAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSY  283 (367)
Q Consensus       217 ~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~  283 (367)
                      +|..+|.+||..+|++++.||++||++++.||+++..+.|.+++.+.++..++++++.||++...++
T Consensus       206 ~~~~aL~~y~~~~~p~~~~Rf~~LL~~L~~Lr~~~~~~~e~l~~~~~~g~~~~~~Ll~Eml~~~~~~  272 (279)
T 1hg4_A          206 KVYACLDEHCRLEHPGDDGRFAQLLLRLPALRSISLKCQDHLFLFRITSDRPLEELFLEQLEAPPPP  272 (279)
T ss_dssp             HHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHTCBCSSCHHHHHHHHHTSCCCC
T ss_pred             HHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCcHHHHHHHHHhCCCCc
Confidence            9999999999999999999999999999999999999999999999999999999999999977653

>1l2j_A Estrogen receptor beta; nuclear receptor, transcription factor, antagonist transcription receptor; HET: ETC; 2.95A {Homo sapiens} SCOP: a.123.1.1

Probab=100.00  E-value=2.5e-36  Score=279.31  Aligned_cols=209  Identities=21%  Similarity=0.267  Sum_probs=171.4

Q ss_pred             cCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEec
Q psy6602          71 ATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN  150 (367)
Q Consensus        71 ~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~  150 (367)
                      ..+++..|++..   ..+.++++++++.++.+|+|||++|+|.+|+.+||++|||++|+|+++|+.|||++...+..++.
T Consensus        47 ~~~~~~~~~~~~---~~~~~l~~~a~~~l~~~VewAK~lP~F~~L~~~DQi~LLk~~w~el~iL~~a~rs~~~~~~l~~~  123 (271)
T 1l2j_A           47 LISRPSAPFTEA---SMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFA  123 (271)
T ss_dssp             CCCC-----CHH---HHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHTTHHHHHHHHHHHHTSSSTTEECSS
T ss_pred             cccCCCCCCcch---hHHHHHHHHHHHHHHHHHHHHHhCcccccCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCeeeec
Confidence            444444554443   23788999999999999999999999999999999999999999999999999999876544444


Q ss_pred             CCccccCCCCC-ccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCC-------hhHHHHHHHHHHHHH
Q psy6602         151 CEKARERLPPD-DVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVD-------AQPVEMLQDQAQCIL  222 (367)
Q Consensus       151 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~-------~~~v~~~q~~~~~~L  222 (367)
                      ++..+.+.... ..+..+.++.+.+++.+|++|++|++||+|||||+||+||++|+++       +.+|+.+|+.|.++|
T Consensus       124 ~g~~~~~~~~~~~~g~~~~~~~l~~~~~~l~~L~ld~~E~~lLkAIvLfnpd~~gLs~~~~~~~~~~~v~~~q~~~~~aL  203 (271)
T 1l2j_A          124 PDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNAVTDAL  203 (271)
T ss_dssp             SSCCEETGGGGGSTTHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC----CCCCGGGHHHHHHHHHHHHHHHHHH
T ss_pred             CCccccchhhhhhccHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHcCCCcCCCccchhhHHHHHHHHHHHHHHHHHH
Confidence            44444433211 2356677788999999999999999999999999999999999976       357889999999999


Q ss_pred             HHHHHhh---CCCcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCC
Q psy6602         223 GDYVRGR---YSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKS  282 (367)
Q Consensus       223 ~~y~~~~---~~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s  282 (367)
                      ..||..+   +++++.||++||++++.||+++..+.|.+++.+.++..++++|+.|||+....
T Consensus       204 ~~y~~~~~~~~~~~~~Rf~~LLl~Lp~Lr~i~~~~~e~l~~~~~~g~~~~~~Ll~Eml~~~~~  266 (271)
T 1l2j_A          204 VWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEMLNAHVL  266 (271)
T ss_dssp             HHHHHTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCTTSSCCHHHHHHHHHHHHTT
T ss_pred             HHHHHhcCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCChHHHHHHHHcCCcc
Confidence            9999986   35788999999999999999999999999999999999999999999987653

>1n83_A Nuclear receptor ROR-alpha; three-layered alpha helical sandwich, transcription regulation, nuclear protein, DNA binding, lipid binding protein; HET: CLR; 1.63A {Homo sapiens} SCOP: a.123.1.1 PDB: 1s0x_A*

Probab=100.00  E-value=5.8e-36  Score=276.59  Aligned_cols=194  Identities=16%  Similarity=0.203  Sum_probs=170.4

Q ss_pred             ccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccc
Q psy6602          85 LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVR  164 (367)
Q Consensus        85 ~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~  164 (367)
                      ...+..+++.+++.++.+|+|||++|||.+|+.+||++|||++|+|+++++.||++...++..++ ++...........+
T Consensus        64 ~~~~~~~~~~~~~~l~~~VewaK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~~~~~~~~~~l~-~g~~~~~~~~~~~~  142 (270)
T 1n83_A           64 EVMWQLCAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQNNTVYF-DGKYASPDVFKSLG  142 (270)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSTTTTTSCHHHHHHHHHHHHHHHHHHHGGGGEETTTTEEEE-TTEEECGGGGGGGS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCCChhhcCHHHHHHHHHHhHHHHHHHHHHHHhcCCCCeEEe-CCccccHHHHHhcC
Confidence            34588899999999999999999999999999999999999999999999999998876555554 44333332222335


Q ss_pred             hHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhh
Q psy6602         165 VNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLML  244 (367)
Q Consensus       165 ~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l  244 (367)
                      ..+.++.+.+++.+|++|++|++||+|||||+||+||++|+++...|+++|++|..+|.+||..+|+ ++.||++|++++
T Consensus       143 ~~~~~~~i~~~~~~l~~L~ld~~E~~lLkAivLfnpd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~-~~~Rf~~LL~~L  221 (270)
T 1n83_A          143 CEDFISFVFEFGKSLCSMHLTEDEIALFSAFVLMSADRSWLQEKVKIEKLQQKIQLALQHVLQKNHR-EDGILTKLICKV  221 (270)
T ss_dssp             CHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCT-TSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCC-chhHHHHHHHHH
Confidence            6778899999999999999999999999999999999999999999999999999999999999987 689999999999


Q ss_pred             hHhHhhhhhHHHHHHhhhccCC----chhHhHHHHHHccc
Q psy6602         245 PSLRAVRQSTIERLFFKETIGD----IPIQRLLGDMYTME  280 (367)
Q Consensus       245 ~~Lr~l~~~~~e~l~~~~~~~~----~~~~~Ll~eml~~~  280 (367)
                      +.||+++..+.|.+++.+..+.    .++++|+.|||+..
T Consensus       222 ~~Lr~l~~~~~e~l~~~~~~~~~~~~~~~~~Ll~Em~~~~  261 (270)
T 1n83_A          222 STLRALCGRHTEKLMAFKAIYPDIVRLHFPPLYKELFTSE  261 (270)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCHHHHHHHSCHHHHHHC---
T ss_pred             HHHHHHHHHHHHHHHHHHhcCcccccCCcCHHHHHHhCCC
Confidence            9999999999999999998765    47899999999866

>1xvp_B Orphan nuclear receptor NR1I3; CAR, RXR, citco, SRC1, DNA binding protein; HET: F15 CID; 2.60A {Homo sapiens} SCOP: a.123.1.1 PDB: 1xv9_B* 1xnx_A* 1xls_E*

Probab=100.00  E-value=1.8e-36  Score=276.66  Aligned_cols=191  Identities=18%  Similarity=0.284  Sum_probs=166.4

Q ss_pred             ccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccc
Q psy6602          85 LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVR  164 (367)
Q Consensus        85 ~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~  164 (367)
                      ...++++++++++.++.+|+|||++|||.+|+.+||++|||++|+|+++++.||+++...+. ++.++..+........+
T Consensus        53 ~~~~~~~~e~~~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~l~~a~~~~~~~~~-~~~~~~~~~~~~~~~~~  131 (246)
T 1xvp_B           53 LPLVTHFADINTFMVLQVIKFTKDLPVFRSLPIEDQISLLKGAAVEICHIVLNTTFCLQTQN-FLCGPLRYTIEDGARVG  131 (246)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTCHHHHHSCHHHHHHHHHHHHHHHHHHHHGGGEETTTTE-EECSSCEECHHHHHHHT
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHcCcchhhCCHHHHHHHHHhhHHHHHHHHHHHHhccccCe-EeeCCeeecHHHHHHcc
Confidence            34588999999999999999999999999999999999999999999999999998875443 45444333322111123


Q ss_pred             hH-HHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhh--CCCcchHHHHHH
Q psy6602         165 VN-NEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGR--YSRQPTRFGRLL  241 (367)
Q Consensus       165 ~~-~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~--~~~~~~Rf~~LL  241 (367)
                      .. +.++.+.+++.+|++|++|++||+|||||+||+||++|+++...|+++|++|..+|.+||..+  +++++.||++|+
T Consensus       132 ~~~~~~~~i~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~~rf~~LL  211 (246)
T 1xvp_B          132 FQVEFLELLFHFHGTLRKLQLQEPEYVLLAAMALFSPDRPGVTQRDEIDQLQEEMALTLQSYIKGQQRRPRDRFLYAKLL  211 (246)
T ss_dssp             CCHHHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHSCSSSTTCSCHHHHHHHHHHHHHHHHHHHHTCSSCCSCSSHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCCchhHHHHHH
Confidence            33 566888999999999999999999999999999999999999999999999999999999954  578899999999


Q ss_pred             HhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHc
Q psy6602         242 LMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT  278 (367)
Q Consensus       242 ~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~  278 (367)
                      ++++.||+++..+.|.+++.  .+..++++|+.|||+
T Consensus       212 ~~L~~Lr~i~~~~~e~l~~~--~~~~~~~~Ll~Em~~  246 (246)
T 1xvp_B          212 GLLAELRSINEAYGYQIQHI--QGLSAMMPLLQEICS  246 (246)
T ss_dssp             HHHHHHHHHHHHHHHHHHHS--TTHHHHCHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHHHHH--hCCCCccHHHHHhcC
Confidence            99999999999999999985  577899999999985

>1nrl_A Orphan nuclear receptor PXR; PXR, xenobiotic, SRC-1, ligand binding domain, transcription; HET: SRL; 2.00A {Homo sapiens} SCOP: a.123.1.1 PDB: 1ilh_A* 1ilg_A* 1m13_A* 2qnv_A* 3r8d_A* 3ctb_A 3ctc_A 3hvl_A* 1skx_A* 2o9i_A*

Probab=100.00  E-value=3.6e-36  Score=282.98  Aligned_cols=195  Identities=17%  Similarity=0.222  Sum_probs=174.6

Q ss_pred             hccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCcc
Q psy6602          84 ILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDV  163 (367)
Q Consensus        84 ~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~  163 (367)
                      ....+.++++++++.++.+|+|||+||+|.+|+.+||++|||++|+|+++|+.||+++..++..++ ++..+..... ..
T Consensus       118 ~~~~~~~l~e~~~~~L~~~VewAK~lP~F~~L~~~DQi~LLk~~w~el~lL~~a~~~~~~~~~~l~-~~~~~~~~~~-~~  195 (316)
T 1nrl_A          118 IFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWEC-GRLSYCLEDT-AG  195 (316)
T ss_dssp             GGTTHHHHHHHHHHHHHHHHHHHHHCHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTEETTTTEEEE-TTEEEEECCC-SS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhCcchhhcCHHHHHHHHHHHHHHHHHHHHHHHhhcCCCeEEE-CCEeecHHHH-hc
Confidence            355699999999999999999999999999999999999999999999999999999876555544 4444444433 34


Q ss_pred             chH-HHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCC--CcchHHHHH
Q psy6602         164 RVN-NEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYS--RQPTRFGRL  240 (367)
Q Consensus       164 ~~~-~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~--~~~~Rf~~L  240 (367)
                      ++. +.++.+.+|+.+|++|++|++||+|||||+||+||++|+++...|+++|++|..+|.+||..+|+  +++.||++|
T Consensus       196 g~~~~~~~~i~~~~~~l~~L~ld~~E~alLkAIvLfnpd~~gL~~~~~Ve~lqe~~~~aL~~y~~~~~p~~~~~~RF~kL  275 (316)
T 1nrl_A          196 GFQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLKI  275 (316)
T ss_dssp             CHHHHTTSHHHHHHHHHHHTCCCHHHHHHHHHHHHTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCCSGGGTTHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCCchhHHHHHH
Confidence            455 56688899999999999999999999999999999999999999999999999999999999998  789999999


Q ss_pred             HHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccC
Q psy6602         241 LLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEK  281 (367)
Q Consensus       241 L~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~  281 (367)
                      |++|+.||+++..+.|.+++.+..+. ++++|+.|||+...
T Consensus       276 Ll~Lp~LR~l~~~~~e~l~~~k~~~~-~i~~Ll~Eml~~~~  315 (316)
T 1nrl_A          276 MAMLTELRSINAQHTQRLLRIQDIHP-FATPLMQELFGITG  315 (316)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSC-CCCHHHHHHTTCCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCC-chHHHHHHHHcCCC
Confidence            99999999999999999999998876 89999999998643

>2hc4_A Vitamin D receptor; alpha helical sandwich, gene regulation; HET: VDX; 2.20A {Danio rerio} PDB: 2hbh_A* 2hcd_A* 3dr1_A* 3o1d_A* 3o1e_A*

Probab=100.00  E-value=5.1e-36  Score=281.04  Aligned_cols=198  Identities=16%  Similarity=0.172  Sum_probs=171.1

Q ss_pred             hhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecC--CccccCCCC
Q psy6602          83 QILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINC--EKARERLPP  160 (367)
Q Consensus        83 ~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~--~~~~~~~~~  160 (367)
                      .....+.++++++++.++.+|+|||+||||.+|+.+||++|||++|+|+++|+.|+++... +..++++  +..+.....
T Consensus        99 ~~~~~~~~l~e~~~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w~el~lL~~a~~~~~~-~~~~l~~~~~~~~~~~~~  177 (302)
T 2hc4_A           99 SRLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLRSNQSFSLE-DMSWSCGGPDFKYCINDV  177 (302)
T ss_dssp             -CCTTHHHHHHHHHHHHHHHHHHHTTSTTTTTSCHHHHHHHHHHHHHHHHHHHGGGTEETT-TTEEECSSSTTEECHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhccC-CCeEEecCCCeeecHHHH
Confidence            3456689999999999999999999999999999999999999999999999999876554 4444444  233322211


Q ss_pred             Cccch-HHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHH
Q psy6602         161 DDVRV-NNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGR  239 (367)
Q Consensus       161 ~~~~~-~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~  239 (367)
                      ...+. .+.++.+.+++.+|++|++|++||+|||||+||+||++|+++...|+++|++|..+|.+||..+|++++.||++
T Consensus       178 ~~~g~~~~~~~~l~~~~~~l~~L~ld~~E~alLkAIvLfnpd~~gL~~~~~Ve~lqe~~~~aL~~y~~~~~p~~~~RF~~  257 (302)
T 2hc4_A          178 TKAGHTLELLEPLVKFQVGLKKLKLHEEEHVLLMAICLLSPDRPGVQDHVRIEALQDRLCDVLQAYIRIQHPGGRLLYAK  257 (302)
T ss_dssp             HTTTCCHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHTCSCSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHH
T ss_pred             HHccCcHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHHHHHHHHHHHHHCCChhHHHHH
Confidence            11223 56778899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhHhHhhhhhHHHHHHhhhccCC--chhHhHHHHHHcccC
Q psy6602         240 LLLMLPSLRAVRQSTIERLFFKETIGD--IPIQRLLGDMYTMEK  281 (367)
Q Consensus       240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~--~~~~~Ll~eml~~~~  281 (367)
                      ||++++.||+++..+.|.+++.+..+.  .++++|+.|||+...
T Consensus       258 LLl~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~~~Ll~Em~~~~~  301 (302)
T 2hc4_A          258 MIQKLADLRSLNEEHSKQYRSLSFQPEHSMQLTPLVLEVFGSEV  301 (302)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHCHHHHTTSCHHHHHHSSSCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhccCCCCCCccHHHHHHHcCCC
Confidence            999999999999999999999887643  678999999998653

>2o4j_A Vitamin D3 receptor; nuclear receptor-ligand complex, hormone/growth factor receptor complex; HET: VD4; 1.74A {Rattus norvegicus} SCOP: a.123.1.1 PDB: 1rk3_A* 1rjk_A* 1rkh_A* 1rkg_A* 2o4r_A*

Probab=100.00  E-value=2.8e-36  Score=281.75  Aligned_cols=198  Identities=18%  Similarity=0.243  Sum_probs=172.5

Q ss_pred             hccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecC-CccccCCCCCc
Q psy6602          84 ILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINC-EKARERLPPDD  162 (367)
Q Consensus        84 ~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~-~~~~~~~~~~~  162 (367)
                      ....+.++++++++.++.+|+|||++|||.+|+.+||++|||++|+|+++|+.||++...++..++.+ +..+.......
T Consensus        57 ~~~~~~~l~~~~~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~  136 (292)
T 2o4j_A           57 PLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMSWDCGSQDYKYDVTDVSK  136 (292)
T ss_dssp             CCTTHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHGGGTEETTTTEEECSSGGGEECHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHcCcchhhccHHHHHHHHHHhHHHHHHHHHHHHhcCCCCeEEecCCCeEEcHHHHHh
Confidence            34569999999999999999999999999999999999999999999999999998876555544443 33333221111


Q ss_pred             cchH-HHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCC--CcchHHHH
Q psy6602         163 VRVN-NEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYS--RQPTRFGR  239 (367)
Q Consensus       163 ~~~~-~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~--~~~~Rf~~  239 (367)
                      .++. +.++.+.+++.+|++|++|++||+|||||+||+||++|+++...|+++|++|..+|.+||..+|+  +++.||++
T Consensus       137 ~g~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkAIvLfnpd~~gL~~~~~Ve~lq~~~~~aL~~y~~~~~p~~~~~~Rf~~  216 (292)
T 2o4j_A          137 AGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAK  216 (292)
T ss_dssp             TTCCHHHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHSCTTTTTTHHHH
T ss_pred             cCCcHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCCchhhHHHH
Confidence            2333 67788999999999999999999999999999999999999999999999999999999999998  88999999


Q ss_pred             HHHhhhHhHhhhhhHHHHHHhhhcc--CCchhHhHHHHHHcccC
Q psy6602         240 LLLMLPSLRAVRQSTIERLFFKETI--GDIPIQRLLGDMYTMEK  281 (367)
Q Consensus       240 LL~~l~~Lr~l~~~~~e~l~~~~~~--~~~~~~~Ll~eml~~~~  281 (367)
                      ||++++.||+++..+.|.+++.+.+  +..++++|+.|||+...
T Consensus       217 LL~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~~~Ll~Eml~~~~  260 (292)
T 2o4j_A          217 MIQKLADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFGNEI  260 (292)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSHHHHTTSCHHHHHHHCCC-
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhccccCCCChhHHHHHHHcCCc
Confidence            9999999999999999999999884  46789999999998765

>3tx7_B Nuclear receptor subfamily 5 group A member 2; LRH-1, beta-catenin, armadillo repeat, nuclear receptor LIGA binding domain, protein binding; HET: P6L; 2.76A {Homo sapiens}

Probab=100.00  E-value=2.5e-36  Score=287.67  Aligned_cols=199  Identities=30%  Similarity=0.442  Sum_probs=157.8

Q ss_pred             hhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCC-CceEecCCc-cccCCC
Q psy6602          82 LQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD-LSLLINCEK-ARERLP  159 (367)
Q Consensus        82 ~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~-~~~l~~~~~-~~~~~~  159 (367)
                      ..+...+..+++++++.++.+|+|||+||+|.+|+.+||++|||++|+|+++|+.|||+.... .+.+++.++ .+....
T Consensus       147 ~~r~~~~~~l~e~a~~~L~~~VewAK~iP~F~~L~~~DQi~LLk~~w~ElllL~~a~rs~~~~~~~~ll~~~G~~i~~~~  226 (352)
T 3tx7_B          147 HEKLSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSI  226 (352)
T ss_dssp             --CCCHHHHHHHHHHHHHHHHHHHTCCC----------CHHHHHHHHHHHHHHHHHHHHHHTCCSSCCBCTTCCBCCHHH
T ss_pred             cchhHHHHHHHHHHHHHHHHHHHHHHcChhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEecCCCcccHHH
Confidence            345678999999999999999999999999999999999999999999999999999987543 234433433 322211


Q ss_pred             CC-ccc--hHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchH
Q psy6602         160 PD-DVR--VNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTR  236 (367)
Q Consensus       160 ~~-~~~--~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~R  236 (367)
                      .. ..+  ..+.++.+.+++.+|++|++|++||+|||||+||+||++|+++..+|+++|++|..+|.+||..+|++++.|
T Consensus       227 ~~~~~g~~~~~l~~~l~~l~~~l~~L~ld~~EyalLkAIvLfnpd~~gLs~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~R  306 (352)
T 3tx7_B          227 IASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEK  306 (352)
T ss_dssp             HHHTSCHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHSCSCC------CHHHHHHHHHHHHHHHHHHHHCTTCTTH
T ss_pred             HHHhccccHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHHHHhCCCccHH
Confidence            00 111  256678899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHccc
Q psy6602         237 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  280 (367)
Q Consensus       237 f~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~  280 (367)
                      |++||++|+.||+++..+.|.+++++.++..++++++.|||+..
T Consensus       307 F~kLLllLp~LR~ls~~~~e~L~~~kl~g~~~i~~LL~EMl~ak  350 (352)
T 3tx7_B          307 FGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHAK  350 (352)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSCSSCHHHHHHHC-
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCccHHHHHHHhcc
Confidence            99999999999999999999999999999999999999999864

>1sqn_A PR, progesterone receptor; nuclear receptor, steroid receptor, norethindrone, birth control, hormone/growth factor receptior complex; HET: NDR; 1.45A {Homo sapiens} SCOP: a.123.1.1 PDB: 3g8o_A* 3g8n_A* 3d90_A* 1e3k_A* 1sr7_A* 1zuc_B* 3zr7_A* 2w8y_A* 3zra_A* 3zrb_A* 4a2j_A* 4apu_A* 1a28_A* 2ovh_A* 2ovm_A* 3hq5_A* 3kba_A*

Probab=100.00  E-value=5.6e-36  Score=275.54  Aligned_cols=211  Identities=19%  Similarity=0.263  Sum_probs=176.8

Q ss_pred             CCcccccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCC
Q psy6602          65 HPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD  144 (367)
Q Consensus        65 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~  144 (367)
                      +|..+++++++..|++....   ++++++++++.++.+|+|||++|+|.+|+.+||++|||++|+|+++++.||+++...
T Consensus        23 ep~~~~~~~~~~~~~~~~~~---~~~l~e~a~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~   99 (261)
T 1sqn_A           23 EPDVIYAGHDNTKPDTSSSL---LTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHV   99 (261)
T ss_dssp             SCCCCCCCCCC--CCCHHHH---HHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCcccccCCCCCCCCchhhH---HHHHHHHHHHHHHHHHHHHHhCccHhhCCHHHHHHHHHhhHHHHHHHHHHHHhhhcC
Confidence            34456777776777765443   678999999999999999999999999999999999999999999999999998654


Q ss_pred             Cc--eEecCCccccCCCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCC-CCCCCCChhHHHHHHHHHHHH
Q psy6602         145 LS--LLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTP-ETPGLVDAQPVEMLQDQAQCI  221 (367)
Q Consensus       145 ~~--~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~p-d~~~L~~~~~v~~~q~~~~~~  221 (367)
                      ++  .++.++....+......++.+.++.+.+++.+|++|++|++||+|||||+||+| |++|+++..+|+++|++|..+
T Consensus       100 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~l~~L~ld~~E~~lLkAIvLfnp~~~~gL~~~~~ve~lq~~~~~a  179 (261)
T 1sqn_A          100 SGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRE  179 (261)
T ss_dssp             TTSSEEEETTEEECGGGCCSHHHHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHTSEECTTCCTTHHHHHHHHHHHHHH
T ss_pred             CCCeEEeCCCcccchHhhhhhhHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCcccccccHHHHHHHHHHHHHH
Confidence            43  345555555544433445667778899999999999999999999999999999 899999999999999999999


Q ss_pred             HHHHHHhh---CCCcchHHHHHHHhhhHhHhhhhhHHHHHHhhhcc-----CCchhHhHHHHHHccc
Q psy6602         222 LGDYVRGR---YSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETI-----GDIPIQRLLGDMYTME  280 (367)
Q Consensus       222 L~~y~~~~---~~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~-----~~~~~~~Ll~eml~~~  280 (367)
                      |.+||..+   +++++.||++|+++++.+|+++...  ..++.+.+     +..++++++.||+...
T Consensus       180 L~~y~~~~~~~~~~~~~Rf~~LL~~L~~Lr~~~~~~--~~~~~~~~~q~~~~~~~~~~Ll~Ei~~~~  244 (261)
T 1sqn_A          180 LIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDLVKQL--HLYCLNTFIQSRALSVEFPEMMSEVIAAQ  244 (261)
T ss_dssp             HHHHHHTTC-CHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHTHHHHTCCCCHHHHHHHHHH
T ss_pred             HHHHHHhhCCCCCchHHHHHHHHHHhHHHHHHHHHH--HHHHHHHHHHhcCCCCChHHHHHHHHhcC
Confidence            99999875   3578999999999999999999876  33344555     7889999999999854

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

Probab=100.00  E-value=5.1e-36  Score=273.01  Aligned_cols=200  Identities=20%  Similarity=0.257  Sum_probs=153.4

Q ss_pred             CCCcccccCCCCCCCCChh----hhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHh
Q psy6602          64 HHPSMFLATHQPPPHPGLL----QILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQW  139 (367)
Q Consensus        64 ~~~~~~~~~~~~~~~~~~~----~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~  139 (367)
                      .++..++++|+...|++..    .....|+.+++.+++.++.+|+|||++|+|.+|+.+||++|||++|+|+++|+.|++
T Consensus        39 ~~~~~~~~~~~~~~p~~~~~~~~s~~~~~~~~~~~~~~~l~~~VewAK~lP~F~~L~~~DQ~~LLk~~~~el~lL~~a~~  118 (245)
T 3n00_A           39 SSPGNFNANHASGSPYPHGRSGRTVQEIWEDFSMSFTPAVREVVEFAKHIPGFRDLSQHDQVTLLKAGTFEVLMVRFASL  118 (245)
T ss_dssp             ------------------------CCHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCcccCCCCCCccccccCHHHHHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3456777877766665443    223558899999999999999999999999999999999999999999999999998


Q ss_pred             hccCCCceEecCCccccCCCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHH
Q psy6602         140 SIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQ  219 (367)
Q Consensus       140 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~  219 (367)
                      +....+..++.++..+........+..+.++.+.+++.+|++|++|++||+|||||+||+||++|+++...|+++|++|.
T Consensus       119 ~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~i~~~~~~l~~L~ld~~E~~lLkAIvL~npd~~gL~~~~~ve~lq~~~~  198 (245)
T 3n00_A          119 FNVKDQTVMFLSRTTYSLQELGAMGMGDLLSAMFDFSEKLNSLALTEEELGLFTAVVLVSADRSGMENSASVEQLQETLL  198 (245)
T ss_dssp             CCSCC--------------CCGGGTTHHHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHHTSCCTTCSSHHHHHHHHHHHH
T ss_pred             hcCCCCeEEecCCCeecHHHHhhccHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHH
Confidence            66544444444444444433334457788899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhCCCcchHHHHHHHhhhHhHhhhhhHHHHHHhhhc
Q psy6602         220 CILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKET  263 (367)
Q Consensus       220 ~~L~~y~~~~~~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~  263 (367)
                      .+|.+||..+|++++.||++||++|+.||+++..+.|.+++.+.
T Consensus       199 ~aL~~y~~~~~p~~~~RF~~LLl~Lp~LR~l~~~~~E~L~~~k~  242 (245)
T 3n00_A          199 RALRALVLKNRPLETSRFTKLLLKLPDLRTLNNMHSEKLLSFRV  242 (245)
T ss_dssp             HHHHHHHHHHCTTCTTHHHHHHTHHHHHHHHHHHHTTCEEEEEC
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHhHHHHHHHHHHHHHHHHhcC
Confidence            99999999999999999999999999999999999999988764

>1pdu_A DHR38, nuclear hormone receptor HR38; nuclear receptor, ligand-binding domain, hormone/growth factor receptor complex; 2.30A {Drosophila melanogaster} SCOP: a.123.1.1

Probab=100.00  E-value=3e-36  Score=274.50  Aligned_cols=193  Identities=24%  Similarity=0.277  Sum_probs=170.5

Q ss_pred             cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccch
Q psy6602          86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRV  165 (367)
Q Consensus        86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~  165 (367)
                      ..+.++++++++.++.+|+|||++|||.+|+.+||++|||++|+|+++++.||+++...+..++.++..+.+... ..+.
T Consensus        47 ~~~~~~~~~~~~~l~~~VewAK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~rs~~~~~~l~~~~g~~~~~~~~-~~~~  125 (244)
T 1pdu_A           47 DKVQQFYQLLTSSVDVIKQFAEKIPGYFDLLPEDQELLFQSASLELFVLRLAYRARIDDTKLIFCNGTVLHRTQC-LRSF  125 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHCCSSCSEEECTTSBEEEHHHH-HHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCceEeeCCeeecHHHH-HhHH
Confidence            448889999999999999999999999999999999999999999999999999986545444444433332211 1134


Q ss_pred             HHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCC--CcchHHHHHHHh
Q psy6602         166 NNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYS--RQPTRFGRLLLM  243 (367)
Q Consensus       166 ~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~--~~~~Rf~~LL~~  243 (367)
                      .+.++.+.+++.+|++|++|++||+|||||+||+ |++|+++...|+++|++|..+|.+||..+|+  +++.||++|+++
T Consensus       126 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkAIvLfn-d~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~~~Rf~~LL~~  204 (244)
T 1pdu_A          126 GEWLNDIMEFSRSLHNLEIDISAFACLCALTLIT-ERHGLREPKKVEQLQMKIIGSLRDHVTYNAEAQKKQHYFSRLLGK  204 (244)
T ss_dssp             TTHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHSS-CCTTCSCHHHHHHHHHHHHHHHHHHHHHCHHHHTSTTHHHHHHTH
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC-CCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHH
Confidence            4567788999999999999999999999999998 9999999999999999999999999998875  689999999999


Q ss_pred             hhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHccc
Q psy6602         244 LPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  280 (367)
Q Consensus       244 l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~  280 (367)
                      ++.||+++..+.|.+++.+.++..++++++.||+...
T Consensus       205 L~~Lr~l~~~~~e~l~~~~~~g~~~~~~Ll~Eml~~~  241 (244)
T 1pdu_A          205 LPELRSLSVQGLQRIFYLKLEDLVPAPALIENMFVTT  241 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHTTTCC
T ss_pred             HHHHHHHHHHHHHHHHHHccCCCCCchHHHHHHHhCC
Confidence            9999999999999999999999999999999999753

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

Probab=100.00  E-value=4.9e-36  Score=279.68  Aligned_cols=215  Identities=17%  Similarity=0.208  Sum_probs=178.2

Q ss_pred             CCCcccccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccC
Q psy6602          64 HHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPW  143 (367)
Q Consensus        64 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~  143 (367)
                      .+|..+++++++..|++....   ++++++++++.++.+|+|||++|+|.+|+.+||++|||++|+|+++|+.||+++..
T Consensus        55 ~eP~~~~~~~~~~~p~~~~~~---~~~l~e~a~~~l~~~VewAK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~rS~~~  131 (294)
T 3vhu_A           55 IEPEIVYAGYDSSKPDTAENL---LSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQYSWMSLLSFALSWRSYKH  131 (294)
T ss_dssp             HCCCCCCCCCCTTSCCCHHHH---HHHHHHHHHHHHHHHHHHHHTCTTTTSSCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCccccCCCCCCCCChHHH---HHHHHHHHHHHHHHHHHHHHhCcchhhCCHHHHHHHHHHhHHHHHHHHHHHHhhhc
Confidence            468888999888888776544   78899999999999999999999999999999999999999999999999998764


Q ss_pred             CC--ceEecCCccccCCCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCC-CCCCCCChhHHHHHHHHHHH
Q psy6602         144 DL--SLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTP-ETPGLVDAQPVEMLQDQAQC  220 (367)
Q Consensus       144 ~~--~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~p-d~~~L~~~~~v~~~q~~~~~  220 (367)
                      .+  ..++.++..+.+......+..+.++.+.+++.+|++|++|++||+|||||+||+| |++|+++...|+++|++|..
T Consensus       132 ~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~l~~~~~~l~~L~ld~~EyalLkAIvLfnp~d~~gL~~~~~Ve~lQe~~~~  211 (294)
T 3vhu_A          132 TNSQFLYFAPDLVFNEEKMHQSAMYELCQGMHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKDGLKSQAAFEEMRTNYIK  211 (294)
T ss_dssp             HTTSSEEEETTEEECHHHHHHTTCHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHTSEEETTCCTTHHHHHHHHHHHHH
T ss_pred             CCCCeEEeCCCccccHHHhhcccHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCcHHHHHHHHHHHHH
Confidence            33  3344444433332211224567778899999999999999999999999999999 99999999999999999999


Q ss_pred             HHHHHHHhhCCCc---chHHHHHHHhhhHhHhhhhhHHHHHHhhhc---cCCchhHhHHHHHHcccC
Q psy6602         221 ILGDYVRGRYSRQ---PTRFGRLLLMLPSLRAVRQSTIERLFFKET---IGDIPIQRLLGDMYTMEK  281 (367)
Q Consensus       221 ~L~~y~~~~~~~~---~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~---~~~~~~~~Ll~eml~~~~  281 (367)
                      +|.+||..++++.   +.||++||.+++.||+++..+.|.+++...   .....+++|+.|||+...
T Consensus       212 aL~~y~~~~~~~~~~~~~RF~~LL~lLp~Lr~l~~~~~e~lff~~~q~~~~~~~~p~Ll~Ei~~~~~  278 (294)
T 3vhu_A          212 ELRKMVTKCPNNSGQSWQRFYQLTKLLDSMHDLVSDLLEFCFYTFRESHALKVEFPAMLVEIISDQL  278 (294)
T ss_dssp             HHHHHHC------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTCCCCHHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCCccHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCcCCCCHHHHHHHcCCC
Confidence            9999999887654   789999999999999999999999886443   345668999999998543

>3cqv_A Nuclear receptor subfamily 1 group D member 2; reverb beta, heme, NR1D2, DNA-binding, metal-binding, nucleus, repressor, transcription; HET: HEM; 1.90A {Homo sapiens} PDB: 2v7c_A 2v0v_A

Probab=100.00  E-value=8.6e-36  Score=263.58  Aligned_cols=178  Identities=19%  Similarity=0.239  Sum_probs=154.7

Q ss_pred             CHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccchH
Q psy6602          87 SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVN  166 (367)
Q Consensus        87 ~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  166 (367)
                      .+..+++.+++.++.+|+|||++|||.+|+.+||++|||++|+|+++++.|+++....+...+.++..+........+..
T Consensus        21 ~~~~~~~~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~e~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~~~~~  100 (199)
T 3cqv_A           21 IWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLFDAKERTVTFLSGKKYSVDDLHSMGAG  100 (199)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTSGGGGGSCHHHHHHHHHHHHHHHHHHHTGGGEETTTTEEECTTSCEEEHHHHHHTTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCChhhCCHHHHHHHHHHhHHHHHHHHHHHHhCCCCCeEEecCCCeecHHHHHhcCcH
Confidence            38889999999999999999999999999999999999999999999999998765444444433333332211112344


Q ss_pred             HHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhhhH
Q psy6602         167 NEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPS  246 (367)
Q Consensus       167 ~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~~  246 (367)
                      +.++.+.+++.+|++|++|++||+|||||+||+||++|+++...|+++|++|..+|.+||..+|++++.||++|+.+++.
T Consensus       101 ~~~~~i~~~~~~~~~L~ld~~E~~lLkaivL~~pd~~gL~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LL~~L~~  180 (199)
T 3cqv_A          101 DLLNSMFEFSEKLNALQLSDEEMSLFTAVVLVSADRSGIENVNSVEALQETLIRALRTLIMKNHPNEASIFTKLLLKLPD  180 (199)
T ss_dssp             HHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHTSCCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCCCCcCHHHHHHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHH
Confidence            67788899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHhhhhhHHHHHHhhhcc
Q psy6602         247 LRAVRQSTIERLFFKETI  264 (367)
Q Consensus       247 Lr~l~~~~~e~l~~~~~~  264 (367)
                      ||+++..+.|.+++.++.
T Consensus       181 Lr~l~~~~~E~l~~~k~~  198 (199)
T 3cqv_A          181 LRSLNNMHSEELLAFKVH  198 (199)
T ss_dssp             HHHHHHHHHHHHHTCC--
T ss_pred             HHHHHHHHHHHHHHhcCC
Confidence            999999999999988754

>1t7r_A Androgen receptor; nuclear receptor, transcription factor, ligand binding domain, AF-2, androgen, testosterone, DHT, alpha-helical sandwich; HET: DHT; 1.40A {Pan troglodytes} SCOP: a.123.1.1 PDB: 1t73_A* 1t76_A* 1t74_A* 1t79_A* 1t7m_A* 1t7f_A* 1t7t_A* 2am9_A* 2ama_A* 2amb_A* 2pnu_A* 1e3g_A* 2q7i_A* 1xj7_A* 2q7j_A* 3g0w_A* 2ihq_A* 2nw4_A* 1i37_A* 2q7k_A* ...

Probab=100.00  E-value=6.2e-36  Score=276.41  Aligned_cols=214  Identities=19%  Similarity=0.274  Sum_probs=178.7

Q ss_pred             CCcccccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCC
Q psy6602          65 HPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD  144 (367)
Q Consensus        65 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~  144 (367)
                      +|..+++++++..|++....   ++++++++++.++.+|+|||++|+|.+|+.+||++|||++|+|+++|+.|||++...
T Consensus        31 ep~~~~~~~~~~~p~~~~~~---~~~l~e~a~~~l~~~VewAK~ip~F~~L~~~DQv~LLk~~w~el~iL~~a~rs~~~~  107 (269)
T 1t7r_A           31 EPGVVCAGHDNNQPDSFAAL---LSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNV  107 (269)
T ss_dssp             CCCCCCCCCCTTSCCCHHHH---HHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCcccCCCCCCCCchhHH---HHHHHHHHHHHHHHHHHHHHhCccHhhCCHHHHHHHHHHhHHHHHHHHHHHHhcccC
Confidence            45667778777777765443   778999999999999999999999999999999999999999999999999987653


Q ss_pred             Cc-eEec-CCccccCCCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCC-CCCCCCChhHHHHHHHHHHHH
Q psy6602         145 LS-LLIN-CEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTP-ETPGLVDAQPVEMLQDQAQCI  221 (367)
Q Consensus       145 ~~-~l~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~p-d~~~L~~~~~v~~~q~~~~~~  221 (367)
                      ++ .+++ ++....+......+..+.++.+.+++.+|++|++|++||+|||||+||+| |++|+++...|+++|++|..+
T Consensus       108 ~~~~l~~~~g~~~~~~~~~~~~~~~~~~~i~~~~~~l~~L~ld~~E~~lLkAIvLfnp~~~~gL~~~~~ve~lq~~~~~a  187 (269)
T 1t7r_A          108 NSRMLYFAPDLVFNEYRMHKSRMYSQCVRMRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFFDELRMNYIKE  187 (269)
T ss_dssp             TTSSEEEETTEEECHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHTSEEETTCCTTHHHHHHHHHHHHHH
T ss_pred             CCCeEEeCCCceecHHhhhhhhHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHcCCCccCCCccHHHHHHHHHHHHHH
Confidence            33 4444 44333322111223446678889999999999999999999999999999 899999999999999999999


Q ss_pred             HHHHHHhhC---CCcchHHHHHHHhhhHhHhhhhhHHHHHHhh--h-ccCCchhHhHHHHHHcccC
Q psy6602         222 LGDYVRGRY---SRQPTRFGRLLLMLPSLRAVRQSTIERLFFK--E-TIGDIPIQRLLGDMYTMEK  281 (367)
Q Consensus       222 L~~y~~~~~---~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~--~-~~~~~~~~~Ll~eml~~~~  281 (367)
                      |.+||..++   ++++.||++||++++.||+++..+.|.++..  + ..+..++++++.|||+...
T Consensus       188 L~~y~~~~~~~~~~~~~Rf~~LL~~L~~Lr~l~~~~~e~lf~~~~~~~~~~~~~~~Ll~E~~~~~~  253 (269)
T 1t7r_A          188 LDRIIACKRKNPTSCSRRFYQLTKLLDSVQPIARELHQFTFDLLIKSHMVSVDFPEMMAEIISVQV  253 (269)
T ss_dssp             HHHHHHTTCCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTCCCCHHHHHHHHHTH
T ss_pred             HHHHHHHhCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCcChHHHHHHHHhCcC
Confidence            999998875   3678999999999999999999999998843  2 2367789999999998544

>2p1t_A Retinoic acid receptor RXR-alpha; protein-ligand complex, hormone receptor; HET: 3TN; 1.80A {Homo sapiens} SCOP: a.123.1.1 PDB: 1mvc_A* 1mzn_A* 1mv9_A* 2p1u_A* 2p1v_A* 2zxz_A* 2zy0_A* 3fug_A* 3nsp_A 3nsq_A* 3r29_A 3r2a_A* 3r5m_A* 3e94_A* 3kwy_A* 1fby_A* 3uvv_B* 3fc6_A* 1rdt_A* 3fal_A* ...

Probab=100.00  E-value=1.6e-35  Score=269.36  Aligned_cols=195  Identities=30%  Similarity=0.600  Sum_probs=171.9

Q ss_pred             CHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccchH
Q psy6602          87 SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVN  166 (367)
Q Consensus        87 ~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  166 (367)
                      .++++++++.+.++.+|+|||++|+|..|+.+||++|||++|+++++++.|||++..++..++.++....+......+..
T Consensus        42 ~~~~l~~~~~~~l~~~vewak~ip~F~~L~~~DQ~~LLk~~w~e~~il~~a~rs~~~~~~~~~~~g~~~~~~~~~~~~~~  121 (240)
T 2p1t_A           42 PVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVG  121 (240)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTSSSEEECTTSCEEEHHHHHTTTCH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCcChhcCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCcccccchhhhhchH
Confidence            47889999999999999999999999999999999999999999999999999988776666544433322211112233


Q ss_pred             HHH-HHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhhh
Q psy6602         167 NEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLP  245 (367)
Q Consensus       167 ~~~-~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~  245 (367)
                      ..+ +.+.+++.+|++|++|++||+|||||+||+||++|+++..+|+++|+++..+|++||..++++++.||++|+.+++
T Consensus       122 ~~~~~~~~~~~~~l~~L~ld~~E~~~Lkai~l~~pd~~gl~~~~~ve~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~  201 (240)
T 2p1t_A          122 AIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLP  201 (240)
T ss_dssp             HHHHHHHHHTHHHHHHTTCCHHHHHHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTTHH
T ss_pred             HHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCchhHHHHHHHHHH
Confidence            444 3457899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccC
Q psy6602         246 SLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEK  281 (367)
Q Consensus       246 ~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~  281 (367)
                      .||+++..+.|.+++.+.++..++++++.||++...
T Consensus       202 ~Lr~~~~~~~e~l~~~~~~~~~~~~~ll~eml~~~~  237 (240)
T 2p1t_A          202 ALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEAPH  237 (240)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCCSCCCHHHHHHTSCC-
T ss_pred             HHHHHHHHHHHHHHHhCcCCCCchHHHHHHHHcCCC
Confidence            999999999999999999999999999999998654

>2nxx_E Ecdysone receptor (ECR, NRH1); hormone receptor, APO and holo ligand binding pocket, hormone/growth factor complex; HET: P1A; 2.75A {Tribolium castaneum}

Probab=100.00  E-value=1.4e-35  Score=270.89  Aligned_cols=195  Identities=21%  Similarity=0.292  Sum_probs=170.8

Q ss_pred             hccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCcc
Q psy6602          84 ILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDV  163 (367)
Q Consensus        84 ~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~  163 (367)
                      ....+.++++++.+.++.+|+|||++|||.+|+.+||++|||++|+|+++|+.||++....+..++.++..+.+......
T Consensus        50 ~~~~~~~l~~~~~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~~~~~~~~~~~~~g~~~~~~~~~~~  129 (248)
T 2nxx_E           50 CDVRFRHITEITILTVQLIVEFAKRLPGFDKLLREDQIALLKACSSEVMMFRMARRYDVQTDSILFVNNQPYSRDSYNLA  129 (248)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEETTTTEEECTTSCEECHHHHHHT
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHcCCchhhCCHHHHHHHHHHhHHHHHHHHHHHHhcCCCCeEEecCCceecHHHHHhc
Confidence            44558999999999999999999999999999999999999999999999999999886555544444433333221123


Q ss_pred             chHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhC-CCcchHHHHHHH
Q psy6602         164 RVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRY-SRQPTRFGRLLL  242 (367)
Q Consensus       164 ~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~-~~~~~Rf~~LL~  242 (367)
                      +..+.++.+.+++.+|++|++|++||+|||||+||+ |++|+++...|+++|++|..+|.+||..+| ++++.||++|++
T Consensus       130 ~~~~~~~~i~~~~~~l~~L~ld~~E~~lLkAivL~~-d~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~Rf~~LL~  208 (248)
T 2nxx_E          130 GMGETIEDLLHFCRTMYSMRVDNAEYALLTAIVIFS-ERPALIEGWKVEKIQEIYLEALRAYVDNRRKPKPGTIFAKLLS  208 (248)
T ss_dssp             TCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHTC-CCSSCTTHHHHHHHHHHHHHHHHHHHHHSCCSSHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHcC-CCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCchhhHHHHHHH
Confidence            455778889999999999999999999999999997 999999999999999999999999999998 468999999999


Q ss_pred             hhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHccc
Q psy6602         243 MLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  280 (367)
Q Consensus       243 ~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~  280 (367)
                      +++.||+++..+.|.+++.+..+ .++++|+.|||+..
T Consensus       209 ~L~~Lr~l~~~~~e~l~~~~~~~-~~~~~Ll~Em~~~~  245 (248)
T 2nxx_E          209 VLTELRTLGNQNSEMCFSLKLKN-KKLPPFLAEIWDVD  245 (248)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTT-CCCCHHHHHHTTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCC-CCccHHHHHHhcCc
Confidence            99999999999999999988875 58999999999854

>1z5x_E Ecdysone receptor ligand binding domain; ponasterone A, nuclear receptor, ECR, USP, hormone/growth factor receptor complex; HET: P1A; 3.07A {Bemisia tabaci}

Probab=100.00  E-value=1.6e-35  Score=278.20  Aligned_cols=196  Identities=20%  Similarity=0.270  Sum_probs=171.8

Q ss_pred             hhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCc
Q psy6602          83 QILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDD  162 (367)
Q Consensus        83 ~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~  162 (367)
                      .....+.++++++.+.++.+|+|||+||||.+|+.+||++|||++|+|+++|+.||+++...+..++.++..+.+.....
T Consensus       113 ~~~~~~~~l~el~~~~l~~~VewAK~lP~F~~L~~~DQi~LLk~~w~el~lL~~a~rs~~~~~~l~~~~g~~~~~~~~~~  192 (310)
T 1z5x_E          113 VAEERFRHITEITILTVQLIVEFSKRLPGFDKLIREDQIALLKACSSEVMMFRMARRYDAETDSILFATNQPYTRESYTV  192 (310)
T ss_dssp             SSHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEETTTTEEECTTSCEECHHHHHH
T ss_pred             chhhHHHHHHHHHHHHHHHHHHHHHcCcchhhCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCeEEeCCCccccHHHHHh
Confidence            34455899999999999999999999999999999999999999999999999999998755554444443333322122


Q ss_pred             cchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhC-CCcchHHHHHH
Q psy6602         163 VRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRY-SRQPTRFGRLL  241 (367)
Q Consensus       163 ~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~-~~~~~Rf~~LL  241 (367)
                      .++.+.++.+.+++.+|++|++|++||+|||||+||+ |++|+++...|+++|++|..+|.+||..+| ++++.||++||
T Consensus       193 ~g~~~~~~~i~~~~~~l~~L~ld~~E~alLkAIvLf~-d~~gL~~~~~Ve~lqe~~~~aL~~y~~~~~~~~~~~RF~kLL  271 (310)
T 1z5x_E          193 AGMGDTVEDLLRFCRHMCAMKVDNAEYALLTAIVIFS-ERPSLSEGWKVEKIQEIYIEALKAYVENRRKPYATTIFAKLL  271 (310)
T ss_dssp             TTTHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHTC-CCTTCTTHHHHHHHHHHHHHHHHHHHHTTTCTTHHHHHHHHH
T ss_pred             cchhHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHcC-CCCCCccHHHHHHHHHHHHHHHHHHHHHHCCCcHHHHHHHHH
Confidence            3456778889999999999999999999999999997 999999999999999999999999999998 57899999999


Q ss_pred             HhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHccc
Q psy6602         242 LMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  280 (367)
Q Consensus       242 ~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~  280 (367)
                      ++|+.||+++..+.|.+++.+..+ .++++|+.|||+..
T Consensus       272 l~Lp~LR~l~~~~~e~l~~~~~~~-~~~~~Ll~Eml~~~  309 (310)
T 1z5x_E          272 SVLTELRTLGNMNSETCFSLKLKN-RKVPSFLEEIWDVV  309 (310)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTT-CCCCHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCC-CCchHHHHHHHcCC
Confidence            999999999999999999988875 58999999999853

>3l0l_A Nuclear receptor ROR-gamma; nuclear receptor, rorgamma, alternative splicing, DNA-bindin binding, nucleus, receptor, zinc-finger, acetylation, activator; HET: HC3; 1.74A {Homo sapiens} SCOP: a.123.1.0 PDB: 3b0w_A* 3kyt_A* 3l0j_A*

Probab=100.00  E-value=1.2e-35  Score=271.34  Aligned_cols=191  Identities=17%  Similarity=0.222  Sum_probs=169.6

Q ss_pred             hccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCcc
Q psy6602          84 ILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDV  163 (367)
Q Consensus        84 ~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~  163 (367)
                      +...|.++++.+++.++.+|+|||++|||.+|+.+||++|||++|+|+++++.||++...++..++ ++...........
T Consensus        54 ~~~~~~~~~~~~~~~l~~~VewaK~iP~F~~L~~~DQi~LLk~~~~el~lL~~a~~~~~~~~~~~~-~g~~~~~~~~~~~  132 (248)
T 3l0l_A           54 MWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNRTVFF-EGKYGGMELFRAL  132 (248)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHGGGGEETTTTEEEE-TTEEECGGGGGGG
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcCCCCEEEe-CCCcccHHHHhhc
Confidence            445689999999999999999999999999999999999999999999999999998876655555 4433332222234


Q ss_pred             chHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHh
Q psy6602         164 RVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLM  243 (367)
Q Consensus       164 ~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~  243 (367)
                      +..+.++.+.+++.+|++|++|++||+|||||+||+||++|+++..+|+++|++|..+|.+||..+++  +.||++|+++
T Consensus       133 ~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkAivLfnpd~~gL~~~~~ve~lqe~~~~aL~~y~~~~~~--~~rf~~LLl~  210 (248)
T 3l0l_A          133 GCSELISSIFDFSHSLSALHFSEDEIALYTALVLINAHRPGLQEKRKVEQLQYNLELAFHHHLCKTHR--QSILAKLPPK  210 (248)
T ss_dssp             SCHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHTTC--GGGGGGSCCT
T ss_pred             cHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCCccHHHHHHHHHHHHHHHHHHHHhhCh--HHHHHHhhcc
Confidence            56788899999999999999999999999999999999999999999999999999999999999874  5799999999


Q ss_pred             hhHhHhhhhhHHHHHHhhhccCC----chhHhHHHHHHc
Q psy6602         244 LPSLRAVRQSTIERLFFKETIGD----IPIQRLLGDMYT  278 (367)
Q Consensus       244 l~~Lr~l~~~~~e~l~~~~~~~~----~~~~~Ll~eml~  278 (367)
                       ++||+++..+.|.+++.+..+.    .++++|+.|||.
T Consensus       211 -p~LR~i~~~~~e~l~~~k~~~p~~~~~~~p~Ll~Emf~  248 (248)
T 3l0l_A          211 -GKLRSLCSQHVERLQIFQHLHPIVVQAAFPPLYKELFS  248 (248)
T ss_dssp             -THHHHHHHHHHHHHHHHHHHCHHHHHHHSCHHHHHHHC
T ss_pred             -HHHHHHHHHHHHHHHHHHhhCcccccCCCChHHHHhhC
Confidence             9999999999999999999873    578999999984

>1lbd_A RXR_LBD, retinoid X receptor; transcription factor, nuclear receptor, structural proteomic europe, spine, structural genomics; 2.70A {Homo sapiens} SCOP: a.123.1.1 PDB: 1z5x_U* 2q60_A

Probab=100.00  E-value=1.4e-35  Score=276.03  Aligned_cols=196  Identities=30%  Similarity=0.588  Sum_probs=173.1

Q ss_pred             cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccch
Q psy6602          86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRV  165 (367)
Q Consensus        86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~  165 (367)
                      .+++++++++.+.++.+|+|||+||+|..|+.+||++|||++|+++++++.||+++...+..++.++..+.+......+.
T Consensus        83 ~~~~~~~~~a~~~l~~~vewaK~ip~F~~L~~~DQ~~LLk~~~~el~il~~a~rs~~~~~~~~~~~g~~~~~~~~~~~~~  162 (282)
T 1lbd_A           83 DPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGV  162 (282)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHGGGGSSSEEECTTSCEEEHHHHHHTTT
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHhCcChhcCCHHHHHHHHHHHHHHHHHHHHHHhcccCCCceEecCCcccccchhhhccc
Confidence            34788999999999999999999999999999999999999999999999999999877766664443333221111223


Q ss_pred             HHHHH-HHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhh
Q psy6602         166 NNEIK-LIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLML  244 (367)
Q Consensus       166 ~~~~~-~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l  244 (367)
                      ...++ .+.+++.+|++|++|.+||+|||||+||+||++|+++..+|+++|++|..+|.+||..+|++++.||++||.+|
T Consensus       163 ~~~~~~~~~~~~~~l~~L~ld~~E~~lLkaivL~~pd~~gLs~~~~v~~lq~~~~~~L~~y~~~~~~~~~~Rf~~LL~~L  242 (282)
T 1lbd_A          163 GAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRL  242 (282)
T ss_dssp             HHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHSCCSTTTHHHHHTTH
T ss_pred             HHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCchhHHHHHHHHH
Confidence            44443 45689999999999999999999999999999999998889999999999999999999999999999999999


Q ss_pred             hHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccC
Q psy6602         245 PSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEK  281 (367)
Q Consensus       245 ~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~  281 (367)
                      +.||+++..+.|.+++.+.++..++++++.||++...
T Consensus       243 ~~Lr~~~~~~~e~l~~~~~~~~~~i~~ll~eml~~~~  279 (282)
T 1lbd_A          243 PALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEAPH  279 (282)
T ss_dssp             HHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHTSCC
T ss_pred             HHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHcCCC
Confidence            9999999999999999999999999999999998654

>1osh_A BIle acid receptor; nuclear receptor, ligand binding domain, transcription; HET: FEX; 1.80A {Homo sapiens} SCOP: a.123.1.1 PDB: 3l1b_A* 3bej_A* 3fli_A* 3hc5_A* 3rvf_A* 3dct_A* 3dcu_A* 3ruu_A* 3rut_A* 3olf_A* 3okh_A* 3fxv_A* 3oki_A* 3omk_A* 3omm_A* 3oof_A* 3ook_A* 3hc6_A* 3p89_A* 3p88_A* ...

Probab=100.00  E-value=2.7e-35  Score=266.53  Aligned_cols=189  Identities=21%  Similarity=0.221  Sum_probs=163.3

Q ss_pred             cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccch
Q psy6602          86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRV  165 (367)
Q Consensus        86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~  165 (367)
                      ..+.++++++.+.++.+|+|||++|||.+|+.+||++|||++|+|+++++.|+++......    ++...........+.
T Consensus        42 ~~~~~~~~~~~~~l~~~vewaK~lp~F~~L~~~DQ~~LLk~~~~e~~~l~~a~~~~~~~~~----~~~~~~~~~~~~~~~  117 (232)
T 1osh_A           42 ENFLILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLPS----GHSDLLEERIRNSGI  117 (232)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHTSCH----HHHHHHHHHHHTSSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCchhhCCHHHHHHHHHHhHHHHHHHHHHHHhCCccCC----CCceecHHHHHHcCC
Confidence            4488999999999999999999999999999999999999999999999999987643111    111111000000112


Q ss_pred             -HHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhh
Q psy6602         166 -NNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLML  244 (367)
Q Consensus       166 -~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l  244 (367)
                       .+.++.+.+++.+|++|++|++||+|||||+||+||++|++++..|+++|++|..+|.+||..++++++.||++|++++
T Consensus       118 ~~~~~~~i~~~~~~l~~L~ld~~E~~lLkaivL~~pd~~gL~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LL~~L  197 (232)
T 1osh_A          118 SDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRL  197 (232)
T ss_dssp             CTTTHHHHHHHHHHHHTTCCCHHHHHHHHHHHHTCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCCChHHHHHHHHHHHHHHHHHHHHHCCCchhHHHHHHHHH
Confidence             2346788899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcc
Q psy6602         245 PSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM  279 (367)
Q Consensus       245 ~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~  279 (367)
                      +.||+++..+.|.+++.+. +..++++++.|||+.
T Consensus       198 ~~Lr~l~~~~~e~l~~~k~-~~~~~~~Ll~Em~~~  231 (232)
T 1osh_A          198 TELRTFNHHHAEMLMSWRV-NDHKFTPLLCEIWDV  231 (232)
T ss_dssp             HHHHTHHHHHHHHHHHHHH-TTCCCCHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHHHh-CCCCCChHHHHHhcC
Confidence            9999999999999999887 688999999999975

>1ovl_A Orphan nuclear receptor NURR1 (MSe 414, 496, 511); NUUR1, LBD, transcription; 2.20A {Homo sapiens} SCOP: a.123.1.1

Probab=100.00  E-value=1.3e-34  Score=268.01  Aligned_cols=191  Identities=24%  Similarity=0.338  Sum_probs=168.7

Q ss_pred             cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccch
Q psy6602          86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRV  165 (367)
Q Consensus        86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~  165 (367)
                      ..+.++++++++.++.+|+|||++|||.+|+.+||++|||++|+|+++|+.||+++..++..++.++..+..... ..+.
T Consensus        74 ~~~~~~~~~~~~~l~~~v~waK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~~l~~~~g~~~~~~~~-~~~~  152 (271)
T 1ovl_A           74 QHIQQFYDLLTGSMEIIRGWAEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIFCNGVVLHRLQC-VRGF  152 (271)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHSBTTTTEEECTTSBEEEHHHH-TTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCCcccCChHHHHHHHHHhHHHHHHHHHHHHhcCCCCeEEeeCCeeecHHHH-HhhH
Confidence            347889999999999999999999999999999999999999999999999999998766444444433332211 1234


Q ss_pred             HHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhC--CCcchHHHHHHHh
Q psy6602         166 NNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRY--SRQPTRFGRLLLM  243 (367)
Q Consensus       166 ~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~--~~~~~Rf~~LL~~  243 (367)
                      .+.++.+.+++.+|++|++|++||+|||||+||+| ++|+++...|+++|++|..+|.+||..++  ++++.||++||++
T Consensus       153 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkAivL~~~-~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~~Rf~~LL~~  231 (271)
T 1ovl_A          153 GEWIDSIVEFSSNLQNMNIDISAFSCIAALAMVTE-RHGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLGK  231 (271)
T ss_dssp             TTHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHSSC-CTTCSCHHHHHHHHHHHHHHHHHHHHGGGTTTTSTTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC-CCCCCcHHHHHHHHHHHHHHHHHHHHhcCCCCccccHHHHHHHH
Confidence            56778889999999999999999999999999995 89999999999999999999999999874  6889999999999


Q ss_pred             hhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHc
Q psy6602         244 LPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT  278 (367)
Q Consensus       244 l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~  278 (367)
                      ++.||+++..+.|.+++.+.++..++++++.+||.
T Consensus       232 L~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~el~~  266 (271)
T 1ovl_A          232 LPELRTLCTQGLQRIFYLKLEDLVPPPAIIDKLFL  266 (271)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTSSCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHcCCCCCCcHHHHHHHH
Confidence            99999999999999999999999999888888875

>3u9q_A Peroxisome proliferator-activated receptor gamma; nuclear receptor, adipogenesis, RXRA, nucleus, transcription; HET: DKA; 1.52A {Homo sapiens} SCOP: a.123.1.1 PDB: 1i7i_A* 3ty0_A* 1zeo_A* 2p4y_A* 3et3_A* 3et0_A* 2hwq_A* 2ath_A* 2f4b_A* 2g0g_A* 2g0h_A* 2gtk_A* 2fvj_A* 2hwr_A* 2prg_A* 2q8s_A* 3fej_A* 3g9e_A* 3gbk_A* 3ia6_A* ...

Probab=100.00  E-value=1.8e-34  Score=266.28  Aligned_cols=187  Identities=21%  Similarity=0.271  Sum_probs=159.5

Q ss_pred             HHHHHHHH-HHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccc-cCCC--CCccch
Q psy6602          90 KCQETTAR-LLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKAR-ERLP--PDDVRV  165 (367)
Q Consensus        90 ~l~e~~~~-~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~-~~~~--~~~~~~  165 (367)
                      ++|+.+.+ .++.+|+|||++|||.+|+.+||++|||++|+|+++|+.|+++..  +..++.++..+ .+..  ....++
T Consensus        76 ~~c~~~~~~~v~~~VewAK~iP~F~~L~~~DQi~LLk~~~~el~lL~~a~~~~~--~~~~~~~g~~~~~~~~~~~~~~~~  153 (269)
T 3u9q_A           76 QGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNK--DGVLISEGQGFMTREFLKSLRKPF  153 (269)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEET--TEEEETTTTEEEEHHHHHHSCTTG
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCChhhcCHHHHHHHHHHhhHHHHHHHHHHhcCC--CCeEEeCCCccccHHHHHHhhhhH
Confidence            34555554 588999999999999999999999999999999999999987653  44555554432 2211  011234


Q ss_pred             HHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhhh
Q psy6602         166 NNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLP  245 (367)
Q Consensus       166 ~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~  245 (367)
                      .+.++.+.+++.+|++|++|++||+|||||+||+||++|+++...|+++|++|..+|.+||..+||+++.||++||++++
T Consensus       154 ~~~~~~l~~~~~~l~~L~ld~~E~alLkAIvLfnpd~~gL~~~~~Ve~lqe~~~~aL~~y~~~~~p~~~~Rf~kLL~~Lp  233 (269)
T 3u9q_A          154 GDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMT  233 (269)
T ss_dssp             GGSSHHHHHHHHHHHTTCCCHHHHHHHHHHHHTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTSTTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHhH
Confidence            45567889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhHhhhhhHHHHHHhhh-ccCCchhHhHHHHHHc
Q psy6602         246 SLRAVRQSTIERLFFKE-TIGDIPIQRLLGDMYT  278 (367)
Q Consensus       246 ~Lr~l~~~~~e~l~~~~-~~~~~~~~~Ll~eml~  278 (367)
                      .||+++..+.+++++.+ ..+..++++|+.|||+
T Consensus       234 ~LR~i~~~~~~~l~~~k~~~~~~~~~~Ll~Em~~  267 (269)
T 3u9q_A          234 DLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYK  267 (269)
T ss_dssp             HHHHHHHHHHHHHHHHHHSCSSCCCCHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHHhCcCCCCCcCHHHHHHHh
Confidence            99999999999996554 5778999999999997

>1pzl_A Hepatocyte nuclear factor 4-alpha; transcription; HET: MYR; 2.10A {Homo sapiens} SCOP: a.123.1.1 PDB: 3fs1_A* 1m7w_A* 1lv2_A*

Probab=100.00  E-value=1.1e-33  Score=256.59  Aligned_cols=199  Identities=28%  Similarity=0.443  Sum_probs=174.0

Q ss_pred             hhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCC
Q psy6602          82 LQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPD  161 (367)
Q Consensus        82 ~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~  161 (367)
                      ..+..+++++++++.+.++.+|+|||++|+|..|+.+||++|||++|+++++|+.||++....+..++.++.........
T Consensus        37 ~~~~~~~~~~~~~~~~~l~~~v~wak~~p~F~~L~~~DQ~~LLk~~~~~~~~L~~a~~s~~~~~~~~~~~g~~~~~~~~~  116 (237)
T 1pzl_A           37 AKKIASIADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVLLLGNDYIVPRHCPE  116 (237)
T ss_dssp             TSCBCCHHHHHHHHHHHHHHHHHHHTTCHHHHTSCHHHHHHHHHHSHHHHHHHHHHHHHTTSSSEEECTTSCEEESSCGG
T ss_pred             ccccCCHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCceeecCCcccCccchh
Confidence            35567799999999999999999999999999999999999999999999999999999875444444333333333222


Q ss_pred             ccchHHHHHH-HHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHH
Q psy6602         162 DVRVNNEIKL-IQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRL  240 (367)
Q Consensus       162 ~~~~~~~~~~-~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~L  240 (367)
                      ..+....... +.+++.+|++|++|++||+|||||+||+||++|+++...|+++|+.+.++|++|+..++++++.||++|
T Consensus       117 ~~~~~~~~~~~~~~l~~~l~~L~ld~~E~~~L~ai~l~~~~~~~l~~~~~ve~~q~~~~~~L~~y~~~~~~~~~~Rf~~L  196 (237)
T 1pzl_A          117 LAEMSRVSIRILDELVLPFQELQIDDNEYAYLKAIIFFDPDAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGEL  196 (237)
T ss_dssp             GGGGHHHHHHHHHHTHHHHHHHTCCHHHHHHHHHHHHCCTTCTTCSCHHHHHHHHHHHHHHHHHHHHSSSSCCTTHHHHH
T ss_pred             hhhhHHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHHHHHhcCCChhhHHHHH
Confidence            2234444444 568999999999999999999999999999999999999999999999999999999999899999999


Q ss_pred             HHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHccc
Q psy6602         241 LLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  280 (367)
Q Consensus       241 L~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~  280 (367)
                      +.+++.+|++...+.|.+++.+.++..+++.++.|||..+
T Consensus       197 L~~l~~lr~~~~~~~e~l~~~~~~~~~~~~~l~~em~~~~  236 (237)
T 1pzl_A          197 LLLLPTLQSITWQMIEQIQFIKLFGMAKIDNLLQEMLLGG  236 (237)
T ss_dssp             HTHHHHHHHHHHHHHHHHHHHHHTTCSCCCHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHhhhHHHhCCCcHHHHHHHHHcCC
Confidence            9999999999999999999999999999999999999753

>3up3_A Acedaf-12; ligand binding domain, nematode, steroid binding protein- transcription complex; HET: XCA; 1.25A {Ancylostoma ceylanicum} PDB: 3up0_A*

Probab=100.00  E-value=5.7e-35  Score=265.67  Aligned_cols=189  Identities=14%  Similarity=0.191  Sum_probs=161.8

Q ss_pred             HHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceE---ecCCccccCCCCC--c
Q psy6602          88 AEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLL---INCEKARERLPPD--D  162 (367)
Q Consensus        88 ~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l---~~~~~~~~~~~~~--~  162 (367)
                      .+++++++++.++.+|+|||++|||.+|+.+||++|||++|+|+++++.||++++..+...   +.++..+.+....  .
T Consensus        43 p~~l~~l~~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w~Ell~L~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~  122 (243)
T 3up3_A           43 PADIMNIMDVTMRRFVKMAKRLPAFNDLSQDGKFALLKGGMIEMLTVRGVRRFDSSSGSWTTPTLGESSEVSINMFDQLN  122 (243)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHCHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHEETTTTEECCTTSCTTCCEEGGGGGGSC
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcccCCeeeecccCCCccccHHHHhhhc
Confidence            4579999999999999999999999999999999999999999999999999987666542   2233233322111  1


Q ss_pred             cchHH-HHHHHHHHHHHHHh-cCCCcchhhhhHHHHhcCCCCCCCCCh---hHHHHHHHHHHHHHHHHHHhhC-CCcchH
Q psy6602         163 VRVNN-EIKLIQEILARFRQ-LSPDGSECGCMKAVILFTPETPGLVDA---QPVEMLQDQAQCILGDYVRGRY-SRQPTR  236 (367)
Q Consensus       163 ~~~~~-~~~~~~~~~~~l~~-L~ld~~E~alLkai~L~~pd~~~L~~~---~~v~~~q~~~~~~L~~y~~~~~-~~~~~R  236 (367)
                      .|+.+ .++.+.+++.+|+. |++|++||+|||||+||+|+ +|+++.   ..|+++|++|..+|++||..+| |+++.|
T Consensus       123 ~g~~~~~~~~l~~~~~~~~~~L~ld~~E~alLkAivLfsp~-~gL~~~~~~~~Ve~lQe~~~~aL~~y~~~~~~p~~~~r  201 (243)
T 3up3_A          123 ADVRSEQKMRFLQFFKIFHEDIRSNDLVISMIMLIVLFSPR-DSITDPEDRRIIARHHEQFSALLNRYLESLYGDDAHQL  201 (243)
T ss_dssp             TTTHHHHHHHHHHHHHTSCHHHHTCHHHHHHHHHHHHSCCC-TTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHGGGHHHH
T ss_pred             ccccHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhcCCC-CCCCCcchHHHHHHHHHHHHHHHHHHHHHhcCCChhHH
Confidence            34555 57889999999997 99999999999999999998 999875   8999999999999999999777 788999


Q ss_pred             HHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcc
Q psy6602         237 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM  279 (367)
Q Consensus       237 f~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~  279 (367)
                      |++||++++.||+++. +.|.+++.+. +..++++|+.|||+.
T Consensus       202 f~kLL~~Lp~LR~i~~-~~e~lf~~k~-~~~~~~pLl~E~f~~  242 (243)
T 3up3_A          202 NEQLPTALRMLREISA-SSGMLFLGTV-NTSEAEPLPREFFKV  242 (243)
T ss_dssp             HHHHHHHHHHHHHHHH-TCTTTTTTSC-CGGGSCHHHHTTSCC
T ss_pred             HHHHHHHHHHHHHHHH-HHHHHHhccc-CCCCCCcHHHHHhCC
Confidence            9999999999999999 8888887664 567899999999874

>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=9.4e-34  Score=279.89  Aligned_cols=192  Identities=30%  Similarity=0.595  Sum_probs=169.9

Q ss_pred             HHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccchHHH
Q psy6602          89 EKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNE  168 (367)
Q Consensus        89 ~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~  168 (367)
                      ..+++++++.++.+|+|||+||+|.+|+.+||++|||++|+|+++++.|||++...+..++.++..+........+..+.
T Consensus       271 ~~l~e~a~~~L~~vVeWAK~iP~F~~L~~~DQi~LLK~~w~elliL~~a~rs~~~~~~~ll~~g~~i~~~~~~~~~~~~~  350 (467)
T 3dzy_A          271 TNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAI  350 (467)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHSTTSTTSCHHHHHHHHHHHHHHHHHHHHHHHTSSSTTBCCCSSSCCCBTHHHHTTTCHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhCcchhcCCHHHHHHHHHhHHHHHHHHHHHHHhccCCCceEecCCceechhhhhhhcchHH
Confidence            34899999999999999999999999999999999999999999999999998877776665554443332222234455


Q ss_pred             HHHHH-HHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhhhHh
Q psy6602         169 IKLIQ-EILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSL  247 (367)
Q Consensus       169 ~~~~~-~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~~L  247 (367)
                      ++.+. +++.+|++|++|++||+|||||+||+||++||++...|+++|+++..+|++|+..++++++.||++||++|+.|
T Consensus       351 ~~~il~~lv~~l~~L~ld~~E~~lLkAIvLfnpd~~gL~~~~~Ve~lQe~~~~aL~~Y~~~~~p~~p~Rf~kLLl~Lp~L  430 (467)
T 3dzy_A          351 FDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPAL  430 (467)
T ss_dssp             HHHHHHHTHHHHHHHTCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTHHHHH
T ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCcCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHH
Confidence            55444 99999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhhhhHHHHHHhhhccCCchhHhHHHHHHccc
Q psy6602         248 RAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  280 (367)
Q Consensus       248 r~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~  280 (367)
                      |+++..+.|.+++.++++.++++.|+.|||+..
T Consensus       431 Rsi~~~~~E~l~~~kl~g~v~i~~Ll~EMl~a~  463 (467)
T 3dzy_A          431 RSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEAP  463 (467)
T ss_dssp             HHHHHHHHHTTTTTSTTSCCCCCSHHHHCC---
T ss_pred             HHHHHHHHHHHHHhhccCCccHHHHHHHHHcCC
Confidence            999999999999999999999999999999854

>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=6.9e-33  Score=270.74  Aligned_cols=189  Identities=22%  Similarity=0.297  Sum_probs=162.1

Q ss_pred             HHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCcc-ccCCC--CCccc
Q psy6602          88 AEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKA-RERLP--PDDVR  164 (367)
Q Consensus        88 ~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~-~~~~~--~~~~~  164 (367)
                      +..+...+...++.+|+|||+||||.+|+.+||++|||++|+|+++|++|+.++.  +..++..+.. ..+..  ....+
T Consensus       224 ~~~~~~~~~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w~Ell~L~~a~~~~~--~~~~~~~~~~~~~~~~~~~~~~~  301 (419)
T 3dzy_D          224 FQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNK--DGVLISEGQGFMTREFLKSLRKP  301 (419)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTSTTTTTSCHHHHHHHHHHHHHHHHHHHHGGGBCS--SEEEEGGGTEEEEHHHHHSSSGG
T ss_pred             HHHHHHHHHHHHHHHHHHhccCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcC--CCceeecCcccccHHHHHhhhhh
Confidence            4455666677899999999999999999999999999999999999999966643  4445544432 22111  11223


Q ss_pred             hHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhh
Q psy6602         165 VNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLML  244 (367)
Q Consensus       165 ~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l  244 (367)
                      +.+.++.+++|+.+|++|+||++||+|||||+||+||++||.+...|+++|+++..+|.+|+..+||+++.||++||++|
T Consensus       302 ~~~l~~~i~~f~~~l~~L~ld~~E~alLkAivLf~pD~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~rf~kLLl~L  381 (419)
T 3dzy_D          302 FGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKM  381 (419)
T ss_dssp             GSGGGHHHHHHHHHHHHTCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHH
Confidence            45667889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHhHhhhhhHHHHHHhhh-ccCCchhHhHHHHHHc
Q psy6602         245 PSLRAVRQSTIERLFFKE-TIGDIPIQRLLGDMYT  278 (367)
Q Consensus       245 ~~Lr~l~~~~~e~l~~~~-~~~~~~~~~Ll~eml~  278 (367)
                      +.||+++..+.+.+++.+ ..+..++++|+.|||+
T Consensus       382 p~LR~i~~~~~~~l~~~k~~~~~~~l~~Ll~Em~~  416 (419)
T 3dzy_D          382 TDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYK  416 (419)
T ss_dssp             HHHHHHHHHHHHHHHHHTTSCSCCCCCHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHhhccCCCCCccHHHHHHHH
Confidence            999999999999996654 5678899999999997

>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=99.98  E-value=1.6e-32  Score=248.94  Aligned_cols=188  Identities=15%  Similarity=0.206  Sum_probs=151.4

Q ss_pred             CHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccC----CCCCc
Q psy6602          87 SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARER----LPPDD  162 (367)
Q Consensus        87 ~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~----~~~~~  162 (367)
                      +.++++++++..++.+|+|||++|||.+|+.+||++|||++|+|+++++.|++++...+...+.++..+..    .....
T Consensus        42 ~p~~i~~l~~~~l~~iVefAK~iPgF~~L~~~DQi~LLK~~~~ElliLr~a~~~~~~~~~~~~~~~~~~~~~~~~l~~l~  121 (244)
T 3gyt_A           42 NPTDILNVMDITMRRLVKMAKRLGAFNEISEAGKFSLLKGGMIEMLTIRGVTVFNADKGVWQTPVDGHSQISFNMFDKLR  121 (244)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHTCGGGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETTTTEECCTTSTTCCEEGGGGGGSC
T ss_pred             CHHHHHHHHHHHHHHHHHHHccCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcccCCeEeecCCcccchhHHHHHHhh
Confidence            35579999999999999999999999999999999999999999999999999876555444433211100    00001


Q ss_pred             cch-----HHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCC---ChhHHHHHHHHHHHHHHHHHHhhC-CCc
Q psy6602         163 VRV-----NNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLV---DAQPVEMLQDQAQCILGDYVRGRY-SRQ  233 (367)
Q Consensus       163 ~~~-----~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~---~~~~v~~~q~~~~~~L~~y~~~~~-~~~  233 (367)
                      .+.     .+.++.+.+|...++.   ++.||+|||||+||+||++|+.   ++..|+++|+++..+|++|+..+| |++
T Consensus       122 ~~~~~~~~~~~~~~~~~f~~~l~~---~~~E~alLkAivLfspDr~gL~~~~d~~~Ve~lQe~~~~aL~~y~~~~~~p~~  198 (244)
T 3gyt_A          122 PDIKDTQKKGFLHFFNLLHSDVRK---NDLAIDIIVLMVLFDSKREGLVSQQDKETVEKLHRNYESLLHRYLYSIHKEEA  198 (244)
T ss_dssp             TTTHHHHHHHHHHHHHHSCHHHHT---CHHHHHHHHHHHHSCTTSTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHCSSSH
T ss_pred             hcchhhHHHHHHHHHHHHHHHHHH---hHHHHHHHHHHHHHhccCCCCCccccHHHHHHHHHHHHHHHHHHHHHhCCCCc
Confidence            111     2334555666666665   5679999999999999999999   789999999999999999999888 788


Q ss_pred             chHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcc
Q psy6602         234 PTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM  279 (367)
Q Consensus       234 ~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~  279 (367)
                      +.||++||++++.||+++..+.+ +++ ...+..++++|+.|||+.
T Consensus       199 ~~rf~kLL~~Lp~LR~i~~~~~~-lf~-~~~~~~~~~pLl~Eif~~  242 (244)
T 3gyt_A          199 EQRFASIPKALVALRKVAENAVT-LFL-GAGNTTEAASLPKEFFAT  242 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTTT-TTT-TSCCCTTSCTTGGGTSCC
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHH-HHH-hccCCccCCcHHHHHhCc
Confidence            99999999999999999999999 444 445566899999999874

>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=99.72  E-value=8.5e-18  Score=154.53  Aligned_cols=113  Identities=22%  Similarity=0.254  Sum_probs=104.2

Q ss_pred             HHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCC
Q psy6602         236 RFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSR  315 (367)
Q Consensus       236 Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~  315 (367)
                      -...+..+...++.+..+..|+++++.+.-               .++|++|+.+..+|+++|+++..||.+|+..+||+
T Consensus       155 ~i~~l~~~~~~l~~L~ld~~E~~lLkAivL---------------~npd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~  219 (268)
T 3f5c_B          155 AVQAIKSFFFKCWSLNIDTKEYAYLKGTVL---------------FNPDLPGLQCVKYIEGLQWRTQQILTEHIRMMQRE  219 (268)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHHHHH---------------SCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHSSC
T ss_pred             HHHHHHHHHHHHHHhCCCHHHHHHHHHHHH---------------hcCCCCCCchHHHHHHHHHHHHHHHHHHHHHHCCC
Confidence            345666788889999999999999987752               24789999999999999999999999999999999


Q ss_pred             CcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhcc
Q psy6602         316 QPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  363 (367)
Q Consensus       316 ~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~  363 (367)
                      ++.||++||++||+||+++.+++|++||++++|.+||++||.|||++|
T Consensus       220 ~~~Rf~~LL~~Lp~LR~i~~~~~e~l~~~k~~g~~~i~~Ll~Eml~a~  267 (268)
T 3f5c_B          220 YQIRSAELNSALFLLRFINSDVVTELFFRPIIGAVSMDDMMLEMLCAK  267 (268)
T ss_dssp             SSHHHHHHHHHHHHHTTSCSSHHHHHHTHHHHCSCCHHHHHHHHTTSC
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCchHHHHHHHhCc
Confidence            999999999999999999999999999999999999999999999986

>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=99.71  E-value=1.9e-17  Score=151.50  Aligned_cols=110  Identities=31%  Similarity=0.449  Sum_probs=99.9

Q ss_pred             HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcCh
Q psy6602         240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTR  319 (367)
Q Consensus       240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r  319 (367)
                      +..+...++.+..+..|+++++.+.-               .+||++|+.+..+|+++|+++..||.+|+..+||+++.|
T Consensus       147 l~~~~~~l~~L~ld~~E~~lLkAivL---------------~npd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~R  211 (257)
T 3plz_A          147 AQELVAKLRSLQFDQREFVCLKFLVL---------------FSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEK  211 (257)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHH---------------SCTTCCSCTTHHHHHHHHHHHHHHHHHHHHHHCTTSTTH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHH---------------hcCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCchhH
Confidence            44566778888899999999887752               247899999999999999999999999999999999999


Q ss_pred             HHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhccc
Q psy6602         320 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEK  364 (367)
Q Consensus       320 ~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~~  364 (367)
                      |++||++||+||+++..++|++||++++|.+|+++||.|||++|+
T Consensus       212 f~~LL~~Lp~Lr~l~~~~~e~l~~~~~~g~~~i~~Ll~Eml~~k~  256 (257)
T 3plz_A          212 FGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHAKR  256 (257)
T ss_dssp             HHHHHTHHHHHHHHHHHHHHHHHHHHHTTCSCCCSHHHHHHTC--
T ss_pred             HHHHHHHhHHHHHHHHHHHHHHhhhhhcCCCCHHHHHHHHHhccc
Confidence            999999999999999999999999999999999999999999985

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

Probab=99.70  E-value=2.5e-17  Score=149.44  Aligned_cols=113  Identities=13%  Similarity=0.098  Sum_probs=101.3

Q ss_pred             HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCc
Q psy6602         238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP  317 (367)
Q Consensus       238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~  317 (367)
                      ..+..+...++.+..+..|+++++.+.-               .+||++|+.+..+|+++|+++..||.+|+..+||+++
T Consensus       121 ~~i~~~~~~l~~L~ld~~E~~lLkaivL---------------~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~p~~~  185 (243)
T 3ltx_A          121 EQVAAVSEQMMQNHLHKDELLLLQAMVL---------------VNAEVRRLASYNQIFNMQQSLLDAIVDTAQKYHPDNV  185 (243)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHH---------------HTSCCSCCTTHHHHHHHHHHHHHHHHHHHHHHSTTCS
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHH---------------hCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCChh
Confidence            3445567778888899999998887652               2479999999999999999999999999999999999


Q ss_pred             ChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhcccc
Q psy6602         318 TRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKS  365 (367)
Q Consensus       318 ~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~~~  365 (367)
                      .||++||++||+||+++..++|++|+.+++|.+|+++||.|||++++.
T Consensus       186 ~Rf~~LL~~Lp~Lr~l~~~~~e~l~~~~~~g~~~~~~Ll~Eml~~~~~  233 (243)
T 3ltx_A          186 RHVPAVLLLLTHIRQAGERGIAFFQRLKSEGVVTFCDLLKEMLDAQDF  233 (243)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHHHHHC--
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHhCccc
Confidence            999999999999999999999999999999999999999999998754

>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=99.69  E-value=1.9e-17  Score=150.79  Aligned_cols=114  Identities=30%  Similarity=0.484  Sum_probs=102.4

Q ss_pred             HHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCC
Q psy6602         236 RFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSR  315 (367)
Q Consensus       236 Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~  315 (367)
                      +...+..+...++.+..+..|+++++...-               .+||++|+.+..+|+++|+++..||.+|+..+||+
T Consensus       124 ~i~~l~~~~~~l~~L~ld~~E~~lLkAivL---------------~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~  188 (249)
T 3p0u_A          124 HIWKLQEFCNSMAKLDIDGYEYAYLKAIVL---------------FSPDHPGLTSTSQIEKFQEAAQMELQDYVQATYSE  188 (249)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHHHHH---------------TCSCSTTCCCSHHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHhhCCCHHHHHHHHHHHH---------------hcCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence            344455677888999999999999987752               24789999999999999999999999999999999


Q ss_pred             CcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhccc
Q psy6602         316 QPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEK  364 (367)
Q Consensus       316 ~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~~  364 (367)
                      ++.||++||++||+||+++.+++|++||++++|.+|+++||.|||++++
T Consensus       189 ~~~Rf~~LL~~L~~Lr~i~~~~~e~l~f~~~~g~~~i~~Ll~eml~~~~  237 (249)
T 3p0u_A          189 DTYRLARILVRLPALRLMSSNITEELFFTGLIGNVSIDSIIPYILKMET  237 (249)
T ss_dssp             CSTHHHHHHTTHHHHHTSCHHHHHHHHCCSSHHHHCHHHHHHHHTTC--
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHeeeecccCCCCHHHHHHHHHhCCc
Confidence            9999999999999999999999999999999999999999999999874

>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=99.67  E-value=8.2e-17  Score=153.13  Aligned_cols=110  Identities=31%  Similarity=0.449  Sum_probs=94.0

Q ss_pred             HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcCh
Q psy6602         240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTR  319 (367)
Q Consensus       240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r  319 (367)
                      +..+...++.+..+..|+++++.++-               .++|++||.+..+|+++|+++..||.+|+..+||+++.|
T Consensus       242 l~~l~~~l~~L~ld~~EyalLkAIvL---------------fnpd~~gLs~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~R  306 (352)
T 3tx7_B          242 AQELVAKLRSLQFDQREFVCLKFLVL---------------FSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEK  306 (352)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHH---------------SCSCC------CHHHHHHHHHHHHHHHHHHHHCTTCTTH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHH---------------hcCCCCCCchHHHHHHHHHHHHHHHHHHHHHhCCCccHH
Confidence            44566778888999999999887752               247899999999999999999999999999999999999


Q ss_pred             HHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhccc
Q psy6602         320 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEK  364 (367)
Q Consensus       320 ~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~~  364 (367)
                      |++||++||+||+++.+++|+|||++++|.+++++||.|||++|+
T Consensus       307 F~kLLllLp~LR~ls~~~~e~L~~~kl~g~~~i~~LL~EMl~akr  351 (352)
T 3tx7_B          307 FGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHAKR  351 (352)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSCSSCHHHHHHHC--
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCccHHHHHHHhccC
Confidence            999999999999999999999999999999999999999999985

>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=99.67  E-value=7.1e-17  Score=146.91  Aligned_cols=112  Identities=27%  Similarity=0.383  Sum_probs=97.9

Q ss_pred             HHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCC--
Q psy6602         237 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYS--  314 (367)
Q Consensus       237 f~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p--  314 (367)
                      +..+......++.+..+..|+++++.+.-               .+||++|+.+..+|+++|+++..||.+|+..+||  
T Consensus       131 ~~~l~~~~~~l~~L~ld~~E~~lLkAivL---------------~npd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~  195 (248)
T 3k6p_A          131 GAALLQLVRRLQALRLEREEYVLLKALAL---------------ANSDSVHIEDAEAVEQLREALHEALLEYEAGRAGPG  195 (248)
T ss_dssp             HHHHHHHHHHHHTTTCCHHHHHHHHHHHH---------------HTCCCTTCSCHHHHHHHHHHHHHHHHHHHHTC----
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHH---------------hCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCC
Confidence            34455667778899999999999887652               2478999999999999999999999999999999  


Q ss_pred             --CCcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhcc
Q psy6602         315 --RQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  363 (367)
Q Consensus       315 --~~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~  363 (367)
                        +++.||++||++||+||+++.+++|++||++++|.+|+++||.|||++|
T Consensus       196 ~~~~~~Rf~~LL~~Lp~Lr~l~~~~~e~l~~~k~~g~~~i~~Ll~Eml~~k  246 (248)
T 3k6p_A          196 GGAERRRAGRLLLTLPLLRQTAGKVLAHFYGVKLEGKVPMHKLFLEMLEAM  246 (248)
T ss_dssp             CCCCCH-HHHHHTTHHHHHHHHHHHHHHHHCC-CCCSSCHHHHHHHHHHHH
T ss_pred             ccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCHHHHHHHHHhcc
Confidence              8999999999999999999999999999999999999999999999986

>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=99.67  E-value=1.1e-16  Score=145.21  Aligned_cols=113  Identities=21%  Similarity=0.377  Sum_probs=103.2

Q ss_pred             HHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCC
Q psy6602         237 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQ  316 (367)
Q Consensus       237 f~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~  316 (367)
                      +..+......++.+..+..|+++++.+.-               .++|++|+.+...|+++|+++..||.+|+..+||++
T Consensus       131 ~~~l~~~~~~l~~L~ld~~E~~lLkAivL---------------~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~  195 (244)
T 2e2r_A          131 NNAILQLVKKYKSMKLEKEEFVTLKAIAL---------------ANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMED  195 (244)
T ss_dssp             HHHHHHHHHHHHHHTCCHHHHHHHHHHHH---------------HTCCCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHH---------------hccCCCCCcCHHHHHHHHHHHHHHHHHHHHhcCCCc
Confidence            34555677888999999999999987752               247899999999999999999999999999999999


Q ss_pred             cChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhccc
Q psy6602         317 PTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEK  364 (367)
Q Consensus       317 ~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~~  364 (367)
                      +.||++||++||+||+++.+++|++||.+++|.+|+++|+.|||+++.
T Consensus       196 ~~Rf~~LL~~L~~Lr~~~~~~~e~l~~~~~~~~~~~~~Ll~Eml~~~~  243 (244)
T 2e2r_A          196 PRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPMHKLFLEMLEAKV  243 (244)
T ss_dssp             TTHHHHHHTTHHHHHHHHHHHHHHHHHHHHHCCSCCCHHHHHHHTSCC
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCChHHHHHHHHhCcC
Confidence            999999999999999999999999999999999999999999999874

>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=99.67  E-value=1.4e-16  Score=143.99  Aligned_cols=109  Identities=20%  Similarity=0.226  Sum_probs=98.8

Q ss_pred             HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCc
Q psy6602         238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP  317 (367)
Q Consensus       238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~  317 (367)
                      ..+......++.+..+..|+++++...-               .+||++|+.+...|+++|+++..||.+|+..+||+++
T Consensus       128 ~~i~~~~~~l~~L~ld~~E~~lLkaivL---------------~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~p~~~  192 (236)
T 1fcy_A          128 DLVFAFAGQLLPLEMDDTETGLLSAICL---------------ICGDRMDLEEPEKVDKLQEPLLEALRLYARRRRPSQP  192 (236)
T ss_dssp             HHHHHHHHHHGGGCCCHHHHHHHHHHHH---------------SCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCT
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHh---------------cCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCch
Confidence            3455566778888899999998877642               3478999999999999999999999999999999999


Q ss_pred             ChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHh
Q psy6602         318 TRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT  361 (367)
Q Consensus       318 ~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~  361 (367)
                      .||++||++||+||+++.+++|++||.+++|.+|+++|+.||++
T Consensus       193 ~Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~Eml~  236 (236)
T 1fcy_A          193 YMFPRMLMKITDLRGISTKGAERAITLKMEIPGPMPPLIREMLE  236 (236)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCCCHHHHHHHC
T ss_pred             hHHHHHHHHhHHHHHHHHHHHHHHHHHHccCCCCccHHHHHHhC
Confidence            99999999999999999999999999999999999999999985

>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=99.66  E-value=2.7e-16  Score=144.84  Aligned_cols=109  Identities=18%  Similarity=0.240  Sum_probs=97.8

Q ss_pred             HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCc
Q psy6602         238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP  317 (367)
Q Consensus       238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~  317 (367)
                      ..+..+...++.+..+..|+++++...-               .++|++|+.+..+|+++|+++..||++|+..+||+++
T Consensus       161 ~~l~~~~~~~~~L~ld~~E~alLkAivL---------------f~pd~~gL~~~~~Ve~lqe~~~~aL~~yi~~~~p~~~  225 (273)
T 3vi8_A          161 EPKFDFAMKFNALELDDSDISLFVAAII---------------CCGDRPGLLNVGHIEKMQEGIVHVLRLHLQSNHPDDI  225 (273)
T ss_dssp             HHHHHHHHHHHTTCCCHHHHHHHHHHHH---------------SCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCT
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHH---------------hCCCCCCcccHHHHHHHHHHHHHHHHHHHHHhCCChh
Confidence            4455567778888899999998887642               2589999999999999999999999999999999999


Q ss_pred             ChHHHHHhhchhhhhhchhhHHHHH-HhhhcCCCChHHHHHHHHh
Q psy6602         318 TRFGRLLLMLPSLRAVRQSTIERLF-FKETIGDIPIQRLLGDMYT  361 (367)
Q Consensus       318 ~r~~~lLl~Lp~lr~i~~~~~e~l~-~~~~~g~~~i~~ll~eml~  361 (367)
                      .||+|||++||+||+|+..+.|.++ |++..|.+++++||.|||.
T Consensus       226 ~rF~kLL~~Lp~LR~l~~~~~e~l~~~k~~~~~~~~~~Ll~Emf~  270 (273)
T 3vi8_A          226 FLFPKLLQKMADLRQLVTEHAQLVQIIKKTESDAALHPLLQEIYR  270 (273)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHT
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCccHHHHHHHH
Confidence            9999999999999999999999998 5667899999999999996

>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=99.65  E-value=1.7e-16  Score=144.20  Aligned_cols=111  Identities=26%  Similarity=0.300  Sum_probs=100.5

Q ss_pred             HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcC
Q psy6602         239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPT  318 (367)
Q Consensus       239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~  318 (367)
                      .+..+...++.+..+..|+++++.+.-               .++|++|+.+...|+++|+++..||.+|+..+||+++.
T Consensus       135 ~~~~~~~~~~~L~ld~~E~~lLkAivL---------------~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~  199 (246)
T 1ymt_A          135 RAQELVLQLHALQLDRQEFVCLKFLIL---------------FSLDVKFLNNHSLVKDAQEKANAALLDYTLSHYPHSGD  199 (246)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHH---------------TCSCGGGSSCHHHHHHHHHHHHHHHHHHHHHHCTTSTT
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHh---------------cCCcccccccHHHHHHHHHHHHHHHHHHHHhcCCchhh
Confidence            344567788999999999999987752               24789999999999999999999999999999999999


Q ss_pred             hHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhccc
Q psy6602         319 RFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEK  364 (367)
Q Consensus       319 r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~~  364 (367)
                      ||++||++||+||+++..+.|++||.+++|.+|+++|+.|||++++
T Consensus       200 Rf~~LL~~L~~Lr~~~~~~~e~l~~~~~~~~~~~~~Ll~Eml~~~~  245 (246)
T 1ymt_A          200 KFQQLLLSLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIEMLQAKQ  245 (246)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSCTTCHHHHHHHC--
T ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHhhcccCCCcHHHHHHHHHhCcc
Confidence            9999999999999999999999999999999999999999999885

>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=99.65  E-value=1.7e-16  Score=145.04  Aligned_cols=109  Identities=19%  Similarity=0.298  Sum_probs=95.5

Q ss_pred             HHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHh--hCC
Q psy6602         237 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRG--RYS  314 (367)
Q Consensus       237 f~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~--~~p  314 (367)
                      +..+......++.+..+..|+++++.+.-           |     +|++||.+..+|+++|+++..||++|+..  .||
T Consensus       134 ~~~l~~~~~~l~~L~ld~~E~a~LkAivL-----------f-----sd~~gL~~~~~Ve~lqe~~~~aL~~yi~~~~~~p  197 (257)
T 3v3e_B          134 IDSILAFSRSLHSLLVDVPAFACLSALVL-----------I-----TDRHGLQEPRRVEELQNRIASCLKEHVAAVAGEP  197 (257)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHH-----------S-----SCCTTCSSHHHHHHHHHHHHHHHHHHHHHHHCSC
T ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHH-----------h-----CCCCCCCCHHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence            33455566678888999999999887652           1     38999999999999999999999999974  479


Q ss_pred             CCcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHh
Q psy6602         315 RQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT  361 (367)
Q Consensus       315 ~~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~  361 (367)
                      +++.||+|||++||+||+|+++++|+|||+|++|.+|+++|+.|||.
T Consensus       198 ~~~~rf~kLL~~Lp~LR~l~~~~~e~l~~~k~~~~~~~~~Ll~Emf~  244 (257)
T 3v3e_B          198 QPASCLSRLLGKLPELRTLCTQGLQRIFYLKLEDLVPPPPIIDKIFM  244 (257)
T ss_dssp             C-CHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHHHH
T ss_pred             cHhhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCccHHHHHHHH
Confidence            99999999999999999999999999999999999999999999995

>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=99.65  E-value=2.7e-16  Score=144.50  Aligned_cols=110  Identities=19%  Similarity=0.231  Sum_probs=98.6

Q ss_pred             HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcC
Q psy6602         239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPT  318 (367)
Q Consensus       239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~  318 (367)
                      .+..+...++.+..+..|+++++.+.-               .+||++|+.+..+|+++|+++..||.+|+..+||+++.
T Consensus       153 ~i~~~~~~l~~L~ld~~E~~lLkAIvL---------------~~pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~  217 (266)
T 3kmr_A          153 LVFAFANQLLPLEMDDAETGLLSAICL---------------ICGDRQDLEQPDRVDMLQEPLLEALKVYVRKRRPSRPH  217 (266)
T ss_dssp             HHHHHHHHHGGGCCCHHHHHHHHHHHH---------------SCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTT
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHH---------------hCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCccc
Confidence            344556778888899999998887642               34789999999999999999999999999999999999


Q ss_pred             hHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhcc
Q psy6602         319 RFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  363 (367)
Q Consensus       319 r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~  363 (367)
                      ||++||++||+||+++.+++|++||.+++|.+++++|+.|||+++
T Consensus       218 Rf~~LL~~Lp~Lr~i~~~~~e~l~~~k~~~~~~~~~Ll~Eml~~~  262 (266)
T 3kmr_A          218 MFPKMLMKITDLRSISAKGAERVITLKMEIPGSMPPLIQEMLENS  262 (266)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSSCCCHHHHHHHC--
T ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHhcCCCCcchHHHHHhcCC
Confidence            999999999999999999999999999999999999999999875

>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=99.64  E-value=4.7e-16  Score=141.17  Aligned_cols=111  Identities=41%  Similarity=0.641  Sum_probs=101.5

Q ss_pred             HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcC
Q psy6602         239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPT  318 (367)
Q Consensus       239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~  318 (367)
                      .+..+...++.+..+..|+++++.+.-               .++|++|+.+...|+++|+++..||.+|+..+||+++.
T Consensus       124 ~~~~~~~~~~~L~ld~~E~~lLkaivL---------------~~pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~  188 (244)
T 3cjw_A          124 IFQEQVEKLKALHVDSAEYSCLKAIVL---------------FTSDACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPT  188 (244)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHH---------------SCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTT
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHH---------------hcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCChhh
Confidence            344566788999999999999987752               24789999999999999999999999999999999999


Q ss_pred             hHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhccc
Q psy6602         319 RFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEK  364 (367)
Q Consensus       319 r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~~  364 (367)
                      ||++||++||+||+++.+++|++|+.+++|.+|+++|+.||++++.
T Consensus       189 Rf~~LLl~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~  234 (244)
T 3cjw_A          189 RFGKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDMLLSGS  234 (244)
T ss_dssp             HHHHHHTTHHHHHHSCHHHHHHHHTHHHHTTCCGGGTHHHHHTCCC
T ss_pred             HHHHHHHHhHHHHhhhHHHHHHHHhhcccCCCcHHHHHHHHHhCCC
Confidence            9999999999999999999999999999999999999999999864

>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_A* 3e00_A*

Probab=99.62  E-value=2.8e-16  Score=155.05  Aligned_cols=150  Identities=27%  Similarity=0.427  Sum_probs=117.0

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhC---------CCcc-------------hHHHHHH-HhhhHhHhhhhhHHH
Q psy6602         200 PETPGLVDAQPVEMLQDQAQCILGDYVRGRY---------SRQP-------------TRFGRLL-LMLPSLRAVRQSTIE  256 (367)
Q Consensus       200 pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~---------~~~~-------------~Rf~~LL-~~l~~Lr~l~~~~~e  256 (367)
                      |....|...+++.-++.-+.+.+.-....+.         +++.             .-+-.++ .++..++.+..+..|
T Consensus       292 P~F~~L~~~DQi~LLK~~w~elliL~~a~rs~~~~~~~ll~~g~~i~~~~~~~~~~~~~~~~il~~lv~~l~~L~ld~~E  371 (467)
T 3dzy_A          292 PHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTE  371 (467)
T ss_dssp             TTSTTSCHHHHHHHHHHHHHHHHHHHHHHHTSSSTTBCCCSSSCCCBTHHHHTTTCHHHHHHHHHHTHHHHHHHTCCHHH
T ss_pred             cchhcCCHHHHHHHHHhHHHHHHHHHHHHHhccCCCceEecCCceechhhhhhhcchHHHHHHHHHHHHHHHHhcCCHHH
Confidence            4566677677777777776665543332221         1110             1122344 566778888888888


Q ss_pred             HHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcChHHHHHhhchhhhhhchh
Q psy6602         257 RLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQS  336 (367)
Q Consensus       257 ~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r~~~lLl~Lp~lr~i~~~  336 (367)
                      +++++.++-               .++|++||.+...|+++|++++.+|.+|+..+||+++.||++||++||+||+++.+
T Consensus       372 ~~lLkAIvL---------------fnpd~~gL~~~~~Ve~lQe~~~~aL~~Y~~~~~p~~p~Rf~kLLl~Lp~LRsi~~~  436 (467)
T 3dzy_A          372 LGCLRAIVL---------------FNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLK  436 (467)
T ss_dssp             HHHHHHHHH---------------SCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTHHHHHHHHHHH
T ss_pred             HHHHHHHHH---------------hCcCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHH
Confidence            888877642               24789999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHhhhcCCCChHHHHHHHHhccc
Q psy6602         337 TIERLFFKETIGDIPIQRLLGDMYTMEK  364 (367)
Q Consensus       337 ~~e~l~~~~~~g~~~i~~ll~eml~~~~  364 (367)
                      ++|+|||++++|.+||+.||.|||++.+
T Consensus       437 ~~E~l~~~kl~g~v~i~~Ll~EMl~a~~  464 (467)
T 3dzy_A          437 CLEHLFFFKLIGDTPIDTFLMEMLEAPH  464 (467)
T ss_dssp             HHHTTTTTSTTSCCCCCSHHHHCC----
T ss_pred             HHHHHHHhhccCCccHHHHHHHHHcCCC
Confidence            9999999999999999999999999864

>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=99.62  E-value=8.3e-16  Score=141.15  Aligned_cols=109  Identities=29%  Similarity=0.424  Sum_probs=100.8

Q ss_pred             HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcCh
Q psy6602         240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTR  319 (367)
Q Consensus       240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r  319 (367)
                      +..+...++.+..+..|+++++.+.-               .++|++|+.+...|+++|+++..+|.+|+..+||+++.|
T Consensus       147 ~~~~~~~~~~L~ld~~E~~lLkAivL---------------~npd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~R  211 (264)
T 1g2n_A          147 LSELSLKMRTLRVDQAEYVALKAIIL---------------LNPDVKGLKNRQEVEVLREKMFLCLDEYCRRSRSSEEGR  211 (264)
T ss_dssp             HHHTHHHHHHTTCCHHHHHHHHHHHH---------------SCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHSTTCTTH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHH---------------hCCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCHhhH
Confidence            44577788999999999999987752               247899999999999999999999999999999999999


Q ss_pred             HHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhcc
Q psy6602         320 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  363 (367)
Q Consensus       320 ~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~  363 (367)
                      |++||++||+||+++..++|++||.+++|.+++++|+.|||+++
T Consensus       212 f~~LL~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~Eml~~~  255 (264)
T 1g2n_A          212 FAALLLRLPALRSISLKSFEHLFFFHLVADTSIAGYIRDALRNH  255 (264)
T ss_dssp             HHHHHTHHHHHHHHHHHHHHHHHHTTCBCTTTHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCChHHHHHHHHhCC
Confidence            99999999999999999999999999999999999999999876

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

Probab=99.62  E-value=1.4e-15  Score=140.83  Aligned_cols=108  Identities=20%  Similarity=0.294  Sum_probs=100.4

Q ss_pred             HhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcChHH
Q psy6602         242 LMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFG  321 (367)
Q Consensus       242 ~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r~~  321 (367)
                      .+...++.+..+..|+++++.+.-               .+||++|+.+...|+++|+++..||.+|+..+||+++.||+
T Consensus       163 ~~~~~~~~L~ld~~E~~lLkAivL---------------~npd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~p~~~~Rf~  227 (279)
T 1hg4_A          163 ELSVKMKRLNLDRRELSCLKAIIL---------------YNPDIRGIKSRAEIEMCREKVYACLDEHCRLEHPGDDGRFA  227 (279)
T ss_dssp             HTHHHHHHHTCCHHHHHHHHHHHH---------------SCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHH
T ss_pred             HHHHHHHHhcCCHHHHHHHHHHHH---------------cCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCChhhHHH
Confidence            467788999999999999987752               24789999999999999999999999999999999999999


Q ss_pred             HHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhccc
Q psy6602         322 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEK  364 (367)
Q Consensus       322 ~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~~  364 (367)
                      +||++||+||+++..+.|++||.+++|.+++++|+.|||+++.
T Consensus       228 ~LL~~L~~Lr~~~~~~~e~l~~~~~~g~~~~~~Ll~Eml~~~~  270 (279)
T 1hg4_A          228 QLLLRLPALRSISLKCQDHLFLFRITSDRPLEELFLEQLEAPP  270 (279)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCBCSSCHHHHHHHHHTSCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhCCCcHHHHHHHHHhCCC
Confidence            9999999999999999999999999999999999999999874

>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=99.61  E-value=6.9e-16  Score=141.88  Aligned_cols=110  Identities=17%  Similarity=0.259  Sum_probs=98.7

Q ss_pred             HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcC
Q psy6602         239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPT  318 (367)
Q Consensus       239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~  318 (367)
                      .+..+...++.+..+..|+++++.+.-               .+||++|+.+..+|+++|+++..||.+|+..+||+++.
T Consensus       155 ~i~~~~~~l~~L~ld~~E~~lLkAivL---------------~~pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~  219 (267)
T 3ilz_A          155 AIFELGKSLSAFNLDDTEVALLQAVLL---------------MSTDRSGLLXVDKIEKSQEAYLLAFEHYVNHRKHNIPH  219 (267)
T ss_dssp             HHHHHHHHHGGGCCCHHHHHHHHHHHH---------------SCCCSSSCSCHHHHHHHHHHHHHHHHHHHHHHTCSSTT
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHh---------------cCCCCCCCchHHHHHHHHHHHHHHHHHHHHHhCCChhh
Confidence            344566778888889999998887642               24789999999999999999999999999999999999


Q ss_pred             hHHHHHhhchhhhhhchhhHHHHHHhhhcCCCCh-HHHHHHHHhcc
Q psy6602         319 RFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI-QRLLGDMYTME  363 (367)
Q Consensus       319 r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i-~~ll~eml~~~  363 (367)
                      ||++||++||+||+++..++|++||.+++|.+++ ++|+.|||++.
T Consensus       220 Rf~~LL~~Lp~Lr~l~~~~~e~l~~~k~~~~~~~~~~Ll~Em~~~~  265 (267)
T 3ilz_A          220 FWPKLLMKVTDLRMIGAXHASRFLHMKVEXPTELFPPLFLEVFEDQ  265 (267)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHC-CCSSCGGGSCHHHHHHTCCS
T ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHhcCCccCCCcHHHHHhcCC
Confidence            9999999999999999999999999999999998 99999999875

>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=99.61  E-value=9.4e-16  Score=143.53  Aligned_cols=113  Identities=17%  Similarity=0.206  Sum_probs=102.2

Q ss_pred             HHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCC
Q psy6602         237 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQ  316 (367)
Q Consensus       237 f~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~  316 (367)
                      +..+..+...++.+..+..|+++++.++-               .++|++||.+...|+++|+++..||.+|+..+||++
T Consensus       154 ~~~i~~~~~~l~~L~ld~~E~~lLkAivL---------------~~pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~  218 (303)
T 1xdk_B          154 TDLVFTFANQLLPLEMDDTETGLLSAICL---------------ICGDRQDLEEPTKVDKLQEPLLEALKIYIRKRRPSK  218 (303)
T ss_dssp             HHHHHHHHHHHGGGCCCHHHHHHHHHHHH---------------SCSCSSSCSSHHHHHHHTHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHH---------------hCCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCc
Confidence            34455567788899999999999887642               247899999999999999999999999999999999


Q ss_pred             cChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhccc
Q psy6602         317 PTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEK  364 (367)
Q Consensus       317 ~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~~  364 (367)
                      +.||++||++||+||+++..++|++||.+++|.+++++||.|||+++.
T Consensus       219 ~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~Eml~~~~  266 (303)
T 1xdk_B          219 PHMFPKILMKITDLRSISAKGAERVITLKMEIPGSMPPLIQEMLENSE  266 (303)
T ss_dssp             TTHHHHHHTHHHHHHHHHHHHHHHHHHHTTTCSSCCCHHHHHHHCCCC
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCccHHHHHHHcCCC
Confidence            999999999999999999999999999999999999999999999764

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

Probab=99.61  E-value=5e-16  Score=140.19  Aligned_cols=108  Identities=30%  Similarity=0.516  Sum_probs=99.1

Q ss_pred             HhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcChHH
Q psy6602         242 LMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFG  321 (367)
Q Consensus       242 ~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r~~  321 (367)
                      .+...++.+..+..|+++++...-               .+||++|+.+...|+++|+++..+|.+|+..+||+++.||+
T Consensus       126 ~~~~~l~~L~ld~~E~~lLkaivL---------------~~pd~~gL~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~  190 (235)
T 2nxx_A          126 ELVNKMKEMKMDKTELGCLRAIIL---------------YNPDVRGIKSVQEVEMLREKIYGVLEEYTRTTHPNEPGRFA  190 (235)
T ss_dssp             HTHHHHHHHTCCHHHHHHHHHHHH---------------CCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHH---------------hcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCChhhHHH
Confidence            467788999999999999987752               24789999999999999999999999999999999999999


Q ss_pred             HHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhccc
Q psy6602         322 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEK  364 (367)
Q Consensus       322 ~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~~  364 (367)
                      +||++||+||+++..++|++||.+++|.+|+++|+.|||+++.
T Consensus       191 ~LL~~L~~Lr~~~~~~~e~l~~~~~~g~~~~~~Ll~eml~~~~  233 (235)
T 2nxx_A          191 KLLLRLPALRSIGLKCLEHLFFFKLIGDVPIDTFLMEMLEGTT  233 (235)
T ss_dssp             HHHTHHHHHHHHHHTCCSCTTTTSSSSCCCHHHHHHHHTTC--
T ss_pred             HHHHHhHHHHHHHHHHHHHHHhhcccCCCcHHHHHHHHHhCCC
Confidence            9999999999999999999999999999999999999999874

>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=99.60  E-value=1.8e-15  Score=136.26  Aligned_cols=111  Identities=19%  Similarity=0.242  Sum_probs=99.7

Q ss_pred             HHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCC
Q psy6602         237 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQ  316 (367)
Q Consensus       237 f~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~  316 (367)
                      ...+..+...++.+..+..|+++++.+.-               .+||++|+.+...|+++|+++..||.+|+..+||++
T Consensus       122 ~~~i~~~~~~l~~L~ld~~E~~lLkaivL---------------~~pd~~gL~~~~~v~~~q~~~~~aL~~y~~~~~~~~  186 (232)
T 1osh_A          122 ITPMFSFYKSIGELKMTQEEYALLTAIVI---------------LSPDRQYIKDREAVEKLQEPLLDVLQKLCKIHQPEN  186 (232)
T ss_dssp             HHHHHHHHHHHHTTCCCHHHHHHHHHHHH---------------TCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHH---------------hCCCCCCCCChHHHHHHHHHHHHHHHHHHHHHCCCc
Confidence            44555567889999999999999887642               247899999999999999999999999999999999


Q ss_pred             cChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhcc
Q psy6602         317 PTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  363 (367)
Q Consensus       317 ~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~  363 (367)
                      +.||++||++||+||+++..+.|.+||.++ |.+++++|+.|||+.+
T Consensus       187 ~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~k~-~~~~~~~Ll~Em~~~~  232 (232)
T 1osh_A          187 PQHFACLLGRLTELRTFNHHHAEMLMSWRV-NDHKFTPLLCEIWDVQ  232 (232)
T ss_dssp             TTHHHHHHHHHHHHHTHHHHHHHHHHHHHH-TTCCCCHHHHHHHTC-
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCCChHHHHHhcCC
Confidence            999999999999999999999999999997 7999999999999864

>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=99.60  E-value=1.5e-15  Score=139.74  Aligned_cols=109  Identities=22%  Similarity=0.311  Sum_probs=97.4

Q ss_pred             HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcC
Q psy6602         239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPT  318 (367)
Q Consensus       239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~  318 (367)
                      .+..+...++.+..+..|+++++.+.-               .+||++|+.+...|+++|+++..||.+|+..+||+++.
T Consensus       159 ~l~~~~~~l~~L~ld~~E~alLkAIvL---------------fnpd~~gL~~~~~Ve~lqe~~~~aL~~y~~~~~p~~~~  223 (269)
T 3u9q_A          159 PKFEFAVKFNALELDDSDLAIFIAVII---------------LSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQ  223 (269)
T ss_dssp             HHHHHHHHHHTTCCCHHHHHHHHHHHH---------------TCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTSTT
T ss_pred             HHHHHHHHHHhhcCCHHHHHHHHHHHH---------------hCCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCChhh
Confidence            345566788889999999999887752               24789999999999999999999999999999999999


Q ss_pred             hHHHHHhhchhhhhhchhhHHHHH-HhhhcCCCChHHHHHHHHhc
Q psy6602         319 RFGRLLLMLPSLRAVRQSTIERLF-FKETIGDIPIQRLLGDMYTM  362 (367)
Q Consensus       319 r~~~lLl~Lp~lr~i~~~~~e~l~-~~~~~g~~~i~~ll~eml~~  362 (367)
                      ||++||++||+||+++..+++.++ |++..|++|+++||.|||+.
T Consensus       224 Rf~kLL~~Lp~LR~i~~~~~~~l~~~k~~~~~~~~~~Ll~Em~~~  268 (269)
T 3u9q_A          224 LFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKD  268 (269)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHSCSSCCCCHHHHHHHSC
T ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHhCcCCCCCcCHHHHHHHhh
Confidence            999999999999999999999996 55678999999999999963

>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=99.60  E-value=1.4e-15  Score=137.70  Aligned_cols=109  Identities=29%  Similarity=0.524  Sum_probs=99.6

Q ss_pred             HhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcChHH
Q psy6602         242 LMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFG  321 (367)
Q Consensus       242 ~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r~~  321 (367)
                      .+...++.+..+..|+++++..+-               .++|++|+.+..+|+++|+++..+|.+|+..+||+++.||+
T Consensus       130 ~~~~~l~~L~ld~~E~~~Lkai~l---------------~~pd~~gl~~~~~ve~~q~~~~~~L~~y~~~~~~~~~~Rf~  194 (240)
T 2p1t_A          130 ELVSKMRDMQMDKTELGCLRAIVL---------------FNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFA  194 (240)
T ss_dssp             HTHHHHHHTTCCHHHHHHHHHHHH---------------SCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHH
T ss_pred             HHHHHHHhhCCCHHHHHHHHHHHH---------------hcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCchhHHH
Confidence            466788999999999999887752               24789999999999999999999999999999999999999


Q ss_pred             HHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhcccc
Q psy6602         322 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKS  365 (367)
Q Consensus       322 ~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~~~  365 (367)
                      +||++||+||+++.+++|++|+.+++|.+|+++|+.|||+++..
T Consensus       195 ~LL~~l~~Lr~~~~~~~e~l~~~~~~~~~~~~~ll~eml~~~~~  238 (240)
T 2p1t_A          195 KLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEAPHQ  238 (240)
T ss_dssp             HHHTTHHHHHHHHHHHHHHHHHHHHHCCSCCCHHHHHHTSCC--
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCcCCCCchHHHHHHHHcCCCC
Confidence            99999999999999999999999999999999999999998753

>3dzy_D Peroxisome proliferator-activated receptor gamma; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_D* 3e00_D* 2env_A

Probab=99.60  E-value=1.4e-15  Score=148.36  Aligned_cols=148  Identities=20%  Similarity=0.248  Sum_probs=113.0

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCC-Cc------c---h-------------HHHHHHHhhhHhHhhhhhHHH
Q psy6602         200 PETPGLVDAQPVEMLQDQAQCILGDYVRGRYS-RQ------P---T-------------RFGRLLLMLPSLRAVRQSTIE  256 (367)
Q Consensus       200 pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~-~~------~---~-------------Rf~~LL~~l~~Lr~l~~~~~e  256 (367)
                      |....|...++|.-++.-..+.+.-.+...+. ++      .   .             -+..+..+...++.+..+..|
T Consensus       246 P~F~~L~~~DQi~LLk~~w~Ell~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~f~~~l~~L~ld~~E  325 (419)
T 3dzy_D          246 PGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSD  325 (419)
T ss_dssp             TTTTTSCHHHHHHHHHHHHHHHHHHHHGGGBCSSEEEEGGGTEEEEHHHHHSSSGGGSGGGHHHHHHHHHHHHTCCCHHH
T ss_pred             CCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCceeecCcccccHHHHHhhhhhHHHHHHHHHHHHHHHHHhCCCHHH
Confidence            44455555777777777666665543333221 11      0   0             112233455667777777777


Q ss_pred             HHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcChHHHHHhhchhhhhhchh
Q psy6602         257 RLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQS  336 (367)
Q Consensus       257 ~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r~~~lLl~Lp~lr~i~~~  336 (367)
                      +.+++.+.-               .++|++||++..+|+++|++++.||++|+..+||+++.||+|||++||+||+|+..
T Consensus       326 ~alLkAivL---------------f~pD~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~rf~kLLl~Lp~LR~i~~~  390 (419)
T 3dzy_D          326 LAIFIAVII---------------LSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTE  390 (419)
T ss_dssp             HHHHHHHHH---------------SCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHH---------------hCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHHHHHHHHHHH
Confidence            777776542               25899999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHH-HhhhcCCCChHHHHHHHHhc
Q psy6602         337 TIERLF-FKETIGDIPIQRLLGDMYTM  362 (367)
Q Consensus       337 ~~e~l~-~~~~~g~~~i~~ll~eml~~  362 (367)
                      +++.++ |++..|++++++||.|||+.
T Consensus       391 ~~~~l~~~k~~~~~~~l~~Ll~Em~~d  417 (419)
T 3dzy_D          391 HVQLLQVIKKTETDMSLHPLLQEIYKD  417 (419)
T ss_dssp             HHHHHHHHTTSCSCCCCCHHHHHHHTT
T ss_pred             HHHHHHHhhccCCCCCccHHHHHHHHh
Confidence            999995 55678999999999999974

>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=99.58  E-value=1.1e-15  Score=138.45  Aligned_cols=111  Identities=21%  Similarity=0.224  Sum_probs=95.1

Q ss_pred             HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCC-------CchhhhhHHHHHHHHHHHHHh
Q psy6602         239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVD-------AQPVEMLQDQAQCILGDYVRG  311 (367)
Q Consensus       239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~-------~~~ve~lq~~~~~aL~~~~~~  311 (367)
                      .+......++.+..+..|+++++...-               .+||++|+.+       ..+|+.+|+++..||.+|+..
T Consensus       119 ~l~~~~~~l~~L~ld~~E~~lLkAivL---------------~~pd~~gLs~~~~~~~~~~~v~~~q~~~~~aL~~y~~~  183 (240)
T 3oll_A          119 MLLATTSRFRELKLQHKEYLCVKAMIL---------------LNSSMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAK  183 (240)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHH---------------HCSCCCCCCCCC--CHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHH---------------cCCCCCCcccccchhhHHHHHHHHHHHHHHHHHHHHhc
Confidence            344566778888999999999887642               2367777765       346889999999999999987


Q ss_pred             h---CCCCcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhccc
Q psy6602         312 R---YSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEK  364 (367)
Q Consensus       312 ~---~p~~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~~  364 (367)
                      +   ||+++.||++||++||+||+++.+++|++||++++|.+|+++||.|||++|+
T Consensus       184 ~~~~~~~~~~Rf~~LL~~Lp~Lr~l~~~~~e~l~~~~~~g~~~~~~Ll~eml~~~~  239 (240)
T 3oll_A          184 SGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEMLNAHV  239 (240)
T ss_dssp             TCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSCCCHHHHHHHHHC-
T ss_pred             cCCCCcchhhHHHHHHHHhHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHhccc
Confidence            6   4778999999999999999999999999999999999999999999999985

>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=99.58  E-value=3.8e-15  Score=138.05  Aligned_cols=111  Identities=20%  Similarity=0.243  Sum_probs=99.5

Q ss_pred             HHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCC
Q psy6602         237 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQ  316 (367)
Q Consensus       237 f~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~  316 (367)
                      ...+..+...++.+..+..|+++++.++-               .+||++||.+...|+++|+++..||.+|+..+||++
T Consensus       172 ~~~l~~~~~~l~~L~ld~~E~~lLkAIvL---------------~npd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~  236 (283)
T 3ipq_A          172 INPIFEFSRAMNELQLNDAEFALLIAISI---------------FSADRPNVQDQLQVERLQHTYVEALHAYVSIHHPHD  236 (283)
T ss_dssp             HHHHHHHHHHHHHHTCCHHHHHHHHHHHH---------------TCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHSTTC
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHH---------------HCCCCCCCCcHHHHHHHHHHHHHHHHHHHHHhCCCh
Confidence            34455677788899999999999887752               247899999999999999999999999999999999


Q ss_pred             cChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhcc
Q psy6602         317 PTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  363 (367)
Q Consensus       317 ~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~  363 (367)
                      +.||++||++||+||+++.+++|++||.+++|. ++++|+.|||+.+
T Consensus       237 ~~Rf~~LL~~Lp~Lr~l~~~~~e~l~~~k~~~~-~~~~Ll~Em~~~~  282 (283)
T 3ipq_A          237 RLMFPRMLMKLVSLRTLSSVHSEQVFALRLQDK-KLPPLLSEIWDVH  282 (283)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC-CCCHHHHHHHCC-
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCC-CCChHHHHHhcCC
Confidence            999999999999999999999999999999975 9999999999865

>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=99.57  E-value=1.9e-15  Score=137.88  Aligned_cols=110  Identities=17%  Similarity=0.267  Sum_probs=99.1

Q ss_pred             HHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCC--
Q psy6602         237 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYS--  314 (367)
Q Consensus       237 f~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p--  314 (367)
                      +..+..+...++.+..+..|+++++.+.-               .+||++|+.+...|+++|+++..||.+|+..+||  
T Consensus       141 ~~~l~~~~~~l~~L~ld~~E~~lLkAivL---------------~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~  205 (254)
T 3b0t_A          141 IEPLIKFQVGLKKLNLHEEEHVLLMAICI---------------VSPDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPP  205 (254)
T ss_dssp             HHHHHHHHHHHHTTCCCHHHHHHHHHHHH---------------SCSCSTTCSCHHHHHHHHHHHHHHHHHHHHHHCCTT
T ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHHH---------------hCCCccCCcCHHHHHHHHHHHHHHHHHHHHHhCCCC
Confidence            34455677888999999999999887752               3478999999999999999999999999999999  


Q ss_pred             CCcChHHHHHhhchhhhhhchhhHHHHHHhhh--cCCCChHHHHHHHHh
Q psy6602         315 RQPTRFGRLLLMLPSLRAVRQSTIERLFFKET--IGDIPIQRLLGDMYT  361 (367)
Q Consensus       315 ~~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~--~g~~~i~~ll~eml~  361 (367)
                      +++.||++||++||+||+++..++|++||.++  .|.+++++|+.|||+
T Consensus       206 ~~~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~~~Ll~Em~~  254 (254)
T 3b0t_A          206 GSHLLYAKMIQKLADLRSLNEEHSKQYRCLSFQPECSMKLTPLVLEVFG  254 (254)
T ss_dssp             TTTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTTHHHHSCHHHHHHHC
T ss_pred             CchhHHHHHHHHhHHHHHHHHHHHHHHHHHhccccCCCCCChHHHHhcC
Confidence            78999999999999999999999999999999  778899999999984

>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=2.9e-15  Score=135.83  Aligned_cols=110  Identities=23%  Similarity=0.292  Sum_probs=98.3

Q ss_pred             HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCC--C
Q psy6602         238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYS--R  315 (367)
Q Consensus       238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p--~  315 (367)
                      ..+......++.+..+..|+++++...-           |    + |++|+.+...|+++|+++..||.+|+..+||  +
T Consensus       130 ~~l~~~~~~l~~L~ld~~E~~lLkAIvL-----------f----n-d~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~  193 (244)
T 1pdu_A          130 NDIMEFSRSLHNLEIDISAFACLCALTL-----------I----T-ERHGLREPKKVEQLQMKIIGSLRDHVTYNAEAQK  193 (244)
T ss_dssp             HHHHHHHHHHHHHCCCHHHHHHHHHHHH-----------S----S-CCTTCSCHHHHHHHHHHHHHHHHHHHHHCHHHHT
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHH-----------h----C-CCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCcc
Confidence            3455677788899999999999887651           1    1 6899999999999999999999999999987  5


Q ss_pred             CcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhcc
Q psy6602         316 QPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  363 (367)
Q Consensus       316 ~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~  363 (367)
                      ++.||++||++||+||+++.+++|++||.+++|.+|+++|+.||+.+.
T Consensus       194 ~~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~g~~~~~~Ll~Eml~~~  241 (244)
T 1pdu_A          194 KQHYFSRLLGKLPELRSLSVQGLQRIFYLKLEDLVPAPALIENMFVTT  241 (244)
T ss_dssp             STTHHHHHHTHHHHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHTTTCC
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCchHHHHHHHhCC
Confidence            889999999999999999999999999999999999999999999763

>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=99.56  E-value=4.1e-15  Score=139.02  Aligned_cols=112  Identities=17%  Similarity=0.253  Sum_probs=101.5

Q ss_pred             HHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCC
Q psy6602         237 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQ  316 (367)
Q Consensus       237 f~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~  316 (367)
                      +..+..+...++.+..+..|+++++.++-               .+||++||.+...|+++|+++..||.+|+..+||++
T Consensus       187 ~~~l~~~~~~l~~L~ld~~E~alLkAIvL---------------fnpd~~gL~~~~~Ve~lqe~~~~aL~~y~~~~~p~~  251 (302)
T 2hc4_A          187 LEPLVKFQVGLKKLKLHEEEHVLLMAICL---------------LSPDRPGVQDHVRIEALQDRLCDVLQAYIRIQHPGG  251 (302)
T ss_dssp             HHHHHHHHHHHHTTCCCHHHHHHHHHHHH---------------TCSCSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHHH---------------hCCCCCCCcCHHHHHHHHHHHHHHHHHHHHHHCCCh
Confidence            34555677789999999999999987752               247899999999999999999999999999999999


Q ss_pred             cChHHHHHhhchhhhhhchhhHHHHHHhhhcCC--CChHHHHHHHHhcc
Q psy6602         317 PTRFGRLLLMLPSLRAVRQSTIERLFFKETIGD--IPIQRLLGDMYTME  363 (367)
Q Consensus       317 ~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~--~~i~~ll~eml~~~  363 (367)
                      +.||++||++||+||+++..++|++|+.+++|.  +++++|+.|||+++
T Consensus       252 ~~RF~~LLl~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~~~Ll~Em~~~~  300 (302)
T 2hc4_A          252 RLLYAKMIQKLADLRSLNEEHSKQYRSLSFQPEHSMQLTPLVLEVFGSE  300 (302)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHTTSCHHHHHHSSSC
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCccHHHHHHHcCC
Confidence            999999999999999999999999999999875  89999999999876

>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=99.55  E-value=5e-15  Score=138.96  Aligned_cols=108  Identities=19%  Similarity=0.298  Sum_probs=97.8

Q ss_pred             HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCC--CCc
Q psy6602         240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYS--RQP  317 (367)
Q Consensus       240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p--~~~  317 (367)
                      +..+...++.+..+..|+++++.++-               .+||++||.+...|+++|+++..||.+|+..+||  +++
T Consensus       205 i~~~~~~l~~L~ld~~E~alLkAIvL---------------fnpd~~gL~~~~~Ve~lqe~~~~aL~~y~~~~~p~~~~~  269 (316)
T 1nrl_A          205 MLKFHYMLKKLQLHEEEYVLMQAISL---------------FSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHR  269 (316)
T ss_dssp             HHHHHHHHHHTCCCHHHHHHHHHHHH---------------TCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCCSGGGT
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHH---------------hCCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCCchh
Confidence            34456778888899999998887652               3478999999999999999999999999999999  789


Q ss_pred             ChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhcc
Q psy6602         318 TRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  363 (367)
Q Consensus       318 ~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~  363 (367)
                      .||++||++||+||+++..++|++||.+.+|. ++++||.|||+++
T Consensus       270 ~RF~kLLl~Lp~LR~l~~~~~e~l~~~k~~~~-~i~~Ll~Eml~~~  314 (316)
T 1nrl_A          270 FLFLKIMAMLTELRSINAQHTQRLLRIQDIHP-FATPLMQELFGIT  314 (316)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHHHHHHHHHSC-CCCHHHHHHTTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-chHHHHHHHHcCC
Confidence            99999999999999999999999999999988 9999999999876

>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=99.55  E-value=2.9e-15  Score=138.80  Aligned_cols=109  Identities=29%  Similarity=0.524  Sum_probs=99.8

Q ss_pred             HhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcChHH
Q psy6602         242 LMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFG  321 (367)
Q Consensus       242 ~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r~~  321 (367)
                      .+...++.+..+..|+++++.++-               .++|++|+.+..+|+.+|+++..+|.+|+..+||+++.||+
T Consensus       172 ~~~~~l~~L~ld~~E~~lLkaivL---------------~~pd~~gLs~~~~v~~lq~~~~~~L~~y~~~~~~~~~~Rf~  236 (282)
T 1lbd_A          172 ELVSKMRDMQMDKTELGCLRAIVL---------------FNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFA  236 (282)
T ss_dssp             HHHHHTTTTCCCHHHHHHHHHHHH---------------SCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHSCCSTTTHH
T ss_pred             HHHHHHHhhcCCHHHHHHHHHHHH---------------cCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCchhHHH
Confidence            366778888999999998887642               34789999999999999999999999999999999999999


Q ss_pred             HHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhcccc
Q psy6602         322 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKS  365 (367)
Q Consensus       322 ~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~~~  365 (367)
                      +||++||+||+++.+++|++||.+++|.+|+++||.|||+++..
T Consensus       237 ~LL~~L~~Lr~~~~~~~e~l~~~~~~~~~~i~~ll~eml~~~~~  280 (282)
T 1lbd_A          237 KLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEAPHQ  280 (282)
T ss_dssp             HHHTTHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHTSCCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHcCCCC
Confidence            99999999999999999999999999999999999999998753

>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=99.55  E-value=6.1e-15  Score=133.79  Aligned_cols=108  Identities=15%  Similarity=0.183  Sum_probs=97.3

Q ss_pred             HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCc
Q psy6602         238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP  317 (367)
Q Consensus       238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~  317 (367)
                      ..+..+...++.+..+..|+++++...-               .+||++|+.+...|+++|+++..||.+|+..+||+++
T Consensus       133 ~~i~~~~~~l~~L~ld~~E~~lLkAivL---------------~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~  197 (244)
T 1nq7_A          133 NEAFDFAKNLCSLQLTEEEIALFSSAVL---------------ISPDRAWLLEPRKVQKLQEKIYFALQHVIQKNHLDDE  197 (244)
T ss_dssp             HHHHHHHHHHHTTCCCHHHHHHHHHHHH---------------SCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCSCTT
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHH---------------cCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcc
Confidence            3445567788889999999999887752               3478999999999999999999999999999999998


Q ss_pred             ChHHHHHhhchhhhhhchhhHHHHHHhhhcCCC----ChHHHHHHHHh
Q psy6602         318 TRFGRLLLMLPSLRAVRQSTIERLFFKETIGDI----PIQRLLGDMYT  361 (367)
Q Consensus       318 ~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~----~i~~ll~eml~  361 (367)
                       ||++||++||+||+++..+.|++||.+++|..    ++++|+.|||+
T Consensus       198 -Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~~~~~Ll~Em~~  244 (244)
T 1nq7_A          198 -TLAKLIAKIPTITAVCNLHGEKLQVFKQSHPDIVNTLFPPLYKELFN  244 (244)
T ss_dssp             -HHHHHHHTHHHHHHHHHHHHHHHHHHHHHCHHHHHHTSCHHHHHHHC
T ss_pred             -HHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcccccCCCChHHHHhhC
Confidence             99999999999999999999999999999976    89999999984

>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=99.54  E-value=7.2e-15  Score=136.75  Aligned_cols=113  Identities=19%  Similarity=0.271  Sum_probs=100.7

Q ss_pred             HHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCC--
Q psy6602         237 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYS--  314 (367)
Q Consensus       237 f~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p--  314 (367)
                      +..+..+...++.+..+..|+++++.++-               .+||++||.+...|+++|+++..||.+|+..+||  
T Consensus       144 ~~~l~~~~~~l~~L~ld~~E~~lLkAIvL---------------fnpd~~gL~~~~~Ve~lq~~~~~aL~~y~~~~~p~~  208 (292)
T 2o4j_A          144 IEPLIKFQVGLKKLNLHEEEHVLLMAICI---------------VSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPP  208 (292)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHH---------------SCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHSCTT
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHH---------------hCCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCC
Confidence            34455677788999999999999887752               2478999999999999999999999999999999  


Q ss_pred             CCcChHHHHHhhchhhhhhchhhHHHHHHhhhc--CCCChHHHHHHHHhccc
Q psy6602         315 RQPTRFGRLLLMLPSLRAVRQSTIERLFFKETI--GDIPIQRLLGDMYTMEK  364 (367)
Q Consensus       315 ~~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~--g~~~i~~ll~eml~~~~  364 (367)
                      +++.||++||++||+||+++..++|++|+.+++  |.+++++|+.|||+++.
T Consensus       209 ~~~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~~~Ll~Eml~~~~  260 (292)
T 2o4j_A          209 GSHQLYAKMIQKLADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFGNEI  260 (292)
T ss_dssp             TTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHTTSCHHHHHHHCCC-
T ss_pred             chhhHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCCCChhHHHHHHHcCCc
Confidence            889999999999999999999999999999995  68899999999998763

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

Probab=99.54  E-value=2.9e-15  Score=139.69  Aligned_cols=114  Identities=20%  Similarity=0.264  Sum_probs=94.6

Q ss_pred             HHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCC--------CCCCCCchhhhhHHHHHHHHHHH
Q psy6602         237 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYET--------PGLVDAQPVEMLQDQAQCILGDY  308 (367)
Q Consensus       237 f~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~--------~gl~~~~~ve~lq~~~~~aL~~~  308 (367)
                      +..+..+...++.+..+..|+++++.++-           |    ++|+        +|+++...|+++|+++..||.+|
T Consensus       128 ~~~l~~~~~~l~~L~ld~~Ey~lLkAIvL-----------f----npd~~~LS~~~~~gL~~~~~ve~lqe~~~~aL~~y  192 (298)
T 2ocf_A          128 FDMLLATSSRFRMMNLQGEEFVCLKSIIL-----------L----NSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHL  192 (298)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHH-----------H----HCSCCC-----------CHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhHhhhCcCHHHHHHHHHHHH-----------c----CCCccccccccccccccHHHHHHHHHHHHHHHHHH
Confidence            34455567789999999999999987752           1    1344        88999999999999999999999


Q ss_pred             HHhhC---CCCcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhcccc
Q psy6602         309 VRGRY---SRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKS  365 (367)
Q Consensus       309 ~~~~~---p~~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~~~  365 (367)
                      +..+|   |+++.||++||++||+||+++.+++|++||++++|.+|+++||.|||++++.
T Consensus       193 ~~~~~~~~~~~~~RF~~LLl~Lp~Lr~i~~~~~e~l~~~kl~g~~~i~~Ll~Eml~~~~~  252 (298)
T 2ocf_A          193 MAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLSDLLLEMLDAHRL  252 (298)
T ss_dssp             HHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSSCCCHHHHHHHHTTC-
T ss_pred             HHhcCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHcCCCc
Confidence            99874   6788999999999999999999999999999999999999999999998753

>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=99.54  E-value=8.2e-15  Score=134.63  Aligned_cols=111  Identities=16%  Similarity=0.232  Sum_probs=98.3

Q ss_pred             HHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhC---
Q psy6602         237 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRY---  313 (367)
Q Consensus       237 f~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~---  313 (367)
                      +..+..+...++.+..+..|+++++.+.-               .+ |++|+.+...|+++|+++..||.+|+..+|   
T Consensus       151 ~~~l~~~~~~l~~L~ld~~E~~lLkAivL---------------~n-d~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~  214 (266)
T 2r40_D          151 IEDLLHFCRCMYSMMMDNVHYALLTAIVI---------------FS-DRPGLEQPLLVEEIQRYYLNTLRVYILNQNSAS  214 (266)
T ss_dssp             HHHHHHHHHHHHTTTCCHHHHHHHHHHHH---------------TS-CCTTCSCHHHHHHHHHHHHHHHHHHHHHHTTTC
T ss_pred             HHHHHHHHHHHhcccCCHHHHHHHhhhee---------------ec-CCCCCcCHHHHHHHHHHHHHHHHHHHHHhCCCC
Confidence            34455567788999999999998887651               12 789999999999999999999999999999   


Q ss_pred             CCCcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhccc
Q psy6602         314 SRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEK  364 (367)
Q Consensus       314 p~~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~~  364 (367)
                      |+++.||++||++||+||+++.+++|++|+.+++| +++++|+.|||+.+.
T Consensus       215 ~~~~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~~-~~~~~Ll~Em~~~~~  264 (266)
T 2r40_D          215 PRCAVIFGKILGILTEIRTLGMQNSNMCISLKLKN-RKLPPFLEEIWDVAD  264 (266)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-CCCCHHHHHHTTCC-
T ss_pred             CchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCccHHHHHHhCCCC
Confidence            88899999999999999999999999999999999 699999999998764

>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=99.53  E-value=1.8e-15  Score=137.63  Aligned_cols=114  Identities=19%  Similarity=0.232  Sum_probs=98.3

Q ss_pred             HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCC--------CCCCCCchhhhhHHHHHHHHHHHH
Q psy6602         238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYET--------PGLVDAQPVEMLQDQAQCILGDYV  309 (367)
Q Consensus       238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~--------~gl~~~~~ve~lq~~~~~aL~~~~  309 (367)
                      ..+..+...++.+..+..|+++++.+.-           |    ++|+        +|+++...|+++|+++..||.+|+
T Consensus       120 ~~l~~~~~~l~~L~ld~~E~~lLkAivL-----------~----~pd~~~ls~~~~~gl~~~~~v~~lq~~~~~aL~~y~  184 (248)
T 1xpc_A          120 DMLLATSSRFRMMNLQGEEFVCLKSIIL-----------L----NSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLM  184 (248)
T ss_dssp             HHHHHHHHHHHHHTCCHHHHHHHHHHHH-----------H----HTTTTCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHH-----------c----CCcccccccccccccccHHHHHHHHHHHHHHHHHHH
Confidence            4455567788899999999999887752           1    1333        677788899999999999999999


Q ss_pred             HhhC---CCCcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhccccC
Q psy6602         310 RGRY---SRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSY  366 (367)
Q Consensus       310 ~~~~---p~~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~~~~  366 (367)
                      ..+|   |+++.||++||++||+||+++..++|++||.+++|.+|+++|+.|||++++.+
T Consensus       185 ~~~~~~~~~~~~Rf~~LL~~L~~Lr~~~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~~~  244 (248)
T 1xpc_A          185 AKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDAHRLH  244 (248)
T ss_dssp             HHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCCSSCHHHHHHHHHSCCSTT
T ss_pred             HccCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHhCCccC
Confidence            9875   57889999999999999999999999999999999999999999999998654

>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=99.53  E-value=1e-14  Score=132.49  Aligned_cols=106  Identities=21%  Similarity=0.329  Sum_probs=93.9

Q ss_pred             HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHh--hCCCC
Q psy6602         239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRG--RYSRQ  316 (367)
Q Consensus       239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~--~~p~~  316 (367)
                      .+..+...++.+..+..|+++++...-               .+||++|+.+...|+++|+++..||.+|+..  .+|++
T Consensus       139 ~i~~~~~~l~~L~ld~~E~~lLkAivL---------------~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~  203 (246)
T 1xvp_B          139 LLFHFHGTLRKLQLQEPEYVLLAAMAL---------------FSPDRPGVTQRDEIDQLQEEMALTLQSYIKGQQRRPRD  203 (246)
T ss_dssp             HHHHHHHHHHHTCCCHHHHHHHHHHHH---------------SCSSSTTCSCHHHHHHHHHHHHHHHHHHHHTCSSCCSC
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHH---------------cCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCCc
Confidence            344556778899999999999887752               2479999999999999999999999999994  47889


Q ss_pred             cChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHh
Q psy6602         317 PTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT  361 (367)
Q Consensus       317 ~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~  361 (367)
                      +.||++||++||+||+++..++|++|+.  +|.+|+++||.|||+
T Consensus       204 ~~rf~~LL~~L~~Lr~i~~~~~e~l~~~--~~~~~~~~Ll~Em~~  246 (246)
T 1xvp_B          204 RFLYAKLLGLLAELRSINEAYGYQIQHI--QGLSAMMPLLQEICS  246 (246)
T ss_dssp             SSHHHHHHHHHHHHHHHHHHHHHHHHHS--TTHHHHCHHHHHHTC
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHH--hCCCCccHHHHHhcC
Confidence            9999999999999999999999999995  699999999999984

>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=99.53  E-value=4.1e-15  Score=136.78  Aligned_cols=113  Identities=20%  Similarity=0.216  Sum_probs=94.6

Q ss_pred             HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCC-------CCchhhhhHHHHHHHHHHHHH
Q psy6602         238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLV-------DAQPVEMLQDQAQCILGDYVR  310 (367)
Q Consensus       238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~-------~~~~ve~lq~~~~~aL~~~~~  310 (367)
                      ..+..+...++.+..+..|+++++.++-               .++|++|+.       +...|+++|+++..||.+|+.
T Consensus       116 ~~l~~~~~~l~~L~ld~~E~~lLkAIvL---------------fnpd~~gLs~~~~~~~~~~~v~~~q~~~~~aL~~y~~  180 (268)
T 1yye_A          116 DMLLATTSRFRELKLQHKEYLCVKAMIL---------------LNSSMYPLVTATQDADSSRKLAHLLNAVTDALVWVIA  180 (268)
T ss_dssp             HHHHHHHHHHHHHTCCHHHHHHHHHHHH---------------HTCCC----------CCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHH---------------cCCCCCCcccchhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444566788899999999999987752               236677765       467899999999999999999


Q ss_pred             hh---CCCCcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhcccc
Q psy6602         311 GR---YSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKS  365 (367)
Q Consensus       311 ~~---~p~~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~~~  365 (367)
                      .+   ||+++.||++||++||+||+++.+++|++||++++|.+|+++|+.|||+++..
T Consensus       181 ~~~~~~~~~~~Rf~~LLl~Lp~Lr~i~~~~~e~l~~~~~~g~~~~~~Ll~Eml~~~~~  238 (268)
T 1yye_A          181 KSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEMLNAHVL  238 (268)
T ss_dssp             HTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSCCCHHHHHHHHHHHC
T ss_pred             hcCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCHHHHHHHHHhCccc
Confidence            87   47788999999999999999999999999999999999999999999998753

>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=99.52  E-value=9.2e-15  Score=134.52  Aligned_cols=110  Identities=19%  Similarity=0.198  Sum_probs=95.5

Q ss_pred             HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCc
Q psy6602         238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP  317 (367)
Q Consensus       238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~  317 (367)
                      ..+..+...++.+..+..|+++++.+.-               .+||++|+.+...|+++|+++..||.+|+..+|| ++
T Consensus       148 ~~i~~~~~~l~~L~ld~~E~~lLkAivL---------------fnpd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~-~~  211 (270)
T 1n83_A          148 SFVFEFGKSLCSMHLTEDEIALFSAFVL---------------MSADRSWLQEKVKIEKLQQKIQLALQHVLQKNHR-ED  211 (270)
T ss_dssp             HHHHHHHHHHHTTCCCHHHHHHHHHHHH---------------SCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCT-TS
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHH---------------hCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCC-ch
Confidence            3444566778888889999998887642               3478999999999999999999999999999998 68


Q ss_pred             ChHHHHHhhchhhhhhchhhHHHHHHhhhcCC----CChHHHHHHHHhcc
Q psy6602         318 TRFGRLLLMLPSLRAVRQSTIERLFFKETIGD----IPIQRLLGDMYTME  363 (367)
Q Consensus       318 ~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~----~~i~~ll~eml~~~  363 (367)
                      .||++||++||+||+++.+++|++|+.+++|.    +++++|+.|||+++
T Consensus       212 ~Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~~~~~Ll~Em~~~~  261 (270)
T 1n83_A          212 GILTKLICKVSTLRALCGRHTEKLMAFKAIYPDIVRLHFPPLYKELFTSE  261 (270)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHSCHHHHHHC---
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccccCCcCHHHHHHhCCC
Confidence            99999999999999999999999999999986    58999999999876

>1l2j_A Estrogen receptor beta; nuclear receptor, transcription factor, antagonist transcription receptor; HET: ETC; 2.95A {Homo sapiens} SCOP: a.123.1.1

Probab=99.50  E-value=7.7e-15  Score=135.13  Aligned_cols=113  Identities=21%  Similarity=0.219  Sum_probs=94.3

Q ss_pred             HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCC-------chhhhhHHHHHHHHHHHHHh
Q psy6602         239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDA-------QPVEMLQDQAQCILGDYVRG  311 (367)
Q Consensus       239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~-------~~ve~lq~~~~~aL~~~~~~  311 (367)
                      .+..+...++.+..+..|+++++.++-           |    +||++|+.+.       ..|+++|+++..||.+|+..
T Consensus       145 ~l~~~~~~l~~L~ld~~E~~lLkAIvL-----------f----npd~~gLs~~~~~~~~~~~v~~~q~~~~~aL~~y~~~  209 (271)
T 1l2j_A          145 MLLATTSRFRELKLQHKEYLCVKAMIL-----------L----NSSMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAK  209 (271)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHH-----------H----HC----CCCCGGGHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHH-----------c----CCCcCCCccchhhHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            344566788999999999999987752           1    3567777663       46888999999999999988


Q ss_pred             h---CCCCcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhccccC
Q psy6602         312 R---YSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSY  366 (367)
Q Consensus       312 ~---~p~~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~~~~  366 (367)
                      +   +|+++.||++||++||+||+++..++|++||.+++|.+|+++|+.|||++++.+
T Consensus       210 ~~~~~~~~~~Rf~~LLl~Lp~Lr~i~~~~~e~l~~~~~~g~~~~~~Ll~Eml~~~~~~  267 (271)
T 1l2j_A          210 SGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEMLNAHVLR  267 (271)
T ss_dssp             TCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCTTSSCCHHHHHHHHHHHHTTC
T ss_pred             cCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCChHHHHHHHHcCCccc
Confidence            6   477899999999999999999999999999999999999999999999988654

>1ovl_A Orphan nuclear receptor NURR1 (MSe 414, 496, 511); NUUR1, LBD, transcription; 2.20A {Homo sapiens} SCOP: a.123.1.1

Probab=99.47  E-value=1.1e-13  Score=127.47  Aligned_cols=110  Identities=19%  Similarity=0.267  Sum_probs=97.4

Q ss_pred             HHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhh--C
Q psy6602         236 RFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGR--Y  313 (367)
Q Consensus       236 Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~--~  313 (367)
                      -+..+..+...++.+..+..|+++++.+.-           |    + +++|+.+...|+++|+++..||.+|+..+  +
T Consensus       155 ~~~~l~~~~~~l~~L~ld~~E~~lLkAivL-----------~----~-~~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~  218 (271)
T 1ovl_A          155 WIDSIVEFSSNLQNMNIDISAFSCIAALAM-----------V----T-ERHGLKEPKRVEELQNKIVNCLKDHVTFNNGG  218 (271)
T ss_dssp             HHHHHHHHHHHHHTTCCCHHHHHHHHHHHH-----------S----S-CCTTCSCHHHHHHHHHHHHHHHHHHHHGGGTT
T ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHHH-----------h----C-CCCCCCcHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence            344556678889999999999999987651           1    1 47899999999999999999999999987  4


Q ss_pred             CCCcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHh
Q psy6602         314 SRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT  361 (367)
Q Consensus       314 p~~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~  361 (367)
                      |+++.||++||++||+||+++.+++|++||.+++|.+|+++|+.||+.
T Consensus       219 ~~~~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~el~~  266 (271)
T 1ovl_A          219 LNRPNYLSKLLGKLPELRTLCTQGLQRIFYLKLEDLVPPPAIIDKLFL  266 (271)
T ss_dssp             TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSSCCCHHHHHHHH
T ss_pred             CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCcHHHHHHHH
Confidence            788999999999999999999999999999999999999999999885

>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=99.47  E-value=6.6e-14  Score=127.25  Aligned_cols=111  Identities=23%  Similarity=0.345  Sum_probs=97.4

Q ss_pred             HHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhC-CC
Q psy6602         237 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRY-SR  315 (367)
Q Consensus       237 f~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~-p~  315 (367)
                      +..+......++.+..+..|+++++.+.-           |    + |++|+.+...|+++|+++..||.+|+..+| |+
T Consensus       135 ~~~i~~~~~~l~~L~ld~~E~~lLkAivL-----------~----~-d~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~  198 (248)
T 2nxx_E          135 IEDLLHFCRTMYSMRVDNAEYALLTAIVI-----------F----S-ERPALIEGWKVEKIQEIYLEALRAYVDNRRKPK  198 (248)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHH-----------T----C-CCSSCTTHHHHHHHHHHHHHHHHHHHHHSCCSS
T ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHHH-----------c----C-CCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCc
Confidence            34455667788999999999998886641           1    1 789999999999999999999999999999 45


Q ss_pred             CcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhccc
Q psy6602         316 QPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEK  364 (367)
Q Consensus       316 ~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~~  364 (367)
                      ++.||++||++||+||+++.++.|++|+.++.| +++++|+.|||+.+.
T Consensus       199 ~~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~~-~~~~~Ll~Em~~~~~  246 (248)
T 2nxx_E          199 PGTIFAKLLSVLTELRTLGNQNSEMCFSLKLKN-KKLPPFLAEIWDVDL  246 (248)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-CCCCHHHHHHTTTTC
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC-CCccHHHHHHhcCcC
Confidence            789999999999999999999999999999987 599999999999873

>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=99.46  E-value=1.4e-13  Score=124.04  Aligned_cols=107  Identities=28%  Similarity=0.424  Sum_probs=98.1

Q ss_pred             HhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcChHH
Q psy6602         242 LMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFG  321 (367)
Q Consensus       242 ~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r~~  321 (367)
                      .++..++.+..+..|+++++...-               .+++++|+.+...|+++|+.+..+|.+|+..+||+.+.||+
T Consensus       130 ~l~~~l~~L~ld~~E~~~L~ai~l---------------~~~~~~~l~~~~~ve~~q~~~~~~L~~y~~~~~~~~~~Rf~  194 (237)
T 1pzl_A          130 ELVLPFQELQIDDNEYAYLKAIIF---------------FDPDAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFG  194 (237)
T ss_dssp             HTHHHHHHHTCCHHHHHHHHHHHH---------------CCTTCTTCSCHHHHHHHHHHHHHHHHHHHHSSSSCCTTHHH
T ss_pred             HHHHHHHhhCCCHHHHHHHHHHHH---------------hCCCCCCCCcHHHHHHHHHHHHHHHHHHHHhcCCChhhHHH
Confidence            456678888999999999887652               24789999999999999999999999999999999999999


Q ss_pred             HHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhcc
Q psy6602         322 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  363 (367)
Q Consensus       322 ~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~  363 (367)
                      +||++||+||+++..+.|++++.+++|.+++++|+.||+++.
T Consensus       195 ~LL~~l~~lr~~~~~~~e~l~~~~~~~~~~~~~l~~em~~~~  236 (237)
T 1pzl_A          195 ELLLLLPTLQSITWQMIEQIQFIKLFGMAKIDNLLQEMLLGG  236 (237)
T ss_dssp             HHHTHHHHHHHHHHHHHHHHHHHHHTTCSCCCHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhHHHhCCCcHHHHHHHHHcCC
Confidence            999999999999999999999999999999999999999875

>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=99.46  E-value=2.5e-14  Score=130.01  Aligned_cols=107  Identities=18%  Similarity=0.221  Sum_probs=94.4

Q ss_pred             HHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCC
Q psy6602         237 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQ  316 (367)
Q Consensus       237 f~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~  316 (367)
                      +..+......++.+..+..|+++++...-               .+||++||.+..+|+++|+++..||.+|+..+||  
T Consensus       138 ~~~l~~~~~~l~~L~ld~~E~~lLkAivL---------------fnpd~~gL~~~~~ve~lqe~~~~aL~~y~~~~~~--  200 (248)
T 3l0l_A          138 ISSIFDFSHSLSALHFSEDEIALYTALVL---------------INAHRPGLQEKRKVEQLQYNLELAFHHHLCKTHR--  200 (248)
T ss_dssp             HHHHHHHHHHHHTTCCCHHHHHHHHHHHH---------------SCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHTTC--
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHH---------------HCCCCCCCccHHHHHHHHHHHHHHHHHHHHhhCh--
Confidence            34455677788888899999998887742               2479999999999999999999999999999986  


Q ss_pred             cChHHHHHhhchhhhhhchhhHHHHHHhhhcC----CCChHHHHHHHHh
Q psy6602         317 PTRFGRLLLMLPSLRAVRQSTIERLFFKETIG----DIPIQRLLGDMYT  361 (367)
Q Consensus       317 ~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g----~~~i~~ll~eml~  361 (367)
                      +.||++||++ |+||+++++++|+|||.+++|    ++++++|+.||+.
T Consensus       201 ~~rf~~LLl~-p~LR~i~~~~~e~l~~~k~~~p~~~~~~~p~Ll~Emf~  248 (248)
T 3l0l_A          201 QSILAKLPPK-GKLRSLCSQHVERLQIFQHLHPIVVQAAFPPLYKELFS  248 (248)
T ss_dssp             GGGGGGSCCT-THHHHHHHHHHHHHHHHHHHCHHHHHHHSCHHHHHHHC
T ss_pred             HHHHHHhhcc-HHHHHHHHHHHHHHHHHHhhCcccccCCCChHHHHhhC
Confidence            5799999999 999999999999999999999    4789999999983

>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=99.45  E-value=1e-13  Score=129.85  Aligned_cols=110  Identities=23%  Similarity=0.312  Sum_probs=96.8

Q ss_pred             HHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhC-CC
Q psy6602         237 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRY-SR  315 (367)
Q Consensus       237 f~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~-p~  315 (367)
                      +..+..+...++.+..+..|+++++.++-           |    + |++||.+...|+.+|+++..||.+|+..+| |+
T Consensus       199 ~~~i~~~~~~l~~L~ld~~E~alLkAIvL-----------f----~-d~~gL~~~~~Ve~lqe~~~~aL~~y~~~~~~~~  262 (310)
T 1z5x_E          199 VEDLLRFCRHMCAMKVDNAEYALLTAIVI-----------F----S-ERPSLSEGWKVEKIQEIYIEALKAYVENRRKPY  262 (310)
T ss_dssp             HHHHHHHHHHHHHHTCCHHHHHHHHHHHH-----------T----C-CCTTCTTHHHHHHHHHHHHHHHHHHHHTTTCTT
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHH-----------c----C-CCCCCccHHHHHHHHHHHHHHHHHHHHHHCCCc
Confidence            34455567788899999999998886651           1    2 789999999999999999999999999998 66


Q ss_pred             CcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhcc
Q psy6602         316 QPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  363 (367)
Q Consensus       316 ~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~  363 (367)
                      ++.||++||++||+||+++..++|++||.++.|. ++++|+.|||+.+
T Consensus       263 ~~~RF~kLLl~Lp~LR~l~~~~~e~l~~~~~~~~-~~~~Ll~Eml~~~  309 (310)
T 1z5x_E          263 ATTIFAKLLSVLTELRTLGNMNSETCFSLKLKNR-KVPSFLEEIWDVV  309 (310)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC-CCCHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC-CchHHHHHHHcCC
Confidence            8899999999999999999999999999999875 9999999999875

>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=99.43  E-value=1e-13  Score=126.78  Aligned_cols=110  Identities=15%  Similarity=0.100  Sum_probs=91.8

Q ss_pred             HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCC-CCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCC-
Q psy6602         239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSY-ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQ-  316 (367)
Q Consensus       239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~-d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~-  316 (367)
                      .+......++.+..+..|+++++...-               .++ |++|+.+...|+++|+++..||.+|+..+||++ 
T Consensus       127 ~l~~~~~~l~~L~ld~~E~~lLkAIvL---------------fnp~d~~gL~~~~~ve~lqe~~~~aL~~y~~~~~~~~~  191 (260)
T 3vhv_A          127 GMHQISLQFVRLQLTFEEYTIMKVLLL---------------LSTIPKDGLKSQAAFEEMRTNYIKELRKMVTKCPNNSG  191 (260)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHHHHHH---------------TSEEETTCCTTHHHHHHHHHHHHHHHHHHHHC-----C
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHH---------------cCCcCCCCCcCHHHHHHHHHHHHHHHHHHHHhcCCCCC
Confidence            344566778888899999999887642               236 899999999999999999999999999999977 


Q ss_pred             --cChHHHHHhhchhhhhhchhhHHHHHHhhh---cCCCChHHHHHHHHhcc
Q psy6602         317 --PTRFGRLLLMLPSLRAVRQSTIERLFFKET---IGDIPIQRLLGDMYTME  363 (367)
Q Consensus       317 --~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~---~g~~~i~~ll~eml~~~  363 (367)
                        +.||++||++||+||+++.+++|++||...   .+.+++++|+.|||..+
T Consensus       192 ~~~~RF~~LL~~Lp~Lr~l~~~~~e~lff~~~~~~~~~~~~p~Ll~Ei~~~~  243 (260)
T 3vhv_A          192 QSWQRFYQLTKLLDSMHDLVSDLLEFCFYTFRESHALKVEFPAMLVEIISDQ  243 (260)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTCCCCHHHHHHHHHH
T ss_pred             cHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCcHHHHHHHhcc
Confidence              689999999999999999999999997664   57899999999999864

>3up3_A Acedaf-12; ligand binding domain, nematode, steroid binding protein- transcription complex; HET: XCA; 1.25A {Ancylostoma ceylanicum} PDB: 3up0_A*

Probab=99.43  E-value=2.2e-14  Score=129.86  Aligned_cols=106  Identities=15%  Similarity=0.221  Sum_probs=87.0

Q ss_pred             HHHhhhHhHh-hhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCC---chhhhhHHHHHHHHHHHHHhhC-C
Q psy6602         240 LLLMLPSLRA-VRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDA---QPVEMLQDQAQCILGDYVRGRY-S  314 (367)
Q Consensus       240 LL~~l~~Lr~-l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~---~~ve~lq~~~~~aL~~~~~~~~-p  314 (367)
                      +......++. +..+..|+++++...-               .+|+ +|+.+.   .+|+++|+++..||.+|+..+| |
T Consensus       133 l~~~~~~~~~~L~ld~~E~alLkAivL---------------fsp~-~gL~~~~~~~~Ve~lQe~~~~aL~~y~~~~~~p  196 (243)
T 3up3_A          133 FLQFFKIFHEDIRSNDLVISMIMLIVL---------------FSPR-DSITDPEDRRIIARHHEQFSALLNRYLESLYGD  196 (243)
T ss_dssp             HHHHHHTSCHHHHTCHHHHHHHHHHHH---------------SCCC-TTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHGG
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHhh---------------cCCC-CCCCCcchHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence            3444555664 6677778877776541               1355 899876   7999999999999999998776 8


Q ss_pred             CCcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhcc
Q psy6602         315 RQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  363 (367)
Q Consensus       315 ~~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~  363 (367)
                      +++.||++||++||+||+++. +.+++|+.++ ++.++++|+.|||+.+
T Consensus       197 ~~~~rf~kLL~~Lp~LR~i~~-~~e~lf~~k~-~~~~~~pLl~E~f~~~  243 (243)
T 3up3_A          197 DAHQLNEQLPTALRMLREISA-SSGMLFLGTV-NTSEAEPLPREFFKVE  243 (243)
T ss_dssp             GHHHHHHHHHHHHHHHHHHHH-TCTTTTTTSC-CGGGSCHHHHTTSCCC
T ss_pred             ChhHHHHHHHHHHHHHHHHHH-HHHHHHhccc-CCCCCCcHHHHHhCCC
Confidence            899999999999999999999 9999999875 5679999999999753

>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=99.38  E-value=1e-13  Score=125.29  Aligned_cols=80  Identities=23%  Similarity=0.359  Sum_probs=72.2

Q ss_pred             CCCCCCCC---CCchhhhhHHHHHHHHHHHHHhhC-CCCcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHH
Q psy6602         282 SYETPGLV---DAQPVEMLQDQAQCILGDYVRGRY-SRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLG  357 (367)
Q Consensus       282 s~d~~gl~---~~~~ve~lq~~~~~aL~~~~~~~~-p~~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~  357 (367)
                      +||++||.   +...|+++|++++.||++|+..+| |+++.||+|||++||+||+|+..+++ +|+. ..++.++++|+.
T Consensus       160 spDr~gL~~~~d~~~Ve~lQe~~~~aL~~y~~~~~~p~~~~rf~kLL~~Lp~LR~i~~~~~~-lf~~-~~~~~~~~pLl~  237 (244)
T 3gyt_A          160 DSKREGLVSQQDKETVEKLHRNYESLLHRYLYSIHKEEAEQRFASIPKALVALRKVAENAVT-LFLG-AGNTTEAASLPK  237 (244)
T ss_dssp             CTTSTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHHHHHTTTT-TTTT-SCCCTTSCTTGG
T ss_pred             hccCCCCCccccHHHHHHHHHHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHHHHHHHHHHH-HHHh-ccCCccCCcHHH
Confidence            58999999   688999999999999999999888 78899999999999999999999999 7664 445778999999


Q ss_pred             HHHhcc
Q psy6602         358 DMYTME  363 (367)
Q Consensus       358 eml~~~  363 (367)
                      |||+..
T Consensus       238 Eif~~~  243 (244)
T 3gyt_A          238 EFFATN  243 (244)
T ss_dssp             GTSCCC
T ss_pred             HHhCcC
Confidence            999754

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

Probab=99.35  E-value=5.7e-13  Score=123.84  Aligned_cols=110  Identities=15%  Similarity=0.100  Sum_probs=90.6

Q ss_pred             HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCC-CCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCC-
Q psy6602         239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSY-ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQ-  316 (367)
Q Consensus       239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~-d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~-  316 (367)
                      .+..+...++.+..+..|+++++.+.-               .++ |++||.+...|+++|+++..||.+|+..++|+. 
T Consensus       161 ~l~~~~~~l~~L~ld~~EyalLkAIvL---------------fnp~d~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~~~~~  225 (294)
T 3vhu_A          161 GMHQISLQFVRLQLTFEEYTIMKVLLL---------------LSTIPKDGLKSQAAFEEMRTNYIKELRKMVTKCPNNSG  225 (294)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHHHHHH---------------TSEEETTCCTTHHHHHHHHHHHHHHHHHHHC------C
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHH---------------hCCCCCCCCCcHHHHHHHHHHHHHHHHHHHHhcCCCCc
Confidence            344566778888999999999987752               236 899999999999999999999999999998876 


Q ss_pred             --cChHHHHHhhchhhhhhchhhHHHHHHhhh---cCCCChHHHHHHHHhcc
Q psy6602         317 --PTRFGRLLLMLPSLRAVRQSTIERLFFKET---IGDIPIQRLLGDMYTME  363 (367)
Q Consensus       317 --~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~---~g~~~i~~ll~eml~~~  363 (367)
                        +.||++||++||+||+++.+++|++||...   .+.+++++|+.|||..+
T Consensus       226 ~~~~RF~~LL~lLp~Lr~l~~~~~e~lff~~~q~~~~~~~~p~Ll~Ei~~~~  277 (294)
T 3vhu_A          226 QSWQRFYQLTKLLDSMHDLVSDLLEFCFYTFRESHALKVEFPAMLVEIISDQ  277 (294)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTCCCCHHHHHHHHHH
T ss_pred             cHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCcCCCCHHHHHHHcCC
Confidence              789999999999999999999999997654   57889999999999864

>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=99.35  E-value=8.1e-13  Score=116.00  Aligned_cols=96  Identities=23%  Similarity=0.305  Sum_probs=85.2

Q ss_pred             HHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCC
Q psy6602         237 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQ  316 (367)
Q Consensus       237 f~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~  316 (367)
                      +..+......++.+..+..|+++++...-               .+||++|+.+...|+++|+++..+|.+|+..+||++
T Consensus       103 ~~~i~~~~~~~~~L~ld~~E~~lLkaivL---------------~~pd~~gL~~~~~v~~~q~~~~~aL~~y~~~~~~~~  167 (199)
T 3cqv_A          103 LNSMFEFSEKLNALQLSDEEMSLFTAVVL---------------VSADRSGIENVNSVEALQETLIRALRTLIMKNHPNE  167 (199)
T ss_dssp             HHHHHHHHHHHHTTCCCHHHHHHHHHHHH---------------HTSCCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHH---------------hcCCCCCCcCHHHHHHHHHHHHHHHHHHHHHHCCCh
Confidence            44556677889999999999999887752               247899999999999999999999999999999999


Q ss_pred             cChHHHHHhhchhhhhhchhhHHHHHHhhhc
Q psy6602         317 PTRFGRLLLMLPSLRAVRQSTIERLFFKETI  347 (367)
Q Consensus       317 ~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~  347 (367)
                      +.||++||++||+||++++.++|++||.|++
T Consensus       168 ~~Rf~~LL~~L~~Lr~l~~~~~E~l~~~k~~  198 (199)
T 3cqv_A          168 ASIFTKLLLKLPDLRSLNNMHSEELLAFKVH  198 (199)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHHHHHTCC--
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence            9999999999999999999999999999875

>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=99.32  E-value=7.6e-13  Score=121.64  Aligned_cols=110  Identities=14%  Similarity=0.157  Sum_probs=94.6

Q ss_pred             HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCC-CCCCCCCCchhhhhHHHHHHHHHHHHHhhC---C
Q psy6602         239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSY-ETPGLVDAQPVEMLQDQAQCILGDYVRGRY---S  314 (367)
Q Consensus       239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~-d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~---p  314 (367)
                      .+..+...++.+..+..|+++++.++-               .++ +++||.+...|+++|+++..+|.+|+..++   |
T Consensus       136 ~i~~~~~~l~~L~ld~~E~~lLkAIvL---------------fnp~~~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~  200 (269)
T 1t7r_A          136 RMRHLSQEFGWLQITPQEFLCMKALLL---------------FSIIPVDGLKNQKFFDELRMNYIKELDRIIACKRKNPT  200 (269)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHH---------------TSEEETTCCTTHHHHHHHHHHHHHHHHHHHHTTCCSHH
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHH---------------cCCCccCCCccHHHHHHHHHHHHHHHHHHHHHhCCCCC
Confidence            345567788999999999999987752               235 789999999999999999999999998875   5


Q ss_pred             CCcChHHHHHhhchhhhhhchhhHHHHHHh--h-hcCCCChHHHHHHHHhcc
Q psy6602         315 RQPTRFGRLLLMLPSLRAVRQSTIERLFFK--E-TIGDIPIQRLLGDMYTME  363 (367)
Q Consensus       315 ~~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~--~-~~g~~~i~~ll~eml~~~  363 (367)
                      +++.||++||++||+||+++..++|++|..  + ..|.+++++|+.|||...
T Consensus       201 ~~~~Rf~~LL~~L~~Lr~l~~~~~e~lf~~~~~~~~~~~~~~~Ll~E~~~~~  252 (269)
T 1t7r_A          201 SCSRRFYQLTKLLDSVQPIARELHQFTFDLLIKSHMVSVDFPEMMAEIISVQ  252 (269)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTCCCCHHHHHHHHHT
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCcChHHHHHHHHhCc
Confidence            678999999999999999999999999842  3 348999999999999854

>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=99.32  E-value=1.3e-12  Score=119.60  Aligned_cols=111  Identities=20%  Similarity=0.184  Sum_probs=97.1

Q ss_pred             HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCC-CCCCCCCCchhhhhHHHHHHHHHHHHHhhCCC-
Q psy6602         238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSY-ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSR-  315 (367)
Q Consensus       238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~-d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~-  315 (367)
                      ..+......++.+..+..|+++++.+.-               .++ |++|+.+..+|+++|+++..||.+|+..+||+ 
T Consensus       128 ~~l~~~~~~l~~L~ld~~E~~lLkAIvL---------------~np~d~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~  192 (261)
T 3mnp_A          128 KHMLFISTELQRLQVSYEEYLCMKTLLL---------------LSSVPKEGLKSQELFDEIRMTYIKELGKAIAKRGGNS  192 (261)
T ss_dssp             HHHHHHHHHHHHHTCCHHHHHHHHHHHH---------------TSEEETTCCTTHHHHHHHHHHHHHHHHHHHHTTCCCH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHH---------------cCCCCcCCCccHHHHHHHHHHHHHHHHHHHHhhCCCC
Confidence            3445667778999999999999987752               236 89999999999999999999999999999995 


Q ss_pred             --CcChHHHHHhhchhhhhhchhhHHHHHHhhhc--CCCChHHHHHHHHhcc
Q psy6602         316 --QPTRFGRLLLMLPSLRAVRQSTIERLFFKETI--GDIPIQRLLGDMYTME  363 (367)
Q Consensus       316 --~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~--g~~~i~~ll~eml~~~  363 (367)
                        ++.||++||++||+||+++..+.+++|+.++.  +.+.+++|+.|||+.+
T Consensus       193 ~~~~~Rf~~LL~lL~~Lr~l~~~~~e~~f~~~~~~~~~~~~p~Ll~Ei~~~~  244 (261)
T 3mnp_A          193 SQNWQRFYQLTKLLDSMHDVVENLLSYCFQTFLDKSMSIEFPEMLAEIITNQ  244 (261)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGGGCCCCCHHHHHHHHHH
T ss_pred             chhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCcHHHHHHHhcc
Confidence              48999999999999999999999999988776  5778999999999853

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

Probab=99.30  E-value=1.2e-12  Score=118.60  Aligned_cols=94  Identities=23%  Similarity=0.299  Sum_probs=83.3

Q ss_pred             HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCc
Q psy6602         238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP  317 (367)
Q Consensus       238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~  317 (367)
                      ..+..+...++.+..+..|+++++.+.-               .+||++|+.+...|+++|+++..||.+|+..+||+++
T Consensus       149 ~~i~~~~~~l~~L~ld~~E~~lLkAIvL---------------~npd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~  213 (245)
T 3n00_A          149 SAMFDFSEKLNSLALTEEELGLFTAVVL---------------VSADRSGMENSASVEQLQETLLRALRALVLKNRPLET  213 (245)
T ss_dssp             HHHHHHHHHHHHTCCCHHHHHHHHHHHH---------------HTSCCTTCSSHHHHHHHHHHHHHHHHHHHHHHCTTCT
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHH---------------hCCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCHH
Confidence            3445566778888888888888887642               2478999999999999999999999999999999999


Q ss_pred             ChHHHHHhhchhhhhhchhhHHHHHHhhh
Q psy6602         318 TRFGRLLLMLPSLRAVRQSTIERLFFKET  346 (367)
Q Consensus       318 ~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~  346 (367)
                      .||++||++||+||++++.++|+|||.|+
T Consensus       214 ~RF~~LLl~Lp~LR~l~~~~~E~L~~~k~  242 (245)
T 3n00_A          214 SRFTKLLLKLPDLRTLNNMHSEKLLSFRV  242 (245)
T ss_dssp             THHHHHHTHHHHHHHHHHHHTTCEEEEEC
T ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHHHhcC
Confidence            99999999999999999999999999886

>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=99.30  E-value=1.1e-12  Score=120.10  Aligned_cols=107  Identities=15%  Similarity=0.152  Sum_probs=92.5

Q ss_pred             HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCC-CCCCCCCCchhhhhHHHHHHHHHHHHHhh---CCC
Q psy6602         240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSY-ETPGLVDAQPVEMLQDQAQCILGDYVRGR---YSR  315 (367)
Q Consensus       240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~-d~~gl~~~~~ve~lq~~~~~aL~~~~~~~---~p~  315 (367)
                      +..+...++.+..+..|+++++...-               .++ |++|+++..+|+++|+++..||.+|+..+   +|+
T Consensus       129 i~~~~~~l~~L~ld~~E~~lLkAIvL---------------fnp~~~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~  193 (261)
T 1sqn_A          129 MWQIPQEFVKLQVSQEEFLCMKVLLL---------------LNTIPLEGLRSQTQFEEMRSSYIRELIKAIGLRQKGVVS  193 (261)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHHHHH---------------TSEECTTCCTTHHHHHHHHHHHHHHHHHHHHTTC-CHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHH---------------cCCCcccccccHHHHHHHHHHHHHHHHHHHHhhCCCCCc
Confidence            33456788889999999999987752               236 78999999999999999999999999874   577


Q ss_pred             CcChHHHHHhhchhhhhhchhhHHHHHHhhhc-----CCCChHHHHHHHHhcc
Q psy6602         316 QPTRFGRLLLMLPSLRAVRQSTIERLFFKETI-----GDIPIQRLLGDMYTME  363 (367)
Q Consensus       316 ~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~-----g~~~i~~ll~eml~~~  363 (367)
                      ++.||++||++||+||+++..+  ++|+.+++     |.+++++|+.|||...
T Consensus       194 ~~~Rf~~LL~~L~~Lr~~~~~~--~~~~~~~~~q~~~~~~~~~~Ll~Ei~~~~  244 (261)
T 1sqn_A          194 SSQRFYQLTKLLDNLHDLVKQL--HLYCLNTFIQSRALSVEFPEMMSEVIAAQ  244 (261)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHTHHHHTCCCCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHhHHHHHHHHHH--HHHHHHHHHHhcCCCCChHHHHHHHHhcC
Confidence            8999999999999999999765  67778888     9999999999999854

---

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	367
d1pzla_	233	a.123.1.1 (A:) Hepatocyte nuclear factor 4-alpha {	2e-45
d1pzla_	233	a.123.1.1 (A:) Hepatocyte nuclear factor 4-alpha {	4e-16
d1pk5a_	242	a.123.1.1 (A:) Orphan nuclear receptor NR5a2 (LRH-	7e-45
d1pk5a_	242	a.123.1.1 (A:) Orphan nuclear receptor NR5a2 (LRH-	8e-18
d1fcya_	236	a.123.1.1 (A:) Retinoic acid receptor gamma (RAR-g	2e-44
d1fcya_	236	a.123.1.1 (A:) Retinoic acid receptor gamma (RAR-g	8e-16
d1g2na_	256	a.123.1.1 (A:) Ultraspiracle protein, usp {Helioth	7e-43
d1g2na_	256	a.123.1.1 (A:) Ultraspiracle protein, usp {Helioth	1e-18
d3d24a1	227	a.123.1.1 (A:194-420) Steroid hormone receptor ERR	4e-42
d3d24a1	227	a.123.1.1 (A:194-420) Steroid hormone receptor ERR	7e-15
d1hg4a_	265	a.123.1.1 (A:) Ultraspiracle protein, usp {Drosoph	7e-42
d2e2ra1	223	a.123.1.1 (A:234-456) Orphan nuclear receptor ERR3	1e-41
d2e2ra1	223	a.123.1.1 (A:234-456) Orphan nuclear receptor ERR3	6e-17
d2fvja1	271	a.123.1.1 (A:207-477) Peroxisome proliferator acti	5e-41
d2fvja1	271	a.123.1.1 (A:207-477) Peroxisome proliferator acti	3e-16
d2b50b1	265	a.123.1.1 (B:211-475) Peroxisome proliferator-acti	1e-40
d2b50b1	265	a.123.1.1 (B:211-475) Peroxisome proliferator-acti	3e-14
d2p1ta1	230	a.123.1.1 (A:229-458) Retinoid-X receptor alpha (R	9e-40
d2p1ta1	230	a.123.1.1 (A:229-458) Retinoid-X receptor alpha (R	1e-15
d2qw4a1	233	a.123.1.1 (A:32-264) Orphan nuclear receptor NR4A1	4e-39
d2qw4a1	233	a.123.1.1 (A:32-264) Orphan nuclear receptor NR4A1	2e-14
d2p54a1	267	a.123.1.1 (A:202-468) Peroxisome proliferator acti	4e-38
d2p54a1	267	a.123.1.1 (A:202-468) Peroxisome proliferator acti	1e-15
d2j7ya1	236	a.123.1.1 (A:217-452) Estrogen receptor beta {Rat	3e-37
d2j7ya1	236	a.123.1.1 (A:217-452) Estrogen receptor beta {Rat	2e-12
d1xpca_	245	a.123.1.1 (A:) Estrogen receptor alpha {Human (Hom	3e-37
d1xpca_	245	a.123.1.1 (A:) Estrogen receptor alpha {Human (Hom	1e-14
d1ovla_	236	a.123.1.1 (A:) Orphan nuclear receptor NURR1 {Huma	7e-37
d1ovla_	236	a.123.1.1 (A:) Orphan nuclear receptor NURR1 {Huma	3e-14
d1n46a_	251	a.123.1.1 (A:) Thyroid hormone receptor beta (TR-b	9e-37
d1n46a_	251	a.123.1.1 (A:) Thyroid hormone receptor beta (TR-b	1e-13
d1nrla_	292	a.123.1.1 (A:) Pregnane x receptor, PXR {Human (Ho	7e-36
d1nrla_	292	a.123.1.1 (A:) Pregnane x receptor, PXR {Human (Ho	6e-10
d1pdua_	230	a.123.1.1 (A:) Nuclear hormone receptor HR38 {Frui	9e-36
d1pdua_	230	a.123.1.1 (A:) Nuclear hormone receptor HR38 {Frui	5e-14
d1xvpb_	246	a.123.1.1 (B:) Orphan nuclear receptor NR1I3 (CAR)	2e-33
d1xvpb_	246	a.123.1.1 (B:) Orphan nuclear receptor NR1I3 (CAR)	2e-12
d1sqna_	251	a.123.1.1 (A:) Progesterone receptor {Human (Homo	3e-33
d1sqna_	251	a.123.1.1 (A:) Progesterone receptor {Human (Homo	1e-09
d1osha_	231	a.123.1.1 (A:) Bile acid receptor FXR {Human (Homo	6e-33
d1osha_	231	a.123.1.1 (A:) Bile acid receptor FXR {Human (Homo	2e-13
d1t7ra_	250	a.123.1.1 (A:) Androgen receptor {Chimpanzee (Pan	6e-33
d1t7ra_	250	a.123.1.1 (A:) Androgen receptor {Chimpanzee (Pan	2e-10
d1pq9a_	239	a.123.1.1 (A:) Oxysterols receptor LXR-beta {Human	1e-32
d1pq9a_	239	a.123.1.1 (A:) Oxysterols receptor LXR-beta {Human	2e-12
d1nhza_	247	a.123.1.1 (A:) Glucocorticoid receptor {Human (Hom	2e-32
d1nhza_	247	a.123.1.1 (A:) Glucocorticoid receptor {Human (Hom	1e-09
d2r40d1	243	a.123.1.1 (D:287-529) Ecdysone receptor {Noctuid m	7e-32
d2r40d1	243	a.123.1.1 (D:287-529) Ecdysone receptor {Noctuid m	1e-09
d1nq7a_	244	a.123.1.1 (A:) Orphan nuclear receptor ROR-beta {R	2e-31
d1nq7a_	244	a.123.1.1 (A:) Orphan nuclear receptor ROR-beta {R	9e-11
d1ie9a_	255	a.123.1.1 (A:) Vitamin D nuclear receptor {Human (	4e-30
d1ie9a_	255	a.123.1.1 (A:) Vitamin D nuclear receptor {Human (	1e-08
d1n83a_	251	a.123.1.1 (A:) Orphan nuclear receptor ROR-alpha {	6e-30
d1n83a_	251	a.123.1.1 (A:) Orphan nuclear receptor ROR-alpha {	3e-09
d1xnxa_	232	a.123.1.1 (A:) Orphan nuclear receptor NR1I3 (CAR)	3e-28
d1xnxa_	232	a.123.1.1 (A:) Orphan nuclear receptor NR1I3 (CAR)	5e-08

>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 =  153 bits (388), Expect = 2e-45
 Identities = 56/186 (30%), Positives = 94/186 (50%), Gaps = 1/186 (0%)

Query: 92  QETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINC 151
            E+    L + V W + +  F  L   DQ+ LL+    E  LL   + S+ +   LL+  
Sbjct: 43  CESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVLLLGN 102

Query: 152 EKARERLPPDDVRVNNE-IKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQP 210
           +    R  P+   ++   I+++ E++  F++L  D +E   +KA+I F P+  GL D   
Sbjct: 103 DYIVPRHCPELAEMSRVSIRILDELVLPFQELQIDDNEYAYLKAIIFFDPDAKGLSDPGK 162

Query: 211 VEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQ 270
           ++ L+ Q Q  L DY+  R      RFG LLL+LP+L+++    IE++ F +  G   I 
Sbjct: 163 IKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFIKLFGMAKID 222

Query: 271 RLLGDM 276
            LL +M
Sbjct: 223 NLLQEM 228

>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 = 74.7 bits (183), Expect = 4e-16
 Identities = 27/76 (35%), Positives = 41/76 (53%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 343
           +  GL D   ++ L+ Q Q  L DY+  R      RFG LLL+LP+L+++    IE++ F
Sbjct: 153 DAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQF 212

Query: 344 KETIGDIPIQRLLGDM 359
            +  G   I  LL +M
Sbjct: 213 IKLFGMAKIDNLLQEM 228

>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 =  152 bits (385), Expect = 7e-45
 Identities = 64/227 (28%), Positives = 98/227 (43%), Gaps = 5/227 (2%)

Query: 55  LKSPPPPSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQT 114
           LK  P        +     Q   +    + L +     +   + LF  V W R    F+ 
Sbjct: 11  LKCEPDEPQVQAKIMAYLQQEQSNRNRQEKLSAFGLLCKMADQTLFSIVEWARSSIFFRE 70

Query: 115 LSKRDQLLLLQESWKELFLLHLAQWSIPWD----LSLLINCEKARERLPPDDVRVNNE-I 169
           L   DQ+ LLQ  W EL +L      +       + L+         +        N  +
Sbjct: 71  LKVDDQMKLLQNCWSELLILDHIYRQVAHGKEGTIFLVTGEHVDYSTIISHTEVAFNNLL 130

Query: 170 KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGR 229
            L QE++ R R L  D  E  C+K ++LF+ +   L + Q VE +Q+Q    L DY    
Sbjct: 131 SLAQELVVRLRSLQFDQREFVCLKFLVLFSSDVKNLENLQLVEGVQEQVNAALLDYTVCN 190

Query: 230 YSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDM 276
           Y +Q  +FG+LLL LP LRA+ +   + L++K   GD+P   LL +M
Sbjct: 191 YPQQTEKFGQLLLRLPELRAISKQAEDYLYYKHVNGDVPYNNLLIEM 237

>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 = 79.7 bits (196), Expect = 8e-18
 Identities = 29/74 (39%), Positives = 42/74 (56%)

Query: 286 PGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKE 345
             L + Q VE +Q+Q    L DY    Y +Q  +FG+LLL LP LRA+ +   + L++K 
Sbjct: 164 KNLENLQLVEGVQEQVNAALLDYTVCNYPQQTEKFGQLLLRLPELRAISKQAEDYLYYKH 223

Query: 346 TIGDIPIQRLLGDM 359
             GD+P   LL +M
Sbjct: 224 VNGDVPYNNLLIEM 237

>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 =  151 bits (382), Expect = 2e-44
 Identities = 44/205 (21%), Positives = 81/205 (39%), Gaps = 1/205 (0%)

Query: 72  THQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKEL 131
           T+    H   L + +  +K  E   + +   V + + L  F  LS  DQ+ LL+ +  ++
Sbjct: 31  TNSSADHRVQLDLGLW-DKFSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDI 89

Query: 132 FLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGC 191
            +L +     P   ++  +      R    +        L+     +   L  D +E G 
Sbjct: 90  LMLRICTRYTPEQDTMTFSDGLTLNRTQMHNAGFGPLTDLVFAFAGQLLPLEMDDTETGL 149

Query: 192 MKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVR 251
           + A+ L   +   L + + V+ LQ+     L  Y R R   QP  F R+L+ +  LR + 
Sbjct: 150 LSAICLICGDRMDLEEPEKVDKLQEPLLEALRLYARRRRPSQPYMFPRMLMKITDLRGIS 209

Query: 252 QSTIERLFFKETIGDIPIQRLLGDM 276
               ER    +     P+  L+ +M
Sbjct: 210 TKGAERAITLKMEIPGPMPPLIREM 234

>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 = 73.9 bits (181), Expect = 8e-16
 Identities = 20/78 (25%), Positives = 33/78 (42%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
             +   L + + V+ LQ+     L  Y R R   QP  F R+L+ +  LR +     ER 
Sbjct: 157 CGDRMDLEEPEKVDKLQEPLLEALRLYARRRRPSQPYMFPRMLMKITDLRGISTKGAERA 216

Query: 342 FFKETIGDIPIQRLLGDM 359
              +     P+  L+ +M
Sbjct: 217 ITLKMEIPGPMPPLIREM 234

>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 =  147 bits (372), Expect = 7e-43
 Identities = 61/242 (25%), Positives = 102/242 (42%), Gaps = 25/242 (10%)

Query: 55  LKSPPPPSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQT 114
           L + P        +   ++ PP     +  L       +   + +   V W R +  F  
Sbjct: 17  LVADPSEEFQFLRVGPDSNVPPKFRAPVSSLC------QIGNKQIAALVVWARDIPHFSQ 70

Query: 115 LSKRDQLLLLQESWKELFLLHLAQWSIPW--DLSLLINCEKARERLPPDDVRVNNEIKL- 171
           L   DQ+LL++ SW EL L  +A  S+ +  +    ++    R   PP  + +   + L 
Sbjct: 71  LEMEDQILLIKGSWNELLLFAIAWRSMEFLTEERDGVDGTGNRTTSPPQLMCLMPGMTLH 130

Query: 172 ----------------IQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQ 215
                           + E+  + R L  D +E   +KA+IL  P+  GL + Q VE+L+
Sbjct: 131 RNSALQAGVGQIFDRVLSELSLKMRTLRVDQAEYVALKAIILLNPDVKGLKNRQEVEVLR 190

Query: 216 DQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGD 275
           ++    L +Y R   S +  RF  LLL LP+LR++   + E LFF   + D  I   + D
Sbjct: 191 EKMFLCLDEYCRRSRSSEEGRFAALLLRLPALRSISLKSFEHLFFFHLVADTSIAGYIRD 250

Query: 276 MY 277
             
Sbjct: 251 AL 252

>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 = 82.4 bits (203), Expect = 1e-18
 Identities = 26/79 (32%), Positives = 41/79 (51%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
           + +  GL + Q VE+L+++    L +Y R   S +  RF  LLL LP+LR++   + E L
Sbjct: 174 NPDVKGLKNRQEVEVLREKMFLCLDEYCRRSRSSEEGRFAALLLRLPALRSISLKSFEHL 233

Query: 342 FFKETIGDIPIQRLLGDMY 360
           FF   + D  I   + D  
Sbjct: 234 FFFHLVADTSIAGYIRDAL 252

>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 =  144 bits (365), Expect = 4e-42
 Identities = 50/224 (22%), Positives = 90/224 (40%), Gaps = 15/224 (6%)

Query: 58  PPPPSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSK 117
           P                P  H   +  L       +   R + + + W + +  F +LS 
Sbjct: 13  PEKLYAMPDPA-----GPDGHLPAVATLC------DLFDREIVVTISWAKSIPGFSSLSL 61

Query: 118 RDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILA 177
            DQ+ +LQ  W E+ +L +AQ S+P    L    +   +        +      + +++ 
Sbjct: 62  SDQMSVLQSVWMEVLVLGVAQRSLPLQDELAFAEDLVLDEEGARAAGLGELGAALLQLVR 121

Query: 178 RFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSR----Q 233
           R + L  +  E   +KA+ L   ++  + DA+ VE L++     L +Y  GR       +
Sbjct: 122 RLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQLREALHEALLEYEAGRAGPGGGAE 181

Query: 234 PTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMY 277
             R GRLLL LP LR      +   +  +  G +P+ +L  +M 
Sbjct: 182 RRRAGRLLLTLPLLRQTAGKVLAHFYGVKLEGKVPMHKLFLEML 225

>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 = 70.9 bits (173), Expect = 7e-15
 Identities = 23/83 (27%), Positives = 39/83 (46%), Gaps = 4/83 (4%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSR----QPTRFGRLLLMLPSLRAVRQST 337
           + ++  + DA+ VE L++     L +Y  GR       +  R GRLLL LP LR      
Sbjct: 143 NSDSVHIEDAEAVEQLREALHEALLEYEAGRAGPGGGAERRRAGRLLLTLPLLRQTAGKV 202

Query: 338 IERLFFKETIGDIPIQRLLGDMY 360
           +   +  +  G +P+ +L  +M 
Sbjct: 203 LAHFYGVKLEGKVPMHKLFLEML 225

>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 =  145 bits (366), Expect = 7e-42
 Identities = 52/246 (21%), Positives = 95/246 (38%), Gaps = 30/246 (12%)

Query: 60  PPSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRD 119
                    FL            +  +SA    +   + LF  V + R +  F  +   D
Sbjct: 15  TQCGDRALTFLRVGPYSTVQPDYKGAVSA--LCQVVNKQLFQMVEYARMMPHFAQVPLDD 72

Query: 120 QLLLLQESWKELFLLHLAQWSIPWDLSLLINC-----------EKARERLPPDDVRVNNE 168
           Q++LL+ +W EL + ++A  SI                     E+    L P  + +N  
Sbjct: 73  QVILLKAAWIELLIANVAWCSIVSLDDGGAGGGGGGLGHDGSFERRSPGLQPQQLFLNQS 132

Query: 169 IKL-----------------IQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPV 211
                               + E+  + ++L+ D  E  C+KA+IL+ P+  G+     +
Sbjct: 133 FSYHRNSAIKAGVSAIFDRILSELSVKMKRLNLDRRELSCLKAIILYNPDIRGIKSRAEI 192

Query: 212 EMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQR 271
           EM +++    L ++ R  +     RF +LLL LP+LR++     + LF      D P++ 
Sbjct: 193 EMCREKVYACLDEHCRLEHPGDDGRFAQLLLRLPALRSISLKCQDHLFLFRITSDRPLEE 252

Query: 272 LLGDMY 277
           L  +  
Sbjct: 253 LFLEQL 258

>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 =  143 bits (362), Expect = 1e-41
 Identities = 43/185 (23%), Positives = 89/185 (48%)

Query: 93  ETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCE 152
           +   R L + + W + +  F TLS  DQ+ LLQ +W E+ +L +   S+ ++  L+   +
Sbjct: 37  DLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDELVYADD 96

Query: 153 KARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVE 212
              +        + +    I +++ +++ +  +  E   +KA+ L   ++  + D + V+
Sbjct: 97  YIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQ 156

Query: 213 MLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRL 272
            LQD     L DY  G++   P R G++L+ LP LR      ++  +  +  G +P+ +L
Sbjct: 157 KLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPMHKL 216

Query: 273 LGDMY 277
             +M 
Sbjct: 217 FLEML 221

>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 = 76.6 bits (188), Expect = 6e-17
 Identities = 21/79 (26%), Positives = 40/79 (50%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
           + ++  + D + V+ LQD     L DY  G++   P R G++L+ LP LR      ++  
Sbjct: 143 NSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHF 202

Query: 342 FFKETIGDIPIQRLLGDMY 360
           +  +  G +P+ +L  +M 
Sbjct: 203 YNIKLEGKVPMHKLFLEML 221

>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 =  143 bits (361), Expect = 5e-41
 Identities = 40/206 (19%), Positives = 79/206 (38%), Gaps = 2/206 (0%)

Query: 74  QPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFL 133
            P         +   + CQ  +   +     + + +  F  L   DQ+ LL+    E+  
Sbjct: 62  TPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIY 121

Query: 134 LHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNE-IKLIQEILARFRQLSPDGSECGCM 192
             LA       + +                +   + ++   E   +F  L  D S+    
Sbjct: 122 TMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIF 181

Query: 193 KAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQ 252
            AVI+ + + PGL++ +P+E +QD     L   ++  +      F +LL  +  LR +  
Sbjct: 182 IAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVT 241

Query: 253 STIERLF-FKETIGDIPIQRLLGDMY 277
             ++ L   K+T  D+ +  LL ++Y
Sbjct: 242 EHVQLLQVIKKTETDMSLHPLLQEIY 267

>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 = 75.4 bits (185), Expect = 3e-16
 Identities = 20/79 (25%), Positives = 39/79 (49%), Gaps = 1/79 (1%)

Query: 283 YETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLF 342
            + PGL++ +P+E +QD     L   ++  +      F +LL  +  LR +    ++ L 
Sbjct: 189 GDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQ 248

Query: 343 -FKETIGDIPIQRLLGDMY 360
             K+T  D+ +  LL ++Y
Sbjct: 249 VIKKTETDMSLHPLLQEIY 267

>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 =  142 bits (358), Expect = 1e-40
 Identities = 45/237 (18%), Positives = 82/237 (34%), Gaps = 11/237 (4%)

Query: 52  PSGLKSPPPPSHHH---------PSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMA 102
            +G  S   P   H           +          P     +    +CQ TT   +   
Sbjct: 27  LTGKASHTAPFVIHDIETLWQAEKGLVWKQLVNGLPPYKEISVHVFYRCQCTTVETVREL 86

Query: 103 VRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDD 162
             + + +  F +L   DQ+ LL+    E     LA       L +               
Sbjct: 87  TEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNKDGLLVANGSGFVTREFLRSL 146

Query: 163 VRVNNE-IKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCI 221
            +  ++ I+   E   +F  L  D S+     A I+   + PGL++   VE +QD     
Sbjct: 147 RKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRA 206

Query: 222 LGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLF-FKETIGDIPIQRLLGDMY 277
           L  +++  +      F +LL  +  LR +     + +   K+T  +  +  LL ++Y
Sbjct: 207 LEFHLQANHPDAQQLFPKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIY 263

>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 = 70.0 bits (171), Expect = 3e-14
 Identities = 18/80 (22%), Positives = 36/80 (45%), Gaps = 1/80 (1%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
             + PGL++   VE +QD     L  +++  +      F +LL  +  LR +     + +
Sbjct: 184 CGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQQLFPKLLQKMADLRQLVTEHAQMM 243

Query: 342 F-FKETIGDIPIQRLLGDMY 360
              K+T  +  +  LL ++Y
Sbjct: 244 QRIKKTETETSLHPLLQEIY 263

>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 =  138 bits (349), Expect = 9e-40
 Identities = 58/189 (30%), Positives = 97/189 (51%), Gaps = 1/189 (0%)

Query: 89  EKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLL 148
               +   + LF  V W + +  F  L   DQ++LL+  W EL +   +  SI     +L
Sbjct: 38  TNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGIL 97

Query: 149 INCEKARERLPPDDVRVNNE-IKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVD 207
           +       R       V     +++ E++++ R +  D +E GC++A++LF P++ GL +
Sbjct: 98  LATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSN 157

Query: 208 AQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDI 267
              VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF + IGD 
Sbjct: 158 PAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDT 217

Query: 268 PIQRLLGDM 276
           PI   L +M
Sbjct: 218 PIDTFLMEM 226

>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 = 72.8 bits (178), Expect = 1e-15
 Identities = 30/74 (40%), Positives = 43/74 (58%)

Query: 286 PGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKE 345
            GL +   VE L+++    L  Y + +Y  QP RF +LLL LP+LR++    +E LFF +
Sbjct: 153 KGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFK 212

Query: 346 TIGDIPIQRLLGDM 359
            IGD PI   L +M
Sbjct: 213 LIGDTPIDTFLMEM 226

>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 =  137 bits (345), Expect = 4e-39
 Identities = 45/208 (21%), Positives = 84/208 (40%), Gaps = 4/208 (1%)

Query: 72  THQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKEL 131
             +        +     ++  +  +  L +  +W   +  F  LS  DQ LLL+ ++ EL
Sbjct: 25  FQELVLPHFGKEDAGDVQQFYDLLSGSLEVIRKWAEKIPGFAELSPADQDLLLESAFLEL 84

Query: 132 FLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGC 191
           F+L LA  S P +  L+        RL        + I  I         L  D     C
Sbjct: 85  FILRLAYRSKPGEGKLIFCSGLVLHRLQCAR-GFGDWIDSILAFSRSLHSLLVDVPAFAC 143

Query: 192 MKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGR--YSRQPTRFGRLLLMLPSLRA 249
           + A ++   +  GL + + VE LQ++    L ++V       +  +   RLL  LP LR 
Sbjct: 144 LSA-LVLITDRHGLQEPRRVEELQNRIASCLKEHVAAVAGEPQPASCLSRLLGKLPELRT 202

Query: 250 VRQSTIERLFFKETIGDIPIQRLLGDMY 277
           +    ++R+F+ +    +P   ++  ++
Sbjct: 203 LCTQGLQRIFYLKLEDLVPPPPIIDKIF 230

>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 = 69.7 bits (170), Expect = 2e-14
 Identities = 18/79 (22%), Positives = 38/79 (48%), Gaps = 2/79 (2%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGR--YSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
           +  GL + + VE LQ++    L ++V       +  +   RLL  LP LR +    ++R+
Sbjct: 152 DRHGLQEPRRVEELQNRIASCLKEHVAAVAGEPQPASCLSRLLGKLPELRTLCTQGLQRI 211

Query: 342 FFKETIGDIPIQRLLGDMY 360
           F+ +    +P   ++  ++
Sbjct: 212 FYLKLEDLVPPPPIIDKIF 230

>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 =  135 bits (341), Expect = 4e-38
 Identities = 34/189 (17%), Positives = 72/189 (38%), Gaps = 2/189 (1%)

Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
           CQ T+   +     + + +  F  L   DQ+ LL+    E     L+       + +   
Sbjct: 75  CQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGMLVAYG 134

Query: 151 CEKARERLPPDDVRVNNE-IKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
                        +   + ++   +   +F  L  D S+     A I+   + PGL++  
Sbjct: 135 NGFITREFLKSLRKPFCDIMEPKFDFAMKFNALELDDSDISLFVAAIICCGDRPGLLNVG 194

Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLF-FKETIGDIP 268
            +E +Q+    +L  +++  +      F +LL  +  LR +     + +   K+T  D  
Sbjct: 195 HIEKMQEGIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQLVTEHAQLVQIIKKTESDAA 254

Query: 269 IQRLLGDMY 277
           +  LL ++Y
Sbjct: 255 LHPLLQEIY 263

>d2p54a1 a.123.1.1 (A:202-468) Peroxisome proliferator activated receptor alpha, PPAR-alpha {Human (Homo sapiens) [TaxId: 9606]} Length = 267

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Peroxisome proliferator activated receptor alpha, PPAR-alpha
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 74.3 bits (182), Expect = 1e-15
 Identities = 17/80 (21%), Positives = 37/80 (46%), Gaps = 1/80 (1%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
             + PGL++   +E +Q+    +L  +++  +      F +LL  +  LR +     + +
Sbjct: 184 CGDRPGLLNVGHIEKMQEGIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQLVTEHAQLV 243

Query: 342 F-FKETIGDIPIQRLLGDMY 360
              K+T  D  +  LL ++Y
Sbjct: 244 QIIKKTESDAALHPLLQEIY 263

>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 =  132 bits (332), Expect = 3e-37
 Identities = 43/195 (22%), Positives = 74/195 (37%), Gaps = 11/195 (5%)

Query: 93  ETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCE 152
           +   + L   + W + +  F  LS  DQ+ LL+  W E+ ++ L   SI     L+   +
Sbjct: 39  KLADKELVHMIGWAKKIPGFVELSLLDQVRLLESCWMEVLMVGLMWRSIDHPGKLIFAPD 98

Query: 153 KARERLPPDDVRVNNE-IKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPV 211
              +R     V    E   ++    +RFR+L     E  C+KA+IL       L  A   
Sbjct: 99  LVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLASANQE 158

Query: 212 EMLQDQAQCILGDYV----------RGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFK 261
                +   +L                   +Q  R   LL++L  +R +    +E L   
Sbjct: 159 AESSRKLTHLLNAVTDALVWVIAKSGISSQQQSVRLANLLMLLSHVRHISNKGMEHLLSM 218

Query: 262 ETIGDIPIQRLLGDM 276
           +    +P+  LL +M
Sbjct: 219 KCKNVVPVYDLLLEM 233

>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 = 64.0 bits (155), Expect = 2e-12
 Identities = 15/88 (17%), Positives = 28/88 (31%), Gaps = 10/88 (11%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYV----------RGRYSRQPTRFGRLLLMLPSLR 331
           +     L  A        +   +L                   +Q  R   LL++L  +R
Sbjct: 146 NSSMYPLASANQEAESSRKLTHLLNAVTDALVWVIAKSGISSQQQSVRLANLLMLLSHVR 205

Query: 332 AVRQSTIERLFFKETIGDIPIQRLLGDM 359
            +    +E L   +    +P+  LL +M
Sbjct: 206 HISNKGMEHLLSMKCKNVVPVYDLLLEM 233

>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 =  132 bits (333), Expect = 3e-37
 Identities = 42/196 (21%), Positives = 79/196 (40%), Gaps = 12/196 (6%)

Query: 93  ETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCE 152
               R L   + W + +  F  L+  DQ+ LL+ +W E+ ++ L   S+     LL    
Sbjct: 42  NLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPN 101

Query: 153 KARERLPPDDVRVNNE-IKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQP- 210
              +R     V    E   ++    +RFR ++  G E  C+K++IL        + +   
Sbjct: 102 LLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLK 161

Query: 211 -------VEMLQDQAQCILGDYVR---GRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFF 260
                  +  + D+    L   +        +Q  R  +LLL+L  +R +    +E L+ 
Sbjct: 162 SLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYS 221

Query: 261 KETIGDIPIQRLLGDM 276
            +    +P+  LL +M
Sbjct: 222 MKCKNVVPLYDLLLEM 237

>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 = 70.5 bits (172), Expect = 1e-14
 Identities = 17/81 (20%), Positives = 33/81 (40%), Gaps = 3/81 (3%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVR---GRYSRQPTRFGRLLLMLPSLRAVRQSTI 338
           S     L +   +  + D+    L   +        +Q  R  +LLL+L  +R +    +
Sbjct: 157 SSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGM 216

Query: 339 ERLFFKETIGDIPIQRLLGDM 359
           E L+  +    +P+  LL +M
Sbjct: 217 EHLYSMKCKNVVPLYDLLLEM 237

>d1ovla_ a.123.1.1 (A:) Orphan nuclear receptor NURR1 {Human (Homo sapiens) [TaxId: 9606]} Length = 236

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NURR1
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  131 bits (330), Expect = 7e-37
 Identities = 47/212 (22%), Positives = 86/212 (40%), Gaps = 4/212 (1%)

Query: 68  MFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQES 127
            +      P +          ++  +     + +   W   +  F  L K DQ LL + +
Sbjct: 21  DYSRFQANPDYQMSGDDTQHIQQFYDLLTGSMEIIRGWAEKIPGFADLPKADQDLLFESA 80

Query: 128 WKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGS 187
           + ELF+L LA  S P +  L+        RL          I  I E  +  + ++ D S
Sbjct: 81  FLELFVLRLAYRSNPVEGKLIFCNGVVLHRLQCVR-GFGEWIDSIVEFSSNLQNMNIDIS 139

Query: 188 ECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSR--QPTRFGRLLLMLP 245
              C+ A+ + T    GL + + VE LQ++    L D+V        +P    +LL  LP
Sbjct: 140 AFSCIAALAMVTE-RHGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLGKLP 198

Query: 246 SLRAVRQSTIERLFFKETIGDIPIQRLLGDMY 277
            LR +    ++R+F+ +    +P   ++  ++
Sbjct: 199 ELRTLCTQGLQRIFYLKLEDLVPPPAIIDKLF 230

>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 = 69.3 bits (169), Expect = 3e-14
 Identities = 19/77 (24%), Positives = 37/77 (48%), Gaps = 2/77 (2%)

Query: 286 PGLVDAQPVEMLQDQAQCILGDYVRGRYSR--QPTRFGRLLLMLPSLRAVRQSTIERLFF 343
            GL + + VE LQ++    L D+V        +P    +LL  LP LR +    ++R+F+
Sbjct: 154 HGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLGKLPELRTLCTQGLQRIFY 213

Query: 344 KETIGDIPIQRLLGDMY 360
            +    +P   ++  ++
Sbjct: 214 LKLEDLVPPPAIIDKLF 230

>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 =  131 bits (331), Expect = 9e-37
 Identities = 41/213 (19%), Positives = 74/213 (34%), Gaps = 1/213 (0%)

Query: 66  PSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQ 125
           P             G    L +     +     +   V + + L  F  L   DQ++LL+
Sbjct: 37  PEDIGQAPIVNAPEGGKVDLEAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLK 96

Query: 126 ESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPD 185
               E+  L  A    P   +L +N E A  R    +  +      I ++       + D
Sbjct: 97  GCCMEIMSLRAAVRYDPESETLTLNGEMAVTRGQLKNGGLGVVSDAIFDLGMSLSSFNLD 156

Query: 186 GSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLP 245
            +E   ++AV+L + + PGL   + +E  QD        Y+  R       + +LL+ + 
Sbjct: 157 DTEVALLQAVLLMSSDRPGLACVERIEKYQDSFLLAFEHYINYRKHHVTHFWPKLLMKVT 216

Query: 246 SLRAVRQSTIERLF-FKETIGDIPIQRLLGDMY 277
            LR +      R    K          L  +++
Sbjct: 217 DLRMIGACHASRFLHMKVECPTELFPPLFLEVF 249

>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 = 68.1 bits (166), Expect = 1e-13
 Identities = 16/80 (20%), Positives = 28/80 (35%), Gaps = 1/80 (1%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
           S + PGL   + +E  QD        Y+  R       + +LL+ +  LR +      R 
Sbjct: 170 SSDRPGLACVERIEKYQDSFLLAFEHYINYRKHHVTHFWPKLLMKVTDLRMIGACHASRF 229

Query: 342 F-FKETIGDIPIQRLLGDMY 360
              K          L  +++
Sbjct: 230 LHMKVECPTELFPPLFLEVF 249

>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 =  130 bits (327), Expect = 7e-36
 Identities = 42/278 (15%), Positives = 95/278 (34%), Gaps = 14/278 (5%)

Query: 12  IHNAHHQ---DSKLEPHNPHHSPDLLPPNGISSVKIPPTVLYPPSGLKSPPPPSHHHPS- 67
           + +A  +    +     N      L     +      P+        +          S 
Sbjct: 13  LMDAQMKTFDTTFSHFKNFRLPGVLSSGCELPESLQAPSREEAAKWSQVRKDLCSLKVSL 72

Query: 68  ------MFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQL 121
                   +  ++PP   G  +I        + +  +    + + + ++ F+ L   DQ+
Sbjct: 73  QLRGEDGSVWNYKPPADSGGKEIFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQI 132

Query: 122 LLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQ 181
            LL+ +  EL  L           +                 +    ++ + +     ++
Sbjct: 133 SLLKGAAFELCQLRFNTVFNAETGTWECGRLSYCLEDTAGGFQ-QLLLEPMLKFHYMLKK 191

Query: 182 LSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP--TRFGR 239
           L     E   M+A+ LF+P+ PG++  + V+ LQ+Q    L  Y+     +      F +
Sbjct: 192 LQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLK 251

Query: 240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMY 277
           ++ ML  LR++     +RL   + I       L+ +++
Sbjct: 252 IMAMLTELRSINAQHTQRLLRIQDI-HPFATPLMQELF 288

>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 = 57.4 bits (138), Expect = 6e-10
 Identities = 18/81 (22%), Positives = 37/81 (45%), Gaps = 3/81 (3%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP--TRFGRLLLMLPSLRAVRQSTIE 339
           S + PG++  + V+ LQ+Q    L  Y+     +      F +++ ML  LR++     +
Sbjct: 209 SPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLKIMAMLTELRSINAQHTQ 268

Query: 340 RLFFKETIGDIPIQRLLGDMY 360
           RL   + I       L+ +++
Sbjct: 269 RLLRIQDI-HPFATPLMQELF 288

>d1pdua_ a.123.1.1 (A:) Nuclear hormone receptor HR38 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 230

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Nuclear hormone receptor HR38
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score =  128 bits (322), Expect = 9e-36
 Identities = 50/225 (22%), Positives = 87/225 (38%), Gaps = 12/225 (5%)

Query: 55  LKSPPPPSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQT 114
           + + P PS    S +    +              ++  +     + +  ++   +  +  
Sbjct: 13  VDTTPDPSCLDYSHY---EEQSMSE-----ADKVQQFYQLLTSSVDVIKQFAEKIPGYFD 64

Query: 115 LSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQE 174
           L   DQ LL Q +  ELF+L LA  +   D  L+        R           +  I E
Sbjct: 65  LLPEDQELLFQSASLELFVLRLAYRARIDDTKLIFCNGTVLHR-TQCLRSFGEWLNDIME 123

Query: 175 ILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYS--R 232
                  L  D S   C+ A+ L T    GL + + VE LQ +    L D+V       +
Sbjct: 124 FSRSLHNLEIDISAFACLCALTLITE-RHGLREPKKVEQLQMKIIGSLRDHVTYNAEAQK 182

Query: 233 QPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMY 277
           +   F RLL  LP LR++    ++R+F+ +    +P   L+ +M+
Sbjct: 183 KQHYFSRLLGKLPELRSLSVQGLQRIFYLKLEDLVPAPALIENMF 227

>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 = 68.5 bits (167), Expect = 5e-14
 Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 2/79 (2%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYS--RQPTRFGRLLLMLPSLRAVRQSTIERL 341
           E  GL + + VE LQ +    L D+V       ++   F RLL  LP LR++    ++R+
Sbjct: 149 ERHGLREPKKVEQLQMKIIGSLRDHVTYNAEAQKKQHYFSRLLGKLPELRSLSVQGLQRI 208

Query: 342 FFKETIGDIPIQRLLGDMY 360
           F+ +    +P   L+ +M+
Sbjct: 209 FYLKLEDLVPAPALIENMF 227

>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 =  122 bits (306), Expect = 2e-33
 Identities = 40/216 (18%), Positives = 88/216 (40%), Gaps = 6/216 (2%)

Query: 65  HPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLL 124
            P+     HQP P      +L       +    ++   +++ + L  F++L   DQ+ LL
Sbjct: 35  PPAHLFIHHQPLPTLA--PVLPLVTHFADINTFMVLQVIKFTKDLPVFRSLPIEDQISLL 92

Query: 125 QESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSP 184
           + +  E+  + L         + L    +               ++L+       R+L  
Sbjct: 93  KGAAVEICHIVLNTTFCLQTQNFLCGPLRYTIEDGARVGFQVEFLELLFHFHGTLRKLQL 152

Query: 185 DGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSR--QPTRFGRLLL 242
              E   + A+ LF+P+ PG+     ++ LQ++    L  Y++G+  R      + +LL 
Sbjct: 153 QEPEYVLLAAMALFSPDRPGVTQRDEIDQLQEEMALTLQSYIKGQQRRPRDRFLYAKLLG 212

Query: 243 MLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT 278
           +L  LR++ ++   ++   +  G   +  LL ++ +
Sbjct: 213 LLAELRSINEAYGYQIQHIQ--GLSAMMPLLQEICS 246

>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 = 64.3 bits (156), Expect = 2e-12
 Identities = 17/82 (20%), Positives = 40/82 (48%), Gaps = 4/82 (4%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSR--QPTRFGRLLLMLPSLRAVRQSTIE 339
           S + PG+     ++ LQ++    L  Y++G+  R      + +LL +L  LR++ ++   
Sbjct: 167 SPDRPGVTQRDEIDQLQEEMALTLQSYIKGQQRRPRDRFLYAKLLGLLAELRSINEAYGY 226

Query: 340 RLFFKETIGDIPIQRLLGDMYT 361
           ++   +  G   +  LL ++ +
Sbjct: 227 QIQHIQ--GLSAMMPLLQEICS 246

>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 =  122 bits (306), Expect = 3e-33
 Identities = 40/212 (18%), Positives = 70/212 (33%), Gaps = 15/212 (7%)

Query: 74  QPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFL 133
           +P     LL  L       +   R L   V+W + L  F+ L   DQ+ L+Q SW  L +
Sbjct: 26  KPDTSSSLLTSL------NQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMV 79

Query: 134 LHLAQWSIPWDLS--LLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGC 191
             L   S        L    +         +    +    + +I   F +L     E  C
Sbjct: 80  FGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLC 139

Query: 192 MKAVILFTPETP-GLVDAQPVEMLQDQAQCILGDYVRGR---YSRQPTRFGRLLLMLPSL 247
           MK ++L       GL      E ++      L   +  R         RF +L  +L +L
Sbjct: 140 MKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSSSQRFYQLTKLLDNL 199

Query: 248 RAVRQSTIER---LFFKETIGDIPIQRLLGDM 276
             + +         F +     +    ++ ++
Sbjct: 200 HDLVKQLHLYCLNTFIQSRALSVEFPEMMSEV 231

>d1sqna_ a.123.1.1 (A:) Progesterone receptor {Human (Homo sapiens) [TaxId: 9606]} Length = 251

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Progesterone receptor
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (134), Expect = 1e-09
 Identities = 11/84 (13%), Positives = 26/84 (30%), Gaps = 6/84 (7%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGR---YSRQPTRFGRLLLMLPSLRAVRQSTI 338
           +    GL      E ++      L   +  R         RF +L  +L +L  + +   
Sbjct: 148 TIPLEGLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDLVKQLH 207

Query: 339 ER---LFFKETIGDIPIQRLLGDM 359
                 F +     +    ++ ++
Sbjct: 208 LYCLNTFIQSRALSVEFPEMMSEV 231

>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 =  120 bits (303), Expect = 6e-33
 Identities = 40/187 (21%), Positives = 68/187 (36%), Gaps = 4/187 (2%)

Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
             E     + + V + + L  FQTL   DQ+ LL+ S  E   L  A+    ++  L   
Sbjct: 47  LTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEI---FNKKLPSG 103

Query: 151 CEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQP 210
                E    +    +  I  +        +L     E   + A+++ +P+   + D + 
Sbjct: 104 HSDLLEERIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREA 163

Query: 211 VEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQ 270
           VE LQ+    +L    +      P  F  LL  L  LR       E L     + D    
Sbjct: 164 VEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAEMLMSW-RVNDHKFT 222

Query: 271 RLLGDMY 277
            LL +++
Sbjct: 223 PLLCEIW 229

>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 = 66.6 bits (162), Expect = 2e-13
 Identities = 18/78 (23%), Positives = 28/78 (35%), Gaps = 1/78 (1%)

Query: 283 YETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLF 342
            +   + D + VE LQ+    +L    +      P  F  LL  L  LR       E L 
Sbjct: 153 PDRQYIKDREAVEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAEMLM 212

Query: 343 FKETIGDIPIQRLLGDMY 360
               + D     LL +++
Sbjct: 213 SW-RVNDHKFTPLLCEIW 229

>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 =  121 bits (304), Expect = 6e-33
 Identities = 37/193 (19%), Positives = 76/193 (39%), Gaps = 9/193 (4%)

Query: 93  ETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLI--N 150
           E   R L   V+W + L  F+ L   DQ+ ++Q SW  L +  +   S     S ++   
Sbjct: 38  ELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFA 97

Query: 151 CEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTP-ETPGLVDAQ 209
            +           R+ ++   ++ +   F  L     E  CMKA++LF+     GL + +
Sbjct: 98  PDLVFNEYRMHKSRMYSQCVRMRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQK 157

Query: 210 PVEMLQDQAQCILGDYVRGRYSR---QPTRFGRLLLMLPSLRAVRQSTIER---LFFKET 263
             + L+      L   +  +         RF +L  +L S++ + +   +    L  K  
Sbjct: 158 FFDELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPIARELHQFTFDLLIKSH 217

Query: 264 IGDIPIQRLLGDM 276
           +  +    ++ ++
Sbjct: 218 MVSVDFPEMMAEI 230

>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 = 58.6 bits (141), Expect = 2e-10
 Identities = 11/82 (13%), Positives = 30/82 (36%), Gaps = 6/82 (7%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSR---QPTRFGRLLLMLPSLRAVRQSTIER 340
              GL + +  + L+      L   +  +         RF +L  +L S++ + +   + 
Sbjct: 149 PVDGLKNQKFFDELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPIARELHQF 208

Query: 341 ---LFFKETIGDIPIQRLLGDM 359
              L  K  +  +    ++ ++
Sbjct: 209 TFDLLIKSHMVSVDFPEMMAEI 230

>d1pq9a_ a.123.1.1 (A:) Oxysterols receptor LXR-beta {Human (Homo sapiens) [TaxId: 9606]} Length = 239

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Oxysterols receptor LXR-beta
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  120 bits (301), Expect = 1e-32
 Identities = 44/188 (23%), Positives = 78/188 (41%), Gaps = 2/188 (1%)

Query: 91  CQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLIN 150
             E     +   V + + +  F  L + DQ+ LL+ S  E+ LL  A+        +   
Sbjct: 52  FTELAIISVQEIVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETARRYNHETECITFL 111

Query: 151 CEKARERLPPDDVRVNNE-IKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ 209
            +    +       +  E I  I E     R+L  D +E   + A+ +F+ + P + +  
Sbjct: 112 KDFTYSKDDFHRAGLQVEFINPIFEFSRAMRRLGLDDAEYALLIAINIFSADRPNVQEPG 171

Query: 210 PVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI 269
            VE LQ      L  Y R +  +   RF R+L+ L SLR +     E++F    + D  +
Sbjct: 172 RVEALQQPYVEALLSYTRIKRPQDQLRFPRMLMKLVSLRTLSSVHSEQVFAL-RLQDKKL 230

Query: 270 QRLLGDMY 277
             LL +++
Sbjct: 231 PPLLSEIW 238

>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 = 63.9 bits (155), Expect = 2e-12
 Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 1/79 (1%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
           S + P + +   VE LQ      L  Y R +  +   RF R+L+ L SLR +     E++
Sbjct: 161 SADRPNVQEPGRVEALQQPYVEALLSYTRIKRPQDQLRFPRMLMKLVSLRTLSSVHSEQV 220

Query: 342 FFKETIGDIPIQRLLGDMY 360
           F    + D  +  LL +++
Sbjct: 221 FAL-RLQDKKLPPLLSEIW 238

>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 =  119 bits (300), Expect = 2e-32
 Identities = 44/234 (18%), Positives = 81/234 (34%), Gaps = 25/234 (10%)

Query: 51  PPSGLKSPPPPSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLA 110
            P  L +    S            P     ++  L           R +  AV+W + + 
Sbjct: 11  EPEVLYAGYDSS-----------VPDSTWRIMTTL------NMLGGRQVIAAVKWAKAIP 53

Query: 111 PFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS--LLINCEKARERLPPDDVRVNNE 168
            F+ L   DQ+ LLQ SW  L    L   S     +  L    +            + ++
Sbjct: 54  GFRNLHLDDQMTLLQYSWMSLMAFALGWRSYRQSSANLLCFAPDLIINEQRMTLPDMYDQ 113

Query: 169 IKLIQEILARFRQLSPDGSECGCMKAVILFTPET-PGLVDAQPVEMLQDQAQCILGDYVR 227
            K +  + +   +L     E  CMK ++L +     GL   +  + ++      LG  + 
Sbjct: 114 CKHMLYVSSELHRLQVSYEEYLCMKTLLLLSSVPKDGLKSQELFDEIRMTYIKELGKAIV 173

Query: 228 GRYS---RQPTRFGRLLLMLPSLRAVRQSTIERLF--FKETIGDIPIQRLLGDM 276
            R     +   RF +L  +L S+  V ++ +   F  F +    I    +L ++
Sbjct: 174 KREGNSSQNWQRFYQLTKLLDSMHEVVENLLNYCFQTFLDKTMSIEFPEMLAEI 227

>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 = 55.9 bits (134), Expect = 1e-09
 Identities = 15/79 (18%), Positives = 31/79 (39%), Gaps = 5/79 (6%)

Query: 286 PGLVDAQPVEMLQDQAQCILGDYVRGRYS---RQPTRFGRLLLMLPSLRAVRQSTIERLF 342
            GL   +  + ++      LG  +  R     +   RF +L  +L S+  V ++ +   F
Sbjct: 149 DGLKSQELFDEIRMTYIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEVVENLLNYCF 208

Query: 343 --FKETIGDIPIQRLLGDM 359
             F +    I    +L ++
Sbjct: 209 QTFLDKTMSIEFPEMLAEI 227

>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 =  118 bits (296), Expect = 7e-32
 Identities = 39/209 (18%), Positives = 78/209 (37%), Gaps = 5/209 (2%)

Query: 72  THQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKEL 131
           T             M   +  E T   + + V + + L  F  +S+ DQ+ LL+    E+
Sbjct: 34  TQTWQSDEDDEDSDMPFRQITEMTILTVQLIVEFAKGLPGFAKISQSDQITLLKACSSEV 93

Query: 132 FLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGC 191
            +L +A+       S+L    +A  R       +   I+ +         +  D      
Sbjct: 94  MMLRVARRYDAATDSVLFANNQAYTRDNYRKAGMAYVIEDLLHFCRCMYSMMMDNVHYAL 153

Query: 192 MKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP---TRFGRLLLMLPSLR 248
           + A+++F+   PGL     VE +Q      L  Y+  + S  P     FG++L +L  +R
Sbjct: 154 LTAIVIFSDR-PGLEQPLLVEEIQRYYLNTLRVYILNQNSASPRCAVIFGKILGILTEIR 212

Query: 249 AVRQSTIERLFFKETIGDIPIQRLLGDMY 277
            +           + + +  +   L +++
Sbjct: 213 TLGMQNSNMCISLK-LKNRKLPPFLEEIW 240

>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 = 55.8 bits (134), Expect = 1e-09
 Identities = 16/80 (20%), Positives = 32/80 (40%), Gaps = 4/80 (5%)

Query: 284 ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP---TRFGRLLLMLPSLRAVRQSTIER 340
           + PGL     VE +Q      L  Y+  + S  P     FG++L +L  +R +       
Sbjct: 162 DRPGLEQPLLVEEIQRYYLNTLRVYILNQNSASPRCAVIFGKILGILTEIRTLGMQNSNM 221

Query: 341 LFFKETIGDIPIQRLLGDMY 360
               + + +  +   L +++
Sbjct: 222 CISLK-LKNRKLPPFLEEIW 240

>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 =  117 bits (293), Expect = 2e-31
 Identities = 34/231 (14%), Positives = 84/231 (36%), Gaps = 10/231 (4%)

Query: 47  TVLYPPSGLKSPPPPSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWV 106
           T  Y    L      +H +        +         +    ++C       +   V + 
Sbjct: 19  TCQYTMEELHQLAWQTHTYEE-----IKAYQSKSREALW---QQCAIQITHAIQYVVEFA 70

Query: 107 RCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVN 166
           + +  F  L + DQ+LLL+    E+ L+ + +   P + ++L   +    ++    +  +
Sbjct: 71  KRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPLNNTVLFEGKYGGMQMFKA-LGSD 129

Query: 167 NEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYV 226
           + +    +       L     E     + +L +P+   L++ + V+ LQ++    L   +
Sbjct: 130 DLVNEAFDFAKNLCSLQLTEEEIALFSSAVLISPDRAWLLEPRKVQKLQEKIYFALQHVI 189

Query: 227 RGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMY 277
           +  +        +L+  +P++ AV     E+L   +      +  L   +Y
Sbjct: 190 QKNH-LDDETLAKLIAKIPTITAVCNLHGEKLQVFKQSHPDIVNTLFPPLY 239

>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 = 59.0 bits (142), Expect = 9e-11
 Identities = 14/79 (17%), Positives = 33/79 (41%), Gaps = 1/79 (1%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
           S +   L++ + V+ LQ++    L   ++  +        +L+  +P++ AV     E+L
Sbjct: 162 SPDRAWLLEPRKVQKLQEKIYFALQHVIQKNH-LDDETLAKLIAKIPTITAVCNLHGEKL 220

Query: 342 FFKETIGDIPIQRLLGDMY 360
              +      +  L   +Y
Sbjct: 221 QVFKQSHPDIVNTLFPPLY 239

>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 =  114 bits (285), Expect = 4e-30
 Identities = 35/212 (16%), Positives = 84/212 (39%), Gaps = 6/212 (2%)

Query: 72  THQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKEL 131
                     L  L       +  +  +   + + + +  F+ L+  DQ++LL+ S  E+
Sbjct: 43  NDGGGSVTLELSQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEV 102

Query: 132 FLLHLAQWSIPWDLSLLI--NCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSEC 189
            +L   +     D+S        K R             I+ + +     ++L+    E 
Sbjct: 103 IMLRSNESFTMDDMSWTCGNQDYKYRVSDVTKAGHSLELIEPLIKFQVGLKKLNLHEEEH 162

Query: 190 GCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSR--QPTRFGRLLLMLPSL 247
             + A+ + +P+ PG+ DA  +E +QD+    L  Y+R R+        + +++  L  L
Sbjct: 163 VLLMAICIVSPDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLLYAKMIQKLADL 222

Query: 248 RAVRQSTIERLFFKETIGDIPIQ--RLLGDMY 277
           R++ +   ++        +  ++   L+ +++
Sbjct: 223 RSLNEEHSKQYRCLSFQPECSMKLTPLVLEVF 254

>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 = 52.8 bits (126), Expect = 1e-08
 Identities = 16/83 (19%), Positives = 39/83 (46%), Gaps = 4/83 (4%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSR--QPTRFGRLLLMLPSLRAVRQSTIE 339
           S + PG+ DA  +E +QD+    L  Y+R R+        + +++  L  LR++ +   +
Sbjct: 172 SPDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNEEHSK 231

Query: 340 RLFFKETIGDIPIQ--RLLGDMY 360
           +        +  ++   L+ +++
Sbjct: 232 QYRCLSFQPECSMKLTPLVLEVF 254

>d1n83a_ a.123.1.1 (A:) Orphan nuclear receptor ROR-alpha {Human (Homo sapiens) [TaxId: 9606]} Length = 251

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor ROR-alpha
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  113 bits (283), Expect = 6e-30
 Identities = 35/231 (15%), Positives = 83/231 (35%), Gaps = 10/231 (4%)

Query: 47  TVLYPPSGLKSPPPPSHHHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWV 106
           T  Y    L+     +     +    +Q      + Q+      C       +   V + 
Sbjct: 27  TCQYLREELQQITWQTFLQEEI--ENYQNKQREVMWQL------CAIKITEAIQYVVEFA 78

Query: 107 RCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVN 166
           + +  F  L + DQ++LL+    E+  + + +     + ++  + + A   +    +   
Sbjct: 79  KRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQNNTVYFDGKYASPDVFKS-LGCE 137

Query: 167 NEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYV 226
           + I  + E       +     E     A +L + +   L +   +E LQ + Q  L   +
Sbjct: 138 DFISFVFEFGKSLCSMHLTEDEIALFSAFVLMSADRSWLQEKVKIEKLQQKIQLALQHVL 197

Query: 227 RGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMY 277
           +  + R+     +L+  + +LRA+     E+L   + I    ++     +Y
Sbjct: 198 QKNH-REDGILTKLICKVSTLRALCGRHTEKLMAFKAIYPDIVRLHFPPLY 247

>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 = 54.7 bits (131), Expect = 3e-09
 Identities = 16/79 (20%), Positives = 34/79 (43%), Gaps = 1/79 (1%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341
           S +   L +   +E LQ + Q  L   ++  + R+     +L+  + +LRA+     E+L
Sbjct: 170 SADRSWLQEKVKIEKLQQKIQLALQHVLQKNH-REDGILTKLICKVSTLRALCGRHTEKL 228

Query: 342 FFKETIGDIPIQRLLGDMY 360
              + I    ++     +Y
Sbjct: 229 MAFKAIYPDIVRLHFPPLY 247

>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 =  108 bits (270), Expect = 3e-28
 Identities = 36/195 (18%), Positives = 79/195 (40%), Gaps = 4/195 (2%)

Query: 66  PSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQ 125
           P+     H+P    G   +L       +    ++   +++ + L  F++L+  DQ+ LL+
Sbjct: 35  PAYLFMHHRPFQPRG--PVLPLLTHFADINTFMVQQIIKFTKDLPLFRSLTMEDQISLLK 92

Query: 126 ESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPD 185
            +  E+  + L         +        +             ++ I       + L   
Sbjct: 93  GAAVEILHISLNTTFCLQTENFFCGPLCYKMEDAVHAGFQYEFLESILHFHKNLKGLHLQ 152

Query: 186 GSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTR--FGRLLLM 243
             E   M A  LF+P+ PG+   + ++ LQ++   IL +++  + SR  +R  + +L+ +
Sbjct: 153 EPEYVLMAATALFSPDRPGVTQREEIDQLQEEMALILNNHIMEQQSRLQSRFLYAKLMGL 212

Query: 244 LPSLRAVRQSTIERL 258
           L  LR++  +    L
Sbjct: 213 LADLRSINNAYSYEL 227

>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 = 50.8 bits (121), Expect = 5e-08
 Identities = 15/62 (24%), Positives = 34/62 (54%), Gaps = 2/62 (3%)

Query: 282 SYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTR--FGRLLLMLPSLRAVRQSTIE 339
           S + PG+   + ++ LQ++   IL +++  + SR  +R  + +L+ +L  LR++  +   
Sbjct: 166 SPDRPGVTQREEIDQLQEEMALILNNHIMEQQSRLQSRFLYAKLMGLLADLRSINNAYSY 225

Query: 340 RL 341
            L
Sbjct: 226 EL 227

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	367
d2e2ra1	223	Orphan nuclear receptor ERR3 {Human (Homo sapiens)	100.0
d1xpca_	245	Estrogen receptor alpha {Human (Homo sapiens) [Tax	100.0
d1g2na_	256	Ultraspiracle protein, usp {Heliothis virescens [T	100.0
d3d24a1	227	Steroid hormone receptor ERR1 {Human (Homo sapiens	100.0
d1pq9a_	239	Oxysterols receptor LXR-beta {Human (Homo sapiens)	100.0
d1pzla_	233	Hepatocyte nuclear factor 4-alpha {Human (Homo sap	100.0
d1n46a_	251	Thyroid hormone receptor beta (TR-beta) {Human (Ho	100.0
d1fcya_	236	Retinoic acid receptor gamma (RAR-gamma) {Human (H	100.0
d1hg4a_	265	Ultraspiracle protein, usp {Drosophila melanogaste	100.0
d1pk5a_	242	Orphan nuclear receptor NR5a2 (LRH-1) {Mouse (Mus	100.0
d2j7ya1	236	Estrogen receptor beta {Rat (Rattus norvegicus) [T	100.0
d1ovla_	236	Orphan nuclear receptor NURR1 {Human (Homo sapiens	100.0
d2qw4a1	233	Orphan nuclear receptor NR4A1 {Human (Homo sapiens	100.0
d1pdua_	230	Nuclear hormone receptor HR38 {Fruit fly (Drosophi	100.0
d1xvpb_	246	Orphan nuclear receptor NR1I3 (CAR) {Human (Homo s	100.0
d2r40d1	243	Ecdysone receptor {Noctuid moth (Heliothis viresce	100.0
d2p1ta1	230	Retinoid-X receptor alpha (RXR-alpha) {Human (Homo	100.0
d1osha_	231	Bile acid receptor FXR {Human (Homo sapiens) [TaxI	100.0
d1ie9a_	255	Vitamin D nuclear receptor {Human (Homo sapiens) [	100.0
d1t7ra_	250	Androgen receptor {Chimpanzee (Pan troglodytes) [T	100.0
d1nhza_	247	Glucocorticoid receptor {Human (Homo sapiens) [Tax	100.0
d1xnxa_	232	Orphan nuclear receptor NR1I3 (CAR) {Mouse (Mus mu	100.0
d1sqna_	251	Progesterone receptor {Human (Homo sapiens) [TaxId	100.0
d1n83a_	251	Orphan nuclear receptor ROR-alpha {Human (Homo sap	100.0
d1nrla_	292	Pregnane x receptor, PXR {Human (Homo sapiens) [Ta	100.0
d2p54a1	267	Peroxisome proliferator activated receptor alpha,	100.0
d1nq7a_	244	Orphan nuclear receptor ROR-beta {Rat (Rattus norv	100.0
d2fvja1	271	Peroxisome proliferator activated receptor gamma,	100.0
d2b50b1	265	Peroxisome proliferator-activated receptor delta,	100.0
d1pk5a_	242	Orphan nuclear receptor NR5a2 (LRH-1) {Mouse (Mus	99.75
d1hg4a_	265	Ultraspiracle protein, usp {Drosophila melanogaste	99.74
d1g2na_	256	Ultraspiracle protein, usp {Heliothis virescens [T	99.73
d2e2ra1	223	Orphan nuclear receptor ERR3 {Human (Homo sapiens)	99.68
d1fcya_	236	Retinoic acid receptor gamma (RAR-gamma) {Human (H	99.63
d3d24a1	227	Steroid hormone receptor ERR1 {Human (Homo sapiens	99.63
d1osha_	231	Bile acid receptor FXR {Human (Homo sapiens) [TaxI	99.62
d1pzla_	233	Hepatocyte nuclear factor 4-alpha {Human (Homo sap	99.61
d1pq9a_	239	Oxysterols receptor LXR-beta {Human (Homo sapiens)	99.61
d1pdua_	230	Nuclear hormone receptor HR38 {Fruit fly (Drosophi	99.59
d1ovla_	236	Orphan nuclear receptor NURR1 {Human (Homo sapiens	99.59
d2p1ta1	230	Retinoid-X receptor alpha (RXR-alpha) {Human (Homo	99.59
d2qw4a1	233	Orphan nuclear receptor NR4A1 {Human (Homo sapiens	99.57
d1n46a_	251	Thyroid hormone receptor beta (TR-beta) {Human (Ho	99.57
d2fvja1	271	Peroxisome proliferator activated receptor gamma,	99.54
d2p54a1	267	Peroxisome proliferator activated receptor alpha,	99.54
d2b50b1	265	Peroxisome proliferator-activated receptor delta,	99.53
d1xvpb_	246	Orphan nuclear receptor NR1I3 (CAR) {Human (Homo s	99.5
d1ie9a_	255	Vitamin D nuclear receptor {Human (Homo sapiens) [	99.47
d1n83a_	251	Orphan nuclear receptor ROR-alpha {Human (Homo sap	99.42
d1nq7a_	244	Orphan nuclear receptor ROR-beta {Rat (Rattus norv	99.42
d2r40d1	243	Ecdysone receptor {Noctuid moth (Heliothis viresce	99.41
d1nrla_	292	Pregnane x receptor, PXR {Human (Homo sapiens) [Ta	99.41
d1t7ra_	250	Androgen receptor {Chimpanzee (Pan troglodytes) [T	99.32
d1nhza_	247	Glucocorticoid receptor {Human (Homo sapiens) [Tax	99.27
d1sqna_	251	Progesterone receptor {Human (Homo sapiens) [TaxId	99.25
d1xnxa_	232	Orphan nuclear receptor NR1I3 (CAR) {Mouse (Mus mu	99.21
d1xpca_	245	Estrogen receptor alpha {Human (Homo sapiens) [Tax	98.79
d2j7ya1	236	Estrogen receptor beta {Rat (Rattus norvegicus) [T	98.43

>d2e2ra1 a.123.1.1 (A:234-456) Orphan nuclear receptor ERR3 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor ERR3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=9.9e-41  Score=298.11  Aligned_cols=212  Identities=22%  Similarity=0.387  Sum_probs=193.3

Q ss_pred             CCcccccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCC
Q psy6602          65 HPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD  144 (367)
Q Consensus        65 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~  144 (367)
                      +|..++.+|++..|++....   ++++|+++++.++.+|+|||++|||.+|+.+||++|||+||+|+++++.||++...+
T Consensus        12 ep~~~~~~~~~~~~~~~~~~---~~~l~~~a~~~l~~~V~waK~lp~F~~L~~~DQi~LLk~~~~el~~L~~a~~s~~~~   88 (223)
T d2e2ra1          12 EPEKIYAMPDPTVPDSDIKA---LTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFE   88 (223)
T ss_dssp             CCCCCCCCCCTTSCCCHHHH---HHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTSS
T ss_pred             CCCcccCCCCCCCCCchhHH---HHHHHHHHHHHHHHHHHHHHhCcchhhcCHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence            45556777777777765433   788999999999999999999999999999999999999999999999999999888


Q ss_pred             CceEecCCccccCCCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHH
Q psy6602         145 LSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGD  224 (367)
Q Consensus       145 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~  224 (367)
                      +..++.++....+......+..+.++.+.+++.+|++|++|++||+|||||+||+||++|+.++.+|+++|++|..+|++
T Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~l~~L~ld~~E~~lLkaivL~~pd~~~L~~~~~I~~~q~~~~~aL~~  168 (223)
T d2e2ra1          89 DELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQD  168 (223)
T ss_dssp             SCEEEETTEEECHHHHHHTTCHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHTCCCTTCSCHHHHHHHHHHHHHHHHH
T ss_pred             CeeeecCCcccchHHhhhccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHH
Confidence            88878777666555444456778889999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhCCCcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcc
Q psy6602         225 YVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM  279 (367)
Q Consensus       225 y~~~~~~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~  279 (367)
                      |+..+|++.+.||++|+.+++.+|+++..+.|.+++.+.++..++++++.|||++
T Consensus       169 y~~~~~~~~~~rf~~LL~~Lp~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~E~l~a  223 (223)
T d2e2ra1         169 YEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPMHKLFLEMLEA  223 (223)
T ss_dssp             HHHHHCTTCTTHHHHHHTTHHHHHHHHHHHHHHHHHHHHHCCSCCCHHHHHHHTS
T ss_pred             HHHhcCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCchHHHHHHHcC
Confidence            9999999999999999999999999999999999999999999999999999974

>d1xpca_ a.123.1.1 (A:) Estrogen receptor alpha {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Estrogen receptor alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.3e-40  Score=301.56  Aligned_cols=221  Identities=19%  Similarity=0.301  Sum_probs=187.3

Q ss_pred             CcccccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCC
Q psy6602          66 PSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDL  145 (367)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~  145 (367)
                      |..++++|++..+.+..   ..++.+|+++++.++.+|+|||++|||..|+.+||++|||++|+|+++|+.||++...++
T Consensus        18 p~~~~~~~~~~~~~~~~---~~~~~l~~la~~~l~~~V~waK~ip~F~~L~~~DQi~LLk~~~~el~iL~~a~~s~~~~~   94 (245)
T d1xpca_          18 PPILYSEYDPTRPFSEA---SMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPG   94 (245)
T ss_dssp             CCCCCCCSCTTSCSTTS---CHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTSTT
T ss_pred             CCcccCCCCCCCCCCHH---HHHHHHHHHHHHHHHHHHHHHHhCccHHhcCHHHHHHHHHHHHHHHHHHHHHHHhhccCC
Confidence            34455666666655433   337889999999999999999999999999999999999999999999999999998777


Q ss_pred             ceEecCCccccCCCCC-ccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHH
Q psy6602         146 SLLINCEKARERLPPD-DVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGD  224 (367)
Q Consensus       146 ~~l~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~  224 (367)
                      ..++.++....+.... ..++.+.++.+.+++.+|++|++|++||+|||||+||+||++|+++                 
T Consensus        95 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~ld~~E~~lLkaI~L~~pd~~~l~~-----------------  157 (245)
T d1xpca_          95 KLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS-----------------  157 (245)
T ss_dssp             EEEEETTEEEEHHHHTTSTTHHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTTTCCCC-----------------
T ss_pred             ceeecCCcccchhHHhhhccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCccccccc-----------------
Confidence            6666666555443322 2357788899999999999999999999999999999999776432                 


Q ss_pred             HHHhhCCCcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHH
Q psy6602         225 YVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCI  304 (367)
Q Consensus       225 y~~~~~~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~a  304 (367)
                                                                                .++.|+++..+|+.+|+++..+
T Consensus       158 ----------------------------------------------------------~~r~~l~~~~~v~~~q~~~~~a  179 (245)
T d1xpca_         158 ----------------------------------------------------------STLKSLEEKDHIHRVLDKITDT  179 (245)
T ss_dssp             ----------------------------------------------------------CCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ----------------------------------------------------------cchhhhhHHHHHHHHHHHHHHH
Confidence                                                                      2345666777899999999999


Q ss_pred             HHHHHHhhC---CCCcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhccc
Q psy6602         305 LGDYVRGRY---SRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEK  364 (367)
Q Consensus       305 L~~~~~~~~---p~~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~~  364 (367)
                      |.+|+..++   |+++.||++||++||+||+++..+.|++|+.+++|.+++++|+.|||++|+
T Consensus       180 L~~~~~~~~~~~~~~~~Rf~~LL~~Lp~Lr~~~~~~~e~l~~~~~~~~~~~~~Ll~Eml~~~~  242 (245)
T d1xpca_         180 LIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDAHR  242 (245)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCCSSCHHHHHHHHHSCCS
T ss_pred             HHHHHHhcCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCccHHHHHHHHccc
Confidence            999987644   667789999999999999999999999999999999999999999999986

>d1g2na_ a.123.1.1 (A:) Ultraspiracle protein, usp {Heliothis virescens [TaxId: 7102]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Ultraspiracle protein, usp
species: Heliothis virescens [TaxId: 7102]

Probab=100.00  E-value=2.3e-39  Score=295.26  Aligned_cols=194  Identities=28%  Similarity=0.440  Sum_probs=168.5

Q ss_pred             CHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecC---------------
Q psy6602          87 SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINC---------------  151 (367)
Q Consensus        87 ~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~---------------  151 (367)
                      .+.++|+++.+.++.+|+|||++|||..|+.+||++|||++|+|+++++.|||+...........               
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            37889999999999999999999999999999999999999999999999999986544332211               


Q ss_pred             ---CccccCCCCCccchHHHH-HHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHH
Q psy6602         152 ---EKARERLPPDDVRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVR  227 (367)
Q Consensus       152 ---~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~  227 (367)
                         +...++......++.+.. +.+.+++.+|++|++|.+||+|||||+||+||++|+++...|+++|++|..+|++||.
T Consensus       123 ~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~L~ld~~E~~~LkaIvLfnpd~~gL~~~~~Ie~lqe~~~~aL~~y~~  202 (256)
T d1g2na_         123 LMPGMTLHRNSALQAGVGQIFDRVLSELSLKMRTLRVDQAEYVALKAIILLNPDVKGLKNRQEVEVLREKMFLCLDEYCR  202 (256)
T ss_dssp             EETTEEEEHHHHHHHTCHHHHHHHHHHTHHHHHHTTCCHHHHHHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCcccCHHHHHhcchHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCccCCcccHHHHHHHHHHHHHHHHHHHH
Confidence               111111111222334444 5577999999999999999999999999999999999999999999999999999999


Q ss_pred             hhCCCcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHccc
Q psy6602         228 GRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  280 (367)
Q Consensus       228 ~~~~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~  280 (367)
                      .++++++.||++||++|+.||.++....|.+|+.+++|+.++++++.||++..
T Consensus       203 ~~~p~~~~Rf~~LLl~Lp~LR~l~~~~~e~lff~~l~g~~~i~~ll~eml~~~  255 (256)
T d1g2na_         203 RSRSSEEGRFAALLLRLPALRSISLKSFEHLFFFHLVADTSIAGYIRDALRNH  255 (256)
T ss_dssp             HHSTTCTTHHHHHHTHHHHHHHHHHHHHHHHHHTTCBCTTTHHHHHHHHHTCC
T ss_pred             hcCCChhhHHHHHHHHHHHHHHHHHHHHHHHhcccccCCCChHHHHHHHHhcc
Confidence            99999999999999999999999999999999999999999999999999853

>d3d24a1 a.123.1.1 (A:194-420) Steroid hormone receptor ERR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Steroid hormone receptor ERR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=4.5e-39  Score=288.20  Aligned_cols=211  Identities=24%  Similarity=0.388  Sum_probs=176.0

Q ss_pred             CcccccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCC
Q psy6602          66 PSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDL  145 (367)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~  145 (367)
                      |..+++.+++..|++.   ...++++|+++++.++.+|+|||++|+|.+|+.+||++|||++|+++++++.||+++..++
T Consensus        13 p~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~   89 (227)
T d3d24a1          13 PEKLYAMPDPAGPDGH---LPAVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQD   89 (227)
T ss_dssp             CCCCCCCC-------------CHHHHHHHHHHHHHHHHHHHHHSTTTTTSCHHHHHHHHHHHHHHHHHHHHHHHHTTSSS
T ss_pred             CCccccCCCCCCCCch---hHHHHHHHHHHHHHHHHHHHHHHhCcchhcCCHHHHHHHHHHHHHHHHHHHHHHhhccCCC
Confidence            3344455444444443   3448889999999999999999999999999999999999999999999999999998877


Q ss_pred             ceEecCCccccCCCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHH
Q psy6602         146 SLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDY  225 (367)
Q Consensus       146 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y  225 (367)
                      ...+.++...........+..+.++.+.+++.+|++|++|+.||+|||||+||+||++|+++...|+++|++|.++|++|
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~L~ld~~E~~lLkaivLf~pd~~gL~~~~~I~~~q~~~~~aL~~y  169 (227)
T d3d24a1          90 ELAFAEDLVLDEEGARAAGLGELGAALLQLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQLREALHEALLEY  169 (227)
T ss_dssp             EEEEETTEEEEHHHHHHTTCTTHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTCCCTTCSCHHHHHHHHHHHHHHHHHH
T ss_pred             eeeecCCcccchhhhccccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCcCCCcccHHHHHHHHHHHHHHHHHH
Confidence            76666654444333223345567789999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhCC----CcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcc
Q psy6602         226 VRGRYS----RQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM  279 (367)
Q Consensus       226 ~~~~~~----~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~  279 (367)
                      +..+++    ..+.||++|+.+++.+|+++..+.|.+++.+.+|..++++++.|||++
T Consensus       170 ~~~~~~~~~~~~~~Rf~~LL~~Lp~Lr~l~~~~~e~l~~~~~~g~~~~~~Ll~Eml~~  227 (227)
T d3d24a1         170 EAGRAGPGGGAERRRAGRLLLTLPLLRQTAGKVLAHFYGVKLEGKVPMHKLFLEMLEA  227 (227)
T ss_dssp             HTC--------CHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHSCCSCCCHHHHHHHHC
T ss_pred             HHHhcCCCchhHHhHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCchHHHHHHHcC
Confidence            999873    446799999999999999999999999999999999999999999974

>d1pq9a_ a.123.1.1 (A:) Oxysterols receptor LXR-beta {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Oxysterols receptor LXR-beta
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=2e-38  Score=285.94  Aligned_cols=195  Identities=22%  Similarity=0.243  Sum_probs=174.9

Q ss_pred             hhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCc
Q psy6602          83 QILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDD  162 (367)
Q Consensus        83 ~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~  162 (367)
                      .....+.++++++...++.+|+|||++|||..|+.+||++|||+||+|+++++.|++++...+...+.++..+.+.....
T Consensus        44 ~~~~~~~~~~~~~~~~i~~iVefAK~lP~F~~L~~~DQi~LLk~~~~el~ll~~a~~~~~~~~~~~~~~~~~~~~~~~~~  123 (239)
T d1pq9a_          44 ARQQRFAHFTELAIISVQEIVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETARRYNHETECITFLKDFTYSKDDFHR  123 (239)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTSTTSTTSCHHHHHHHHHHHHHHHHHHHHHHTEETTTTEEEEETTEEECHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHhHhhhcCcCHHhcCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEeecCCCcccHHHHhh
Confidence            34445889999999999999999999999999999999999999999999999999998877777776666554433222


Q ss_pred             cch-HHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHH
Q psy6602         163 VRV-NNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLL  241 (367)
Q Consensus       163 ~~~-~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL  241 (367)
                      .+. .+.++.+.+|+.+|++|++|++||+|||||+||+||++|+.+..+|+++|++|..+|+.|+..+||+++.||++|+
T Consensus       124 ~~~~~~~~~~i~~~~~~l~~L~ld~~E~alLkAivL~~pd~~gl~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~rf~~LL  203 (239)
T d1pq9a_         124 AGLQVEFINPIFEFSRAMRRLGLDDAEYALLIAINIFSADRPNVQEPGRVEALQQPYVEALLSYTRIKRPQDQLRFPRML  203 (239)
T ss_dssp             TTCCHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHH
T ss_pred             hhhhHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcCccccHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHH
Confidence            222 4677899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHc
Q psy6602         242 LMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT  278 (367)
Q Consensus       242 ~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~  278 (367)
                      ++++.||+++..+.|.+++.+.. ...+++|+.|||+
T Consensus       204 ~~L~~LR~l~~~~~e~l~~~k~~-~~~~~~L~~Em~d  239 (239)
T d1pq9a_         204 MKLVSLRTLSSVHSEQVFALRLQ-DKKLPPLLSEIWD  239 (239)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTT-TCCCCHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcC-CCCCcHHHHHhcC
Confidence            99999999999999999988864 5678999999986

>d1pzla_ a.123.1.1 (A:) Hepatocyte nuclear factor 4-alpha {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Hepatocyte nuclear factor 4-alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=3.9e-38  Score=283.22  Aligned_cols=200  Identities=29%  Similarity=0.467  Sum_probs=181.5

Q ss_pred             hhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCC
Q psy6602          81 LLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPP  160 (367)
Q Consensus        81 ~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~  160 (367)
                      ......+++++|+++++.++.+|+|||++|+|..|+.+||++|||++|+++++|+.||++...++..++.++....+...
T Consensus        32 ~~~~~~~~~~l~~~a~~~l~~~vewaK~ip~F~~L~~~DQ~~LLk~~~~el~lL~~a~~s~~~~~~~~l~~~~~~~~~~~  111 (233)
T d1pzla_          32 RAKKIASIADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVLLLGNDYIVPRHCP  111 (233)
T ss_dssp             TTSCBCCHHHHHHHHHHHHHHHHHHHTTCHHHHTSCHHHHHHHHHHSHHHHHHHHHHHHHTTSSSEEECTTSCEEESSCG
T ss_pred             cccccccHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCceeecCCccccchhh
Confidence            33455679999999999999999999999999999999999999999999999999999998887777777766655554


Q ss_pred             CccchHH-HHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHH
Q psy6602         161 DDVRVNN-EIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGR  239 (367)
Q Consensus       161 ~~~~~~~-~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~  239 (367)
                      ...+... ..+.+.+++.+|++|++|.+||+|||||+||+||++|+.+..+|+.+|+++.++|++|+..+|++.+.||++
T Consensus       112 ~~~~~~~~~~~~l~~~~~~~~~L~ld~~E~~lLkaiiL~~pd~~~l~~~~~i~~~q~~~~~~L~~y~~~~~~~~~~Rf~~  191 (233)
T d1pzla_         112 ELAEMSRVSIRILDELVLPFQELQIDDNEYAYLKAIIFFDPDAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGE  191 (233)
T ss_dssp             GGGGGHHHHHHHHHHTHHHHHHHTCCHHHHHHHHHHHHCCTTCTTCSCHHHHHHHHHHHHHHHHHHHHSSSSCCTTHHHH
T ss_pred             hhhhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhcccccCCcccHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHH
Confidence            4443333 347788999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHccc
Q psy6602         240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  280 (367)
Q Consensus       240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~  280 (367)
                      |+++++.+|+++..+.|.+++.+.++..++++++.||+..+
T Consensus       192 LLl~Lp~Lr~i~~~~~e~l~~~~~~~~~~~~~Ll~emL~~~  232 (233)
T d1pzla_         192 LLLLLPTLQSITWQMIEQIQFIKLFGMAKIDNLLQEMLLGG  232 (233)
T ss_dssp             HHTHHHHHHHHHHHHHHHHHHHHHTTCSCCCHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcccCCCCChHHHHHHHhccC
Confidence            99999999999999999999999999999999999998754

>d1n46a_ a.123.1.1 (A:) Thyroid hormone receptor beta (TR-beta) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Thyroid hormone receptor beta (TR-beta)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.7e-38  Score=288.10  Aligned_cols=194  Identities=20%  Similarity=0.244  Sum_probs=174.6

Q ss_pred             ccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccc
Q psy6602          85 LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVR  164 (367)
Q Consensus        85 ~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~  164 (367)
                      ...|.++++++++.|+.+|+|||+||||..|+.+||++|||++|+|+++|++|++++..++...+.++....+......+
T Consensus        56 ~~~~~~~~~~~~~~i~~vV~fAK~iPgF~~L~~~DQi~LLk~~~~El~lL~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~  135 (251)
T d1n46a_          56 LEAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLNGEMAVTRGQLKNGG  135 (251)
T ss_dssp             HHHHHHHHTTHHHHHHHHHHHHHTCTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTCBTTTTBEEETTTEEECHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEeCCCccccHHHHhhcc
Confidence            44489999999999999999999999999999999999999999999999999999887777767666555544333334


Q ss_pred             hHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhh
Q psy6602         165 VNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLML  244 (367)
Q Consensus       165 ~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l  244 (367)
                      ..+..+.+.+|+.+|++|++|++||+|||||+||+||++|+.+..+|+++|+++..+|+.|+..++++.+.||++|+.+|
T Consensus       136 ~~~~~~~i~~f~~~l~~L~ld~~E~alL~AivL~~pdr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~rf~kLL~~L  215 (251)
T d1n46a_         136 LGVVSDAIFDLGMSLSSFNLDDTEVALLQAVLLMSSDRPGLACVERIEKYQDSFLLAFEHYINYRKHHVTHFWPKLLMKV  215 (251)
T ss_dssp             TTTHHHHHHHHHHHHGGGTCCHHHHHHHHHHHHTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCCSSTTHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCCcCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHh
Confidence            55677899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHhHhhhhhHHHHHHhhhcc-CCchhHhHHHHHHc
Q psy6602         245 PSLRAVRQSTIERLFFKETI-GDIPIQRLLGDMYT  278 (367)
Q Consensus       245 ~~Lr~l~~~~~e~l~~~~~~-~~~~~~~Ll~eml~  278 (367)
                      +.||+++..+.|.++..+.. ....+++|+.|||+
T Consensus       216 p~LR~l~~~~~e~l~~~k~~~~~~~~ppLl~E~fd  250 (251)
T d1n46a_         216 TDLRMIGACHASRFLHMKVECPTELFPPLFLEVFE  250 (251)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSCGGGSCHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHhc
Confidence            99999999999999888875 44457899999997

>d1fcya_ a.123.1.1 (A:) Retinoic acid receptor gamma (RAR-gamma) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Retinoic acid receptor gamma (RAR-gamma)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.9e-38  Score=285.59  Aligned_cols=191  Identities=21%  Similarity=0.295  Sum_probs=176.2

Q ss_pred             HHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccchHH
Q psy6602          88 AEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNN  167 (367)
Q Consensus        88 ~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~  167 (367)
                      |+++++.+++.++.+|+|||++|||.+|+.+||++|||++|+|+++++.|++++...+...+.++....+......+..+
T Consensus        46 ~~~~~~~~~~~i~~iV~faK~ip~F~~L~~~DQi~LLk~~~~el~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~  125 (236)
T d1fcya_          46 WDKFSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMTFSDGLTLNRTQMHNAGFGP  125 (236)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETTTTEEECTTCBEEEHHHHHHHTTGG
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcccCCeeeccCCceecHHHHhhcccHH
Confidence            78999999999999999999999999999999999999999999999999999887666666666555544433445566


Q ss_pred             HHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhhhHh
Q psy6602         168 EIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSL  247 (367)
Q Consensus       168 ~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~~L  247 (367)
                      .++.+.+|+.+|++|++|++||+|||||+||+||++|+.++..|+++|++|.++|+.|+..++++++.||++|+.+|+.|
T Consensus       126 l~~~~~~~~~~l~~L~ld~~E~alL~Ai~L~~pd~~gL~~~~~Ve~lq~~~~~aL~~y~~~~~~~~~~rf~~LL~~Lp~L  205 (236)
T d1fcya_         126 LTDLVFAFAGQLLPLEMDDTETGLLSAICLICGDRMDLEEPEKVDKLQEPLLEALRLYARRRRPSQPYMFPRMLMKITDL  205 (236)
T ss_dssp             GHHHHHHHHHHHGGGCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHHHhhccCCCCCcccccHHHHHHHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHH
Confidence            77889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhhhhHHHHHHhhhccCCchhHhHHHHHHc
Q psy6602         248 RAVRQSTIERLFFKETIGDIPIQRLLGDMYT  278 (367)
Q Consensus       248 r~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~  278 (367)
                      |+++..+.|.+++.+..+..++++|+.|||+
T Consensus       206 R~l~~~~~e~l~~~k~~~~~~~~~L~~E~~d  236 (236)
T d1fcya_         206 RGISTKGAERAITLKMEIPGPMPPLIREMLE  236 (236)
T ss_dssp             HHHHHHHHHHHHHHHTTSSSCCCHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHhhCCCCCccHHHHHHcC
Confidence            9999999999999999999999999999986

>d1hg4a_ a.123.1.1 (A:) Ultraspiracle protein, usp {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Ultraspiracle protein, usp
species: Drosophila melanogaster [TaxId: 7227]

Probab=100.00  E-value=9.4e-38  Score=286.06  Aligned_cols=199  Identities=23%  Similarity=0.360  Sum_probs=169.4

Q ss_pred             ccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCcc----------
Q psy6602          85 LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKA----------  154 (367)
Q Consensus        85 ~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~----------  154 (367)
                      ..+++++|+++.+.++.+|+|||++|||..|+.+||++|||++|+|+++|+.||++............+.          
T Consensus        38 ~~~~~~l~~~~~~~L~~~VewaK~lP~F~~L~~~DQ~~LLk~~~~el~iL~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~  117 (265)
T d1hg4a_          38 KGAVSALCQVVNKQLFQMVEYARMMPHFAQVPLDDQVILLKAAWIELLIANVAWCSIVSLDDGGAGGGGGGLGHDGSFER  117 (265)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTTC--------------------
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHcCCchhcCCHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccccchhhhc
Confidence            4458899999999999999999999999999999999999999999999999999986654433222211          


Q ss_pred             -----------------ccCCCCCccchHH-HHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHH
Q psy6602         155 -----------------RERLPPDDVRVNN-EIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQD  216 (367)
Q Consensus       155 -----------------~~~~~~~~~~~~~-~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~  216 (367)
                                       ..+......+... ..+.+.+++.+|++|++|++||+|||||+||+||++|+++...|+++|+
T Consensus       118 ~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~L~ld~~E~~lLkaivLf~pd~~~l~~~~~Ie~lqe  197 (265)
T d1hg4a_         118 RSPGLQPQQLFLNQSFSYHRNSAIKAGVSAIFDRILSELSVKMKRLNLDRRELSCLKAIILYNPDIRGIKSRAEIEMCRE  197 (265)
T ss_dssp             -----CCCEEESSSSCEEEHHHHHHHTCHHHHHHHHHHTHHHHHHHTCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHH
T ss_pred             cCcccCcceeeccCCcccchHHHHHhccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHccccCCCCcCHHHHHHHHH
Confidence                             0000000112222 3366789999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhCCCcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCC
Q psy6602         217 QAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSY  283 (367)
Q Consensus       217 ~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~  283 (367)
                      +++.+|++||..++|+++.||++|+++|+.||.++..+.|.+++.+.++..++++|+.||++...+|
T Consensus       198 ~~~~aL~~y~~~~~p~~~~Rf~~LLl~Lp~Lr~l~~~~~e~l~~~~~~g~~~i~~Ll~Eml~~~~~~  264 (265)
T d1hg4a_         198 KVYACLDEHCRLEHPGDDGRFAQLLLRLPALRSISLKCQDHLFLFRITSDRPLEELFLEQLEAPPPP  264 (265)
T ss_dssp             HHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHTCBCSSCHHHHHHHHHTSCCCC
T ss_pred             HHHHHHHHHHHhhCCChhhHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCChhHHHHHHhcCCCCC
Confidence            9999999999999999999999999999999999999999999999999999999999999987664

>d1pk5a_ a.123.1.1 (A:) Orphan nuclear receptor NR5a2 (LRH-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NR5a2 (LRH-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=100.00  E-value=7.6e-38  Score=282.91  Aligned_cols=197  Identities=31%  Similarity=0.487  Sum_probs=175.5

Q ss_pred             hccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCC-CceEecCCcc-ccCC---
Q psy6602          84 ILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD-LSLLINCEKA-RERL---  158 (367)
Q Consensus        84 ~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~-~~~l~~~~~~-~~~~---  158 (367)
                      ...++..+|+++.+.++.+|+|||++|||.+|+.+||++|||++|+++++|+.||+++... .+.++..++. ....   
T Consensus        40 ~~~~~~~l~~~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~iL~~a~~s~~~~~~~~~~~~~g~~~~~~~~~  119 (242)
T d1pk5a_          40 KLSAFGLLCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVAHGKEGTIFLVTGEHVDYSTII  119 (242)
T ss_dssp             CCCSHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCSSEEECTTSCEEEHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHHHHHHHhCCCHhhcCHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCeeEecCCCcccchHHh
Confidence            4566899999999999999999999999999999999999999999999999999987543 3344444443 2211   


Q ss_pred             CCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHH
Q psy6602         159 PPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFG  238 (367)
Q Consensus       159 ~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~  238 (367)
                      .....+....++.+.+++.+|++|++|++||+|||||+||+||++|+++...|+.+|++|..+|++||..+|++.+.||+
T Consensus       120 ~~~~~~~~~~~~~~~~l~~~l~~L~ld~~E~~lLkai~Lf~pd~~gL~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~  199 (242)
T d1pk5a_         120 SHTEVAFNNLLSLAQELVVRLRSLQFDQREFVCLKFLVLFSSDVKNLENLQLVEGVQEQVNAALLDYTVCNYPQQTEKFG  199 (242)
T ss_dssp             HTSCHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHSCSCCSSCTTHHHHHHHHHHHHHHHHHHHHHHCTTSTTHHH
T ss_pred             hhcccchHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHhcCCCCCCchhHHHHHHHHHHHHHHHHHHHHhhCCCcchHHH
Confidence            12233456677889999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHccc
Q psy6602         239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  280 (367)
Q Consensus       239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~  280 (367)
                      +|+++++.||+++....|.+++++..|..++++++.||+++.
T Consensus       200 ~LLl~Lp~Lr~~~~~~~e~L~~~~~~g~~~~~~Ll~Eml~~~  241 (242)
T d1pk5a_         200 QLLLRLPELRAISKQAEDYLYYKHVNGDVPYNNLLIEMLHAK  241 (242)
T ss_dssp             HHHTTHHHHHHHHHHHHHHHHHHHHTTCSCCCHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHhCC
Confidence            999999999999999999999999999999999999999865

>d2j7ya1 a.123.1.1 (A:217-452) Estrogen receptor beta {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Estrogen receptor beta
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=100.00  E-value=8e-38  Score=281.71  Aligned_cols=199  Identities=21%  Similarity=0.283  Sum_probs=163.7

Q ss_pred             HHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCC-ccchH
Q psy6602          88 AEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPD-DVRVN  166 (367)
Q Consensus        88 ~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~-~~~~~  166 (367)
                      +..+++++++.++.+|+|||++|||.+|+.+||++|||++|+++++++.||+++..++..++.++....+.... ..+..
T Consensus        34 ~~~l~~~a~~~l~~~V~waK~lp~F~~L~~~DQi~LLk~~~~el~~L~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~  113 (236)
T d2j7ya1          34 MMSLTKLADKELVHMIGWAKKIPGFVELSLLDQVRLLESCWMEVLMVGLMWRSIDHPGKLIFAPDLVLDRDEGKCVEGIL  113 (236)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTSTTEEEEETTEEEEGGGGGGSTTHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCchHHHhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcEEecCCcccCHHHHHHHhhHH
Confidence            67799999999999999999999999999999999999999999999999999988777777766555544433 23567


Q ss_pred             HHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhhhH
Q psy6602         167 NEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPS  246 (367)
Q Consensus       167 ~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~~  246 (367)
                      +.++.+.+++.+|++|++|++||+|||||+||+||++|+.+...+++.++++.                           
T Consensus       114 ~~~~~i~~~~~~l~~L~ld~~E~~lLkaIvLf~pd~~~l~~~~~~~~~~~~v~---------------------------  166 (236)
T d2j7ya1         114 EIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLASANQEAESSRKLT---------------------------  166 (236)
T ss_dssp             HHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHTTTTCCCCC------HHHHHHH---------------------------
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCcCCCCcchhHHHHHHHHHH---------------------------
Confidence            88899999999999999999999999999999999999877555544443333                           


Q ss_pred             hHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhh---CCCCcChHHHH
Q psy6602         247 LRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGR---YSRQPTRFGRL  323 (367)
Q Consensus       247 Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~---~p~~~~r~~~l  323 (367)
                                                                       .+|+.+..+|..|+..+   +|+.+.||++|
T Consensus       167 -------------------------------------------------~~~~~~~~~l~~~~~~~~~~~p~~~~Rf~~L  197 (236)
T d2j7ya1         167 -------------------------------------------------HLLNAVTDALVWVIAKSGISSQQQSVRLANL  197 (236)
T ss_dssp             -------------------------------------------------HHHHHHHHHHHHHHHHTCCCHHHHHHHHHHH
T ss_pred             -------------------------------------------------HHHHHHHHHHHHHHhccCCCCcchhHHHHHH
Confidence                                                             33344444444444433   35567899999


Q ss_pred             HhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhc
Q psy6602         324 LLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM  362 (367)
Q Consensus       324 Ll~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~  362 (367)
                      |++||+||+++..++|+|||++++|.+|+++|+.|||++
T Consensus       198 L~~Lp~Lr~l~~~~~e~l~~~~~~g~~~i~~Ll~Eml~a  236 (236)
T d2j7ya1         198 LMLLSHVRHISNKGMEHLLSMKCKNVVPVYDLLLEMLNA  236 (236)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSSCCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCCCccHHHHHHhCc
Confidence            999999999999999999999999999999999999986

>d1ovla_ a.123.1.1 (A:) Orphan nuclear receptor NURR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NURR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.7e-37  Score=278.94  Aligned_cols=190  Identities=25%  Similarity=0.353  Sum_probs=173.5

Q ss_pred             CHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccchH
Q psy6602          87 SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVN  166 (367)
Q Consensus        87 ~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  166 (367)
                      .+++++++.++.+..+|+|||++|||.+|+.+||++|||++|+|++++++||++++.++..++.++....+... ..+..
T Consensus        40 ~~~~f~~~~~~~i~~iv~fAK~iPgF~~L~~~DQi~LLk~~~~ElllL~~a~~~~~~~~~l~~~~~~~~~~~~~-~~~~~  118 (236)
T d1ovla_          40 HIQQFYDLLTGSMEIIRGWAEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIFCNGVVLHRLQC-VRGFG  118 (236)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHSBTTTTEEECTTSBEEEHHHH-TTTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEecCCceechHhh-cccHH
Confidence            37889999999999999999999999999999999999999999999999999998777776666655544332 22355


Q ss_pred             HHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCC--CcchHHHHHHHhh
Q psy6602         167 NEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYS--RQPTRFGRLLLML  244 (367)
Q Consensus       167 ~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~--~~~~Rf~~LL~~l  244 (367)
                      +.++.+.+|+.+|++|++|++||+|||||+||+ |++|+.+..+|+++|+++.++|++|+..+++  +++.||++|+.++
T Consensus       119 ~~~~~i~~~~~~l~~L~ld~~E~alLkAI~L~~-dr~gL~~~~~Ve~lQ~~~~~aL~~~~~~~~~~~~~~~rf~~LL~~L  197 (236)
T d1ovla_         119 EWIDSIVEFSSNLQNMNIDISAFSCIAALAMVT-ERHGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLGKL  197 (236)
T ss_dssp             THHHHHHHHHHHHHTTCCCHHHHHHHHHHHHSS-CCTTCSCHHHHHHHHHHHHHHHHHHHHGGGTTTTSTTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcC-CCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCccHHHHHHHHHHHh
Confidence            678999999999999999999999999999998 9999999999999999999999999999886  6789999999999


Q ss_pred             hHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHc
Q psy6602         245 PSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT  278 (367)
Q Consensus       245 ~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~  278 (367)
                      +.||+++..+.|.+++.+..+..++++++.|||.
T Consensus       198 p~LR~l~~~~~e~l~~~kl~~~~~~~~L~~elf~  231 (236)
T d1ovla_         198 PELRTLCTQGLQRIFYLKLEDLVPPPAIIDKLFL  231 (236)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSSCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhhcCCCCCcHHHHHHHHH
Confidence            9999999999999999999999999999999985

>d2qw4a1 a.123.1.1 (A:32-264) Orphan nuclear receptor NR4A1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NR4A1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=8.5e-37  Score=274.14  Aligned_cols=190  Identities=25%  Similarity=0.366  Sum_probs=171.1

Q ss_pred             CHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccchH
Q psy6602          87 SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVN  166 (367)
Q Consensus        87 ~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  166 (367)
                      .++++++++++.++.+|+|||+||||.+|+.+||++|||++|+|++++++||++++.++..++.++....+... ..+..
T Consensus        40 ~~~~~~~~~~~~i~~iv~wAK~iPgF~~L~~~DQi~LLk~~~~el~lL~~a~~~~~~~~~l~~~~~~~~~~~~~-~~~~~  118 (233)
T d2qw4a1          40 DVQQFYDLLSGSLEVIRKWAEKIPGFAELSPADQDLLLESAFLELFILRLAYRSKPGEGKLIFCSGLVLHRLQC-ARGFG  118 (233)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTSTTTTTSCHHHHHHHHHHHHHHHHHHHHHHHSBGGGTEEECTTSCEEEHHHH-HHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhCCCCCCceeecCCeeecHHhh-hhhhH
Confidence            37889999999999999999999999999999999999999999999999999998777777666655444322 12355


Q ss_pred             HHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhC--CCcchHHHHHHHhh
Q psy6602         167 NEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRY--SRQPTRFGRLLLML  244 (367)
Q Consensus       167 ~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~--~~~~~Rf~~LL~~l  244 (367)
                      +.++.+.+|+.+|++|++|++||+|||||+||+ |++|++++..|+++|+++..+|++|+..++  ++++.||++|+.++
T Consensus       119 ~~~~~i~~~~~~l~~L~ld~~E~alLkAivL~~-d~~gL~~~~~Ve~lq~~~~~aL~~yi~~~~~~~~~~~rf~kLL~~L  197 (233)
T d2qw4a1         119 DWIDSILAFSRSLHSLLVDVPAFACLSALVLIT-DRHGLQEPRRVEELQNRIASCLKEHVAAVAGEPQPASCLSRLLGKL  197 (233)
T ss_dssp             THHHHHHHHHHHHHHHTCCHHHHHHHHHHHHSS-CCTTCSCHHHHHHHHHHHHHHHHHHHHHSCC---CCTTHHHHHTHH
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhcC-cccCccCHHHHHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHH
Confidence            677899999999999999999999999999998 899999999999999999999999998764  68899999999999


Q ss_pred             hHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHc
Q psy6602         245 PSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT  278 (367)
Q Consensus       245 ~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~  278 (367)
                      +.||+++..+.|.+++.+..+..++++|+.|||.
T Consensus       198 p~LR~l~~~~~e~l~~~k~~~~~~~p~L~~Emf~  231 (233)
T d2qw4a1         198 PELRTLCTQGLQRIFYLKLEDLVPPPPIIDKIFM  231 (233)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCCSCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCchHHHHHHcc
Confidence            9999999999999999999999999999999985

>d1pdua_ a.123.1.1 (A:) Nuclear hormone receptor HR38 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Nuclear hormone receptor HR38
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=100.00  E-value=4.5e-37  Score=275.34  Aligned_cols=190  Identities=25%  Similarity=0.286  Sum_probs=171.6

Q ss_pred             HHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccchHH
Q psy6602          88 AEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNN  167 (367)
Q Consensus        88 ~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~  167 (367)
                      +.++++.++..++.+|+|||++|||.+|+.+||++|||++|+|++++++||+++..++..++.++....+... ..+..+
T Consensus        38 ~~~~~~~~~~~i~~ivefAK~iPgF~~L~~~DQi~LLk~~~~El~~L~~a~~~~~~~~~l~~~~g~~~~~~~~-~~~~~~  116 (230)
T d1pdua_          38 VQQFYQLLTSSVDVIKQFAEKIPGYFDLLPEDQELLFQSASLELFVLRLAYRARIDDTKLIFCNGTVLHRTQC-LRSFGE  116 (230)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHCCSSCSEEECTTSBEEEHHHH-HHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCChhcCCHHHHHHHHHHHHHHHHHHHHHHhccCCCCeEEecCCccccHHHH-HHhHHH
Confidence            7889999999999999999999999999999999999999999999999999998777666665555443322 123456


Q ss_pred             HHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCC--CcchHHHHHHHhhh
Q psy6602         168 EIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYS--RQPTRFGRLLLMLP  245 (367)
Q Consensus       168 ~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~--~~~~Rf~~LL~~l~  245 (367)
                      .++.+.+|+.+|++|++|++||+|||||+||+ |++|+.+..+|+++|++|.++|++|+..+++  ..+.||++|+++++
T Consensus       117 ~~~~i~~~~~~~~~L~ld~~E~alL~AivL~~-d~~~L~~~~~Ve~lq~~~~~aL~~~i~~~~~~~~~~~rf~~LL~~Lp  195 (230)
T d1pdua_         117 WLNDIMEFSRSLHNLEIDISAFACLCALTLIT-ERHGLREPKKVEQLQMKIIGSLRDHVTYNAEAQKKQHYFSRLLGKLP  195 (230)
T ss_dssp             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHSS-CCTTCSCHHHHHHHHHHHHHHHHHHHHHCHHHHTSTTHHHHHHTHHH
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHhhheeec-CcccccCHHHHHHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHHhH
Confidence            77899999999999999999999999999995 8999999999999999999999999998887  56789999999999


Q ss_pred             HhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcc
Q psy6602         246 SLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM  279 (367)
Q Consensus       246 ~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~  279 (367)
                      .||+++..+.|.+++.+..+..++++|+.|||..
T Consensus       196 ~LR~l~~~~~e~l~~~k~~~~~~~~~L~~Em~~~  229 (230)
T d1pdua_         196 ELRSLSVQGLQRIFYLKLEDLVPAPALIENMFVT  229 (230)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCSSCCCHHHHHTTTC
T ss_pred             HHHHHHHHHHHHHHHHHcCCCCCccHHHHHHhhc
Confidence            9999999999999999999999999999999863

>d1xvpb_ a.123.1.1 (B:) Orphan nuclear receptor NR1I3 (CAR) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NR1I3 (CAR)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=5.5e-37  Score=277.65  Aligned_cols=190  Identities=17%  Similarity=0.257  Sum_probs=164.6

Q ss_pred             cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCC-ccc
Q psy6602          86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPD-DVR  164 (367)
Q Consensus        86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~-~~~  164 (367)
                      ..+.++++++++.++.+|+|||++|||..|+.+||++|||+||+|++++++++++....... ++++......... ..+
T Consensus        54 ~~~~~~~~~~~~~i~~iV~waK~lP~F~~L~~~DQi~LLk~~~~El~~l~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~  132 (246)
T d1xvpb_          54 PLVTHFADINTFMVLQVIKFTKDLPVFRSLPIEDQISLLKGAAVEICHIVLNTTFCLQTQNF-LCGPLRYTIEDGARVGF  132 (246)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTCHHHHHSCHHHHHHHHHHHHHHHHHHHHGGGEETTTTEE-ECSSCEECHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHhcccCCee-ecCCCccchHHHhcccc
Confidence            34888999999999999999999999999999999999999999999999999887654444 4443333222211 122


Q ss_pred             hHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhC--CCcchHHHHHHH
Q psy6602         165 VNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRY--SRQPTRFGRLLL  242 (367)
Q Consensus       165 ~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~--~~~~~Rf~~LL~  242 (367)
                      ..+.++.+.+|+.+|++|++|++||+|||||+||+||++||.+..+|+++|++|..+|+.|+..+|  ++++.||++||+
T Consensus       133 ~~~~~~~~~~f~~~l~~L~ld~~E~alLkAivL~~pD~~gL~~~~~Ve~lQ~~~~~aL~~y~~~~~~~p~~~~rf~~LL~  212 (246)
T d1xvpb_         133 QVEFLELLFHFHGTLRKLQLQEPEYVLLAAMALFSPDRPGVTQRDEIDQLQEEMALTLQSYIKGQQRRPRDRFLYAKLLG  212 (246)
T ss_dssp             CHHHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHSCSSSTTCSCHHHHHHHHHHHHHHHHHHHHTCSSCCSCSSHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHhCCCHHHHHHHhhhhhccCCCCCCCcHHHHHHHHHHHHHHHHHHHHHcCCCCCcccHHHHHHH
Confidence            457789999999999999999999999999999999999999999999999999999999999876  688999999999


Q ss_pred             hhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHc
Q psy6602         243 MLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT  278 (367)
Q Consensus       243 ~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~  278 (367)
                      +++.||+++..+.|.+++.+  +..++++|+.|||.
T Consensus       213 ~L~~LR~l~~~~~e~l~~~k--~~~~~~pLl~E~fs  246 (246)
T d1xvpb_         213 LLAELRSINEAYGYQIQHIQ--GLSAMMPLLQEICS  246 (246)
T ss_dssp             HHHHHHHHHHHHHHHHHHST--THHHHCHHHHHHTC
T ss_pred             HhHHHHHHHHHHHHHHHHhc--CCCCCChHHHHhcC
Confidence            99999999999999998765  45578899999973

>d2r40d1 a.123.1.1 (D:287-529) Ecdysone receptor {Noctuid moth (Heliothis virescens) [TaxId: 7102]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Ecdysone receptor
species: Noctuid moth (Heliothis virescens) [TaxId: 7102]

Probab=100.00  E-value=1.4e-36  Score=274.41  Aligned_cols=194  Identities=20%  Similarity=0.252  Sum_probs=173.5

Q ss_pred             ccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccc
Q psy6602          85 LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVR  164 (367)
Q Consensus        85 ~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~  164 (367)
                      ...+.+++++++..++.+|+|||++|||..|+.+||++|||+||+|+++++.|++++...+..++.++..+.+......+
T Consensus        47 ~~~~~~~~~~~~~~i~~iV~faK~lP~F~~L~~~DQi~LLk~~~~El~lL~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~  126 (243)
T d2r40d1          47 DMPFRQITEMTILTVQLIVEFAKGLPGFAKISQSDQITLLKACSSEVMMLRVARRYDAATDSVLFANNQAYTRDNYRKAG  126 (243)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEETTTTEEECTTSCEECHHHHHHTT
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHcCcChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCeEEecCCeeecHHHHhhcc
Confidence            34588999999999999999999999999999999999999999999999999999987776666666555554444445


Q ss_pred             hHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCC---CcchHHHHHH
Q psy6602         165 VNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYS---RQPTRFGRLL  241 (367)
Q Consensus       165 ~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~---~~~~Rf~~LL  241 (367)
                      ..+.++.+.+|+.+|++|++|++||+|||||+||+ |++|+.+..+|+++|++|..+|+.|+..+++   +++.||++|+
T Consensus       127 ~~~~~~~l~~f~~~l~~L~ld~~E~alL~AivL~s-d~~~L~~~~~ve~lq~~~~~aL~~y~~~~~~~~p~~~~rf~~LL  205 (243)
T d2r40d1         127 MAYVIEDLLHFCRCMYSMMMDNVHYALLTAIVIFS-DRPGLEQPLLVEEIQRYYLNTLRVYILNQNSASPRCAVIFGKIL  205 (243)
T ss_dssp             CHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHTS-CCTTCSCHHHHHHHHHHHHHHHHHHHHHHTTTCTTHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHhcC-CCCCCCcHHHHHHHHHHHHHHHHHHHHhhCCCCccHhHHHHHHH
Confidence            67888999999999999999999999999999999 9999999999999999999999999999875   4557999999


Q ss_pred             HhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHccc
Q psy6602         242 LMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  280 (367)
Q Consensus       242 ~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~  280 (367)
                      .++++||+++..+.|.++..+.. +..+++|+.|||+.+
T Consensus       206 ~~L~~LR~l~~~~~e~l~~~k~~-~~~~~pLl~E~~d~~  243 (243)
T d2r40d1         206 GILTEIRTLGMQNSNMCISLKLK-NRKLPPFLEEIWDVA  243 (243)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHT-TCCCCHHHHHHTTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcC-CCCCChHHHHHhCCC
Confidence            99999999999999999988765 457899999999863

>d2p1ta1 a.123.1.1 (A:229-458) Retinoid-X receptor alpha (RXR-alpha) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Retinoid-X receptor alpha (RXR-alpha)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=2.1e-36  Score=271.40  Aligned_cols=192  Identities=30%  Similarity=0.609  Sum_probs=174.7

Q ss_pred             HHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccchHH
Q psy6602          88 AEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNN  167 (367)
Q Consensus        88 ~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~  167 (367)
                      +.++|+++.+.++.+|+|||++|||..|+.+||++|||++|+++++|+.||++...++..++.++..+........+..+
T Consensus        37 ~~~l~~~a~~~l~~~v~wak~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  116 (230)
T d2p1ta1          37 VTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGA  116 (230)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTSSSEEECTTSCEEEHHHHHTTTCHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCccccCCHHHHHHHHHHHHHHHHHHHHHHHhhcCCCeEEecCCeeecHhHHHhccchH
Confidence            67899999999999999999999999999999999999999999999999999987777777666554443333333445


Q ss_pred             HH-HHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhhhH
Q psy6602         168 EI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPS  246 (367)
Q Consensus       168 ~~-~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~~  246 (367)
                      .+ +.+.+++.+|++|++|++||+|||||+||+||++|+++...|+++|++|..+|++|+..++++.+.||++|+.+++.
T Consensus       117 ~~~~~~~~~~~~~~~L~ld~~E~~lLkaivL~~pd~~~l~~~~~i~~~q~~~~~aL~~y~~~~~~~~~~R~~~Ll~~L~~  196 (230)
T d2p1ta1         117 IFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPA  196 (230)
T ss_dssp             HHHHHHHHTHHHHHHTTCCHHHHHHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTTHHH
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhccccCCcccHHHHHHHHHHHHHHHHHHHHhhCCCchhHHHHHHHHHHH
Confidence            54 55678999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHhhhhhHHHHHHhhhccCCchhHhHHHHHHcc
Q psy6602         247 LRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM  279 (367)
Q Consensus       247 Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~  279 (367)
                      +|.++..+.|.+++.+.++..++++|+.||++.
T Consensus       197 Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~Eml~~  229 (230)
T d2p1ta1         197 LRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEA  229 (230)
T ss_dssp             HHHHHHHHHHHHHHHHHHCCSCCCHHHHHHTSC
T ss_pred             HHHHHHHHHHHHHhcCcCCCCChhHHHHHHHcC
Confidence            999999999999999999999999999999985

>d1osha_ a.123.1.1 (A:) Bile acid receptor FXR {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Bile acid receptor FXR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.2e-36  Score=272.86  Aligned_cols=188  Identities=20%  Similarity=0.209  Sum_probs=162.0

Q ss_pred             CHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCc-cch
Q psy6602          87 SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDD-VRV  165 (367)
Q Consensus        87 ~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~-~~~  165 (367)
                      .+..+++++++.++.+|+|||++|||.+|+.+||++|||+||+|+++++.|++++...    ..++..+....... ...
T Consensus        43 ~~~~l~~~~~~~i~~iVe~AK~iP~F~~L~~~DQi~LLk~~~~El~~L~~~~~~~~~~----~~~~~~~~~~~~~~~~~~  118 (231)
T d1osha_          43 NFLILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKL----PSGHSDLLEERIRNSGIS  118 (231)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHTS----CHHHHHHHHHHHHTSSCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhcCccc----cCCCccccHHHHHhccch
Confidence            3778999999999999999999999999999999999999999999999999886431    11111111111000 112


Q ss_pred             HHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhhh
Q psy6602         166 NNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLP  245 (367)
Q Consensus       166 ~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~  245 (367)
                      .+.++.+.+|+.+|++|++|++||+|||||+||+||++|+.+...|+++|++|..+|++|+..+||+++.||++|+.+|+
T Consensus       119 ~~~~~~i~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~Ve~lq~~~~~aL~~y~~~~~p~~~~rf~~LL~~L~  198 (231)
T d1osha_         119 DEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLT  198 (231)
T ss_dssp             TTTHHHHHHHHHHHHTTCCCHHHHHHHHHHHHTCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhccCCCCCccHHHHHHHHHHHHHHHHHHHHHHCCCchhHHHHHHHHHH
Confidence            24568899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcc
Q psy6602         246 SLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM  279 (367)
Q Consensus       246 ~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~  279 (367)
                      .||+++..+.|.+++.+. +...+++|+.|||+.
T Consensus       199 ~LR~l~~~~~e~l~~~k~-~~~~~~pLl~E~fd~  231 (231)
T d1osha_         199 ELRTFNHHHAEMLMSWRV-NDHKFTPLLCEIWDV  231 (231)
T ss_dssp             HHHTHHHHHHHHHHHHHH-TTCCCCHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHhc-CCCCCChHHHHHhCc
Confidence            999999999999988775 456889999999973

>d1ie9a_ a.123.1.1 (A:) Vitamin D nuclear receptor {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Vitamin D nuclear receptor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=9e-36  Score=270.96  Aligned_cols=195  Identities=17%  Similarity=0.253  Sum_probs=167.0

Q ss_pred             hhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccC-CC-C
Q psy6602          83 QILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARER-LP-P  160 (367)
Q Consensus        83 ~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~-~~-~  160 (367)
                      .....+.+++++++..++.+|+|||++|||..|+.+||++|||++|+|++++++|++++.......+.++..... .. .
T Consensus        54 ~~~~~~~~~~~l~~~~i~~iVefAK~iPgF~~L~~~DQi~LLK~~~~El~ll~~a~~~~~~~~~~~~~~~~~~~~~~~~~  133 (255)
T d1ie9a_          54 SQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVSDVT  133 (255)
T ss_dssp             HHCTTHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHGGGTEETTTTEEECSSGGGEECHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHhCcccccCCHHHHHHHHHHHHHHHHHHHHHHheeCCCCeEEeCCCCeeecHHHHH
Confidence            444568999999999999999999999999999999999999999999999999998877555544443322211 11 1


Q ss_pred             CccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCC--cchHHH
Q psy6602         161 DDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSR--QPTRFG  238 (367)
Q Consensus       161 ~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~--~~~Rf~  238 (367)
                      ......+.++.+.+|+.+|++|++|++||+|||||+||+||++|+.++..|+++|++|.++|+.||..+|+.  ++.||+
T Consensus       134 ~~~~~~~~~~~i~~f~~~l~~L~ld~~E~~lLkAiiL~~pdr~gL~~~~~Ve~lq~~~~~aL~~y~~~~~~~~~~~~~f~  213 (255)
T d1ie9a_         134 KAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLLYA  213 (255)
T ss_dssp             TTTCCHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHSCSCSTTCSCHHHHHHHHHHHHHHHHHHHHHHCCTTTTTTHHH
T ss_pred             hccchHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHhcCCCcccccCHHHHHHHHHHHHHHHHHHHHHhCCCCCcccHHH
Confidence            112245678899999999999999999999999999999999999999999999999999999999999974  567899


Q ss_pred             HHHHhhhHhHhhhhhHHHHHHhhhccCC--chhHhHHHHHH
Q psy6602         239 RLLLMLPSLRAVRQSTIERLFFKETIGD--IPIQRLLGDMY  277 (367)
Q Consensus       239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~--~~~~~Ll~eml  277 (367)
                      +||++|+.||+++..+.|.++..+..+.  ..+++|+.|||
T Consensus       214 kLL~~L~~LR~l~~~~~e~l~~~~~~~~~~~~lppLl~E~f  254 (255)
T d1ie9a_         214 KMIQKLADLRSLNEEHSKQYRCLSFQPECSMKLTPLVLEVF  254 (255)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSTTHHHHSCHHHHHHH
T ss_pred             HHHHHhHHHHHHHHHHHHHHHHHhhCCCCCCCccHHHHHhc
Confidence            9999999999999999999988777544  35788999998

>d1t7ra_ a.123.1.1 (A:) Androgen receptor {Chimpanzee (Pan troglodytes) [TaxId: 9598]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Androgen receptor
species: Chimpanzee (Pan troglodytes) [TaxId: 9598]

Probab=100.00  E-value=1.9e-36  Score=274.77  Aligned_cols=214  Identities=19%  Similarity=0.283  Sum_probs=179.7

Q ss_pred             CCcccccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCC
Q psy6602          65 HPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD  144 (367)
Q Consensus        65 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~  144 (367)
                      +|..++++|++..|++....   ++.+|+++++.++.+|+|||++|||.+|+.+||++|||++|+|+++++.||++....
T Consensus        13 ep~~~~~~~~~~~p~~~~~~---l~~l~~~a~~~L~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~rs~~~~   89 (250)
T d1t7ra_          13 EPGVVCAGHDNNQPDSFAAL---LSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNV   89 (250)
T ss_dssp             CCCCCCCCCCTTSCCCHHHH---HHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCcccCCCCCCCCCchHHH---HHHHHHHHHHHHHHHHHHHHhCccHHHhhHHHHHHHHHHHHHHHHHHHHHHHhhccC
Confidence            57778888887778777655   466999999999999999999999999999999999999999999999999987654


Q ss_pred             Cce-E-ecCCccccCCCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCC-CCCCChhHHHHHHHHHHHH
Q psy6602         145 LSL-L-INCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPET-PGLVDAQPVEMLQDQAQCI  221 (367)
Q Consensus       145 ~~~-l-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~-~~L~~~~~v~~~q~~~~~~  221 (367)
                      +.. + +.++...........+..+.+..+.+++.+|++|++|++||+|||||+|||||+ +|+.+...|+.+|++|..+
T Consensus        90 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~ld~~E~~lLkaIvL~npd~~~~l~~~~~i~~lq~~~~~a  169 (250)
T d1t7ra_          90 NSRMLYFAPDLVFNEYRMHKSRMYSQCVRMRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFFDELRMNYIKE  169 (250)
T ss_dssp             TTSSEEEETTEEECHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHTSEEETTCCTTHHHHHHHHHHHHHH
T ss_pred             CCceEecCCCcccCHHHHhhchhHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhcCCccccCCccHHHHHHHHHHHHHH
Confidence            433 2 333333332222223355667788899999999999999999999999999975 7899999999999999999


Q ss_pred             HHHHHHhhCC---CcchHHHHHHHhhhHhHhhhhhHHHHHH---hhhccCCchhHhHHHHHHcccC
Q psy6602         222 LGDYVRGRYS---RQPTRFGRLLLMLPSLRAVRQSTIERLF---FKETIGDIPIQRLLGDMYTMEK  281 (367)
Q Consensus       222 L~~y~~~~~~---~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~---~~~~~~~~~~~~Ll~eml~~~~  281 (367)
                      |+.|+..+++   +++.||++||.+++++|+++.++.++++   +....+...+++++.||++...
T Consensus       170 L~~y~~~~~~~~~~~p~Rf~~LL~~Lp~lr~l~~~~~~~~~~l~~~~~~~~~~i~~Ll~Eml~~~~  235 (250)
T d1t7ra_         170 LDRIIACKRKNPTSCSRRFYQLTKLLDSVQPIARELHQFTFDLLIKSHMVSVDFPEMMAEIISVQV  235 (250)
T ss_dssp             HHHHHHTTCCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTCCCCHHHHHHHHHTH
T ss_pred             HHHHHHHhCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCChHHHHHHHHhccC
Confidence            9999998886   4577999999999999999999988654   5566778889999999998664

>d1nhza_ a.123.1.1 (A:) Glucocorticoid receptor {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Glucocorticoid receptor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=3e-35  Score=266.39  Aligned_cols=214  Identities=20%  Similarity=0.243  Sum_probs=179.2

Q ss_pred             CCcccccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCC
Q psy6602          65 HPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD  144 (367)
Q Consensus        65 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~  144 (367)
                      +|..++++|++..|++....   ++.+|++++|.+..+|+|||++|||..|+.+||++|||++|+++++|+.||+++..+
T Consensus        11 eP~~~~~~~~~~~p~~~~~~---~~~l~~la~r~L~~~IewaK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~s~~~~   87 (247)
T d1nhza_          11 EPEVLYAGYDSSVPDSTWRI---MTTLNMLGGRQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMSLMAFALGWRSYRQS   87 (247)
T ss_dssp             CCCCCCCCCCTTSCCCHHHH---HHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCCCCCCCCChHHH---HHHHHHHHHHHHHHHHHHHHhcccHhhcCHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence            46667777777777776543   577999999999999999999999999999999999999999999999999986543


Q ss_pred             Cc--eEecCCccccCCCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCC-CCCCCChhHHHHHHHHHHHH
Q psy6602         145 LS--LLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPE-TPGLVDAQPVEMLQDQAQCI  221 (367)
Q Consensus       145 ~~--~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd-~~~L~~~~~v~~~q~~~~~~  221 (367)
                      .+  ..+.++...........+....++.+.+++.+|++|++|++||+|||||+||||| +.++.++..|+++|++|.++
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~l~~~E~~lLkaIvLfnpd~~~~l~~~~~ve~lq~~~~~a  167 (247)
T d1nhza_          88 SANLLCFAPDLIINEQRMTLPDMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSSVPKDGLKSQELFDEIRMTYIKE  167 (247)
T ss_dssp             TTSSEEEETTEEECTTGGGSTTHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHTSEEETTCCTTHHHHHHHHHHHHHH
T ss_pred             CCCeEeccccceecHHhhccccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCcccccHHHHHHHHHHHHHH
Confidence            32  2334444444444444556677789999999999999999999999999999999 78899999999999999999


Q ss_pred             HHHHHHhhCCCc---chHHHHHHHhhhHhHhhhhhHHHHHHhhhc--cCCchhHhHHHHHHcccC
Q psy6602         222 LGDYVRGRYSRQ---PTRFGRLLLMLPSLRAVRQSTIERLFFKET--IGDIPIQRLLGDMYTMEK  281 (367)
Q Consensus       222 L~~y~~~~~~~~---~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~--~~~~~~~~Ll~eml~~~~  281 (367)
                      |.+|+..++++.   +.||++|+++++.+|+++..+.+.++....  .+.+.+++++.||+....
T Consensus       168 L~~y~~~~~~~~~~~~~Rf~~LL~~Lp~lR~~~~~~~~~l~~~~~~~~~~v~~~~Ll~Eml~~~~  232 (247)
T d1nhza_         168 LGKAIVKREGNSSQNWQRFYQLTKLLDSMHEVVENLLNYCFQTFLDKTMSIEFPEMLAEIITNQI  232 (247)
T ss_dssp             HHHHHHHHCCSTHHHHHHHHHHHHHHHHHHHHHHHHTTSCCCCHHHHHHHSCHHHHHHHHHTC--
T ss_pred             HHHHHHHhCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcCCCChhHHHHHHHhccC
Confidence            999999998654   459999999999999999999998875433  456778899999997554

>d1xnxa_ a.123.1.1 (A:) Orphan nuclear receptor NR1I3 (CAR) {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NR1I3 (CAR)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=100.00  E-value=1.3e-35  Score=266.08  Aligned_cols=174  Identities=17%  Similarity=0.209  Sum_probs=151.0

Q ss_pred             CHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCC-ccch
Q psy6602          87 SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPD-DVRV  165 (367)
Q Consensus        87 ~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~-~~~~  165 (367)
                      .+.++++++++.++.+|+|||++|||..|+.+||++|||+||+|++++++|++++...+.. +.+++........ ....
T Consensus        54 ~~~~~~~~~~~~i~~iV~faK~lP~F~~L~~eDQi~LLk~~~~El~~L~~a~~~~~~~~~~-~~~~~~~~~~~~~~~~~~  132 (232)
T d1xnxa_          54 LLTHFADINTFMVQQIIKFTKDLPLFRSLTMEDQISLLKGAAVEILHISLNTTFCLQTENF-FCGPLCYKMEDAVHAGFQ  132 (232)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTCHHHHTSCHHHHHHHHHHHHHHHHHHHHGGGEETTTTEE-EETTEEECHHHHHHTTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCce-eeCCcccchHHHHhcccc
Confidence            3788999999999999999999999999999999999999999999999999988755554 4444433222211 1123


Q ss_pred             HHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCc--chHHHHHHHh
Q psy6602         166 NNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQ--PTRFGRLLLM  243 (367)
Q Consensus       166 ~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~--~~Rf~~LL~~  243 (367)
                      .+.++.+.+|+.+|++|++|++||+|||||+||+||++||.+..+|+++|++|..+|++||..+++..  +.||++||++
T Consensus       133 ~~~~~~i~~f~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~~~~~f~kLL~~  212 (232)
T d1xnxa_         133 YEFLESILHFHKNLKGLHLQEPEYVLMAATALFSPDRPGVTQREEIDQLQEEMALILNNHIMEQQSRLQSRFLYAKLMGL  212 (232)
T ss_dssp             HHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHTTTTCCSTTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCCCcCCHHHHHHHHHHHHHHHHHHHHHhCCCCCcccHHHHHHHH
Confidence            56778999999999999999999999999999999999999999999999999999999999988644  4569999999


Q ss_pred             hhHhHhhhhhHHHHHHhh
Q psy6602         244 LPSLRAVRQSTIERLFFK  261 (367)
Q Consensus       244 l~~Lr~l~~~~~e~l~~~  261 (367)
                      |+.||+++..+.|.+...
T Consensus       213 L~~LR~l~~~h~e~l~~i  230 (232)
T d1xnxa_         213 LADLRSINNAYSYELQRL  230 (232)
T ss_dssp             HHHHHHHHHHTHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHh
Confidence            999999999999988654

>d1sqna_ a.123.1.1 (A:) Progesterone receptor {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Progesterone receptor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=3.1e-35  Score=266.80  Aligned_cols=214  Identities=18%  Similarity=0.225  Sum_probs=178.2

Q ss_pred             CCcccccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCC
Q psy6602          65 HPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD  144 (367)
Q Consensus        65 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~  144 (367)
                      +|..++++|++..|++....   ++.+|++++|.++.+|+|||++|||.+|+.+||++|||++|+++++|+.||++....
T Consensus        14 eP~~~~~~~~~~~~~~~~~~---~~~l~~la~r~L~~~VewaK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~rs~~~~   90 (251)
T d1sqna_          14 EPDVIYAGHDNTKPDTSSSL---LTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHV   90 (251)
T ss_dssp             SCCCCCCCCCC--CCCHHHH---HHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCcccCCCCCCCCCCchHH---HHHHHHHHHHHHHHHHHHHHhccchhhcCHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence            46677778777777776644   677999999999999999999999999999999999999999999999999987643


Q ss_pred             C-ceE-ecCCccccCCCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCC-CCCCCChhHHHHHHHHHHHH
Q psy6602         145 L-SLL-INCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPE-TPGLVDAQPVEMLQDQAQCI  221 (367)
Q Consensus       145 ~-~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd-~~~L~~~~~v~~~q~~~~~~  221 (367)
                      . ..+ +.++...........+..+.++.+.+++.+|++|++|++||+|||||+||||| ++|+.++.+|+++|++|.++
T Consensus        91 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~~lLkAIiL~npd~~~~l~~~~~V~~lq~~~~~a  170 (251)
T d1sqna_          91 SGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRE  170 (251)
T ss_dssp             TTSSEEEETTEEECGGGCCSHHHHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHTSEECTTCCTTHHHHHHHHHHHHHH
T ss_pred             CcceeeccCCceecHHhhccccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCccccCCcCHHHHHHHHHHHHHH
Confidence            3 333 33344444444455567777889999999999999999999999999999996 78999999999999999999


Q ss_pred             HHHHHHhhCCC---cchHHHHHHHhhhHhHhhhhhHHHHHHh---hhccCCchhHhHHHHHHcccC
Q psy6602         222 LGDYVRGRYSR---QPTRFGRLLLMLPSLRAVRQSTIERLFF---KETIGDIPIQRLLGDMYTMEK  281 (367)
Q Consensus       222 L~~y~~~~~~~---~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~---~~~~~~~~~~~Ll~eml~~~~  281 (367)
                      |++||..++++   ++.||++|+++++.+|+++..+.++++.   ....+.+++++++.||++...
T Consensus       171 L~~~~~~~~~~~~~~~~Rf~~LL~lLp~lR~l~~~~~~~~~~~~~~~~~~~v~~p~Ll~E~l~~~~  236 (251)
T d1sqna_         171 LIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDLVKQLHLYCLNTFIQSRALSVEFPEMMSEVIAAQL  236 (251)
T ss_dssp             HHHHHHTTC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTCCCCHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCcChhHHHHHHHHccC
Confidence            99999988754   5679999999999999999999998643   333456778999999998543

>d1n83a_ a.123.1.1 (A:) Orphan nuclear receptor ROR-alpha {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor ROR-alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=7e-35  Score=264.52  Aligned_cols=191  Identities=15%  Similarity=0.183  Sum_probs=170.1

Q ss_pred             ccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccc
Q psy6602          85 LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVR  164 (367)
Q Consensus        85 ~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~  164 (367)
                      ...|.++++.++..|+.+|+|||++|||.+|+.+||++|||++|+|++++++|++++.. +..+++++...........+
T Consensus        57 ~~~~~~~~~~~~~~i~~vV~faK~iPgF~~L~~~DQi~LLk~~~~el~ll~~a~~~~~~-~~~~~~~~~~~~~~~~~~~~  135 (251)
T d1n83a_          57 EVMWQLCAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQ-NNTVYFDGKYASPDVFKSLG  135 (251)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSTTTTTSCHHHHHHHHHHHHHHHHHHHGGGGEETT-TTEEEETTEEECGGGGGGGS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHhCCC-CCEEecCCeeecHHHHhhcc
Confidence            44478999999999999999999999999999999999999999999999999988764 45566666555555555556


Q ss_pred             hHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhh
Q psy6602         165 VNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLML  244 (367)
Q Consensus       165 ~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l  244 (367)
                      ..+.++.+.+|+..|++|++|++||+|||||+||+||++|+.+...|+++|++|..+|+.|+..+++ ++.||++|+.++
T Consensus       136 ~~~~~~~~~~~~~~~~~L~ld~~E~alL~AivL~~pd~~gL~~~~~Ve~lq~~~~~aL~~~~~~~~~-~~~rf~~Ll~~L  214 (251)
T d1n83a_         136 CEDFISFVFEFGKSLCSMHLTEDEIALFSAFVLMSADRSWLQEKVKIEKLQQKIQLALQHVLQKNHR-EDGILTKLICKV  214 (251)
T ss_dssp             CHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCT-TSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHccCccccCCHHHHHHHHHHHHHHHHHHHHhcCC-CccHHHHHHHHh
Confidence            7888999999999999999999999999999999999999999999999999999999999999977 478999999999


Q ss_pred             hHhHhhhhhHHHHHHhhhccCC----chhHhHHHHHH
Q psy6602         245 PSLRAVRQSTIERLFFKETIGD----IPIQRLLGDMY  277 (367)
Q Consensus       245 ~~Lr~l~~~~~e~l~~~~~~~~----~~~~~Ll~eml  277 (367)
                      +.||+++..+.|.+++.+....    ..+++|+.|||
T Consensus       215 p~LR~l~~~~~e~l~~~k~~~~~~~~~~~ppL~~Eif  251 (251)
T d1n83a_         215 STLRALCGRHTEKLMAFKAIYPDIVRLHFPPLYKELF  251 (251)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCHHHHHHHSCHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHccccccCCccHHHHhhC
Confidence            9999999999999988876532    35778999886

>d1nrla_ a.123.1.1 (A:) Pregnane x receptor, PXR {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Pregnane x receptor, PXR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=7.9e-35  Score=269.90  Aligned_cols=194  Identities=17%  Similarity=0.215  Sum_probs=170.7

Q ss_pred             ccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccc
Q psy6602          85 LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVR  164 (367)
Q Consensus        85 ~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~  164 (367)
                      ...+.++++++++.|+.+|+|||+||||.+|+.+||++|||++|+|++++++|++++.. ...+..++..+........+
T Consensus        96 ~~~l~~~~~~~~~~i~~iV~fAK~iP~F~~L~~~DQi~LLk~~~~el~~l~~a~~~~~~-~~~~~~~~~~~~~~~~~~~~  174 (292)
T d1nrla_          96 FSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAE-TGTWECGRLSYCLEDTAGGF  174 (292)
T ss_dssp             GTTHHHHHHHHHHHHHHHHHHHHHCHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTEETT-TTEEEETTEEEEECCCSSCH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCcCHhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCC-CCeeeCCCccccHHHhhhhh
Confidence            44589999999999999999999999999999999999999999999999999998764 44455555555544444444


Q ss_pred             hHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcc--hHHHHHHH
Q psy6602         165 VNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP--TRFGRLLL  242 (367)
Q Consensus       165 ~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~--~Rf~~LL~  242 (367)
                      ..+..+.+.+|+.+|++|++|++||+|||||+||+||++|+.+...|+++|++|..+|+.||..+|++.+  .||++||.
T Consensus       175 ~~~~~~~~~~~~~~l~~L~ld~~E~~lLkAi~L~~pd~~gL~~~~~Ve~lq~~~~~aL~~y~~~~~p~~~~~~~f~kLL~  254 (292)
T d1nrla_         175 QQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLKIMA  254 (292)
T ss_dssp             HHHTTSHHHHHHHHHHHTCCCHHHHHHHHHHHHTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCCSGGGTTHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHhCCCCchhhHHHHHHH
Confidence            5666789999999999999999999999999999999999999999999999999999999999998665  47999999


Q ss_pred             hhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHccc
Q psy6602         243 MLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  280 (367)
Q Consensus       243 ~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~  280 (367)
                      +++.||+++..+.|.++..+..+. .+++|+.|||+..
T Consensus       255 ~l~~LR~l~~~~~e~l~~~k~~~~-~~~pLl~E~f~~~  291 (292)
T d1nrla_         255 MLTELRSINAQHTQRLLRIQDIHP-FATPLMQELFGIT  291 (292)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSC-CCCHHHHHHTTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCC-CCchHHHHHhCcC
Confidence            999999999999999988877543 4578999999864

>d2p54a1 a.123.1.1 (A:202-468) Peroxisome proliferator activated receptor alpha, PPAR-alpha {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Peroxisome proliferator activated receptor alpha, PPAR-alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=2.5e-35  Score=268.77  Aligned_cols=190  Identities=19%  Similarity=0.222  Sum_probs=165.4

Q ss_pred             HHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCC--CCCccch
Q psy6602          88 AEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERL--PPDDVRV  165 (367)
Q Consensus        88 ~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~--~~~~~~~  165 (367)
                      +..+...++..++.+|+|||++|||.+|+.+||++|||++|+|++++++|++++. ++..+.++++.....  .....+.
T Consensus        72 ~~~~~~~~~~~i~~iVewAK~iPgF~~L~~~DQi~LLK~~~~Ellil~~a~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~  150 (267)
T d2p54a1          72 FHCCQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNK-DGMLVAYGNGFITREFLKSLRKPF  150 (267)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHGGGEET-TEEEETTTTEEEEHHHHHHSCTTG
T ss_pred             HHHHHHHHHHHHHHHHHHHhhCcChhhCCHHHHHHHHHHHHHHHHHHHHHHhccC-CCCEEEeCCCccchHHHHHhcchH
Confidence            5667787889999999999999999999999999999999999999999999875 344444444432211  1112234


Q ss_pred             HHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhhh
Q psy6602         166 NNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLP  245 (367)
Q Consensus       166 ~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~  245 (367)
                      .+.++.+.+|+.+|++|++|+.||+|||||+||+||++|+.+..+|+++|++|.++|+.|+..+||+.+.||++|+.+++
T Consensus       151 ~~~~~~~~~~~~~~~~L~ld~~E~alLkAIvLf~pd~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~rf~kLL~~Lp  230 (267)
T d2p54a1         151 CDIMEPKFDFAMKFNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKMQEGIVHVLRLHLQSNHPDDIFLFPKLLQKMA  230 (267)
T ss_dssp             GGTSHHHHHHHHHHHTTCCCHHHHHHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcccHHHHHHHHHHHHHHHHHHHHhcCCChhhHHHHHHHHhH
Confidence            55668899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhHhhhhhHHHHHHhhh-ccCCchhHhHHHHHHc
Q psy6602         246 SLRAVRQSTIERLFFKE-TIGDIPIQRLLGDMYT  278 (367)
Q Consensus       246 ~Lr~l~~~~~e~l~~~~-~~~~~~~~~Ll~eml~  278 (367)
                      .||+++..+.|.++..+ ..+..++++|+.|||.
T Consensus       231 ~LR~l~~~~~e~l~~~k~~~~~~~l~pLl~Eif~  264 (267)
T d2p54a1         231 DLRQLVTEHAQLVQIIKKTESDAALHPLLQEIYR  264 (267)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHhccCCCCCccHHHHHHHH
Confidence            99999999999998654 4678899999999995

>d1nq7a_ a.123.1.1 (A:) Orphan nuclear receptor ROR-beta {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor ROR-beta
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=100.00  E-value=1e-34  Score=262.51  Aligned_cols=192  Identities=15%  Similarity=0.217  Sum_probs=170.6

Q ss_pred             ccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccc
Q psy6602          85 LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVR  164 (367)
Q Consensus        85 ~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~  164 (367)
                      ...|.++++.+++.|+.+|+|||++|||.+|+.+||++|||++|+|++++++|++++..++. ++++++..........+
T Consensus        49 ~~~~~~~~~~~~~~i~~vV~faK~lP~F~~L~~~DQi~LLk~~~~el~~l~~a~~~~~~~~~-~~~~~~~~~~~~~~~~~  127 (244)
T d1nq7a_          49 EALWQQCAIQITHAIQYVVEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPLNNT-VLFEGKYGGMQMFKALG  127 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCHHHHTSCHHHHHHHHHHHHHHHHHHHHGGGEETTTTE-EEETTEEEEGGGGGGGS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHccCCCCe-EeeCCccccHHHHhhcc
Confidence            34588999999999999999999999999999999999999999999999999999875544 44455554444444455


Q ss_pred             hHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhh
Q psy6602         165 VNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLML  244 (367)
Q Consensus       165 ~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l  244 (367)
                      ..+.++.+.+|+.+|++|++|++||+|||||+||+||++|+.+...|+++|++|..+|+.|+..+|++ +.||++|+.++
T Consensus       128 ~~~~~~~~~~~~~~~~~L~l~~~E~all~AivL~~pd~~~l~~~~~Ve~lq~~~~~aL~~~~~~~~~~-~~rf~~LL~~L  206 (244)
T d1nq7a_         128 SDDLVNEAFDFAKNLCSLQLTEEEIALFSSAVLISPDRAWLLEPRKVQKLQEKIYFALQHVIQKNHLD-DETLAKLIAKI  206 (244)
T ss_dssp             CHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCSC-TTHHHHHHHTH
T ss_pred             cHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCcccHHHHHHHHHHHHHHHHHHHHhcCCC-chHHHHHHHHh
Confidence            77888999999999999999999999999999999999999999999999999999999999999985 46999999999


Q ss_pred             hHhHhhhhhHHHHHHhhhccCCchh----HhHHHHHHc
Q psy6602         245 PSLRAVRQSTIERLFFKETIGDIPI----QRLLGDMYT  278 (367)
Q Consensus       245 ~~Lr~l~~~~~e~l~~~~~~~~~~~----~~Ll~eml~  278 (367)
                      +.||+++..+.|.++..+..+...+    ++|+.|||+
T Consensus       207 p~LR~l~~~~~e~l~~~k~~~~~~~~~~lp~L~~E~fd  244 (244)
T d1nq7a_         207 PTITAVCNLHGEKLQVFKQSHPDIVNTLFPPLYKELFN  244 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCHHHHHHTSCHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCccccccchHHHHHHcC
Confidence            9999999999999999888766554    478888885

>d2fvja1 a.123.1.1 (A:207-477) Peroxisome proliferator activated receptor gamma, PPAR-gamma {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Peroxisome proliferator activated receptor gamma, PPAR-gamma
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=7.6e-35  Score=266.42  Aligned_cols=191  Identities=22%  Similarity=0.301  Sum_probs=166.0

Q ss_pred             cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCc-cccC--CCCCc
Q psy6602          86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEK-ARER--LPPDD  162 (367)
Q Consensus        86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~-~~~~--~~~~~  162 (367)
                      ..+..+++.+++.+..+|+|||++|||.+|+.+||++|||++|+|+++++.|++++.  ++..+..+. ....  .....
T Consensus        74 ~~~~~~~~~~~~~i~~vVefAK~iP~F~~L~~~DQi~LLK~~~~ElllL~~a~~~~~--~~~~~~~g~~~~~~~~~~~~~  151 (271)
T d2fvja1          74 RIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNK--DGVLISEGQGFMTREFLKSLR  151 (271)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEET--TEEEETTTTEEEEHHHHHTSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCcChhhCCHHHHHHHHHHHHHHHHHHHHHHHcCC--CCCeeeCCCccchHHHHHHhh
Confidence            348889999999999999999999999999999999999999999999999998864  333333332 2111  11112


Q ss_pred             cchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHH
Q psy6602         163 VRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLL  242 (367)
Q Consensus       163 ~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~  242 (367)
                      .+..+.++.+.+|+.+|++|++|+.||+|||||+||+||++|+.+...|+++|++|.++|+.|+..+||+++.||++|+.
T Consensus       152 ~~~~~~~~~i~~f~~~~~~L~ld~~E~alLkAIvLf~pd~~gL~~~~~Ve~lQ~~~~~aL~~y~~~~~p~~~~rf~kLL~  231 (271)
T d2fvja1         152 KPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQ  231 (271)
T ss_dssp             TTGGGSSHHHHHHHHHHHTTCCCHHHHHHHHHHHHTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHSTTSTTHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcccccCCccHHHHHHHHHHHHHHHHHHHHHhCCCchhHHHHHHH
Confidence            22445568899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhHhHhhhhhHHHHHHhh-hccCCchhHhHHHHHHc
Q psy6602         243 MLPSLRAVRQSTIERLFFK-ETIGDIPIQRLLGDMYT  278 (367)
Q Consensus       243 ~l~~Lr~l~~~~~e~l~~~-~~~~~~~~~~Ll~eml~  278 (367)
                      +++.||+++..+.|.++.. ...+..++++|+.|||.
T Consensus       232 ~Lp~LR~l~~~~~e~l~~~k~~~~~~~l~pLl~Eif~  268 (271)
T d2fvja1         232 KMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYK  268 (271)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHCCSSCCCHHHHHHHT
T ss_pred             HhHHHHHHHHHHHHHHHHHhccCCCCCccHHHHHHHH
Confidence            9999999999999999855 45788999999999996

>d2b50b1 a.123.1.1 (B:211-475) Peroxisome proliferator-activated receptor delta, PPAR-DELTA {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Peroxisome proliferator-activated receptor delta, PPAR-DELTA
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.8e-34  Score=262.89  Aligned_cols=192  Identities=21%  Similarity=0.252  Sum_probs=168.9

Q ss_pred             ccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccC---CCCC
Q psy6602          85 LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARER---LPPD  161 (367)
Q Consensus        85 ~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~---~~~~  161 (367)
                      ...|.+++..++..+..+|+|||++|||.+|+.+||++|||++|+|+++++.|++++.  ++..+..+.....   ....
T Consensus        69 ~~~f~~~~~~~~~~I~~iVefAK~iPgF~~L~~~DQi~LLK~~~~Ellil~~a~~~~~--d~~~~~~g~~~~~~~~~~~~  146 (265)
T d2b50b1          69 VHVFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNK--DGLLVANGSGFVTREFLRSL  146 (265)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTSHHHHTSCHHHHHHHHHHHHHHHHHHHHGGGEET--TEEEETTTTEEEEHHHHHTS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCcChhhCCHHHHHHHHHHHHHHHHHHHHHHHhCC--CCceEeCCcccccHHHHHHh
Confidence            3458889999999999999999999999999999999999999999999999998763  4444444433221   1122


Q ss_pred             ccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHH
Q psy6602         162 DVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLL  241 (367)
Q Consensus       162 ~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL  241 (367)
                      ..+..+..+.+.+|+.+|+.|++|+.||+|||||+||+||++|+.+...|+++|++|.++|+.|+..+|++++.||++|+
T Consensus       147 ~~~~~~~~~~~~~f~~~~~~L~ld~~E~alLkAiiL~~pd~~~L~~~~~Ve~lQ~~~~~aL~~y~~~~~p~~~~rfakLL  226 (265)
T d2b50b1         147 RKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQQLFPKLL  226 (265)
T ss_dssp             CHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHhhcccCccccccHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHH
Confidence            33356677889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhhHhHhhhhhHHHHHHhhh-ccCCchhHhHHHHHHc
Q psy6602         242 LMLPSLRAVRQSTIERLFFKE-TIGDIPIQRLLGDMYT  278 (367)
Q Consensus       242 ~~l~~Lr~l~~~~~e~l~~~~-~~~~~~~~~Ll~eml~  278 (367)
                      .+++.||+++..+.|.++..+ ..+..++++|+.|||.
T Consensus       227 ~~L~~LR~ls~~~~e~L~~~k~~~~~~~l~pLl~Em~~  264 (265)
T d2b50b1         227 QKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYK  264 (265)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHCTTSCCCHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCCCccHHHHHHhc
Confidence            999999999999999999655 4788899999999986

>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=99.75  E-value=1.1e-18  Score=156.25  Aligned_cols=109  Identities=31%  Similarity=0.459  Sum_probs=100.3

Q ss_pred             HHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcChH
Q psy6602         241 LLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRF  320 (367)
Q Consensus       241 L~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r~  320 (367)
                      ..++..++.+..+..|+++++...-               .+||++|+++...|+.+|+++..||.+|+..+||+++.||
T Consensus       134 ~~l~~~l~~L~ld~~E~~lLkai~L---------------f~pd~~gL~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf  198 (242)
T d1pk5a_         134 QELVVRLRSLQFDQREFVCLKFLVL---------------FSSDVKNLENLQLVEGVQEQVNAALLDYTVCNYPQQTEKF  198 (242)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHH---------------SCSCCSSCTTHHHHHHHHHHHHHHHHHHHHHHCTTSTTHH
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHh---------------cCCCCCCchhHHHHHHHHHHHHHHHHHHHHhhCCCcchHH
Confidence            3456668888899999998887752               3489999999999999999999999999999999999999


Q ss_pred             HHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhccc
Q psy6602         321 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEK  364 (367)
Q Consensus       321 ~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~~  364 (367)
                      ++||++||+||+++..++|+|||++++|.+|+++||.|||++|+
T Consensus       199 ~~LLl~Lp~Lr~~~~~~~e~L~~~~~~g~~~~~~Ll~Eml~~~r  242 (242)
T d1pk5a_         199 GQLLLRLPELRAISKQAEDYLYYKHVNGDVPYNNLLIEMLHAKR  242 (242)
T ss_dssp             HHHHTTHHHHHHHHHHHHHHHHHHHHTTCSCCCHHHHHHHTTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHhCCC
Confidence            99999999999999999999999999999999999999999984

>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=99.74  E-value=2.5e-18  Score=155.89  Aligned_cols=111  Identities=21%  Similarity=0.298  Sum_probs=103.6

Q ss_pred             HhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcChHH
Q psy6602         242 LMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFG  321 (367)
Q Consensus       242 ~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r~~  321 (367)
                      .+...++.+..+..|+++++.+.-               .++|++|+.+..+|+++|+++..||++|+..+||+++.||+
T Consensus       155 ~~~~~~~~L~ld~~E~~lLkaivL---------------f~pd~~~l~~~~~Ie~lqe~~~~aL~~y~~~~~p~~~~Rf~  219 (265)
T d1hg4a_         155 ELSVKMKRLNLDRRELSCLKAIIL---------------YNPDIRGIKSRAEIEMCREKVYACLDEHCRLEHPGDDGRFA  219 (265)
T ss_dssp             HTHHHHHHHTCCHHHHHHHHHHHH---------------SCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHH---------------ccccCCCCcCHHHHHHHHHHHHHHHHHHHHhhCCChhhHHH
Confidence            466778999999999999987752               24899999999999999999999999999999999999999


Q ss_pred             HHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhccccCC
Q psy6602         322 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYG  367 (367)
Q Consensus       322 ~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~~~~~  367 (367)
                      +||++||+||+++..++|+|||.+++|.+||++||.|||+++..+|
T Consensus       220 ~LLl~Lp~Lr~l~~~~~e~l~~~~~~g~~~i~~Ll~Eml~~~~~~~  265 (265)
T d1hg4a_         220 QLLLRLPALRSISLKCQDHLFLFRITSDRPLEELFLEQLEAPPPPG  265 (265)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCBCSSCHHHHHHHHHTSCCCCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhcccCCCCChhHHHHHHhcCCCCCC
Confidence            9999999999999999999999999999999999999999998776

>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=99.73  E-value=2.6e-18  Score=155.01  Aligned_cols=107  Identities=29%  Similarity=0.426  Sum_probs=100.0

Q ss_pred             HhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcChHH
Q psy6602         242 LMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFG  321 (367)
Q Consensus       242 ~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r~~  321 (367)
                      .+...++.+..+..|+++++...-               .+||++|+.+...|+++|+++..+|.+|+..+||+++.||+
T Consensus       149 ~l~~~~~~L~ld~~E~~~LkaIvL---------------fnpd~~gL~~~~~Ie~lqe~~~~aL~~y~~~~~p~~~~Rf~  213 (256)
T d1g2na_         149 ELSLKMRTLRVDQAEYVALKAIIL---------------LNPDVKGLKNRQEVEVLREKMFLCLDEYCRRSRSSEEGRFA  213 (256)
T ss_dssp             HTHHHHHHTTCCHHHHHHHHHHHH---------------SCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHSTTCTTHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHH---------------hcCccCCcccHHHHHHHHHHHHHHHHHHHHhcCCChhhHHH
Confidence            466679999999999999988752               24899999999999999999999999999999999999999


Q ss_pred             HHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhcc
Q psy6602         322 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME  363 (367)
Q Consensus       322 ~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~  363 (367)
                      +||++||+||+++++++|+|||.+++|+++|++||.|||+++
T Consensus       214 ~LLl~Lp~LR~l~~~~~e~lff~~l~g~~~i~~ll~eml~~~  255 (256)
T d1g2na_         214 ALLLRLPALRSISLKSFEHLFFFHLVADTSIAGYIRDALRNH  255 (256)
T ss_dssp             HHHTHHHHHHHHHHHHHHHHHHTTCBCTTTHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcccccCCCChHHHHHHHHhcc
Confidence            999999999999999999999999999999999999999875

>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=99.68  E-value=9.9e-17  Score=141.49  Aligned_cols=148  Identities=22%  Similarity=0.288  Sum_probs=118.2

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhC---CC-------------------cchHHHHHHHhhhHhHhhhhhHHHH
Q psy6602         200 PETPGLVDAQPVEMLQDQAQCILGDYVRGRY---SR-------------------QPTRFGRLLLMLPSLRAVRQSTIER  257 (367)
Q Consensus       200 pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~---~~-------------------~~~Rf~~LL~~l~~Lr~l~~~~~e~  257 (367)
                      |...+|...+++.-++..+...+.--...++   .+                   ....+..+......++++..+..|+
T Consensus        54 p~F~~L~~~DQi~LLk~~~~el~~L~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~l~~L~ld~~E~  133 (223)
T d2e2ra1          54 PGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEF  133 (223)
T ss_dssp             TTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTSSSCEEEETTEEECHHHHHHTTCHHHHHHHHHHHHHHHHHTCCHHHH
T ss_pred             cchhhcCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeeeecCCcccchHHhhhccHHHHHHHHHHHHHHHHHcCCCHHHH
Confidence            3444555567777777666664443222221   11                   0123455666777788888888888


Q ss_pred             HHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcChHHHHHhhchhhhhhchhh
Q psy6602         258 LFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQST  337 (367)
Q Consensus       258 l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r~~~lLl~Lp~lr~i~~~~  337 (367)
                      .+++...-               .+||++|+++..+|+.+|+++..||++|+..+||+++.||++||++||+||+++..+
T Consensus       134 ~lLkaivL---------------~~pd~~~L~~~~~I~~~q~~~~~aL~~y~~~~~~~~~~rf~~LL~~Lp~Lr~l~~~~  198 (223)
T d2e2ra1         134 VTLKAIAL---------------ANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKA  198 (223)
T ss_dssp             HHHHHHHH---------------HTCCCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTTHHHHHHHHHHH
T ss_pred             HHHHHHHH---------------hccCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHHHH
Confidence            88876642               258999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhhcCCCChHHHHHHHHhc
Q psy6602         338 IERLFFKETIGDIPIQRLLGDMYTM  362 (367)
Q Consensus       338 ~e~l~~~~~~g~~~i~~ll~eml~~  362 (367)
                      .+++||.+++|.+|+++|+.||+++
T Consensus       199 ~e~l~~~~~~~~~~~~~Ll~E~l~a  223 (223)
T d2e2ra1         199 VQHFYNIKLEGKVPMHKLFLEMLEA  223 (223)
T ss_dssp             HHHHHHHHHHCCSCCCHHHHHHHTS
T ss_pred             HHHHHHhhcCCCCCchHHHHHHHcC
Confidence            9999999999999999999999985

>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=99.63  E-value=2.9e-16  Score=139.68  Aligned_cols=108  Identities=20%  Similarity=0.228  Sum_probs=96.9

Q ss_pred             HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcC
Q psy6602         239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPT  318 (367)
Q Consensus       239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~  318 (367)
                      .+......++.+..+..|+++++.+.-               .++|++||+++..|+++|+++..||++|+..+||+++.
T Consensus       129 ~~~~~~~~l~~L~ld~~E~alL~Ai~L---------------~~pd~~gL~~~~~Ve~lq~~~~~aL~~y~~~~~~~~~~  193 (236)
T d1fcya_         129 LVFAFAGQLLPLEMDDTETGLLSAICL---------------ICGDRMDLEEPEKVDKLQEPLLEALRLYARRRRPSQPY  193 (236)
T ss_dssp             HHHHHHHHHGGGCCCHHHHHHHHHHHH---------------SCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTT
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHhh---------------ccCCCCCcccccHHHHHHHHHHHHHHHHHHHhCCCchh
Confidence            344455667788888888888876642               35899999999999999999999999999999999999


Q ss_pred             hHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHh
Q psy6602         319 RFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT  361 (367)
Q Consensus       319 r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~  361 (367)
                      ||++||++||+||+++..+.|++++.++.|.+++++|+.|||+
T Consensus       194 rf~~LL~~Lp~LR~l~~~~~e~l~~~k~~~~~~~~~L~~E~~d  236 (236)
T d1fcya_         194 MFPRMLMKITDLRGISTKGAERAITLKMEIPGPMPPLIREMLE  236 (236)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCCCHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCccHHHHHHcC
Confidence            9999999999999999999999999999999999999999985

>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=99.63  E-value=1.8e-16  Score=140.24  Aligned_cols=111  Identities=27%  Similarity=0.392  Sum_probs=96.0

Q ss_pred             HHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhC---
Q psy6602         237 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRY---  313 (367)
Q Consensus       237 f~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~---  313 (367)
                      +..+......++.+..+..|+++++...-               .+||++|+++...|+.+|+++..||.+|+..+|   
T Consensus       113 ~~~l~~~~~~~~~L~ld~~E~~lLkaivL---------------f~pd~~gL~~~~~I~~~q~~~~~aL~~y~~~~~~~~  177 (227)
T d3d24a1         113 GAALLQLVRRLQALRLEREEYVLLKALAL---------------ANSDSVHIEDAEAVEQLREALHEALLEYEAGRAGPG  177 (227)
T ss_dssp             HHHHHHHHHHHHTTTCCHHHHHHHHHHHH---------------HTCCCTTCSCHHHHHHHHHHHHHHHHHHHTC-----
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHH---------------hCCcCCCcccHHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence            44566677778888999999998887642               248999999999999999999999999999987   


Q ss_pred             -CCCcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhc
Q psy6602         314 -SRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM  362 (367)
Q Consensus       314 -p~~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~  362 (367)
                       |.++.||++||++||+||+++..+.|++||++++|.+|+++|+.|||++
T Consensus       178 ~~~~~~Rf~~LL~~Lp~Lr~l~~~~~e~l~~~~~~g~~~~~~Ll~Eml~~  227 (227)
T d3d24a1         178 GGAERRRAGRLLLTLPLLRQTAGKVLAHFYGVKLEGKVPMHKLFLEMLEA  227 (227)
T ss_dssp             ---CHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHSCCSCCCHHHHHHHHC
T ss_pred             chhHHhHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCchHHHHHHHcC
Confidence             3456799999999999999999999999999999999999999999985

>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=99.62  E-value=1.6e-15  Score=134.29  Aligned_cols=111  Identities=19%  Similarity=0.227  Sum_probs=99.4

Q ss_pred             hHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCC
Q psy6602         235 TRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYS  314 (367)
Q Consensus       235 ~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p  314 (367)
                      .-...+......++.+..+..|+++++...-               .+||++||++...|+++|+++..||++|+..+||
T Consensus       120 ~~~~~i~~~~~~l~~L~ld~~E~~lLkAivL---------------~~pd~~gL~~~~~Ve~lq~~~~~aL~~y~~~~~p  184 (231)
T d1osha_         120 EYITPMFSFYKSIGELKMTQEEYALLTAIVI---------------LSPDRQYIKDREAVEKLQEPLLDVLQKLCKIHQP  184 (231)
T ss_dssp             TTHHHHHHHHHHHHTTCCCHHHHHHHHHHHH---------------TCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHH---------------hccCCCCCccHHHHHHHHHHHHHHHHHHHHHHCC
Confidence            3456666777788888899999998887742               3589999999999999999999999999999999


Q ss_pred             CCcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHh
Q psy6602         315 RQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT  361 (367)
Q Consensus       315 ~~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~  361 (367)
                      +++.||++||++||+||+++..+.|++++.++ +..++++|+.|||+
T Consensus       185 ~~~~rf~~LL~~L~~LR~l~~~~~e~l~~~k~-~~~~~~pLl~E~fd  230 (231)
T d1osha_         185 ENPQHFACLLGRLTELRTFNHHHAEMLMSWRV-NDHKFTPLLCEIWD  230 (231)
T ss_dssp             TCTTHHHHHHHHHHHHHTHHHHHHHHHHHHHH-TTCCCCHHHHHHHT
T ss_pred             CchhHHHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCCCChHHHHHhC
Confidence            99999999999999999999999999999987 56789999999997

>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=99.61  E-value=5.2e-16  Score=137.74  Aligned_cols=106  Identities=28%  Similarity=0.431  Sum_probs=98.0

Q ss_pred             HhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcChHH
Q psy6602         242 LMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFG  321 (367)
Q Consensus       242 ~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r~~  321 (367)
                      .+...++.+..+..|+++++...-               .+||++|+.+..+|+.+|+++..+|.+|+..+||+++.||+
T Consensus       126 ~~~~~~~~L~ld~~E~~lLkaiiL---------------~~pd~~~l~~~~~i~~~q~~~~~~L~~y~~~~~~~~~~Rf~  190 (233)
T d1pzla_         126 ELVLPFQELQIDDNEYAYLKAIIF---------------FDPDAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFG  190 (233)
T ss_dssp             HTHHHHHHHTCCHHHHHHHHHHHH---------------CCTTCTTCSCHHHHHHHHHHHHHHHHHHHHSSSSCCTTHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHh---------------cccccCCcccHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHH
Confidence            456678889999999999887752               24899999999999999999999999999999999999999


Q ss_pred             HHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhc
Q psy6602         322 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM  362 (367)
Q Consensus       322 ~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~  362 (367)
                      +||++||+||+++..+.|++||.+++|.+++++|+.||+.+
T Consensus       191 ~LLl~Lp~Lr~i~~~~~e~l~~~~~~~~~~~~~Ll~emL~~  231 (233)
T d1pzla_         191 ELLLLLPTLQSITWQMIEQIQFIKLFGMAKIDNLLQEMLLG  231 (233)
T ss_dssp             HHHTHHHHHHHHHHHHHHHHHHHHHTTCSCCCHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcccCCCCChHHHHHHHhcc
Confidence            99999999999999999999999999999999999999965

>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=99.61  E-value=2e-15  Score=134.34  Aligned_cols=109  Identities=22%  Similarity=0.280  Sum_probs=96.9

Q ss_pred             HHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCC
Q psy6602         237 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQ  316 (367)
Q Consensus       237 f~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~  316 (367)
                      ...+......++.+..+..|+++++...-               .+||++|+++...|+++|+++..||+.|+..+||++
T Consensus       131 ~~~i~~~~~~l~~L~ld~~E~alLkAivL---------------~~pd~~gl~~~~~ve~lq~~~~~aL~~y~~~~~p~~  195 (239)
T d1pq9a_         131 INPIFEFSRAMRRLGLDDAEYALLIAINI---------------FSADRPNVQEPGRVEALQQPYVEALLSYTRIKRPQD  195 (239)
T ss_dssp             HHHHHHHHHHHHHHTCCHHHHHHHHHHHH---------------TCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHH---------------hCCCcCccccHHHHHHHHHHHHHHHHHHHHhcCCCc
Confidence            44555566678888888888888877642               258999999999999999999999999999999999


Q ss_pred             cChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHh
Q psy6602         317 PTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT  361 (367)
Q Consensus       317 ~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~  361 (367)
                      +.||++||++||+||+++..+.|++|+.++. +.++++|+.|||+
T Consensus       196 ~~rf~~LL~~L~~LR~l~~~~~e~l~~~k~~-~~~~~~L~~Em~d  239 (239)
T d1pq9a_         196 QLRFPRMLMKLVSLRTLSSVHSEQVFALRLQ-DKKLPPLLSEIWD  239 (239)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-TCCCCHHHHHHHC
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHHHHHHcC-CCCCcHHHHHhcC
Confidence            9999999999999999999999999999975 5689999999996

>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=99.59  E-value=1.8e-15  Score=133.78  Aligned_cols=109  Identities=23%  Similarity=0.284  Sum_probs=94.2

Q ss_pred             HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCC--C
Q psy6602         238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYS--R  315 (367)
Q Consensus       238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p--~  315 (367)
                      ..+......++.+..+..|+.+++...-           |     +|++||++..+|+++|+++..||++|+..+||  +
T Consensus       119 ~~i~~~~~~~~~L~ld~~E~alL~AivL-----------~-----~d~~~L~~~~~Ve~lq~~~~~aL~~~i~~~~~~~~  182 (230)
T d1pdua_         119 NDIMEFSRSLHNLEIDISAFACLCALTL-----------I-----TERHGLREPKKVEQLQMKIIGSLRDHVTYNAEAQK  182 (230)
T ss_dssp             HHHHHHHHHHHHHCCCHHHHHHHHHHHH-----------S-----SCCTTCSCHHHHHHHHHHHHHHHHHHHHHCHHHHT
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhhhee-----------e-----cCcccccCHHHHHHHHHHHHHHHHHHHHHhCCCcc
Confidence            4455556667777777788777765541           1     57999999999999999999999999999998  5


Q ss_pred             CcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhc
Q psy6602         316 QPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM  362 (367)
Q Consensus       316 ~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~  362 (367)
                      .+.||++||++||+||+++..++|++|+.|++|.+|+++|+.|||..
T Consensus       183 ~~~rf~~LL~~Lp~LR~l~~~~~e~l~~~k~~~~~~~~~L~~Em~~~  229 (230)
T d1pdua_         183 KQHYFSRLLGKLPELRSLSVQGLQRIFYLKLEDLVPAPALIENMFVT  229 (230)
T ss_dssp             STTHHHHHHTHHHHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHTTTC
T ss_pred             hhhHHHHHHHHhHHHHHHHHHHHHHHHHHHcCCCCCccHHHHHHhhc
Confidence            57799999999999999999999999999999999999999999863

>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=3.7e-15  Score=132.27  Aligned_cols=109  Identities=19%  Similarity=0.268  Sum_probs=95.3

Q ss_pred             HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCC--C
Q psy6602         238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYS--R  315 (367)
Q Consensus       238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p--~  315 (367)
                      ..+......++.+..+..|+++++.+.-                .+|++|+++..+|+++|+++..||++|+..+||  +
T Consensus       122 ~~i~~~~~~l~~L~ld~~E~alLkAI~L----------------~~dr~gL~~~~~Ve~lQ~~~~~aL~~~~~~~~~~~~  185 (236)
T d1ovla_         122 DSIVEFSSNLQNMNIDISAFSCIAALAM----------------VTERHGLKEPKRVEELQNKIVNCLKDHVTFNNGGLN  185 (236)
T ss_dssp             HHHHHHHHHHHTTCCCHHHHHHHHHHHH----------------SSCCTTCSCHHHHHHHHHHHHHHHHHHHHGGGTTTT
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHH----------------cCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcc
Confidence            4455566677888888888888765431                148999999999999999999999999999987  6


Q ss_pred             CcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhc
Q psy6602         316 QPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM  362 (367)
Q Consensus       316 ~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~  362 (367)
                      ++.||++||++||+||+++..++|++|+.|++|.+|+++|+.||+..
T Consensus       186 ~~~rf~~LL~~Lp~LR~l~~~~~e~l~~~kl~~~~~~~~L~~elf~~  232 (236)
T d1ovla_         186 RPNYLSKLLGKLPELRTLCTQGLQRIFYLKLEDLVPPPAIIDKLFLD  232 (236)
T ss_dssp             STTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSSCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcCCCCCcHHHHHHHHHh
Confidence            78999999999999999999999999999999999999999999864

>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=99.59  E-value=1e-15  Score=135.53  Aligned_cols=106  Identities=30%  Similarity=0.538  Sum_probs=98.2

Q ss_pred             HhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcChHH
Q psy6602         242 LMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFG  321 (367)
Q Consensus       242 ~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r~~  321 (367)
                      .+...++.+..+..|+++++...-               .++|++|+.+..+|+.+|+++..||.+|+..+||+.+.||+
T Consensus       124 ~~~~~~~~L~ld~~E~~lLkaivL---------------~~pd~~~l~~~~~i~~~q~~~~~aL~~y~~~~~~~~~~R~~  188 (230)
T d2p1ta1         124 ELVSKMRDMQMDKTELGCLRAIVL---------------FNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFA  188 (230)
T ss_dssp             HTHHHHHHTTCCHHHHHHHHHHHH---------------SCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHH---------------hccccCCcccHHHHHHHHHHHHHHHHHHHHhhCCCchhHHH
Confidence            466778889999999998887642               34799999999999999999999999999999999999999


Q ss_pred             HHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhc
Q psy6602         322 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM  362 (367)
Q Consensus       322 ~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~  362 (367)
                      +||++||+||+++..+.+++||.+++|.+++++|+.|||++
T Consensus       189 ~Ll~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~Eml~~  229 (230)
T d2p1ta1         189 KLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEA  229 (230)
T ss_dssp             HHHTTHHHHHHHHHHHHHHHHHHHHHCCSCCCHHHHHHTSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCcCCCCChhHHHHHHHcC
Confidence            99999999999999999999999999999999999999986

>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=99.57  E-value=8.3e-15  Score=129.77  Aligned_cols=108  Identities=19%  Similarity=0.305  Sum_probs=89.6

Q ss_pred             HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhh--CCC
Q psy6602         238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGR--YSR  315 (367)
Q Consensus       238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~--~p~  315 (367)
                      ..+......++.+..+..|+++++...-             +   +|++|+++...|+++|+++..||++|+..+  +|+
T Consensus       122 ~~i~~~~~~l~~L~ld~~E~alLkAivL-------------~---~d~~gL~~~~~Ve~lq~~~~~aL~~yi~~~~~~~~  185 (233)
T d2qw4a1         122 DSILAFSRSLHSLLVDVPAFACLSALVL-------------I---TDRHGLQEPRRVEELQNRIASCLKEHVAAVAGEPQ  185 (233)
T ss_dssp             HHHHHHHHHHHHHTCCHHHHHHHHHHHH-------------S---SCCTTCSCHHHHHHHHHHHHHHHHHHHHHSCC---
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHh-------------c---CcccCccCHHHHHHHHHHHHHHHHHHHHHhcCCCc
Confidence            4444455566777777777777665431             1   378999999999999999999999999865  578


Q ss_pred             CcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHh
Q psy6602         316 QPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT  361 (367)
Q Consensus       316 ~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~  361 (367)
                      ++.||+|||++||+||+++..+.|++|+.|++|.+|+++|+.|||.
T Consensus       186 ~~~rf~kLL~~Lp~LR~l~~~~~e~l~~~k~~~~~~~p~L~~Emf~  231 (233)
T d2qw4a1         186 PASCLSRLLGKLPELRTLCTQGLQRIFYLKLEDLVPPPPIIDKIFM  231 (233)
T ss_dssp             CCTTHHHHHTHHHHHHHHHHHHHHHHHHHHHHCCSCCCHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCchHHHHHHcc
Confidence            8999999999999999999999999999999999999999999985

>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=99.57  E-value=8.2e-15  Score=131.17  Aligned_cols=109  Identities=17%  Similarity=0.228  Sum_probs=94.6

Q ss_pred             HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCc
Q psy6602         238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP  317 (367)
Q Consensus       238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~  317 (367)
                      ..+......++.+..+..|+++++...-               .++|++||++...|+++|+.+..||+.|+..+||+++
T Consensus       141 ~~i~~f~~~l~~L~ld~~E~alL~AivL---------------~~pdr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~  205 (251)
T d1n46a_         141 DAIFDLGMSLSSFNLDDTEVALLQAVLL---------------MSSDRPGLACVERIEKYQDSFLLAFEHYINYRKHHVT  205 (251)
T ss_dssp             HHHHHHHHHHGGGTCCHHHHHHHHHHHH---------------TCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCCSST
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHH---------------hcCCCCCCcCHHHHHHHHHHHHHHHHHHHHHhCCCcc
Confidence            4455566677777788888887776642               2589999999999999999999999999999999999


Q ss_pred             ChHHHHHhhchhhhhhchhhHHHHHHhhhcCCC-ChHHHHHHHHh
Q psy6602         318 TRFGRLLLMLPSLRAVRQSTIERLFFKETIGDI-PIQRLLGDMYT  361 (367)
Q Consensus       318 ~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~-~i~~ll~eml~  361 (367)
                      .||+|||++||+||+++..+.+.+++.+..+.. .+++|+.|||+
T Consensus       206 ~rf~kLL~~Lp~LR~l~~~~~e~l~~~k~~~~~~~~ppLl~E~fd  250 (251)
T d1n46a_         206 HFWPKLLMKVTDLRMIGACHASRFLHMKVECPTELFPPLFLEVFE  250 (251)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCGGGSCHHHHHHHC
T ss_pred             cHHHHHHHHhHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHhc
Confidence            999999999999999999999999999988654 46899999997

>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=99.54  E-value=6.3e-15  Score=133.27  Aligned_cols=110  Identities=22%  Similarity=0.305  Sum_probs=96.6

Q ss_pred             HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCc
Q psy6602         238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP  317 (367)
Q Consensus       238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~  317 (367)
                      ..+......++.+..+..|+++++...-               .+||++|+.+...|+++|+++..||++|+..+||+++
T Consensus       159 ~~i~~f~~~~~~L~ld~~E~alLkAIvL---------------f~pd~~gL~~~~~Ve~lQ~~~~~aL~~y~~~~~p~~~  223 (271)
T d2fvja1         159 EPKFEFAVKFNALELDDSDLAIFIAVII---------------LSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESS  223 (271)
T ss_dssp             HHHHHHHHHHHTTCCCHHHHHHHHHHHH---------------TCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHSTTST
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHH---------------HcccccCCccHHHHHHHHHHHHHHHHHHHHHhCCCch
Confidence            3455566677888888888888876642               2589999999999999999999999999999999999


Q ss_pred             ChHHHHHhhchhhhhhchhhHHHHH-HhhhcCCCChHHHHHHHHhc
Q psy6602         318 TRFGRLLLMLPSLRAVRQSTIERLF-FKETIGDIPIQRLLGDMYTM  362 (367)
Q Consensus       318 ~r~~~lLl~Lp~lr~i~~~~~e~l~-~~~~~g~~~i~~ll~eml~~  362 (367)
                      .||++||++||+||+++..+.+.++ ++...|.+++++|+.|||..
T Consensus       224 ~rf~kLL~~Lp~LR~l~~~~~e~l~~~k~~~~~~~l~pLl~Eif~d  269 (271)
T d2fvja1         224 QLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKD  269 (271)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCSSCCCHHHHHHHTT
T ss_pred             hHHHHHHHHhHHHHHHHHHHHHHHHHHhccCCCCCccHHHHHHHHH
Confidence            9999999999999999999999998 56678999999999999963

>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=6.9e-15  Score=132.61  Aligned_cols=110  Identities=18%  Similarity=0.243  Sum_probs=97.0

Q ss_pred             HHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCC
Q psy6602         237 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQ  316 (367)
Q Consensus       237 f~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~  316 (367)
                      ...+......++.+..+..|+.+++...-               .++|++|+.+...|+++|+++..||+.|+..+||++
T Consensus       154 ~~~~~~~~~~~~~L~ld~~E~alLkAIvL---------------f~pd~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~  218 (267)
T d2p54a1         154 MEPKFDFAMKFNALELDDSDISLFVAAII---------------CCGDRPGLLNVGHIEKMQEGIVHVLRLHLQSNHPDD  218 (267)
T ss_dssp             SHHHHHHHHHHHTTCCCHHHHHHHHHHHH---------------SCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHH---------------hcCCCCCcccHHHHHHHHHHHHHHHHHHHHhcCCCh
Confidence            34455566778888888888888876642               258999999999999999999999999999999999


Q ss_pred             cChHHHHHhhchhhhhhchhhHHHHHH-hhhcCCCChHHHHHHHHh
Q psy6602         317 PTRFGRLLLMLPSLRAVRQSTIERLFF-KETIGDIPIQRLLGDMYT  361 (367)
Q Consensus       317 ~~r~~~lLl~Lp~lr~i~~~~~e~l~~-~~~~g~~~i~~ll~eml~  361 (367)
                      +.||+|||++||+||+++..+.+.++. +...+.+++++|+.|||.
T Consensus       219 ~~rf~kLL~~Lp~LR~l~~~~~e~l~~~k~~~~~~~l~pLl~Eif~  264 (267)
T d2p54a1         219 IFLFPKLLQKMADLRQLVTEHAQLVQIIKKTESDAALHPLLQEIYR  264 (267)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHT
T ss_pred             hhHHHHHHHHhHHHHHHHHHHHHHHHHHhccCCCCCccHHHHHHHH
Confidence            999999999999999999999999984 566899999999999995

>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=8.3e-15  Score=132.00  Aligned_cols=109  Identities=19%  Similarity=0.243  Sum_probs=96.5

Q ss_pred             HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCc
Q psy6602         238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP  317 (367)
Q Consensus       238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~  317 (367)
                      ..+......++.+..+..|+++++...-               .++|++|+++...|+.+|+++..||+.|+..+||+.+
T Consensus       155 ~~~~~f~~~~~~L~ld~~E~alLkAiiL---------------~~pd~~~L~~~~~Ve~lQ~~~~~aL~~y~~~~~p~~~  219 (265)
T d2b50b1         155 EPKFEFAVKFNALELDDSDLALFIAAII---------------LCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQ  219 (265)
T ss_dssp             HHHHHHHHHHHTTCCCHHHHHHHHHHHH---------------SCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCT
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHhh---------------cccCccccccHHHHHHHHHHHHHHHHHHHHHhCCChh
Confidence            3445566777888888888888876642               3589999999999999999999999999999999999


Q ss_pred             ChHHHHHhhchhhhhhchhhHHHHHH-hhhcCCCChHHHHHHHHh
Q psy6602         318 TRFGRLLLMLPSLRAVRQSTIERLFF-KETIGDIPIQRLLGDMYT  361 (367)
Q Consensus       318 ~r~~~lLl~Lp~lr~i~~~~~e~l~~-~~~~g~~~i~~ll~eml~  361 (367)
                      .||++||++||+||+++..+.+.|+. ++..|.+|+++|+.|||.
T Consensus       220 ~rfakLL~~L~~LR~ls~~~~e~L~~~k~~~~~~~l~pLl~Em~~  264 (265)
T d2b50b1         220 QLFPKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYK  264 (265)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTTSCCCHHHHHHHC
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCccHHHHHHhc
Confidence            99999999999999999999999995 566899999999999995

>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=99.50  E-value=1e-14  Score=130.19  Aligned_cols=107  Identities=20%  Similarity=0.327  Sum_probs=94.1

Q ss_pred             HHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhC--C
Q psy6602         237 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRY--S  314 (367)
Q Consensus       237 f~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~--p  314 (367)
                      ...+......++.+..+..|+++++...-               .+||++||++...|+++|+++..||++|+..+|  |
T Consensus       137 ~~~~~~f~~~l~~L~ld~~E~alLkAivL---------------~~pD~~gL~~~~~Ve~lQ~~~~~aL~~y~~~~~~~p  201 (246)
T d1xvpb_         137 LELLFHFHGTLRKLQLQEPEYVLLAAMAL---------------FSPDRPGVTQRDEIDQLQEEMALTLQSYIKGQQRRP  201 (246)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHH---------------SCSSSTTCSCHHHHHHHHHHHHHHHHHHHHTCSSCC
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHhhhhh---------------ccCCCCCCCcHHHHHHHHHHHHHHHHHHHHHcCCCC
Confidence            44555667788999999999999987752               258999999999999999999999999998877  7


Q ss_pred             CCcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHH
Q psy6602         315 RQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMY  360 (367)
Q Consensus       315 ~~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml  360 (367)
                      +++.||+|||++||+||+++..+.+++++.+  |..++++|+.||+
T Consensus       202 ~~~~rf~~LL~~L~~LR~l~~~~~e~l~~~k--~~~~~~pLl~E~f  245 (246)
T d1xvpb_         202 RDRFLYAKLLGLLAELRSINEAYGYQIQHIQ--GLSAMMPLLQEIC  245 (246)
T ss_dssp             SCSSHHHHHHHHHHHHHHHHHHHHHHHHHST--THHHHCHHHHHHT
T ss_pred             CcccHHHHHHHHhHHHHHHHHHHHHHHHHhc--CCCCCChHHHHhc
Confidence            8899999999999999999999999999877  5567899999996

>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=99.47  E-value=3.8e-14  Score=127.14  Aligned_cols=109  Identities=17%  Similarity=0.274  Sum_probs=93.8

Q ss_pred             HHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCC
Q psy6602         237 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQ  316 (367)
Q Consensus       237 f~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~  316 (367)
                      +..++.....++.+..+..|+++++.+.-               .+||++||++...|+++|+++..||++|+..+||+.
T Consensus       142 ~~~i~~f~~~l~~L~ld~~E~~lLkAiiL---------------~~pdr~gL~~~~~Ve~lq~~~~~aL~~y~~~~~~~~  206 (255)
T d1ie9a_         142 IEPLIKFQVGLKKLNLHEEEHVLLMAICI---------------VSPDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPP  206 (255)
T ss_dssp             HHHHHHHHHHHHTTCCCHHHHHHHHHHHH---------------SCSCSTTCSCHHHHHHHHHHHHHHHHHHHHHHCCTT
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHh---------------cCCCcccccCHHHHHHHHHHHHHHHHHHHHHhCCCC
Confidence            34455566778888888888888887642               358999999999999999999999999999999864


Q ss_pred             --cChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCC--hHHHHHHHH
Q psy6602         317 --PTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIP--IQRLLGDMY  360 (367)
Q Consensus       317 --~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~--i~~ll~eml  360 (367)
                        +.||+|||++||+||+++..+.+.+++.++.+.++  +++|+.|||
T Consensus       207 ~~~~~f~kLL~~L~~LR~l~~~~~e~l~~~~~~~~~~~~lppLl~E~f  254 (255)
T d1ie9a_         207 GSHLLYAKMIQKLADLRSLNEEHSKQYRCLSFQPECSMKLTPLVLEVF  254 (255)
T ss_dssp             TTTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTTHHHHSCHHHHHHH
T ss_pred             CcccHHHHHHHHhHHHHHHHHHHHHHHHHHhhCCCCCCCccHHHHHhc
Confidence              56799999999999999999999999999877654  688999998

>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=99.42  E-value=2e-13  Score=122.04  Aligned_cols=145  Identities=14%  Similarity=0.138  Sum_probs=111.2

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCC-C-c-------------------chHHHHHHHhhhHhHhhhhhHHHHH
Q psy6602         200 PETPGLVDAQPVEMLQDQAQCILGDYVRGRYS-R-Q-------------------PTRFGRLLLMLPSLRAVRQSTIERL  258 (367)
Q Consensus       200 pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~-~-~-------------------~~Rf~~LL~~l~~Lr~l~~~~~e~l  258 (367)
                      |...+|...+++.=++....+.+.-.+...+. . .                   ..-...+......++.+..+..|++
T Consensus        82 PgF~~L~~~DQi~LLk~~~~el~ll~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~ld~~E~a  161 (251)
T d1n83a_          82 DGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQNNTVYFDGKYASPDVFKSLGCEDFISFVFEFGKSLCSMHLTEDEIA  161 (251)
T ss_dssp             TTTTTSCHHHHHHHHHHHHHHHHHHHGGGGEETTTTEEEETTEEECGGGGGGGSCHHHHHHHHHHHHHHHTTCCCHHHHH
T ss_pred             cchhcCCHHHHHHHHHHHHHHHHHHHHHHHhCCCCCEEecCCeeecHHHHhhccHHHHHHHHHHHHHHHHHcCCCHHHHH
Confidence            45555666777777777666655544443321 1 1                   1134455556667788888888888


Q ss_pred             HhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcChHHHHHhhchhhhhhchhhH
Q psy6602         259 FFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTI  338 (367)
Q Consensus       259 ~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r~~~lLl~Lp~lr~i~~~~~  338 (367)
                      +++...-               .+||++||++...|+++|+.+..||+.|+..+||+ +.||+|||++||+||+++..+.
T Consensus       162 lL~AivL---------------~~pd~~gL~~~~~Ve~lq~~~~~aL~~~~~~~~~~-~~rf~~Ll~~Lp~LR~l~~~~~  225 (251)
T d1n83a_         162 LFSAFVL---------------MSADRSWLQEKVKIEKLQQKIQLALQHVLQKNHRE-DGILTKLICKVSTLRALCGRHT  225 (251)
T ss_dssp             HHHHHHH---------------SCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTT-SCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHH---------------HccCccccCCHHHHHHHHHHHHHHHHHHHHhcCCC-ccHHHHHHHHhHHHHHHHHHHH
Confidence            8776642               34899999999999999999999999999999984 7899999999999999999999


Q ss_pred             HHHHHhhhcC----CCChHHHHHHHH
Q psy6602         339 ERLFFKETIG----DIPIQRLLGDMY  360 (367)
Q Consensus       339 e~l~~~~~~g----~~~i~~ll~eml  360 (367)
                      |.+++.+.++    ..++++|+.|||
T Consensus       226 e~l~~~k~~~~~~~~~~~ppL~~Eif  251 (251)
T d1n83a_         226 EKLMAFKAIYPDIVRLHFPPLYKELF  251 (251)
T ss_dssp             HHHHHHHHHCHHHHHHHSCHHHHHHC
T ss_pred             HHHHHHHHHccccccCCccHHHHhhC
Confidence            9999988764    346789999996

>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=99.42  E-value=1.1e-13  Score=123.21  Aligned_cols=110  Identities=15%  Similarity=0.178  Sum_probs=94.9

Q ss_pred             HHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCC
Q psy6602         236 RFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSR  315 (367)
Q Consensus       236 Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~  315 (367)
                      -+..+......++.+..+..|+++++...-               .+||++|+.+...|+++|+.+..||+.|+..+||+
T Consensus       131 ~~~~~~~~~~~~~~L~l~~~E~all~AivL---------------~~pd~~~l~~~~~Ve~lq~~~~~aL~~~~~~~~~~  195 (244)
T d1nq7a_         131 LVNEAFDFAKNLCSLQLTEEEIALFSSAVL---------------ISPDRAWLLEPRKVQKLQEKIYFALQHVIQKNHLD  195 (244)
T ss_dssp             HHHHHHHHHHHHHTTCCCHHHHHHHHHHHH---------------SCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCSC
T ss_pred             HHHHHHHHHHHHHHhCCCHHHHHHHHHHHH---------------HcCCCCCcccHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence            345555666778888888888888876642               25899999999999999999999999999999995


Q ss_pred             CcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChH----HHHHHHHh
Q psy6602         316 QPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQ----RLLGDMYT  361 (367)
Q Consensus       316 ~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~----~ll~eml~  361 (367)
                       +.||+|||++||+||+++..+.|++++.+..+..+++    +|+.|||+
T Consensus       196 -~~rf~~LL~~Lp~LR~l~~~~~e~l~~~k~~~~~~~~~~lp~L~~E~fd  244 (244)
T d1nq7a_         196 -DETLAKLIAKIPTITAVCNLHGEKLQVFKQSHPDIVNTLFPPLYKELFN  244 (244)
T ss_dssp             -TTHHHHHHHTHHHHHHHHHHHHHHHHHHHHHCHHHHHHTSCHHHHHHHC
T ss_pred             -chHHHHHHHHhHHHHHHHHHHHHHHHHHHHhCCccccccchHHHHHHcC
Confidence             4699999999999999999999999999999887765    78888885

>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=99.41  E-value=2.1e-13  Score=121.29  Aligned_cols=109  Identities=17%  Similarity=0.254  Sum_probs=92.4

Q ss_pred             HHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCC
Q psy6602         237 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQ  316 (367)
Q Consensus       237 f~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~  316 (367)
                      +..+......++.+..+..|+++++...-               .+ |++|+++...|+++|+.+..||++|+..+||..
T Consensus       131 ~~~l~~f~~~l~~L~ld~~E~alL~AivL---------------~s-d~~~L~~~~~ve~lq~~~~~aL~~y~~~~~~~~  194 (243)
T d2r40d1         131 IEDLLHFCRCMYSMMMDNVHYALLTAIVI---------------FS-DRPGLEQPLLVEEIQRYYLNTLRVYILNQNSAS  194 (243)
T ss_dssp             HHHHHHHHHHHHTTTCCHHHHHHHHHHHH---------------TS-CCTTCSCHHHHHHHHHHHHHHHHHHHHHHTTTC
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHh---------------cC-CCCCCCcHHHHHHHHHHHHHHHHHHHHhhCCCC
Confidence            34455566678888888888888766541               12 899999999999999999999999999999766


Q ss_pred             c---ChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhc
Q psy6602         317 P---TRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM  362 (367)
Q Consensus       317 ~---~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~  362 (367)
                      |   .||++||++||+||+++..+.+.+++.++.+ .++++|+.|||+-
T Consensus       195 p~~~~rf~~LL~~L~~LR~l~~~~~e~l~~~k~~~-~~~~pLl~E~~d~  242 (243)
T d2r40d1         195 PRCAVIFGKILGILTEIRTLGMQNSNMCISLKLKN-RKLPPFLEEIWDV  242 (243)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-CCCCHHHHHHTTC
T ss_pred             ccHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-CCCChHHHHHhCC
Confidence            5   5999999999999999999999999999864 5899999999973

>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=99.41  E-value=1.4e-13  Score=125.81  Aligned_cols=108  Identities=19%  Similarity=0.307  Sum_probs=92.9

Q ss_pred             HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcC
Q psy6602         239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPT  318 (367)
Q Consensus       239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~  318 (367)
                      .+......++.+..+..|+++++.+.-               .++|++||++...|+++|+++..||+.|+..+||++++
T Consensus       181 ~~~~~~~~l~~L~ld~~E~~lLkAi~L---------------~~pd~~gL~~~~~Ve~lq~~~~~aL~~y~~~~~p~~~~  245 (292)
T d1nrla_         181 PMLKFHYMLKKLQLHEEEYVLMQAISL---------------FSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAH  245 (292)
T ss_dssp             HHHHHHHHHHHTCCCHHHHHHHHHHHH---------------TCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCCSGGG
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHH---------------hCCCCCCcccHHHHHHHHHHHHHHHHHHHHHhCCCCch
Confidence            344455678888888899988887742               34899999999999999999999999999999998775


Q ss_pred             --hHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhc
Q psy6602         319 --RFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM  362 (367)
Q Consensus       319 --r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~  362 (367)
                        ||+|||++||+||+++..++++++..+..+. .+++|+.|||+.
T Consensus       246 ~~~f~kLL~~l~~LR~l~~~~~e~l~~~k~~~~-~~~pLl~E~f~~  290 (292)
T d1nrla_         246 RFLFLKIMAMLTELRSINAQHTQRLLRIQDIHP-FATPLMQELFGI  290 (292)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSC-CCCHHHHHHTTC
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-CCchHHHHHhCc
Confidence              6999999999999999999999999888765 457899999964

>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=5.1e-13  Score=119.32  Aligned_cols=112  Identities=14%  Similarity=0.163  Sum_probs=96.5

Q ss_pred             HHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCC-CCCCCCCchhhhhHHHHHHHHHHHHHhhCCC
Q psy6602         237 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYE-TPGLVDAQPVEMLQDQAQCILGDYVRGRYSR  315 (367)
Q Consensus       237 f~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d-~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~  315 (367)
                      +..+..+...++.+..+..|+++++...-               .++| .+|+.+...|+.+|+++..||++|+...||+
T Consensus       116 ~~~~~~~~~~~~~L~ld~~E~~lLkaIvL---------------~npd~~~~l~~~~~i~~lq~~~~~aL~~y~~~~~~~  180 (250)
T d1t7ra_         116 CVRMRHLSQEFGWLQITPQEFLCMKALLL---------------FSIIPVDGLKNQKFFDELRMNYIKELDRIIACKRKN  180 (250)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHH---------------TSEEETTCCTTHHHHHHHHHHHHHHHHHHHHTTCCS
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHh---------------cCCccccCCccHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence            44455677788999999999999987752               1244 5789999999999999999999999999985


Q ss_pred             ---CcChHHHHHhhchhhhhhchhhHHH---HHHhhhcCCCChHHHHHHHHhcc
Q psy6602         316 ---QPTRFGRLLLMLPSLRAVRQSTIER---LFFKETIGDIPIQRLLGDMYTME  363 (367)
Q Consensus       316 ---~~~r~~~lLl~Lp~lr~i~~~~~e~---l~~~~~~g~~~i~~ll~eml~~~  363 (367)
                         .|.||++||++||+||+++..+.++   ++|++..|.+++++|+.||++++
T Consensus       181 ~~~~p~Rf~~LL~~Lp~lr~l~~~~~~~~~~l~~~~~~~~~~i~~Ll~Eml~~~  234 (250)
T d1t7ra_         181 PTSCSRRFYQLTKLLDSVQPIARELHQFTFDLLIKSHMVSVDFPEMMAEIISVQ  234 (250)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTCCCCHHHHHHHHHT
T ss_pred             CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCChHHHHHHHHhcc
Confidence               4679999999999999999999884   57889999999999999999976

>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=99.27  E-value=1.3e-12  Score=116.49  Aligned_cols=112  Identities=21%  Similarity=0.237  Sum_probs=95.4

Q ss_pred             HHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCC-CCCCCCCchhhhhHHHHHHHHHHHHHhhCCC
Q psy6602         237 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYE-TPGLVDAQPVEMLQDQAQCILGDYVRGRYSR  315 (367)
Q Consensus       237 f~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d-~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~  315 (367)
                      ...+......++.+..+..|+++++...-               .+|| +.++++...|+++|+++..||.+|+..+|++
T Consensus       114 ~~~~~~~~~~l~~L~l~~~E~~lLkaIvL---------------fnpd~~~~l~~~~~ve~lq~~~~~aL~~y~~~~~~~  178 (247)
T d1nhza_         114 CKHMLYVSSELHRLQVSYEEYLCMKTLLL---------------LSSVPKDGLKSQELFDEIRMTYIKELGKAIVKREGN  178 (247)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHH---------------TSEEETTCCTTHHHHHHHHHHHHHHHHHHHHHHCCS
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHH---------------cCCCCCcccccHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence            35555677778999999999999887752               2466 7899999999999999999999999999987


Q ss_pred             Cc---ChHHHHHhhchhhhhhchhhHHHHH--HhhhcCCCChHHHHHHHHhcc
Q psy6602         316 QP---TRFGRLLLMLPSLRAVRQSTIERLF--FKETIGDIPIQRLLGDMYTME  363 (367)
Q Consensus       316 ~~---~r~~~lLl~Lp~lr~i~~~~~e~l~--~~~~~g~~~i~~ll~eml~~~  363 (367)
                      .+   .||++||++||+||+++.++.+++|  ++.-.+++++++|+.||+.++
T Consensus       179 ~~~~~~Rf~~LL~~Lp~lR~~~~~~~~~l~~~~~~~~~~v~~~~Ll~Eml~~~  231 (247)
T d1nhza_         179 SSQNWQRFYQLTKLLDSMHEVVENLLNYCFQTFLDKTMSIEFPEMLAEIITNQ  231 (247)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHHHHTTSCCCCHHHHHHHSCHHHHHHHHHTC-
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcCCCChhHHHHHHHhcc
Confidence            55   4999999999999999999999998  455567899999999999865

>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=99.25  E-value=2.4e-12  Score=114.88  Aligned_cols=111  Identities=14%  Similarity=0.095  Sum_probs=93.0

Q ss_pred             HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCC-CCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCC
Q psy6602         238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSY-ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQ  316 (367)
Q Consensus       238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~-d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~  316 (367)
                      ..+......++.+..+..|+++++...-               .+| +++|+.+..+|+.+|+++..||.+|+...|++.
T Consensus       118 ~~~~~~~~~l~~L~ld~~E~~lLkAIiL---------------~npd~~~~l~~~~~V~~lq~~~~~aL~~~~~~~~~~~  182 (251)
T d1sqna_         118 LTMWQIPQEFVKLQVSQEEFLCMKVLLL---------------LNTIPLEGLRSQTQFEEMRSSYIRELIKAIGLRQKGV  182 (251)
T ss_dssp             HHHHHHHHHHHHHTCCHHHHHHHHHHHH---------------TSEECTTCCTTHHHHHHHHHHHHHHHHHHHHTTC-CH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHH---------------cCCccccCCcCHHHHHHHHHHHHHHHHHHHHHhCCCC
Confidence            3444566778889999999999887752               235 478999999999999999999999999988664


Q ss_pred             ---cChHHHHHhhchhhhhhchhhHHHH---HHhhhcCCCChHHHHHHHHhcc
Q psy6602         317 ---PTRFGRLLLMLPSLRAVRQSTIERL---FFKETIGDIPIQRLLGDMYTME  363 (367)
Q Consensus       317 ---~~r~~~lLl~Lp~lr~i~~~~~e~l---~~~~~~g~~~i~~ll~eml~~~  363 (367)
                         +.||++||++||+||+++..+.+++   |+....|.+++++|+.||+.++
T Consensus       183 ~~~~~Rf~~LL~lLp~lR~l~~~~~~~~~~~~~~~~~~~v~~p~Ll~E~l~~~  235 (251)
T d1sqna_         183 VSSSQRFYQLTKLLDNLHDLVKQLHLYCLNTFIQSRALSVEFPEMMSEVIAAQ  235 (251)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTCCCCHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCcChhHHHHHHHHcc
Confidence               5799999999999999999999975   4566678999999999999865

>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=99.21  E-value=1.1e-11  Score=109.27  Aligned_cols=94  Identities=21%  Similarity=0.327  Sum_probs=81.0

Q ss_pred             HHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCC
Q psy6602         237 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQ  316 (367)
Q Consensus       237 f~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~  316 (367)
                      +..+......++.+..+..|+++++...-               .+||++||.+..+|+++|+.+..||++|+..+||..
T Consensus       136 ~~~i~~f~~~l~~L~ld~~E~alLkAivL---------------f~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~  200 (232)
T d1xnxa_         136 LESILHFHKNLKGLHLQEPEYVLMAATAL---------------FSPDRPGVTQREEIDQLQEEMALILNNHIMEQQSRL  200 (232)
T ss_dssp             HHHHHHHHHHHHTTCCCHHHHHHHHHHHH---------------TCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHTTTTC
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHH---------------hcCCCCCcCCHHHHHHHHHHHHHHHHHHHHHhCCCC
Confidence            34555566788889999999998887642               258999999999999999999999999999999877


Q ss_pred             cCh--HHHHHhhchhhhhhchhhHHHHHHhh
Q psy6602         317 PTR--FGRLLLMLPSLRAVRQSTIERLFFKE  345 (367)
Q Consensus       317 ~~r--~~~lLl~Lp~lr~i~~~~~e~l~~~~  345 (367)
                      ++|  |+|||++||+||+++..|.|.|...+
T Consensus       201 ~~~~~f~kLL~~L~~LR~l~~~h~e~l~~ik  231 (232)
T d1xnxa_         201 QSRFLYAKLMGLLADLRSINNAYSYELQRLE  231 (232)
T ss_dssp             CSTTHHHHHHHHHHHHHHHHHHTHHHHHHHT
T ss_pred             CcccHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            665  99999999999999999999987653

>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=98.79  E-value=1.2e-09  Score=96.65  Aligned_cols=84  Identities=19%  Similarity=0.303  Sum_probs=75.8

Q ss_pred             cCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhC---CCcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHH
Q psy6602         198 FTPETPGLVDAQPVEMLQDQAQCILGDYVRGRY---SRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLG  274 (367)
Q Consensus       198 ~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~---~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~  274 (367)
                      .+.++.++.++.+|+.+|++|..+|..|+..++   ++.+.||++|+.+++.||+++..+.|.+++.+..+..++++++.
T Consensus       156 ~~~~r~~l~~~~~v~~~q~~~~~aL~~~~~~~~~~~~~~~~Rf~~LL~~Lp~Lr~~~~~~~e~l~~~~~~~~~~~~~Ll~  235 (245)
T d1xpca_         156 LSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLL  235 (245)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCCSSCHHHHHH
T ss_pred             cccchhhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCccHHHH
Confidence            345678888999999999999999999998765   45578999999999999999999999999999999999999999


Q ss_pred             HHHcccC
Q psy6602         275 DMYTMEK  281 (367)
Q Consensus       275 eml~~~~  281 (367)
                      ||++...
T Consensus       236 Eml~~~~  242 (245)
T d1xpca_         236 EMLDAHR  242 (245)
T ss_dssp             HHHSCCS
T ss_pred             HHHHccc
Confidence            9998653

>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=98.43  E-value=1e-07  Score=83.28  Aligned_cols=75  Identities=19%  Similarity=0.255  Sum_probs=68.0

Q ss_pred             CCChhHHHHHHHHHHHHHHHHHHhhC---CCcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcc
Q psy6602         205 LVDAQPVEMLQDQAQCILGDYVRGRY---SRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM  279 (367)
Q Consensus       205 L~~~~~v~~~q~~~~~~L~~y~~~~~---~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~  279 (367)
                      ......+..++++|.++|..|+..++   ++.+.||++|+.+++.||+++..+.|.+++.+.+|..++++++.||+++
T Consensus       159 ~~~~~~v~~~~~~~~~~l~~~~~~~~~~~p~~~~Rf~~LL~~Lp~Lr~l~~~~~e~l~~~~~~g~~~i~~Ll~Eml~a  236 (236)
T d2j7ya1         159 AESSRKLTHLLNAVTDALVWVIAKSGISSQQQSVRLANLLMLLSHVRHISNKGMEHLLSMKCKNVVPVYDLLLEMLNA  236 (236)
T ss_dssp             -HHHHHHHHHHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSCCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhccCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCccHHHHHHhCc
Confidence            34488999999999999999999765   4567899999999999999999999999999999999999999999874