Psyllid ID: psy3092

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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-------
Protein Sequence
MKPDTATLLVNFNSGGANSMSSFGSNNHSSSHNNGSSNSSIISPYPPNHPLCGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIEV
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEccccccccccccccccccccHHHHHHcccccccccccccccccccccccHHHHHHHHHHHHcccHHHHHHcccccccccccccccccccccccHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccEEEcccccccccHHHHccHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccEEccccccEEccEEccEEccHHHHHHHHHHHHHccccccccccccccccccccccHHHHHHHHHHccccHHHcccccccccccccccccccccccccccHHHHHHHHHHcccccccccccccccccHHHHHHHHHHHHHHHHHHHHccccHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEEcccccEEEHHHHHHHccccHHHHHHHHcHHHHHHccccHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHccHHHHHHHcc
Coil and Loop (DISEMBL)
MKPDTATLLVNFnsggansmssfgsnnhssshnngssnssiispyppnhplcgskhlcsicgdrasgkhygvyscegckgffkrTVRKDLSYACREGrnciidkrqrnrcqycrYQKCLNMGMKREAVQEERQrtkerdsnevestsgtliempVERILEAEQrvdmkqepadqdIVNEQQATNICKATDKQLFQLVDWakhiphfttlplEDQVLLLRAGWNELLIASFShrsisvkdgillapgvtvyrssaheagvggIFDRVLTELVSKMREMKMDKTELGCLRTIILfnpdvrglkSQQVVEMLREKVYTSLEEYTrvnhseepGRFAKLLLrlpslrsiev
Flexible Loop (DISEMBL)
MKPDTATLLVNFNSGGANSMSSFGSNNHSSSHNNGSSNSSIISPYPPNHPLCGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREgrnciidkrqrnrcQYCRYQkclnmgmkREAVQEerqrtkerdsnevestsgtliempvERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSsaheagvggifdRVLTELVSKMREMKMDKTELGCLRTIIlfnpdvrglksQQVVEMLREKVYTSLEEytrvnhseepgrfaklllrlpslrsiev
Low Complexity Region (SEG)
MKPDTATLLVNFNSGGAnsmssfgsnnhssshnngssnssiisPYPPNHPLCGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDkrqrnrcqycryqkcLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIEV
Disordered region (IsUnstruct)
*************************************************PLCGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMG***********************************************************ATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRV********FAKLLL**********
Disordered Region (DISOPRED)
**********************************************************SICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKR**********************************************************NICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNH***PGRFAKLLLRLPSLRSIE*
Disordered Region (DISEMBL)
MKPDTATLLVNFNSGGANSMS******************SIISPYPPNHPLCGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMK***********************GTLIEMPVERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIEV
Disordered Region (DISPRO)
****************************************************GSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMK****************************MPVERILEAEQRVD**QEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIEV
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKPDTATLLVNFNSGGANSMSSFGSNNHSSSHNNGSSNSSIISPYPPNHPLCGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIEV
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	347	2.2.26 [Sep-21-2011]
Q5I7G2	436	Retinoic acid receptor RX	N/A	N/A	0.939	0.747	0.691	1e-132
Q8T5C6	436	Retinoic acid receptor RX	N/A	N/A	0.982	0.782	0.645	1e-131
A2T929	430	Retinoic acid receptor RX	yes	N/A	0.948	0.765	0.656	1e-129
P28701	467	Retinoic acid receptor RX	yes	N/A	0.864	0.642	0.714	1e-128
P51129	470	Retinoic acid receptor RX	N/A	N/A	0.884	0.653	0.700	1e-127
P19793	462	Retinoic acid receptor RX	yes	N/A	0.933	0.701	0.668	1e-127
Q90416	441	Retinoic acid receptor RX	no	N/A	0.965	0.759	0.660	1e-127
Q05343	467	Retinoic acid receptor RX	yes	N/A	0.927	0.689	0.663	1e-126
P28700	467	Retinoic acid receptor RX	yes	N/A	0.927	0.689	0.663	1e-126
P51128	488	Retinoic acid receptor RX	N/A	N/A	0.899	0.639	0.669	1e-126

>sp|Q5I7G2|RXR_LYMST Retinoic acid receptor RXR OS=Lymnaea stagnalis GN=RXR PE=1 SV=1

 Score =  472 bits (1214), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 235/340 (69%), Positives = 267/340 (78%), Gaps = 14/340 (4%)

Query: 14  SGGANSMSSFGSNNHSSSHNNGSSNSSIISPYPPN------HPLCGSKHLCSICGDRASG 67
           S G   M S G   HS + + GS     +SP  P+      H    +KH+C+ICGDRASG
Sbjct: 69  SPGPQQMHSPGM--HSPTSSMGSPPMLCLSPTGPSPSPGLPHSSLHTKHICAICGDRASG 126

Query: 68  KHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREA 127
           KHYGVYSCEGCKGFFKRTVRKDL+YACR+ +NC+IDKRQRNRCQYCRY KCL+MGMKREA
Sbjct: 127 KHYGVYSCEGCKGFFKRTVRKDLTYACRDDKNCMIDKRQRNRCQYCRYMKCLSMGMKREA 186

Query: 128 VQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQRVDMKQEPADQDIVNEQQ--ATNI 185
           VQEERQR KE+   EVESTSG   +MPVE+ILEAE  VD    P     ++ Q+   TNI
Sbjct: 187 VQEERQRVKEKGDGEVESTSGANNDMPVEQILEAELAVD----PKIDTYIDAQKDPVTNI 242

Query: 186 CKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAP 245
           C+A DKQLF LV+WAK IPHFT LPLEDQV+LLRAGWNELLIA FSHRSI  KDGILLA 
Sbjct: 243 CQAADKQLFTLVEWAKRIPHFTELPLEDQVILLRAGWNELLIAGFSHRSIMAKDGILLAT 302

Query: 246 GVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQV 305
           G+ V+RSSAH+AGVG IFDRVLTELV+KMREMKMDKTELGCLR ++LFNPD +GL + Q 
Sbjct: 303 GLHVHRSSAHQAGVGTIFDRVLTELVAKMREMKMDKTELGCLRAVVLFNPDAKGLTAVQE 362

Query: 306 VEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           VE LREKVY SLEEYT+  + EEPGRFAKLLLRLP+LRSI
Sbjct: 363 VEQLREKVYASLEEYTKTRYPEEPGRFAKLLLRLPALRSI 402

Ligand-dependent transcription factor probably involved in the retinoic acid response pathway. Binds 9-cis-retinoic acid (By similarity). Involved in embryo development, in particular eye and shell formation. May play a role in growth cone steering.
Lymnaea stagnalis (taxid: 6523)

>sp|Q8T5C6|RXR_BIOGL Retinoic acid receptor RXR OS=Biomphalaria glabrata GN=RXR PE=1 SV=1

 Score =  466 bits (1200), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 240/372 (64%), Positives = 275/372 (73%), Gaps = 31/372 (8%)

Query: 1   MKPDTATL--------LVNFNSGGANSMSSFG--SNNHSSSHNNG--SSNSSIISP---- 44
           +KPD ++L           F  GG  SM+S    S      H+ G  S  SS+ SP    
Sbjct: 35  IKPDISSLTSPTSTHGYYGFGPGGMPSMASSTQPSPGPQQMHSPGMHSPTSSMGSPPMLC 94

Query: 45  ---------YPPNHPLCGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACR 95
                        H    +KH+C+ICGDRASGKHYGVYSCEGCKGFFKRTVRKDL+YACR
Sbjct: 95  LSPSGPSPSPGLPHSSLHTKHICAICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYACR 154

Query: 96  EGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPV 155
           + +NC+IDKRQRNRCQYCRY KCL+MGMKREAVQEERQR KE+   EVESTSG   +MPV
Sbjct: 155 DDKNCMIDKRQRNRCQYCRYMKCLSMGMKREAVQEERQRVKEKGDGEVESTSGANNDMPV 214

Query: 156 ERILEAEQRVDMKQEPADQDIVNEQQ--ATNICKATDKQLFQLVDWAKHIPHFTTLPLED 213
           E+ILEAE  VD    P     ++ Q+   TNIC+A DKQLF LV+WAK IPHFT LPLED
Sbjct: 215 EQILEAELAVD----PKIDTYIDAQKDPVTNICQAADKQLFTLVEWAKRIPHFTELPLED 270

Query: 214 QVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSK 273
           QV+LLRAGWNELLIA FSHRSI  KDGILLA G+ V+RSSAH+AGVG IFDRVLTELV+K
Sbjct: 271 QVILLRAGWNELLIAGFSHRSIMAKDGILLATGLHVHRSSAHQAGVGTIFDRVLTELVAK 330

Query: 274 MREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFA 333
           MR+MKMDKTELGCLR ++LFNPD +GL + Q VE LREKVY SLEEYT+  + EEPGRFA
Sbjct: 331 MRDMKMDKTELGCLRAVVLFNPDAKGLTAVQEVEQLREKVYASLEEYTKSRYPEEPGRFA 390

Query: 334 KLLLRLPSLRSI 345
           KLLLRLP+LRSI
Sbjct: 391 KLLLRLPALRSI 402

Ligand-dependent transcription factor probably involved in the retinoic acid response pathway. Binds 9-cis-retinoic acid (9C-RA) and, to a lesser extent, docosahexaenoic acid (DHA), phytanic acid, methoprene acid and oleic acid. Binds to double-stranded DNA sequences containing direct repeats (DR) with the consensus sequence 5'-[AG]GGTCA-3' and 1, 2, 3, 4 or 5 nucleotides in between (DR1, DR2, DR3. DR4 and DR5, respectively). Binding to DR1 is strongest. Transactivates gene expression when 9C-RA or DHA is bound.

Biomphalaria glabrata (taxid: 6526)

>sp|A2T929|RXRAA_DANRE Retinoic acid receptor RXR-alpha-A OS=Danio rerio GN=rxraa PE=2 SV=2

 Score =  462 bits (1189), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 233/355 (65%), Positives = 268/355 (75%), Gaps = 26/355 (7%)

Query: 16  GANSMSSFGSNNHSS------SHNNGSSNSSIISP------------YPPNHPLCGSKHL 57
           G +SM+S G     S      SH N  S+S  I P             P   PL  +KH+
Sbjct: 43  GPHSMASPGVGYGPSISPQLNSHMNSVSSSEDIKPPLGLNGVMKVPAQPSGTPLSLTKHI 102

Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQK 117
           C+ICGDR+SGKHYGVYSCEGCKGFFKRTVRKDL+Y CR+ ++C+IDKRQRNRCQYCRYQK
Sbjct: 103 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCVIDKRQRNRCQYCRYQK 162

Query: 118 CLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQRVDMKQE------- 170
           CL MGMKREAVQEERQR KER  NEVESTS    +MPVE+ILEAE  V+ K E       
Sbjct: 163 CLAMGMKREAVQEERQRAKERSENEVESTSSANEDMPVEKILEAELAVEPKTETYIETNV 222

Query: 171 PADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASF 230
           P   +  N+   TNIC+A DKQLF LV+WAK IPHF+ LPL+DQV+LLRAGWNELLIASF
Sbjct: 223 PMPSNSPNDP-VTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASF 281

Query: 231 SHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTI 290
           SHRSI+VKDGILLA G+ V+R+SAH AGVG IFDRVLTELVSKMR+M+MDKTELGCLR I
Sbjct: 282 SHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAI 341

Query: 291 ILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +LFNPD +GL +   VE LREKVY SLE Y +  + E+PGRFAKLLLRLP+LRSI
Sbjct: 342 VLFNPDSKGLSNPGEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSI 396

Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The rar/rxr heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. The high affinity ligand for rxrs is 9-cis retinoic acid.

Danio rerio (taxid: 7955)

>sp|P28701|RXRG_CHICK Retinoic acid receptor RXR-gamma OS=Gallus gallus GN=RXRG PE=2 SV=1

 Score =  456 bits (1174), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 218/305 (71%), Positives = 250/305 (81%), Gaps = 5/305 (1%)

Query: 45  YPPNHPLCGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDK 104
           YP   P   +KH+C+ICGDR+SGKHYGVYSCEGCKGFFKRT+RKDL Y CR+ ++C+IDK
Sbjct: 130 YPSTSPGSLAKHICAICGDRSSGKHYGVYSCEGCKGFFKRTIRKDLIYTCRDNKDCLIDK 189

Query: 105 RQRNRCQYCRYQKCLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQR 164
           RQRNRCQYCRYQKCL MGMKREAVQEERQ ++ER  NE ESTSG   +MPVERILEAE  
Sbjct: 190 RQRNRCQYCRYQKCLAMGMKREAVQEERQGSRERSENEAESTSGGSEDMPVERILEAELA 249

Query: 165 VDMKQEPADQDIVNEQQ----ATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRA 220
           V+ K E A  D+  E       TNIC A DKQLF LV+WAK IPHF+ L LEDQV+LLRA
Sbjct: 250 VEPKTE-AYSDVNTESSTNDPVTNICHAADKQLFTLVEWAKRIPHFSDLTLEDQVILLRA 308

Query: 221 GWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMD 280
           GWNELLIASFSHRS+SV+DGILLA G+ V+RSSAH AGVG IFDRVLTELVSKM++M+MD
Sbjct: 309 GWNELLIASFSHRSVSVQDGILLATGLHVHRSSAHSAGVGSIFDRVLTELVSKMKDMQMD 368

Query: 281 KTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLP 340
           K+ELGCLR I+LFNPD +GL S   VE LREKVY +LE YT+  + E+PGRFAKLLLRLP
Sbjct: 369 KSELGCLRAIVLFNPDAKGLSSPSEVESLREKVYATLEAYTKQKYPEQPGRFAKLLLRLP 428

Query: 341 SLRSI 345
           +LRSI
Sbjct: 429 ALRSI 433

Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The RAR/RXR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. The high affinity ligand for RXRs is 9-cis retinoic acid.

Gallus gallus (taxid: 9031)

>sp|P51129|RXRG_XENLA Retinoic acid receptor RXR-gamma OS=Xenopus laevis GN=rxrg PE=2 SV=1

 Score =  456 bits (1172), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 220/314 (70%), Positives = 254/314 (80%), Gaps = 7/314 (2%)

Query: 39  SSIISP----YPPNHPLCGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYAC 94
           SS+ SP    Y  N P   +KH+C+ICGDR+SGKHYGVYSCEGCKGFFKRT+RKDL Y C
Sbjct: 123 SSLGSPCMNNYSCNSPGALTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTIRKDLVYTC 182

Query: 95  REGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMP 154
           R+ ++C+IDKRQRNRCQYCRYQKCL MGMKREAVQEERQR++E+   E ESTS T  EMP
Sbjct: 183 RDSKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRSREKSDTEAESTSSTSEEMP 242

Query: 155 VERILEAEQRVDMKQEP-ADQDIVNEQQ--ATNICKATDKQLFQLVDWAKHIPHFTTLPL 211
           VERILEAE  VD K E   D  + N      TNIC A DKQLF LV+WAK IP+F+ LPL
Sbjct: 243 VERILEAELAVDPKIEAFGDAGLPNSTNDPVTNICHAADKQLFTLVEWAKRIPYFSDLPL 302

Query: 212 EDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELV 271
           EDQV+LLRAGWNELLIASFSHRS+SV+DGILLA G+ V+RSSAH AGVG IFDRVLTELV
Sbjct: 303 EDQVILLRAGWNELLIASFSHRSVSVQDGILLATGLHVHRSSAHNAGVGSIFDRVLTELV 362

Query: 272 SKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGR 331
           SKM++M MDK+ELGCLR I+LFNPD +GL +   VE LREKVY +LE YT+  + ++PGR
Sbjct: 363 SKMKDMDMDKSELGCLRAIVLFNPDAKGLSNAAEVEALREKVYATLESYTKQKYPDQPGR 422

Query: 332 FAKLLLRLPSLRSI 345
           FAKLLLRLP+LRSI
Sbjct: 423 FAKLLLRLPALRSI 436

Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The rar/rxr heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. The high affinity ligand for rxrs is 9-cis retinoic acid.

Xenopus laevis (taxid: 8355)

>sp|P19793|RXRA_HUMAN Retinoic acid receptor RXR-alpha OS=Homo sapiens GN=RXRA PE=1 SV=1

 Score =  455 bits (1171), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 228/341 (66%), Positives = 262/341 (76%), Gaps = 17/341 (4%)

Query: 22  SFGSNNHSSSHNNGSSNSSIISPYP-------PNHP----LCGSKHLCSICGDRASGKHY 70
           S GS   SS  N  SS+  I  P         P HP       +KH+C+ICGDR+SGKHY
Sbjct: 88  STGSPQLSSPMNPVSSSEDIKPPLGLNGVLKVPAHPSGNMASFTKHICAICGDRSSGKHY 147

Query: 71  GVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQE 130
           GVYSCEGCKGFFKRTVRKDL+Y CR+ ++C+IDKRQRNRCQYCRYQKCL MGMKREAVQE
Sbjct: 148 GVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQE 207

Query: 131 ERQRTKERDSNEVESTSGTLIEMPVERILEAEQRVDMKQEPADQDIVN------EQQATN 184
           ERQR K+R+ NEVESTS    +MPVERILEAE  V+ K E   +  +           TN
Sbjct: 208 ERQRGKDRNENEVESTSSANEDMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTN 267

Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           IC+A DKQLF LV+WAK IPHF+ LPL+DQV+LLRAGWNELLIASFSHRSI+VKDGILLA
Sbjct: 268 ICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLA 327

Query: 245 PGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQ 304
            G+ V+R+SAH AGVG IFDRVLTELVSKMR+M+MDKTELGCLR I+LFNPD +GL +  
Sbjct: 328 TGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPA 387

Query: 305 VVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            VE LREKVY SLE Y +  + E+PGRFAKLLLRLP+LRSI
Sbjct: 388 EVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSI 428

Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The RAR/RXR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. The high affinity ligand for RXRs is 9-cis retinoic acid. RXRA serves as a common heterodimeric partner for a number of nuclear receptors. The RXR/RAR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. In the absence of ligand, the RXR-RAR heterodimers associate with a multiprotein complex containing transcription corepressors that induce histone acetylation, chromatin condensation and transcriptional suppression. On ligand binding, the corepressors dissociate from the receptors and associate with the coactivators leading to transcriptional activation. The RXRA/PPARA heterodimer is required for PPARA transcriptional activity on fatty acid oxidation genes such as ACOX1 and the P450 system genes.

Homo sapiens (taxid: 9606)

>sp|Q90416|RXRGA_DANRE Retinoic acid receptor RXR-gamma-A OS=Danio rerio GN=rxrga PE=2 SV=2

 Score =  455 bits (1171), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 224/339 (66%), Positives = 264/339 (77%), Gaps = 4/339 (1%)

Query: 11  NFNSGGANSMSSFGSNNHSSSHN-NGSSNSSIISPYPPNHPLCGSKHLCSICGDRASGKH 69
           N   G  NS      N+ SSS +       + +  YP   P   SKH+C+ICGDR+SGKH
Sbjct: 69  NMGYGALNSPQMNSLNSVSSSEDIKPPPGLAGLGSYPCGSPGSLSKHICAICGDRSSGKH 128

Query: 70  YGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQ 129
           YGVYSCEGCKGFFKRT+RKDL+Y CR+ ++C IDKRQRNRCQYCRYQKCL MGMKREAVQ
Sbjct: 129 YGVYSCEGCKGFFKRTIRKDLTYTCRDNKDCQIDKRQRNRCQYCRYQKCLAMGMKREAVQ 188

Query: 130 EERQRTKERDSNEVESTSGTLIEMPVERILEAEQRVDMKQEPADQDIVNEQQ---ATNIC 186
           EERQR +ER  NEV+S+S    EMPVE+IL+AE  V+ K E   +  ++       TNIC
Sbjct: 189 EERQRGRERSDNEVDSSSSFNEEMPVEKILDAELAVEPKTEAYMESSMSNSTNDPVTNIC 248

Query: 187 KATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPG 246
           +A DKQLF LV+WAK IPHF+ LPL+DQV+LLRAGWNELLIASFSHRS++VKDGILLA G
Sbjct: 249 QAADKQLFTLVEWAKRIPHFSDLPLDDQVILLRAGWNELLIASFSHRSVTVKDGILLATG 308

Query: 247 VTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVV 306
           + V+RSSAH AGVG IFDRVLTELVSKMR+M+MDKTELGCLR I+LFNPD +GL +   V
Sbjct: 309 LHVHRSSAHSAGVGSIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDAKGLSNPSEV 368

Query: 307 EMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           E LREKVY SLE YT+ N+ ++PGRFAKLLLRLP+LRSI
Sbjct: 369 EALREKVYASLEGYTKHNYPDQPGRFAKLLLRLPALRSI 407

Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The rar/rxr heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. The high affinity ligand for rxrs is 9-cis retinoic acid.

Danio rerio (taxid: 7955)

>sp|Q05343|RXRA_RAT Retinoic acid receptor RXR-alpha OS=Rattus norvegicus GN=Rxra PE=2 SV=1

 Score =  452 bits (1164), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 225/339 (66%), Positives = 261/339 (76%), Gaps = 17/339 (5%)

Query: 24  GSNNHSSSHNNGSSNSSIISPYP-------PNHPLCG----SKHLCSICGDRASGKHYGV 72
           GS   +S  N  SS+  I  P         P HP       +KH+C+ICGDR+SGKHYGV
Sbjct: 95  GSPQLNSPMNPVSSSEDIKPPLGLNGVLKVPAHPSGNMSSFTKHICAICGDRSSGKHYGV 154

Query: 73  YSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEER 132
           YSCEGCKGFFKRTVRKDL+Y CR+ ++C+IDKRQRNRCQYCRYQKCL MGMKREAVQEER
Sbjct: 155 YSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER 214

Query: 133 QRTKERDSNEVESTSGTLIEMPVERILEAEQRVDMKQEPADQDIVN------EQQATNIC 186
           QR K+R+ NEVESTS    +MPVE+ILEAE  V+ K E   +  +           TNIC
Sbjct: 215 QRGKDRNENEVESTSSANEDMPVEKILEAELAVEPKTETYVEANMGLNPSSPNDPVTNIC 274

Query: 187 KATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPG 246
           +A DKQLF LV+WAK IPHF+ LPL+DQV+LLRAGWNELLIASFSHRSI+VKDGILLA G
Sbjct: 275 QAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATG 334

Query: 247 VTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVV 306
           + V+R+SAH AGVG IFDRVLTELVSKMR+M+MDKTELGCLR I+LFNPD +GL +   V
Sbjct: 335 LHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEV 394

Query: 307 EMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           E LREKVY SLE Y +  + E+PGRFAKLLLRLP+LRSI
Sbjct: 395 EALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSI 433

Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The RAR/RXR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. The high affinity ligand for RXRs is 9-cis retinoic acid. RXRA serves as a common heterodimeric partner for a number of nuclear receptors. The RXR/RAR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. In the absence of ligand, the RXR-RAR heterodimers associate with a multiprotein complex containing transcription corepressors that induce histone acetylation, chromatin condensation and transcriptional suppression. On ligand binding, the corepressors dissociate from the receptors and associate with the coactivators leading to transcriptional activation (By similarity). The RXRA/PPARA heterodimer is required for PPARA transcriptional activity on fatty acid oxidation genes such as ACOX1 and the P450 system genes.

Rattus norvegicus (taxid: 10116)

>sp|P28700|RXRA_MOUSE Retinoic acid receptor RXR-alpha OS=Mus musculus GN=Rxra PE=1 SV=1

 Score =  452 bits (1163), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 225/339 (66%), Positives = 260/339 (76%), Gaps = 17/339 (5%)

Query: 24  GSNNHSSSHNNGSSNSSIISPYP-------PNHP----LCGSKHLCSICGDRASGKHYGV 72
           GS   +S  N  SS   I  P         P HP       +KH+C+ICGDR+SGKHYGV
Sbjct: 95  GSPQLNSPMNPVSSTEDIKPPLGLNGVLKVPAHPSGNMASFTKHICAICGDRSSGKHYGV 154

Query: 73  YSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEER 132
           YSCEGCKGFFKRTVRKDL+Y CR+ ++C+IDKRQRNRCQYCRYQKCL MGMKREAVQEER
Sbjct: 155 YSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER 214

Query: 133 QRTKERDSNEVESTSGTLIEMPVERILEAEQRVDMKQEPADQDIVN------EQQATNIC 186
           QR K+R+ NEVESTS    +MPVE+ILEAE  V+ K E   +  +           TNIC
Sbjct: 215 QRGKDRNENEVESTSSANEDMPVEKILEAELAVEPKTETYVEANMGLNPSSPNDPVTNIC 274

Query: 187 KATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPG 246
           +A DKQLF LV+WAK IPHF+ LPL+DQV+LLRAGWNELLIASFSHRSI+VKDGILLA G
Sbjct: 275 QAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATG 334

Query: 247 VTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVV 306
           + V+R+SAH AGVG IFDRVLTELVSKMR+M+MDKTELGCLR I+LFNPD +GL +   V
Sbjct: 335 LHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEV 394

Query: 307 EMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           E LREKVY SLE Y +  + E+PGRFAKLLLRLP+LRSI
Sbjct: 395 EALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSI 433

Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The RAR/RXR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. The high affinity ligand for RXRs is 9-cis retinoic acid. RXRA serves as a common heterodimeric partner for a number of nuclear receptors. The RXR/RAR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. In the absence of ligand, the RXR-RAR heterodimers associate with a multiprotein complex containing transcription corepressors that induce histone acetylation, chromatin condensation and transcriptional suppression. On ligand binding, the corepressors dissociate from the receptors and associate with the coactivators leading to transcriptional activation. The RXRA/PPARA heterodimer is required for PPARA transcriptional activity on fatty acid oxidation genes such as ACOX1 and the P450 system genes.

Mus musculus (taxid: 10090)

>sp|P51128|RXRA_XENLA Retinoic acid receptor RXR-alpha OS=Xenopus laevis GN=rxra PE=1 SV=1

 Score =  451 bits (1161), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 221/330 (66%), Positives = 258/330 (78%), Gaps = 18/330 (5%)

Query: 34  NGSSNSSIISPYP--------PNHPLCG----SKHLCSICGDRASGKHYGVYSCEGCKGF 81
           N  S++  I P P        P HP       +KH+C+ICGDR+SGKHYGVYSCEGCKGF
Sbjct: 125 NSVSSTEDIKPPPGINGILKVPMHPSGAMASFTKHICAICGDRSSGKHYGVYSCEGCKGF 184

Query: 82  FKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRTKERDSN 141
           FKRTVRKDL+Y CR+ ++C+IDKRQRNRCQYCRYQKCL MGMKREAVQEERQR KER+ N
Sbjct: 185 FKRTVRKDLTYTCRDSKDCMIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRGKERNEN 244

Query: 142 EVESTSGTLIEMPVERILEAEQRVDMKQEPADQDIVN------EQQATNICKATDKQLFQ 195
           EVES++    +MPVE+ILEAE  V+ K E   +  +           TNIC+A DKQLF 
Sbjct: 245 EVESSNSANEDMPVEKILEAEHAVEPKTETYTEANMGLAPNSPSDPVTNICQAADKQLFT 304

Query: 196 LVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH 255
           LV+WAK IPHF+ LPL+DQV+LLRAGWNELLIASFSHRSI+VKDGILLA G+ V+R+SAH
Sbjct: 305 LVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAH 364

Query: 256 EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYT 315
            AGVG IFDRVLTELVSKMR+M+MDKTELGCLR I+LFNPD +GL +   VE LREKVY 
Sbjct: 365 SAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPLEVEALREKVYA 424

Query: 316 SLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           SLE Y +  + E+PGRFAKLLLRLP+LRSI
Sbjct: 425 SLEAYCKQKYPEQPGRFAKLLLRLPALRSI 454

Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The rar/rxr heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. The high affinity ligand for rxrs is 9-cis retinoic acid.

Xenopus laevis (taxid: 8355)

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	347
410130138	416	retinoid X receptor [Periplaneta america	0.982	0.819	0.736	1e-147
302202572	403	retinoid X receptor [Gryllus firmus]	0.988	0.851	0.750	1e-147
314955486	403	retinoid X receptor [Gryllus firmus]	0.988	0.851	0.747	1e-147
314955556	403	retinoid X receptor [Gryllus firmus]	0.988	0.851	0.747	1e-147
383848789	427	PREDICTED: retinoic acid receptor RXR-al	0.985	0.800	0.738	1e-147
242008309	420	retinoid X receptor, putative [Pediculus	0.976	0.807	0.740	1e-147
449082861	441	ultraspiracle long isoform [Periplaneta	0.991	0.780	0.704	1e-146
380012603	440	PREDICTED: retinoic acid receptor RXR-al	0.985	0.777	0.735	1e-145
58585210	427	ultraspiracle [Apis mellifera] gi|811861	0.985	0.800	0.735	1e-145
340719093	427	PREDICTED: retinoic acid receptor RXR-al	0.985	0.800	0.735	1e-145

>gi|410130138|dbj|BAM63276.2| retinoid X receptor [Periplaneta americana]

 Score =  528 bits (1361), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 265/360 (73%), Positives = 294/360 (81%), Gaps = 19/360 (5%)

Query: 1   MKPDTATLLVNFNS-----GGANSMSSFG-------SNNHSSSHNNGSSNSSIISPYPPN 48
           MKPDTA LL+   S     GG N+  SF        S +  SS +NGS  SS   PYPPN
Sbjct: 29  MKPDTACLLLGSGSFTPTGGGPNTPGSFCIGQSRVFSKSTGSSQSNGSWGSS---PYPPN 85

Query: 49  HPLCGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRN 108
           HPL GSKHLC+ICGDRA GKHYGVY CEGCKGFFK TVRKDLSYACRE +NCIIDKRQRN
Sbjct: 86  HPLSGSKHLCTICGDRACGKHYGVYCCEGCKGFFKWTVRKDLSYACREDKNCIIDKRQRN 145

Query: 109 RCQYCRYQKCLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQRVDMK 168
           RCQYCRYQKCL MGMKREAVQEERQRTKERD NEVESTS    +MPVERILEAE+RV+ K
Sbjct: 146 RCQYCRYQKCLGMGMKREAVQEERQRTKERDQNEVESTSSLHTDMPVERILEAEKRVECK 205

Query: 169 QEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIA 228
            E     +  E   TNIC+AT+KQLFQLV+WAKHIPHFT+LPL DQVLLLRAGWNELLIA
Sbjct: 206 TE---HQVEFESAVTNICQATNKQLFQLVEWAKHIPHFTSLPLSDQVLLLRAGWNELLIA 262

Query: 229 SFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLR 288
           +FSHRS+ VKDGI+LA G+TV+R+SAH+AGVG IFDRVLTELV+KMREMKMDKTEL CLR
Sbjct: 263 AFSHRSVEVKDGIVLATGLTVHRNSAHQAGVGTIFDRVLTELVAKMREMKMDKTELVCLR 322

Query: 289 TIILFNPD-VRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIEV 347
           ++ILFNPD VRGLKS+Q VE+LREKVY +LEEYTR  H +EPGRFAKLL  LPSLRSI +
Sbjct: 323 SVILFNPDVVRGLKSRQEVELLREKVYAALEEYTRTTHPDEPGRFAKLLPSLPSLRSISL 382

Source: Periplaneta americana

Species: Periplaneta americana

Genus: Periplaneta

Family: Blattidae

Order: Blattodea

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|302202572|gb|ADL09403.1| retinoid X receptor [Gryllus firmus]

 Score =  528 bits (1360), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 262/349 (75%), Positives = 292/349 (83%), Gaps = 6/349 (1%)

Query: 1   MKPDTATLLVNFNSGGANSMSSFGSNNHSSSHN-NGSSNSSIISPYPPNHPLCGSKHLCS 59
           MKPDTA+L+ + +          G    +S     G S+SSI   YPPNHPL GSKHLCS
Sbjct: 24  MKPDTASLISSGSFSPTGGGGGGGGGGPNSPTGGQGKSSSSI--QYPPNHPLSGSKHLCS 81

Query: 60  ICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCL 119
           ICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACRE +NCIIDKRQRNRCQYCRYQKCL
Sbjct: 82  ICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREEKNCIIDKRQRNRCQYCRYQKCL 141

Query: 120 NMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQRVDMKQE---PADQDI 176
            MGMKREAVQEERQRTK    NEVESTS    +MPVERILEAE+RV+ K E     +  +
Sbjct: 142 TMGMKREAVQEERQRTKGEAQNEVESTSSLHADMPVERILEAEKRVEYKTENNMEFENTM 201

Query: 177 VNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSIS 236
            N  QA NIC+AT+KQLFQLV+WAKHIPHFT+LPLEDQVLLLRAGWNELLIA+FSHRS+ 
Sbjct: 202 NNICQAANICQATNKQLFQLVEWAKHIPHFTSLPLEDQVLLLRAGWNELLIAAFSHRSME 261

Query: 237 VKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD 296
           VKDGI+LA G+T++R+SAH+AGVG IFDRVLTELV+KMREMKMDKTELGCLR++ILFNPD
Sbjct: 262 VKDGIVLATGLTIHRNSAHQAGVGTIFDRVLTELVAKMREMKMDKTELGCLRSVILFNPD 321

Query: 297 VRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           VRGLKSQQ VEMLREKVY +LEEYTR  H +EPGRFAKLLLRLP+LRSI
Sbjct: 322 VRGLKSQQEVEMLREKVYAALEEYTRTTHPDEPGRFAKLLLRLPALRSI 370

Source: Gryllus firmus

Species: Gryllus firmus

Genus: Gryllus

Family: Gryllidae

Order: Orthoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|314955486|gb|ADT64884.1| retinoid X receptor [Gryllus firmus]

 Score =  526 bits (1356), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 261/349 (74%), Positives = 292/349 (83%), Gaps = 6/349 (1%)

Query: 1   MKPDTATLLVNFNSGGANSMSSFGSNNHSSSHN-NGSSNSSIISPYPPNHPLCGSKHLCS 59
           MKPDTA+L+ + +          G    +S     G S+SSI   YPPNHPL GSKHLCS
Sbjct: 24  MKPDTASLISSGSFSPTGGGGGGGGGGPNSPTGGQGKSSSSI--QYPPNHPLSGSKHLCS 81

Query: 60  ICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCL 119
           ICGDRASGKHYGVYSCEGCKGFFKRTVRK+LSYACRE +NCIIDKRQRNRCQYCRYQKCL
Sbjct: 82  ICGDRASGKHYGVYSCEGCKGFFKRTVRKELSYACREEKNCIIDKRQRNRCQYCRYQKCL 141

Query: 120 NMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQRVDMKQE---PADQDI 176
            MGMKREAVQEERQRTK    NEVESTS    +MPVERILEAE+RV+ K E     +  +
Sbjct: 142 TMGMKREAVQEERQRTKGEAQNEVESTSSLHADMPVERILEAEKRVEYKTENNMEFENTM 201

Query: 177 VNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSIS 236
            N  QA NIC+AT+KQLFQLV+WAKHIPHFT+LPLEDQVLLLRAGWNELLIA+FSHRS+ 
Sbjct: 202 NNICQAANICQATNKQLFQLVEWAKHIPHFTSLPLEDQVLLLRAGWNELLIAAFSHRSME 261

Query: 237 VKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD 296
           VKDGI+LA G+T++R+SAH+AGVG IFDRVLTELV+KMREMKMDKTELGCLR++ILFNPD
Sbjct: 262 VKDGIVLATGLTIHRNSAHQAGVGTIFDRVLTELVAKMREMKMDKTELGCLRSVILFNPD 321

Query: 297 VRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           VRGLKSQQ VEMLREKVY +LEEYTR  H +EPGRFAKLLLRLP+LRSI
Sbjct: 322 VRGLKSQQEVEMLREKVYAALEEYTRTTHPDEPGRFAKLLLRLPALRSI 370

Source: Gryllus firmus

Species: Gryllus firmus

Genus: Gryllus

Family: Gryllidae

Order: Orthoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|314955556|gb|ADT64885.1| retinoid X receptor [Gryllus firmus]

 Score =  526 bits (1356), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 261/349 (74%), Positives = 292/349 (83%), Gaps = 6/349 (1%)

Query: 1   MKPDTATLLVNFNSGGANSMSSFGSNNHSSSHN-NGSSNSSIISPYPPNHPLCGSKHLCS 59
           MKPDTA+L+ + +          G    +S     G S+SSI   YPPNHPL GSKHLCS
Sbjct: 24  MKPDTASLISSGSFSPTGGGGGGGGGGPNSPTGGQGKSSSSI--QYPPNHPLSGSKHLCS 81

Query: 60  ICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCL 119
           ICGDRASGKHYGVYSCEGCKGFFKRTVRK+LSYACRE +NCIIDKRQRNRCQYCRYQKCL
Sbjct: 82  ICGDRASGKHYGVYSCEGCKGFFKRTVRKELSYACREEKNCIIDKRQRNRCQYCRYQKCL 141

Query: 120 NMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQRVDMKQE---PADQDI 176
            MGMKREAVQEERQRTK    NEVESTS    +MPVERILEAE+RV+ K E     +  +
Sbjct: 142 TMGMKREAVQEERQRTKGEAQNEVESTSSLHADMPVERILEAEKRVEYKTENNMEFENTM 201

Query: 177 VNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSIS 236
            N  QA NIC+AT+KQLFQLV+WAKHIPHFT+LPLEDQVLLLRAGWNELLIA+FSHRS+ 
Sbjct: 202 NNICQAANICQATNKQLFQLVEWAKHIPHFTSLPLEDQVLLLRAGWNELLIAAFSHRSME 261

Query: 237 VKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD 296
           VKDGI+LA G+T++R+SAH+AGVG IFDRVLTELV+KMREMKMDKTELGCLR++ILFNPD
Sbjct: 262 VKDGIVLATGLTIHRNSAHQAGVGTIFDRVLTELVAKMREMKMDKTELGCLRSVILFNPD 321

Query: 297 VRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           VRGLKSQQ VEMLREKVY +LEEYTR  H +EPGRFAKLLLRLP+LRSI
Sbjct: 322 VRGLKSQQEVEMLREKVYAALEEYTRTTHPDEPGRFAKLLLRLPALRSI 370

Source: Gryllus firmus

Species: Gryllus firmus

Genus: Gryllus

Family: Gryllidae

Order: Orthoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383848789|ref|XP_003700030.1| PREDICTED: retinoic acid receptor RXR-alpha-A-like [Megachile rotundata]

 Score =  526 bits (1355), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 257/348 (73%), Positives = 293/348 (84%), Gaps = 6/348 (1%)

Query: 1   MKPDTATLL--VNFNSGGANSMSSFGSNNHSSS-HNNGSSNSSIISPYPPNHPLCGSKHL 57
           MKPDTA+L+   NF+  G NS  SF +  HS+    + S  +  ++PYPPNHPL GSKHL
Sbjct: 50  MKPDTASLINAGNFSPSGPNSPGSFNAGCHSNLLSTSPSGQNKAVAPYPPNHPLSGSKHL 109

Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQK 117
           CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACRE ++CIIDKRQRNRCQYCRYQK
Sbjct: 110 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREEKSCIIDKRQRNRCQYCRYQK 169

Query: 118 CLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQRVDMKQEPADQDIV 177
           CL MGMKREAVQEERQRTKERD +EVESTS    +MP+ERILEAE+RV+ K E   Q   
Sbjct: 170 CLAMGMKREAVQEERQRTKERDQSEVESTSSLHSDMPIERILEAEKRVEYKME---QQGN 226

Query: 178 NEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISV 237
            E   ++IC AT+KQLFQLV WAKHIPHFT+LPLEDQVLLLRAGWNELLIASFSHRSI V
Sbjct: 227 YENAVSHICNATNKQLFQLVAWAKHIPHFTSLPLEDQVLLLRAGWNELLIASFSHRSIDV 286

Query: 238 KDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDV 297
           KDGI+LA G+TV+R+SA +AGVG IFDRVL+ELVSKMREMKMD+TELGCLR+IILFNP+V
Sbjct: 287 KDGIVLATGITVHRNSAQQAGVGTIFDRVLSELVSKMREMKMDRTELGCLRSIILFNPEV 346

Query: 298 RGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           RGLKS Q V +LREK+Y +LE Y RV   ++PGRFAKLLLRLP++RSI
Sbjct: 347 RGLKSIQEVTLLREKIYAALEGYCRVAWPDDPGRFAKLLLRLPAIRSI 394

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242008309|ref|XP_002424949.1| retinoid X receptor, putative [Pediculus humanus corporis] gi|212508563|gb|EEB12211.1| retinoid X receptor, putative [Pediculus humanus corporis]

 Score =  526 bits (1354), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 257/347 (74%), Positives = 296/347 (85%), Gaps = 8/347 (2%)

Query: 1   MKPDTATLLV-NFN-SGGANSMSSFGSNNHSSSHNNGSSNSSIISPYPPNHPLCGSKHLC 58
           MKPDTATLL  NF+ +GG NS +SF +  HSS   N S+N   ++ YPPNHPL GSKHLC
Sbjct: 47  MKPDTATLLGGNFSPNGGPNSPNSF-TMGHSSLIGNNSNNK--MASYPPNHPLSGSKHLC 103

Query: 59  SICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKC 118
           SICGDRASGKHYGVYSCEGCKGFFKRTVRKDL+YACRE RNCIIDKRQRNRCQ+CRY KC
Sbjct: 104 SICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYACREERNCIIDKRQRNRCQFCRYNKC 163

Query: 119 LNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQRVDMKQEPADQDIVN 178
           L MGMKREAVQEERQRTKER+  EVES+     +MPVERILEAE+RV+ K E  ++    
Sbjct: 164 LAMGMKREAVQEERQRTKEREQGEVESSGAMQADMPVERILEAEKRVECKVENQNE---Y 220

Query: 179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVK 238
           E    NIC+AT+ QL+QLV+WAKHIPHF++LP+EDQVLLLRAGWNELLIA+FSHRS+ V+
Sbjct: 221 ENAVANICQATNTQLYQLVEWAKHIPHFSSLPIEDQVLLLRAGWNELLIAAFSHRSVEVR 280

Query: 239 DGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVR 298
           DGI+L  G+TV+R+SAH+AGVG IFDRVLTELV+KMR+M MD+TELGCLR+IILFNP+VR
Sbjct: 281 DGIVLGAGITVHRNSAHQAGVGTIFDRVLTELVAKMRDMNMDRTELGCLRSIILFNPEVR 340

Query: 299 GLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           GLKS Q VE+LREKVY +LEEYTRV   EEPGRFAKLLLRLP+LRSI
Sbjct: 341 GLKSGQEVELLREKVYAALEEYTRVTRPEEPGRFAKLLLRLPALRSI 387

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|449082861|dbj|BAM83567.1| ultraspiracle long isoform [Periplaneta americana]

 Score =  524 bits (1349), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 269/382 (70%), Positives = 299/382 (78%), Gaps = 38/382 (9%)

Query: 1   MKPDTATLLVNFNS-----GGANSMSSFG-------SNNHSSSHNNGSSNSSIISPYPPN 48
           MKPDTA LL+   S     GG N+  SF        S +  SS +NGS  SS   PYPPN
Sbjct: 29  MKPDTACLLLGSGSFTPTGGGPNTPGSFCIGQSRVFSKSTGSSQSNGSWGSS---PYPPN 85

Query: 49  HPLCGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRN 108
           HPLCGSKHLC+ICGDRA GKHYGVY CEGCKGFFK TVRKDLSYACRE +NCIIDKRQRN
Sbjct: 86  HPLCGSKHLCTICGDRACGKHYGVYCCEGCKGFFKWTVRKDLSYACREDKNCIIDKRQRN 145

Query: 109 RCQYCRYQKCLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQRVDMK 168
           RCQYCRYQKCL MGMKREAVQEERQRTKERD NEVESTS    +MPVERILEAE+RV+ K
Sbjct: 146 RCQYCRYQKCLGMGMKREAVQEERQRTKERDQNEVESTSSLHTDMPVERILEAEKRVECK 205

Query: 169 QE---------------------PADQDIVNEQQA-TNICKATDKQLFQLVDWAKHIPHF 206
            E                      AD + V  + A TNIC+AT+KQLFQLV+WAKHIPHF
Sbjct: 206 TEHQVEFELRCWNRKTVDAWRGRGADLNGVGPKSAVTNICQATNKQLFQLVEWAKHIPHF 265

Query: 207 TTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRV 266
           T+LPL DQVLLLRAGWNELLIA+FSHRS+ VKDGI+LA G+TV+R+SAH+AGVG IFDRV
Sbjct: 266 TSLPLSDQVLLLRAGWNELLIAAFSHRSVEVKDGIVLATGLTVHRNSAHQAGVGTIFDRV 325

Query: 267 LTELVSKMREMKMDKTELGCLRTIILFNPD-VRGLKSQQVVEMLREKVYTSLEEYTRVNH 325
           LTELV+KMREMKMDKTEL CLR++ILFNPD VRGLKS+Q VE+LREKVY +LEEYTR  H
Sbjct: 326 LTELVAKMREMKMDKTELVCLRSVILFNPDVVRGLKSRQEVELLREKVYAALEEYTRTTH 385

Query: 326 SEEPGRFAKLLLRLPSLRSIEV 347
            +EPGRFAKLL  LPSLRSI +
Sbjct: 386 PDEPGRFAKLLPSLPSLRSISL 407

Source: Periplaneta americana

Species: Periplaneta americana

Genus: Periplaneta

Family: Blattidae

Order: Blattodea

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380012603|ref|XP_003690369.1| PREDICTED: retinoic acid receptor RXR-alpha-A-like [Apis florea]

 Score =  521 bits (1343), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 256/348 (73%), Positives = 292/348 (83%), Gaps = 6/348 (1%)

Query: 1   MKPDTATLL--VNFNSGGANSMSSFGSNNHSSS-HNNGSSNSSIISPYPPNHPLCGSKHL 57
           MKPDTA+L+   NF+  G NS  SF +  HS+    + S  +  ++PYPPNHPL GSKHL
Sbjct: 63  MKPDTASLINPGNFSPSGPNSPGSFTAGCHSNLLSTSPSGQNKAVAPYPPNHPLSGSKHL 122

Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQK 117
           CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACRE ++CIIDKRQRNRCQYCRYQK
Sbjct: 123 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREEKSCIIDKRQRNRCQYCRYQK 182

Query: 118 CLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQRVDMKQEPADQDIV 177
           CL MGMKREAVQEERQRTKERD +EVESTS    +MP+ERILEAE+RV+ K E   Q   
Sbjct: 183 CLAMGMKREAVQEERQRTKERDQSEVESTSSLHSDMPIERILEAEKRVECKME---QQGN 239

Query: 178 NEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISV 237
            E   ++IC AT+KQLFQLV WAKHIPHFT+LPLEDQVLLLRAGWNELLIASFSHRSI V
Sbjct: 240 YENAVSHICNATNKQLFQLVAWAKHIPHFTSLPLEDQVLLLRAGWNELLIASFSHRSIDV 299

Query: 238 KDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDV 297
           KDGI+LA G+TV+R+SA +AGVG IFDRVL+ELVSKMREMKMD+TELGCLR+IILFNP+V
Sbjct: 300 KDGIVLATGITVHRNSAQQAGVGTIFDRVLSELVSKMREMKMDRTELGCLRSIILFNPEV 359

Query: 298 RGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           RGLKS Q V +LREK+Y +LE Y RV   ++ GRFAKLLLRLP++RSI
Sbjct: 360 RGLKSIQEVTLLREKIYGALEGYCRVAWPDDAGRFAKLLLRLPAIRSI 407

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|58585210|ref|NP_001011634.1| ultraspiracle [Apis mellifera] gi|8118613|gb|AAF73057.1|AF263459_1 ultraspiracle protein [Apis mellifera] gi|30691980|gb|AAP33487.1| ultraspiracle protein [Apis mellifera]

 Score =  521 bits (1342), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 256/348 (73%), Positives = 292/348 (83%), Gaps = 6/348 (1%)

Query: 1   MKPDTATLL--VNFNSGGANSMSSFGSNNHSSS-HNNGSSNSSIISPYPPNHPLCGSKHL 57
           MKPDTA+L+   NF+  G NS  SF +  HS+    + S  +  ++PYPPNHPL GSKHL
Sbjct: 50  MKPDTASLINPGNFSPSGPNSPGSFTAGCHSNLLSTSPSGQNKAVAPYPPNHPLSGSKHL 109

Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQK 117
           CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACRE ++CIIDKRQRNRCQYCRYQK
Sbjct: 110 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREEKSCIIDKRQRNRCQYCRYQK 169

Query: 118 CLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQRVDMKQEPADQDIV 177
           CL MGMKREAVQEERQRTKERD +EVESTS    +MP+ERILEAE+RV+ K E   Q   
Sbjct: 170 CLAMGMKREAVQEERQRTKERDQSEVESTSSLHSDMPIERILEAEKRVECKME---QQGN 226

Query: 178 NEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISV 237
            E   ++IC AT+KQLFQLV WAKHIPHFT+LPLEDQVLLLRAGWNELLIASFSHRSI V
Sbjct: 227 YENAVSHICNATNKQLFQLVAWAKHIPHFTSLPLEDQVLLLRAGWNELLIASFSHRSIDV 286

Query: 238 KDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDV 297
           KDGI+LA G+TV+R+SA +AGVG IFDRVL+ELVSKMREMKMD+TELGCLR+IILFNP+V
Sbjct: 287 KDGIVLATGITVHRNSAQQAGVGTIFDRVLSELVSKMREMKMDRTELGCLRSIILFNPEV 346

Query: 298 RGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           RGLKS Q V +LREK+Y +LE Y RV   ++ GRFAKLLLRLP++RSI
Sbjct: 347 RGLKSIQEVTLLREKIYGALEGYCRVAWPDDAGRFAKLLLRLPAIRSI 394

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340719093|ref|XP_003397991.1| PREDICTED: retinoic acid receptor RXR-alpha-A-like isoform 1 [Bombus terrestris] gi|350396161|ref|XP_003484462.1| PREDICTED: retinoic acid receptor RXR-alpha-A-like isoform 1 [Bombus impatiens]

 Score =  520 bits (1340), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 256/348 (73%), Positives = 291/348 (83%), Gaps = 6/348 (1%)

Query: 1   MKPDTATLL--VNFNSGGANSMSSFGSNNHSSS-HNNGSSNSSIISPYPPNHPLCGSKHL 57
           MKPDTA+L+   NF+  G NS  SF +  HS+    + S  +   +PYPPNHPL GSKHL
Sbjct: 50  MKPDTASLINPGNFSPSGPNSPGSFTAGCHSNLLSTSPSGQNKAAAPYPPNHPLSGSKHL 109

Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQK 117
           CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACRE ++CIIDKRQRNRCQYCRYQK
Sbjct: 110 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREEKSCIIDKRQRNRCQYCRYQK 169

Query: 118 CLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQRVDMKQEPADQDIV 177
           CL MGMKREAVQEERQRTKERD +EVESTS    +MP+ERILEAE+RV+ K E   Q   
Sbjct: 170 CLAMGMKREAVQEERQRTKERDQSEVESTSSLHSDMPIERILEAEKRVECKME---QQGN 226

Query: 178 NEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISV 237
            E   ++IC AT+KQLFQLV WAKHIPHFT+LPLEDQVLLLRAGWNELLIASFSHRSI V
Sbjct: 227 YENAVSHICNATNKQLFQLVAWAKHIPHFTSLPLEDQVLLLRAGWNELLIASFSHRSIDV 286

Query: 238 KDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDV 297
           KDGI+LA G+TV+R+SA +AGVG IFDRVL+ELVSKMREMKMD+TELGCLR+IILFNP+V
Sbjct: 287 KDGIVLATGITVHRNSAQQAGVGTIFDRVLSELVSKMREMKMDRTELGCLRSIILFNPEV 346

Query: 298 RGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           RGLKS Q V +LREK+Y +LE Y RV   ++ GRFAKLLLRLP++RSI
Sbjct: 347 RGLKSIQEVTLLREKIYAALEGYCRVAWPDDAGRFAKLLLRLPAIRSI 394

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	347
UNIPROTKB|F1NSP3	467	RXRG "Retinoic acid receptor R	0.864	0.642	0.668	2e-104
ZFIN|ZDB-GENE-070314-2	495	rxraa "retinoid X receptor, al	0.861	0.604	0.667	5.3e-104
ZFIN|ZDB-GENE-980526-36	441	rxrga "retinoid x receptor, ga	0.867	0.682	0.664	6.7e-104
UNIPROTKB|P28701	467	RXRG "Retinoic acid receptor R	0.864	0.642	0.665	1.1e-103
UNIPROTKB|P51129	470	rxrg "Retinoic acid receptor R	0.867	0.640	0.661	3.7e-103
UNIPROTKB|B3KY83	365	RXRA "cDNA FLJ16020 fis, clone	0.867	0.824	0.657	1.3e-102
UNIPROTKB|P19793	462	RXRA "Retinoic acid receptor R	0.867	0.651	0.657	1.3e-102
UNIPROTKB|F1P6M9	486	RXRA "Uncharacterized protein"	0.867	0.619	0.654	2.6e-102
MGI|MGI:98214	467	Rxra "retinoid X receptor alph	0.867	0.644	0.654	2.6e-102
UNIPROTKB|P51128	488	rxra "Retinoic acid receptor R	0.870	0.618	0.650	3.3e-102

UNIPROTKB|F1NSP3 RXRG "Retinoic acid receptor RXR-gamma" [Gallus gallus (taxid:9031)]

 Score = 1034 (369.0 bits), Expect = 2.0e-104, P = 2.0e-104
 Identities = 204/305 (66%), Positives = 236/305 (77%)

Query:    45 YPPNHPLCGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDX 104
             YP   P   +KH+C+ICGDR+SGKHYGVYSCEGCKGFFKRT+RKDL Y CR+ ++C+ID 
Sbjct:   130 YPSTSPGSLAKHICAICGDRSSGKHYGVYSCEGCKGFFKRTIRKDLIYTCRDNKDCLIDK 189

Query:   105 XXXXXXXXXXXXXXLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQR 164
                           L MGMKREAVQEERQR++ER  NE ESTSG   +MPVERILEAE  
Sbjct:   190 RQRNRCQYCRYQKCLAMGMKREAVQEERQRSRERSENEAESTSGGSEDMPVERILEAELA 249

Query:   165 VDMKQEPADQDIVNEQQA----TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRA 220
             V+ K E A  D+  E       TNIC A DKQLF LV+WAK IPHF+ L LEDQV+LLRA
Sbjct:   250 VEPKTE-AYSDVNTESSTNDPVTNICHAADKQLFTLVEWAKRIPHFSDLTLEDQVILLRA 308

Query:   221 GWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMD 280
             GWNELLIASFSHRS+SV+DGILLA G+ V+RSSAH AGVG IFDRVLTELVSKM++M+MD
Sbjct:   309 GWNELLIASFSHRSVSVQDGILLATGLHVHRSSAHSAGVGSIFDRVLTELVSKMKDMQMD 368

Query:   281 KTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLP 340
             K+ELGCLR I+LFNPD +GL S   VE LREKVY +LE YT+  + E+PGRFAKLLLRLP
Sbjct:   369 KSELGCLRAIVLFNPDAKGLSSPSEVESLREKVYATLEAYTKQKYPEQPGRFAKLLLRLP 428

Query:   341 SLRSI 345
             +LRSI
Sbjct:   429 ALRSI 433

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0004886 "9-cis retinoic acid receptor activity" evidence=IEA

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

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

ZFIN|ZDB-GENE-070314-2 rxraa "retinoid X receptor, alpha a" [Danio rerio (taxid:7955)]

 Score = 1030 (367.6 bits), Expect = 5.3e-104, P = 5.3e-104
 Identities = 205/307 (66%), Positives = 237/307 (77%)

Query:    46 PPNHPLCGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXX 105
             P   PL  +KH+C+ICGDR+SGKHYGVYSCEGCKGFFKRTVRKDL+Y CR+ ++C+ID  
Sbjct:   156 PSGTPLSLTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCVIDKR 215

Query:   106 XXXXXXXXXXXXXLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQRV 165
                          L MGMKREAVQEERQR KER  NEVESTS    +MPVE+ILEAE  V
Sbjct:   216 QRNRCQYCRYQKCLAMGMKREAVQEERQRAKERSENEVESTSSANEDMPVEKILEAELAV 275

Query:   166 DMKQE-------PADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLL 218
             + K E       P   +  N+   TNIC+A DKQLF LV+WAK IPHF+ LPL+DQV+LL
Sbjct:   276 EPKTETYIETNVPMPSNSPNDP-VTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILL 334

Query:   219 RAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMK 278
             RAGWNELLIASFSHRSI+VKDGILLA G+ V+R+SAH AGVG IFDRVLTELVSKMR+M+
Sbjct:   335 RAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQ 394

Query:   279 MDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLR 338
             MDKTELGCLR I+LFNPD +GL +   VE LREKVY SLE Y +  + E+PGRFAKLLLR
Sbjct:   395 MDKTELGCLRAIVLFNPDSKGLSNPGEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLR 454

Query:   339 LPSLRSI 345
             LP+LRSI
Sbjct:   455 LPALRSI 461

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

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

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

GO:0005634 "nucleus" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

GO:0046872 "metal ion binding" evidence=IEA

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

ZFIN|ZDB-GENE-980526-36 rxrga "retinoid x receptor, gamma a" [Danio rerio (taxid:7955)]

 Score = 1029 (367.3 bits), Expect = 6.7e-104, P = 6.7e-104
 Identities = 202/304 (66%), Positives = 237/304 (77%)

Query:    45 YPPNHPLCGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDX 104
             YP   P   SKH+C+ICGDR+SGKHYGVYSCEGCKGFFKRT+RKDL+Y CR+ ++C ID 
Sbjct:   104 YPCGSPGSLSKHICAICGDRSSGKHYGVYSCEGCKGFFKRTIRKDLTYTCRDNKDCQIDK 163

Query:   105 XXXXXXXXXXXXXXLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQR 164
                           L MGMKREAVQEERQR +ER  NEV+S+S    EMPVE+IL+AE  
Sbjct:   164 RQRNRCQYCRYQKCLAMGMKREAVQEERQRGRERSDNEVDSSSSFNEEMPVEKILDAELA 223

Query:   165 VDMKQEP-ADQDIVNEQQ--ATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAG 221
             V+ K E   +  + N      TNIC+A DKQLF LV+WAK IPHF+ LPL+DQV+LLRAG
Sbjct:   224 VEPKTEAYMESSMSNSTNDPVTNICQAADKQLFTLVEWAKRIPHFSDLPLDDQVILLRAG 283

Query:   222 WNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDK 281
             WNELLIASFSHRS++VKDGILLA G+ V+RSSAH AGVG IFDRVLTELVSKMR+M+MDK
Sbjct:   284 WNELLIASFSHRSVTVKDGILLATGLHVHRSSAHSAGVGSIFDRVLTELVSKMRDMQMDK 343

Query:   282 TELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPS 341
             TELGCLR I+LFNPD +GL +   VE LREKVY SLE YT+ N+ ++PGRFAKLLLRLP+
Sbjct:   344 TELGCLRAIVLFNPDAKGLSNPSEVEALREKVYASLEGYTKHNYPDQPGRFAKLLLRLPA 403

Query:   342 LRSI 345
             LRSI
Sbjct:   404 LRSI 407

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

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

GO:0004886 "9-cis retinoic acid receptor activity" evidence=IDA

GO:0046872 "metal ion binding" evidence=IEA

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

UNIPROTKB|P28701 RXRG "Retinoic acid receptor RXR-gamma" [Gallus gallus (taxid:9031)]

 Score = 1027 (366.6 bits), Expect = 1.1e-103, P = 1.1e-103
 Identities = 203/305 (66%), Positives = 235/305 (77%)

Query:    45 YPPNHPLCGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDX 104
             YP   P   +KH+C+ICGDR+SGKHYGVYSCEGCKGFFKRT+RKDL Y CR+ ++C+ID 
Sbjct:   130 YPSTSPGSLAKHICAICGDRSSGKHYGVYSCEGCKGFFKRTIRKDLIYTCRDNKDCLIDK 189

Query:   105 XXXXXXXXXXXXXXLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQR 164
                           L MGMKREAVQEERQ ++ER  NE ESTSG   +MPVERILEAE  
Sbjct:   190 RQRNRCQYCRYQKCLAMGMKREAVQEERQGSRERSENEAESTSGGSEDMPVERILEAELA 249

Query:   165 VDMKQEPADQDIVNEQQA----TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRA 220
             V+ K E A  D+  E       TNIC A DKQLF LV+WAK IPHF+ L LEDQV+LLRA
Sbjct:   250 VEPKTE-AYSDVNTESSTNDPVTNICHAADKQLFTLVEWAKRIPHFSDLTLEDQVILLRA 308

Query:   221 GWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMD 280
             GWNELLIASFSHRS+SV+DGILLA G+ V+RSSAH AGVG IFDRVLTELVSKM++M+MD
Sbjct:   309 GWNELLIASFSHRSVSVQDGILLATGLHVHRSSAHSAGVGSIFDRVLTELVSKMKDMQMD 368

Query:   281 KTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLP 340
             K+ELGCLR I+LFNPD +GL S   VE LREKVY +LE YT+  + E+PGRFAKLLLRLP
Sbjct:   369 KSELGCLRAIVLFNPDAKGLSSPSEVESLREKVYATLEAYTKQKYPEQPGRFAKLLLRLP 428

Query:   341 SLRSI 345
             +LRSI
Sbjct:   429 ALRSI 433

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0004886 "9-cis retinoic acid receptor activity" evidence=IEA

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

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

UNIPROTKB|P51129 rxrg "Retinoic acid receptor RXR-gamma" [Xenopus laevis (taxid:8355)]

 Score = 1022 (364.8 bits), Expect = 3.7e-103, P = 3.7e-103
 Identities = 201/304 (66%), Positives = 234/304 (76%)

Query:    45 YPPNHPLCGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDX 104
             Y  N P   +KH+C+ICGDR+SGKHYGVYSCEGCKGFFKRT+RKDL Y CR+ ++C+ID 
Sbjct:   133 YSCNSPGALTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTIRKDLVYTCRDSKDCLIDK 192

Query:   105 XXXXXXXXXXXXXXLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQR 164
                           L MGMKREAVQEERQR++E+   E ESTS T  EMPVERILEAE  
Sbjct:   193 RQRNRCQYCRYQKCLAMGMKREAVQEERQRSREKSDTEAESTSSTSEEMPVERILEAELA 252

Query:   165 VDMKQEP-ADQDIVNEQQ--ATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAG 221
             VD K E   D  + N      TNIC A DKQLF LV+WAK IP+F+ LPLEDQV+LLRAG
Sbjct:   253 VDPKIEAFGDAGLPNSTNDPVTNICHAADKQLFTLVEWAKRIPYFSDLPLEDQVILLRAG 312

Query:   222 WNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDK 281
             WNELLIASFSHRS+SV+DGILLA G+ V+RSSAH AGVG IFDRVLTELVSKM++M MDK
Sbjct:   313 WNELLIASFSHRSVSVQDGILLATGLHVHRSSAHNAGVGSIFDRVLTELVSKMKDMDMDK 372

Query:   282 TELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPS 341
             +ELGCLR I+LFNPD +GL +   VE LREKVY +LE YT+  + ++PGRFAKLLLRLP+
Sbjct:   373 SELGCLRAIVLFNPDAKGLSNAAEVEALREKVYATLESYTKQKYPDQPGRFAKLLLRLPA 432

Query:   342 LRSI 345
             LRSI
Sbjct:   433 LRSI 436

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

GO:0046966 "thyroid hormone receptor binding" evidence=IPI

GO:0046982 "protein heterodimerization activity" evidence=IPI

UNIPROTKB|B3KY83 RXRA "cDNA FLJ16020 fis, clone BRAMY2003287, highly similar to RETINOIC ACID RECEPTOR RXR-ALPHA" [Homo sapiens (taxid:9606)]

 Score = 1017 (363.1 bits), Expect = 1.3e-102, P = 1.3e-102
 Identities = 202/307 (65%), Positives = 239/307 (77%)

Query:    45 YPPNHPLCGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDX 104
             +P  +    +KH+C+ICGDR+SGKHYGVYSCEGCKGFFKRTVRKDL+Y CR+ ++C+ID 
Sbjct:    25 HPSGNMASFTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDK 84

Query:   105 XXXXXXXXXXXXXXLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQR 164
                           L MGMKREAVQEERQR K+R+ NEVESTS    +MPVERILEAE  
Sbjct:    85 RQRNRCQYCRYQKCLAMGMKREAVQEERQRGKDRNENEVESTSSANEDMPVERILEAELA 144

Query:   165 VDMKQEP-ADQDI-VNEQQ----ATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLL 218
             V+ K E   + ++ +N        TNIC+A DKQLF LV+WAK IPHF+ LPL+DQV+LL
Sbjct:   145 VEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILL 204

Query:   219 RAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMK 278
             RAGWNELLIASFSHRSI+VKDGILLA G+ V+R+SAH AGVG IFDRVLTELVSKMR+M+
Sbjct:   205 RAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQ 264

Query:   279 MDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLR 338
             MDKTELGCLR I+LFNPD +GL +   VE LREKVY SLE Y +  + E+PGRFAKLLLR
Sbjct:   265 MDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLR 324

Query:   339 LPSLRSI 345
             LP+LRSI
Sbjct:   325 LPALRSI 331

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0001701 "in utero embryonic development" evidence=IEA

GO:0001893 "maternal placenta development" evidence=IEA

GO:0004886 "9-cis retinoic acid receptor activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0007566 "embryo implantation" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IEA

GO:0031490 "chromatin DNA binding" evidence=IEA

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

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

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

GO:0055010 "ventricular cardiac muscle tissue morphogenesis" evidence=IEA

GO:0055012 "ventricular cardiac muscle cell differentiation" evidence=IEA

GO:0060038 "cardiac muscle cell proliferation" evidence=IEA

GO:0060528 "secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development" evidence=IEA

GO:0060687 "regulation of branching involved in prostate gland morphogenesis" evidence=IEA

UNIPROTKB|P19793 RXRA "Retinoic acid receptor RXR-alpha" [Homo sapiens (taxid:9606)]

 Score = 1017 (363.1 bits), Expect = 1.3e-102, P = 1.3e-102
 Identities = 202/307 (65%), Positives = 239/307 (77%)

Query:    45 YPPNHPLCGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDX 104
             +P  +    +KH+C+ICGDR+SGKHYGVYSCEGCKGFFKRTVRKDL+Y CR+ ++C+ID 
Sbjct:   122 HPSGNMASFTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDK 181

Query:   105 XXXXXXXXXXXXXXLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQR 164
                           L MGMKREAVQEERQR K+R+ NEVESTS    +MPVERILEAE  
Sbjct:   182 RQRNRCQYCRYQKCLAMGMKREAVQEERQRGKDRNENEVESTSSANEDMPVERILEAELA 241

Query:   165 VDMKQEP-ADQDI-VNEQQ----ATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLL 218
             V+ K E   + ++ +N        TNIC+A DKQLF LV+WAK IPHF+ LPL+DQV+LL
Sbjct:   242 VEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILL 301

Query:   219 RAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMK 278
             RAGWNELLIASFSHRSI+VKDGILLA G+ V+R+SAH AGVG IFDRVLTELVSKMR+M+
Sbjct:   302 RAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQ 361

Query:   279 MDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLR 338
             MDKTELGCLR I+LFNPD +GL +   VE LREKVY SLE Y +  + E+PGRFAKLLLR
Sbjct:   362 MDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLR 421

Query:   339 LPSLRSI 345
             LP+LRSI
Sbjct:   422 LPALRSI 428

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0001701 "in utero embryonic development" evidence=IEA

GO:0001893 "maternal placenta development" evidence=IEA

GO:0004886 "9-cis retinoic acid receptor activity" evidence=IEA

GO:0007566 "embryo implantation" evidence=IEA

GO:0031490 "chromatin DNA binding" evidence=IEA

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

GO:0055010 "ventricular cardiac muscle tissue morphogenesis" evidence=IEA

GO:0055012 "ventricular cardiac muscle cell differentiation" evidence=IEA

GO:0060038 "cardiac muscle cell proliferation" evidence=IEA

GO:0060528 "secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development" evidence=IEA

GO:0060687 "regulation of branching involved in prostate gland morphogenesis" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0019899 "enzyme binding" evidence=IPI

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

GO:0046982 "protein heterodimerization activity" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0035357 "peroxisome proliferator activated receptor signaling pathway" evidence=IDA

GO:0019048 "virus-host interaction" evidence=IDA

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

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

GO:0006766 "vitamin metabolic process" evidence=TAS

GO:0003713 "transcription coactivator activity" evidence=TAS

GO:0003677 "DNA binding" evidence=IDA

GO:0005654 "nucleoplasm" evidence=TAS

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

GO:0010467 "gene expression" evidence=TAS

GO:0044255 "cellular lipid metabolic process" evidence=TAS

GO:0044281 "small molecule metabolic process" evidence=TAS

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

GO:0008203 "cholesterol metabolic process" evidence=TAS

GO:0032526 "response to retinoic acid" evidence=IMP

GO:0048384 "retinoic acid receptor signaling pathway" evidence=IMP

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

GO:0000790 "nuclear chromatin" evidence=IDA

GO:0070644 "vitamin D response element binding" evidence=IDA

GO:0042809 "vitamin D receptor binding" evidence=IPI

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

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

UNIPROTKB|F1P6M9 RXRA "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 1014 (362.0 bits), Expect = 2.6e-102, P = 2.6e-102
 Identities = 201/307 (65%), Positives = 239/307 (77%)

Query:    45 YPPNHPLCGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDX 104
             +P  +    +KH+C+ICGDR+SGKHYGVYSCEGCKGFFKRTVRKDL+Y CR+ ++C+ID 
Sbjct:   146 HPSGNMASFTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDK 205

Query:   105 XXXXXXXXXXXXXXLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQR 164
                           L MGMKREAVQEERQR K+R+ NEVESTS    +MPVE+ILEAE  
Sbjct:   206 RQRNRCQYCRYQKCLAMGMKREAVQEERQRGKDRNENEVESTSSANEDMPVEKILEAELA 265

Query:   165 VDMKQEP-ADQDI-VNEQQ----ATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLL 218
             V+ K E   D ++ +N        TNIC+A DKQLF LV+WAK IPHF+ LPL+DQV+LL
Sbjct:   266 VEPKTETYVDANMGLNPNSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILL 325

Query:   219 RAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMK 278
             RAGWNELLIASFSHRSI+VKDGILLA G+ V+R+SAH AGVG IFDRVLTELVSKMR+M+
Sbjct:   326 RAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQ 385

Query:   279 MDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLR 338
             MDK+ELGCLR I+LFNPD +GL +   VE LREKVY SLE Y +  + E+PGRFAKLLLR
Sbjct:   386 MDKSELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLR 445

Query:   339 LPSLRSI 345
             LP+LRSI
Sbjct:   446 LPALRSI 452

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

MGI|MGI:98214 Rxra "retinoid X receptor alpha" [Mus musculus (taxid:10090)]

 Score = 1014 (362.0 bits), Expect = 2.6e-102, P = 2.6e-102
 Identities = 201/307 (65%), Positives = 239/307 (77%)

Query:    45 YPPNHPLCGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDX 104
             +P  +    +KH+C+ICGDR+SGKHYGVYSCEGCKGFFKRTVRKDL+Y CR+ ++C+ID 
Sbjct:   127 HPSGNMASFTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDK 186

Query:   105 XXXXXXXXXXXXXXLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQR 164
                           L MGMKREAVQEERQR K+R+ NEVESTS    +MPVE+ILEAE  
Sbjct:   187 RQRNRCQYCRYQKCLAMGMKREAVQEERQRGKDRNENEVESTSSANEDMPVEKILEAELA 246

Query:   165 VDMKQEP-ADQDI-VNEQQ----ATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLL 218
             V+ K E   + ++ +N        TNIC+A DKQLF LV+WAK IPHF+ LPL+DQV+LL
Sbjct:   247 VEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILL 306

Query:   219 RAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMK 278
             RAGWNELLIASFSHRSI+VKDGILLA G+ V+R+SAH AGVG IFDRVLTELVSKMR+M+
Sbjct:   307 RAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQ 366

Query:   279 MDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLR 338
             MDKTELGCLR I+LFNPD +GL +   VE LREKVY SLE Y +  + E+PGRFAKLLLR
Sbjct:   367 MDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLR 426

Query:   339 LPSLRSI 345
             LP+LRSI
Sbjct:   427 LPALRSI 433

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

GO:0000790 "nuclear chromatin" evidence=ISO

GO:0001701 "in utero embryonic development" evidence=IGI

GO:0001890 "placenta development" evidence=IMP

GO:0001893 "maternal placenta development" evidence=IGI

GO:0003007 "heart morphogenesis" evidence=TAS

GO:0003677 "DNA binding" evidence=ISO;IDA;IPI

GO:0003690 "double-stranded DNA binding" evidence=ISO

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

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

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

GO:0004886 "9-cis retinoic acid receptor activity" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO;IDA

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

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

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

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

GO:0007566 "embryo implantation" evidence=IGI

GO:0008134 "transcription factor binding" evidence=IPI

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0010629 "negative regulation of gene expression" evidence=TAS

GO:0019048 "virus-host interaction" evidence=ISO

GO:0019899 "enzyme binding" evidence=ISO

GO:0019904 "protein domain specific binding" evidence=ISO

GO:0030424 "axon" evidence=ISO

GO:0031490 "chromatin DNA binding" evidence=IDA

GO:0031641 "regulation of myelination" evidence=ISO

GO:0032403 "protein complex binding" evidence=ISO

GO:0032526 "response to retinoic acid" evidence=ISO

GO:0035357 "peroxisome proliferator activated receptor signaling pathway" evidence=ISO

GO:0042809 "vitamin D receptor binding" evidence=ISO

GO:0042974 "retinoic acid receptor binding" evidence=ISO

GO:0043065 "positive regulation of apoptotic process" evidence=ISO

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

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

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

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

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IGI;TAS

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

GO:0046872 "metal ion binding" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=ISO

GO:0048384 "retinoic acid receptor signaling pathway" evidence=ISO;IDA

GO:0051384 "response to glucocorticoid stimulus" evidence=ISO

GO:0055007 "cardiac muscle cell differentiation" evidence=TAS

GO:0055010 "ventricular cardiac muscle tissue morphogenesis" evidence=IMP

GO:0055012 "ventricular cardiac muscle cell differentiation" evidence=IGI;IMP

GO:0060038 "cardiac muscle cell proliferation" evidence=IGI;IMP;TAS

GO:0060485 "mesenchyme development" evidence=TAS

GO:0060528 "secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development" evidence=IMP

GO:0060687 "regulation of branching involved in prostate gland morphogenesis" evidence=IMP

GO:0060978 "angiogenesis involved in coronary vascular morphogenesis" evidence=TAS

GO:0061032 "visceral serous pericardium development" evidence=TAS

UNIPROTKB|P51128 rxra "Retinoic acid receptor RXR-alpha" [Xenopus laevis (taxid:8355)]

 Score = 1013 (361.7 bits), Expect = 3.3e-102, P = 3.3e-102
 Identities = 201/309 (65%), Positives = 239/309 (77%)

Query:    44 PYPPNHPLCG-SKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCII 102
             P  P+  +   +KH+C+ICGDR+SGKHYGVYSCEGCKGFFKRTVRKDL+Y CR+ ++C+I
Sbjct:   146 PMHPSGAMASFTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDSKDCMI 205

Query:   103 DXXXXXXXXXXXXXXXLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAE 162
             D               L MGMKREAVQEERQR KER+ NEVES++    +MPVE+ILEAE
Sbjct:   206 DKRQRNRCQYCRYQKCLAMGMKREAVQEERQRGKERNENEVESSNSANEDMPVEKILEAE 265

Query:   163 QRVDMKQEP---ADQDIVNEQQA---TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVL 216
               V+ K E    A+  +     +   TNIC+A DKQLF LV+WAK IPHF+ LPL+DQV+
Sbjct:   266 HAVEPKTETYTEANMGLAPNSPSDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVI 325

Query:   217 LLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMRE 276
             LLRAGWNELLIASFSHRSI+VKDGILLA G+ V+R+SAH AGVG IFDRVLTELVSKMR+
Sbjct:   326 LLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRD 385

Query:   277 MKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLL 336
             M+MDKTELGCLR I+LFNPD +GL +   VE LREKVY SLE Y +  + E+PGRFAKLL
Sbjct:   386 MQMDKTELGCLRAIVLFNPDSKGLSNPLEVEALREKVYASLEAYCKQKYPEQPGRFAKLL 445

Query:   337 LRLPSLRSI 345
             LRLP+LRSI
Sbjct:   446 LRLPALRSI 454

GO:0046966 "thyroid hormone receptor binding" evidence=IPI

GO:0046982 "protein heterodimerization activity" evidence=IPI

---

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)
P51129	RXRG_XENLA	No assigned EC number	0.7006	0.8847	0.6531	N/A	N/A
Q05343	RXRA_RAT	No assigned EC number	0.6637	0.9279	0.6895	yes	N/A
P19793	RXRA_HUMAN	No assigned EC number	0.6686	0.9337	0.7012	yes	N/A
P28701	RXRG_CHICK	No assigned EC number	0.7147	0.8645	0.6423	yes	N/A
P28700	RXRA_MOUSE	No assigned EC number	0.6637	0.9279	0.6895	yes	N/A
P28705	RXRG_MOUSE	No assigned EC number	0.7006	0.8674	0.6501	no	N/A
Q0GFF6	RXRG_PIG	No assigned EC number	0.7006	0.8674	0.6501	yes	N/A
Q0VC20	RXRG_BOVIN	No assigned EC number	0.6973	0.8674	0.6501	yes	N/A
A2T929	RXRAA_DANRE	No assigned EC number	0.6563	0.9481	0.7651	yes	N/A
Q5REL6	RXRG_PONAB	No assigned EC number	0.7006	0.8674	0.6501	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	347
cd06943	207	cd06943, NR_LBD_RXR_like, The ligand binding domai	1e-123
cd06930	165	cd06930, NR_LBD_F2, Ligand-binding domain of nucle	8e-57
cd06956	77	cd06956, NR_DBD_RXR, DNA-binding domain of retinoi	2e-53
cd06931	222	cd06931, NR_LBD_HNF4_like, The ligand binding doma	2e-49
cd06916	72	cd06916, NR_DBD_like, DNA-binding domain of nuclea	2e-47
cd06157	168	cd06157, NR_LBD, The ligand binding domain of nucl	3e-45
smart00430	163	smart00430, HOLI, Ligand binding domain of hormone	2e-43
pfam00105	70	pfam00105, zf-C4, Zinc finger, C4 type (two domain	5e-42
cd06960	76	cd06960, NR_DBD_HNF4A, DNA-binding domain of hepto	2e-41
cd06967	87	cd06967, NR_DBD_TR2_like, DNA-binding domain of th	3e-40
cd06948	236	cd06948, NR_LBD_COUP-TF, Ligand binding domain of	6e-40
cd06961	85	cd06961, NR_DBD_TR, DNA-binding domain of thyroid	2e-39
cd06969	75	cd06969, NR_DBD_NGFI-B, DNA-binding domain of the	3e-39
cd07164	78	cd07164, NR_DBD_PNR_like_1, DNA-binding domain of	3e-39
cd06944	237	cd06944, NR_LBD_Ftz-F1_like, The ligand binding do	6e-38
cd07068	221	cd07068, NR_LBD_ER_like, The ligand binding domain	2e-37
cd06950	206	cd06950, NR_LBD_Tlx_PNR_like, The ligand binding d	5e-37
pfam00104	186	pfam00104, Hormone_recep, Ligand-binding domain of	7e-37
cd07167	93	cd07167, NR_DBD_Lrh-1_like, The DNA-binding domain	3e-36
smart00399	70	smart00399, ZnF_C4, c4 zinc finger in nuclear horm	4e-36
cd06958	73	cd06958, NR_DBD_COUP_TF, DNA-binding domain of chi	1e-35
cd07169	90	cd07169, NR_DBD_GCNF_like, DNA-binding domain of G	1e-33
cd06968	95	cd06968, NR_DBD_ROR, DNA-binding domain of Retinoi	4e-33
cd06965	84	cd06965, NR_DBD_Ppar, DNA-binding domain of peroxi	5e-33
cd06957	82	cd06957, NR_DBD_PNR_like_2, DNA-binding domain of	8e-33
cd06964	85	cd06964, NR_DBD_RAR, DNA-binding domain of retinoi	8e-33
cd07168	90	cd07168, NR_DBD_DHR4_like, DNA-binding domain of e	1e-32
cd06970	92	cd06970, NR_DBD_PNR, DNA-binding domain of the pho	3e-32
cd07154	73	cd07154, NR_DBD_PNR_like, The DNA-binding domain o	1e-31
cd07158	73	cd07158, NR_DBD_Ppar_like, The DNA-binding domain	2e-31
cd07165	81	cd07165, NR_DBD_DmE78_like, DNA-binding domain of	3e-31
cd07163	92	cd07163, NR_DBD_TLX, DNA-binding domain of Tailles	1e-30
cd07166	89	cd07166, NR_DBD_REV_ERB, DNA-binding domain of REV	2e-30
cd06929	174	cd06929, NR_LBD_F1, Ligand-binding domain of nucle	4e-30
cd07069	241	cd07069, NR_LBD_Lrh-1, The ligand binding domain o	7e-30
cd07155	75	cd07155, NR_DBD_ER_like, DNA-binding domain of est	4e-29
cd06946	221	cd06946, NR_LBD_ERR, The ligand binding domain of	4e-28
cd07179	74	cd07179, 2DBD_NR_DBD2, The second DNA-binding doma	5e-28
cd06959	73	cd06959, NR_DBD_EcR_like, The DNA-binding domain o	6e-28
cd07170	97	cd07170, NR_DBD_ERR, DNA-binding domain of estroge	8e-28
cd07171	82	cd07171, NR_DBD_ER, DNA-binding domain of estrogen	2e-27
cd07161	91	cd07161, NR_DBD_EcR, DNA-binding domain of Ecdyson	2e-26
cd06952	222	cd06952, NR_LBD_TR2_like, The ligand binding domai	5e-26
cd07156	72	cd07156, NR_DBD_VDR_like, The DNA-binding domain o	5e-26
cd07160	101	cd07160, NR_DBD_LXR, DNA-binding domain of Liver X	7e-26
cd06962	84	cd06962, NR_DBD_FXR, DNA-binding domain of Farneso	3e-24
cd06937	231	cd06937, NR_LBD_RAR, The ligand binding domain (LB	6e-24
cd06953	213	cd06953, NR_LBD_DHR4_like, The ligand binding doma	1e-23
cd06949	235	cd06949, NR_LBD_ER, Ligand binding domain of Estro	5e-23
cd07162	87	cd07162, NR_DBD_PXR, DNA-binding domain of pregnan	2e-22
cd07157	86	cd07157, 2DBD_NR_DBD1, The first DNA-binding domai	3e-22
cd06955	107	cd06955, NR_DBD_VDR, DNA-binding domain of vitamin	2e-21
cd07172	78	cd07172, NR_DBD_GR_PR, DNA-binding domain of gluco	3e-21
cd07070	237	cd07070, NR_LBD_SF-1, The ligand binding domain of	5e-21
cd06940	189	cd06940, NR_LBD_REV_ERB, The ligand binding domain	7e-21
cd06954	236	cd06954, NR_LBD_LXR, The ligand binding domain of	2e-20
cd06963	73	cd06963, NR_DBD_GR_like, The DNA binding domain of	2e-19
cd06966	94	cd06966, NR_DBD_CAR, DNA-binding domain of constit	2e-19
cd06932	259	cd06932, NR_LBD_PPAR, The ligand binding domain of	2e-17
cd06951	222	cd06951, NR_LBD_Dax1_like, The ligand binding doma	8e-17
cd06935	243	cd06935, NR_LBD_TR, The ligand binding domain of t	1e-16
cd07350	232	cd07350, NR_LBD_Dax1, The ligand binding domain of	2e-16
cd07173	82	cd07173, NR_DBD_AR, DNA-binding domain of androgen	2e-16
cd06945	239	cd06945, NR_LBD_Nurr1_like, The ligand binding dom	9e-16
cd06936	221	cd06936, NR_LBD_Fxr, The ligand binding domain of	2e-14
cd07348	238	cd07348, NR_LBD_NGFI-B, The ligand binding domain	2e-14
cd07071	238	cd07071, NR_LBD_Nurr1, The ligand binding domain o	7e-14
cd07349	222	cd07349, NR_LBD_SHP, The ligand binding domain of	2e-13
cd06939	241	cd06939, NR_LBD_ROR_like, The ligand binding domai	4e-13
cd06938	231	cd06938, NR_LBD_EcR, The ligand binding domain (LB	1e-12
cd06941	195	cd06941, NR_LBD_DmE78_like, The ligand binding dom	1e-12
cd07072	239	cd07072, NR_LBD_DHR38_like, Ligand binding domain	3e-10
cd06934	226	cd06934, NR_LBD_PXR_like, The ligand binding domai	1e-09
cd06947	246	cd06947, NR_LBD_GR_Like, Ligand binding domain of	3e-08
cd06933	238	cd06933, NR_LBD_VDR, The ligand binding domain of	4e-08
cd07076	247	cd07076, NR_LBD_GR, Ligand binding domain of the g	1e-07
cd07075	248	cd07075, NR_LBD_MR, Ligand binding domain of the m	5e-07
cd07074	248	cd07074, NR_LBD_PR, Ligand binding domain of the p	9e-07
cd07073	246	cd07073, NR_LBD_AR, Ligand binding domain of the n	3e-06

>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 =  352 bits (906), Expect = e-123
 Identities = 139/195 (71%), Positives = 164/195 (84%), Gaps = 1/195 (0%)

Query: 152 EMPVERILEAEQRVDMKQEP-ADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLP 210
           +MP+ERILEAE  V+ K E  A          +NIC+A DKQLFQLV+WAK IPHF+ LP
Sbjct: 1   DMPIERILEAELAVEPKSEAVAMVPPEYRDPVSNICQAADKQLFQLVEWAKRIPHFSELP 60

Query: 211 LEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTEL 270
           L+DQV+LLRAGWNELLIA+F+HRSI+VKDGILLA G+ ++R+SAH+AGVG IFDR+LTEL
Sbjct: 61  LDDQVILLRAGWNELLIAAFAHRSIAVKDGILLATGLHLHRNSAHQAGVGAIFDRILTEL 120

Query: 271 VSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPG 330
           V KMR++KMD+TELGCLR IILFNPDV+GLKS+Q VE LREKVY SLEEY R  H E+PG
Sbjct: 121 VVKMRDLKMDRTELGCLRAIILFNPDVKGLKSRQEVESLREKVYASLEEYCRQKHPEQPG 180

Query: 331 RFAKLLLRLPSLRSI 345
           RFAKLLLRLP+LRSI
Sbjct: 181 RFAKLLLRLPALRSI 195

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

 Score =  181 bits (462), Expect = 8e-57
 Identities = 73/163 (44%), Positives = 108/163 (66%), Gaps = 3/163 (1%)

Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSI--SVKDGIL 242
           +C+  D+ LF+ VDWAK++P F  LPL+DQ+ LL+  W ELL+   + RS+   + + +L
Sbjct: 4   LCELADRVLFKTVDWAKNLPAFRNLPLDDQLTLLQNSWAELLLLGLAQRSVHFELSELLL 63

Query: 243 LAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKS 302
            +P + +        G+  +  R L EL+SK+R +++D  E  CL+ I+LFNPD+ GLK+
Sbjct: 64  PSPLLVILTEREALLGLAELVQR-LQELLSKLRSLQLDPKEYACLKAIVLFNPDLPGLKN 122

Query: 303 QQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           QQ VE L+EK   +L+EY R  + ++P RFAKLLLRLP LRSI
Sbjct: 123 QQQVEELQEKAQQALQEYIRKRYPQQPARFAKLLLRLPELRSI 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|143514 cd06956, NR_DBD_RXR, DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers

 Score =  170 bits (431), Expect = 2e-53
 Identities = 67/77 (87%), Positives = 74/77 (96%)

Query: 56  HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRY 115
           H+C+ICGDRASGKHYGVYSCEGCKGFFKRTVRKDL+Y CR+ ++C+IDKRQRNRCQYCRY
Sbjct: 1   HICAICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRY 60

Query: 116 QKCLNMGMKREAVQEER 132
           QKCL MGMKREAVQEER
Sbjct: 61  QKCLAMGMKREAVQEER 77

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

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

 Score =  164 bits (418), Expect = 2e-49
 Identities = 73/196 (37%), Positives = 114/196 (58%), Gaps = 6/196 (3%)

Query: 155 VERILEAEQRVDMKQEPA---DQDIVNEQQAT--NICKATDKQLFQLVDWAKHIPHFTTL 209
           +  +L+AE     +  P      DI  ++ A+  ++C++  +QL  LV+WAK+IP F  L
Sbjct: 2   ISVLLQAEALSRQQSSPIPTCSGDIRPKKIASINDVCESMKQQLLVLVEWAKYIPAFCEL 61

Query: 210 PLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTE 269
           PL+DQV LLRA   E L+   + RS+  KD +LL   + + R    E  +  + +R+L E
Sbjct: 62  PLDDQVALLRAHAGEHLLLGVARRSMPYKDILLLGNDLIIPRHCP-EPEISRVANRILDE 120

Query: 270 LVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEP 329
           LV  +R++ +D  E  CL+ I+ F+PD +GL   Q ++ LR +V  SLE+Y      +  
Sbjct: 121 LVLPLRDLNIDDNEYACLKAIVFFDPDAKGLSDPQKIKRLRFQVQVSLEDYINDRQYDSR 180

Query: 330 GRFAKLLLRLPSLRSI 345
           GRF +LLL LP+L+SI
Sbjct: 181 GRFGELLLLLPTLQSI 196

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

 Score =  154 bits (392), Expect = 2e-47
 Identities = 47/72 (65%), Positives = 61/72 (84%)

Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQK 117
           C++CGD+ASG HYGV +CEGCKGFF+R+VR++L Y C  G NC+IDKR RNRCQ CR +K
Sbjct: 1   CAVCGDKASGYHYGVLTCEGCKGFFRRSVRRNLEYTCPAGGNCVIDKRNRNRCQACRLKK 60

Query: 118 CLNMGMKREAVQ 129
           CL +GM++EAV+
Sbjct: 61  CLAVGMRKEAVR 72

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

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

 Score =  152 bits (385), Expect = 3e-45
 Identities = 66/168 (39%), Positives = 101/168 (60%), Gaps = 5/168 (2%)

Query: 183 TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGIL 242
             +C+   + L  +V+WAK IP F  LPLEDQ++LL++ W ELL+   ++RS      +L
Sbjct: 1   ELLCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLL 60

Query: 243 LAPGVTVYRSSAHE---AGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDV-R 298
           LAP          +     + G   R+L E V+ +R +K+D  E   L+ I+LF+PD   
Sbjct: 61  LAPNGGHTDDDKEDEMKLLLKGELIRLLFEFVNPLRALKLDDEEYALLKAIVLFSPDRKE 120

Query: 299 GLKSQQVVEMLREKVYTSLEEYTRVNHSEE-PGRFAKLLLRLPSLRSI 345
            L+ +++VE L+E++  +L++Y R N+ EE P RFAKLLL LPSLR +
Sbjct: 121 SLEDRKIVEELQERLLEALQDYLRKNYPEEAPSRFAKLLLLLPSLRKL 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|214658 smart00430, HOLI, Ligand binding domain of hormone receptors

 Score =  147 bits (372), Expect = 2e-43
 Identities = 71/163 (43%), Positives = 99/163 (60%), Gaps = 6/163 (3%)

Query: 189 TDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVT 248
            ++QL   V+WAK  P F  L LEDQ++LL++ W ELL+   ++RS+ +K  +LLAP  T
Sbjct: 1   AERQLLLTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKELLLAPDGT 60

Query: 249 VYRSSAH---EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGL--KSQ 303
             R  A            DR+L+ELV  +RE+K+D  E   L+ I+LFNP V GL  + +
Sbjct: 61  YIRPDAVLELRKLFSPFLDRILSELVKPLRELKLDDEEYALLKAIVLFNPAVPGLSEEGK 120

Query: 304 QVVEMLREKVYTSLEEYTRVNHSEE-PGRFAKLLLRLPSLRSI 345
           ++VE L+EK   +L +Y   N+    PGRFAKLLL LP LR I
Sbjct: 121 EIVEKLQEKYANALHDYYLKNYPMNYPGRFAKLLLILPELRKI 163

Length = 163

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

 Score =  140 bits (355), Expect = 5e-42
 Identities = 42/70 (60%), Positives = 57/70 (81%)

Query: 56  HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRY 115
            LC +CGD+ASG HYGV +CEGCKGFF+R+++K++ Y C   ++C+IDKR RNRCQYCR 
Sbjct: 1   ELCKVCGDKASGYHYGVLTCEGCKGFFRRSIQKNIVYTCPFNKDCVIDKRNRNRCQYCRL 60

Query: 116 QKCLNMGMKR 125
           +KCL +GM +
Sbjct: 61  KKCLEVGMSK 70

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

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

 Score =  138 bits (351), Expect = 2e-41
 Identities = 49/75 (65%), Positives = 63/75 (84%)

Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQK 117
           C++CGDRA+GKHYGV SC GCKGFF+R+VRK+ +Y CR G NC++DK +RN C+YCR++K
Sbjct: 1   CAVCGDRATGKHYGVLSCNGCKGFFRRSVRKNRTYTCRFGGNCVVDKDKRNACRYCRFKK 60

Query: 118 CLNMGMKREAVQEER 132
           CL +GM  EAVQ ER
Sbjct: 61  CLEVGMDPEAVQNER 75

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

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

 Score =  136 bits (344), Expect = 3e-40
 Identities = 51/83 (61%), Positives = 65/83 (78%)

Query: 57  LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQ 116
           LC +CGD+ASG+HYG  SCEGCKGFFKR++RK+L Y+CR  ++C+I+K  RNRCQYCR Q
Sbjct: 5   LCVVCGDKASGRHYGAVSCEGCKGFFKRSIRKNLGYSCRGSKDCVINKHHRNRCQYCRLQ 64

Query: 117 KCLNMGMKREAVQEERQRTKERD 139
           KCL MGMK ++VQ ER+      
Sbjct: 65  KCLAMGMKSDSVQCERKPIDVSR 87

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

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

 Score =  140 bits (355), Expect = 6e-40
 Identities = 63/171 (36%), Positives = 92/171 (53%), Gaps = 17/171 (9%)

Query: 184 NICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL 243
           NIC+   + LF  V+WA++IP F  L + DQV LLR  W+EL + + +   + +    LL
Sbjct: 34  NICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLSWSELFVLNAAQCCMPLHVAPLL 93

Query: 244 APGVTVYRSSAHEAGVGGIFDRVLT---------ELVSKMREMKMDKTELGCLRTIILFN 294
           A       +  H + +    DRV+          E V K++ + +D  E  CL+ I+LF 
Sbjct: 94  AA------AGLHASPMSA--DRVVAFMDHIRIFQEQVEKLKALHVDSAEFSCLKAIVLFT 145

Query: 295 PDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            D  GL     +E L+EK   +LEEY R  +  +P RF KLLLRLPSLR++
Sbjct: 146 SDACGLSDPAHIESLQEKSQCALEEYVRTQYPNQPTRFGKLLLRLPSLRTV 196

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

 Score =  134 bits (338), Expect = 2e-39
 Identities = 42/82 (51%), Positives = 61/82 (74%)

Query: 57  LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQ 116
            C +CGD+A+G HY   +CEGCKGFF+RTV+K LSY+C+    C IDK  RN+CQ CR++
Sbjct: 1   PCVVCGDKATGYHYRCITCEGCKGFFRRTVQKKLSYSCKGEGKCEIDKVTRNQCQECRFK 60

Query: 117 KCLNMGMKREAVQEERQRTKER 138
           KC+ +GM ++ V ++R+R  +R
Sbjct: 61  KCIAVGMAKDLVLDDRKRGAKR 82

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

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

 Score =  133 bits (336), Expect = 3e-39
 Identities = 46/73 (63%), Positives = 60/73 (82%)

Query: 57  LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQ 116
           LC++CGD A+ +HYGV +CEGCKGFFKRTV+K+  Y C   +NC +DKR+RNRCQYCR+Q
Sbjct: 2   LCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQ 61

Query: 117 KCLNMGMKREAVQ 129
           KCL +GM +E V+
Sbjct: 62  KCLQVGMVKEVVR 74

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

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

 Score =  133 bits (336), Expect = 3e-39
 Identities = 45/76 (59%), Positives = 63/76 (82%)

Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQK 117
           C +CGDRASGKHYGV SC+GC+GFFKR++R++L+Y C+E  +C++D  +RN+CQ CR++K
Sbjct: 1   CRVCGDRASGKHYGVPSCDGCRGFFKRSIRRNLAYVCKENGSCVVDVARRNQCQACRFKK 60

Query: 118 CLNMGMKREAVQEERQ 133
           CL + M R+AVQ ER 
Sbjct: 61  CLQVNMNRDAVQHERA 76

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

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

 Score =  135 bits (341), Expect = 6e-38
 Identities = 69/166 (41%), Positives = 112/166 (67%), Gaps = 6/166 (3%)

Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSI--SVKDGIL 242
           +CK  D+ LF +V+WA++   F  L ++DQ+ LL+  W+ELL+    +R +    +D IL
Sbjct: 43  MCKMADQTLFSIVEWARNSVFFKELKVDDQMKLLQNCWSELLVLDHIYRQVHHGKEDSIL 102

Query: 243 LAPGVTVYRSS-AHEAGVG--GIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRG 299
           L  G  V  S+ A +AG+G   + DR   ELV+K+RE++ D+ E  CL+ +ILFNPDV+G
Sbjct: 103 LVTGQEVDLSTLASQAGLGLSSLVDR-AQELVNKLRELQFDRQEFVCLKFLILFNPDVKG 161

Query: 300 LKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           L+++Q+VE ++E+V  +L +YT  N+ ++  +F +LLLRLP +R+I
Sbjct: 162 LENRQLVESVQEQVNAALLDYTLCNYPQQTDKFGQLLLRLPEIRAI 207

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

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

 Score =  133 bits (337), Expect = 2e-37
 Identities = 66/191 (34%), Positives = 108/191 (56%), Gaps = 4/191 (2%)

Query: 155 VERILEAE-QRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLED 213
           +  +L AE  ++    +P   D      AT +    D++L  ++ WAKHIP F+ L L D
Sbjct: 2   LSALLVAEPDKLYAMNDPTGPDTEVSLLAT-LSDLADRELVHIISWAKHIPGFSDLSLND 60

Query: 214 QVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSK 273
           Q+ LL++ W E+L+     RS+     ++ AP + + R  A   G+  IFD +L +LV +
Sbjct: 61  QMHLLQSAWLEILMLGLVWRSLPHPGKLVFAPDLLLDREQARVEGLLEIFDMLL-QLVRR 119

Query: 274 MREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEY-TRVNHSEEPGRF 332
            RE+ + + E  CL+ IIL N DVR L+ ++ V+ LR+ +  +L +   + + S++P R 
Sbjct: 120 FRELGLQREEYVCLKAIILANSDVRHLEDREAVQQLRDAILDALVDVEAKRHGSQQPRRL 179

Query: 333 AKLLLRLPSLR 343
           A+LLL LP LR
Sbjct: 180 AQLLLLLPHLR 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|132748 cd06950, NR_LBD_Tlx_PNR_like, The ligand binding domain of Tailless-like proteins, orphan nuclear receptors

 Score =  131 bits (332), Expect = 5e-37
 Identities = 64/164 (39%), Positives = 96/164 (58%), Gaps = 5/164 (3%)

Query: 184 NICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL 243
           ++C++  + LF  V WAK IP F+TLP  DQ++LL   W+EL +   +  S+ +    LL
Sbjct: 30  SVCESAARLLFMAVKWAKSIPAFSTLPFRDQLILLEESWSELFLLGAAQWSLPLDSCPLL 89

Query: 244 A-PGVTVYRSSAHEAGVGGIFD-RVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLK 301
           A PG+        EA    + + R L E +S+ R++++D TE  CL+ I+LF P+ RGLK
Sbjct: 90  AVPGL---SPDNTEAERTFLSEVRALQETLSRFRQLRVDATEFACLKAIVLFKPETRGLK 146

Query: 302 SQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
               VE L+++    L ++ R  +  +P RF KLLL LPSLR I
Sbjct: 147 DPAQVEALQDQAQLMLNKHIRTRYPTQPARFGKLLLLLPSLRFI 190

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

 Score =  130 bits (330), Expect = 7e-37
 Identities = 58/171 (33%), Positives = 89/171 (52%), Gaps = 7/171 (4%)

Query: 183 TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSI-SVKDGI 241
             + +  ++ L  +V+WAK  P F  L L+DQ+ LL++ W E L    + RS    KD +
Sbjct: 3   NELFEIWERDLLLVVEWAKRFPGFRELSLDDQLALLKSSWFEWLRLELASRSAECEKDDL 62

Query: 242 LLAPGVTVYRSSAHEAGVGGIFD--RVLTELVSKMREMKMDKTELGCLRTIILFNPDVRG 299
           L + G+ + R       V  I +  R L ELV  ++E+K+   EL  L+ ++LFNP  + 
Sbjct: 63  LFSNGLYLDRDELKSIEVNYINEQIRQLFELVQPLKELKLTDEELAALKALLLFNPAGKR 122

Query: 300 L--KSQQVVEMLREKVYTSLEEY--TRVNHSEEPGRFAKLLLRLPSLRSIE 346
           L  +  +VVE L+E +  +L  Y     +     GR AKLL  LP+LR I 
Sbjct: 123 LSGEILEVVEKLQEVIANALHNYYKDENSPPNYSGRLAKLLKLLPALRKIS 173

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

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

 Score =  126 bits (318), Expect = 3e-36
 Identities = 47/77 (61%), Positives = 58/77 (75%)

Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQK 117
           C +CGD+ SG HYG+ +CE CKGFFKRTV+    Y C E +NC IDK QR RC YCR+QK
Sbjct: 1   CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKRYTCIENQNCQIDKTQRKRCPYCRFQK 60

Query: 118 CLNMGMKREAVQEERQR 134
           CL++GMK EAV+ +R R
Sbjct: 61  CLSVGMKLEAVRADRMR 77

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

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

 Score =  124 bits (315), Expect = 4e-36
 Identities = 38/70 (54%), Positives = 45/70 (64%)

Query: 57  LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQ 116
           LC +CGD ASG H+GV SC  CK FF+RTV     Y C    NC I+KR R RC+ CR +
Sbjct: 1   LCCVCGDHASGFHFGVCSCRACKAFFRRTVNLRYKYRCDRKNNCSINKRYRCRCRACRLK 60

Query: 117 KCLNMGMKRE 126
           KCL +GM  E
Sbjct: 61  KCLGVGMDPE 70

Length = 70

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

 Score =  124 bits (312), Expect = 1e-35
 Identities = 47/72 (65%), Positives = 61/72 (84%)

Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQK 117
           C +CGD++SGKHYG ++CEGCK FFKR+VR++L+Y CR  RNC ID+  RN+CQYCR +K
Sbjct: 1   CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRGNRNCPIDQHHRNQCQYCRLKK 60

Query: 118 CLNMGMKREAVQ 129
           CL +GM+REAVQ
Sbjct: 61  CLKVGMRREAVQ 72

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

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

 Score =  119 bits (299), Expect = 1e-33
 Identities = 44/77 (57%), Positives = 57/77 (74%)

Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQK 117
           C ICGDRA+G HYG+ SCEGCKGFFKR++     Y C   +NC++ ++QRNRCQYCR  K
Sbjct: 9   CLICGDRATGLHYGIISCEGCKGFFKRSICNKRVYRCSRDKNCVMSRKQRNRCQYCRLLK 68

Query: 118 CLNMGMKREAVQEERQR 134
           CL MGM R+A++E+   
Sbjct: 69  CLQMGMNRKAIREDGMP 85

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

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

 Score =  118 bits (296), Expect = 4e-33
 Identities = 49/88 (55%), Positives = 66/88 (75%)

Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQK 117
           C ICGD++SG HYGV +CEGCKGFF+R+ + ++SY+C   +NC+ID+  RNRCQ+CR QK
Sbjct: 8   CKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVSYSCPRQKNCLIDRTNRNRCQHCRLQK 67

Query: 118 CLNMGMKREAVQEERQRTKERDSNEVES 145
           CL +GM R+AV+  R   K+RDS   E 
Sbjct: 68  CLALGMSRDAVKFGRMSKKQRDSLYAEV 95

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

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

 Score =  117 bits (294), Expect = 5e-33
 Identities = 44/82 (53%), Positives = 58/82 (70%), Gaps = 1/82 (1%)

Query: 57  LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQ 116
            C +CGD+ASG HYGV++CEGCKGFF+RT+R  L Y      +C I K+ RN+CQYCR+Q
Sbjct: 1   ECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLVYK-PCDLSCKIHKKSRNKCQYCRFQ 59

Query: 117 KCLNMGMKREAVQEERQRTKER 138
           KCLN+GM   A++  R    E+
Sbjct: 60  KCLNVGMSHNAIRFGRMPRVEK 81

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

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

 Score =  116 bits (293), Expect = 8e-33
 Identities = 45/76 (59%), Positives = 56/76 (73%), Gaps = 1/76 (1%)

Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGR-NCIIDKRQRNRCQYCRYQ 116
           C +CGD++ GKHYGVY C+GC  FFKR+VRK + Y C  G  NC++DK +RN C +CR Q
Sbjct: 1   CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKGIIYTCIAGNGNCVVDKARRNWCPFCRLQ 60

Query: 117 KCLNMGMKREAVQEER 132
           KC  +GM R AVQEER
Sbjct: 61  KCFAVGMNRAAVQEER 76

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

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

 Score =  116 bits (293), Expect = 8e-33
 Identities = 43/79 (54%), Positives = 61/79 (77%)

Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQK 117
           C +C D++SG HYGV +CEGCKGFF+R+++K++ Y C   +NCII+K  RNRCQYCR QK
Sbjct: 7   CFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQK 66

Query: 118 CLNMGMKREAVQEERQRTK 136
           C  +GM +E+V+ +R + K
Sbjct: 67  CFEVGMSKESVRNDRNKKK 85

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

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

 Score =  116 bits (293), Expect = 1e-32
 Identities = 46/79 (58%), Positives = 56/79 (70%)

Query: 54  SKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYC 113
           S  LCSIC D+A+G HYG+ +CEGCKGFFKRTV+    Y C     C I K QRNRCQYC
Sbjct: 5   SPKLCSICEDKATGLHYGIITCEGCKGFFKRTVQNKRVYTCVGDGRCEITKAQRNRCQYC 64

Query: 114 RYQKCLNMGMKREAVQEER 132
           R++KC+  GM   AV+E+R
Sbjct: 65  RFRKCIRKGMMLAAVREDR 83

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

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

 Score =  115 bits (290), Expect = 3e-32
 Identities = 46/78 (58%), Positives = 58/78 (74%), Gaps = 1/78 (1%)

Query: 57  LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGR-NCIIDKRQRNRCQYCRY 115
           LC +CGD +SGKHYG+Y+C GC GFFKR+VR+ L Y C+ G   C +DK  RN+CQ CR 
Sbjct: 8   LCRVCGDTSSGKHYGIYACNGCSGFFKRSVRRKLIYRCQAGTGMCPVDKAHRNQCQACRL 67

Query: 116 QKCLNMGMKREAVQEERQ 133
           +KCL  GM ++AVQ ERQ
Sbjct: 68  KKCLQAGMNKDAVQNERQ 85

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

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

 Score =  113 bits (284), Expect = 1e-31
 Identities = 42/73 (57%), Positives = 60/73 (82%), Gaps = 1/73 (1%)

Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGR-NCIIDKRQRNRCQYCRYQ 116
           C +CGDR+SGKHYGVY+C+GC GFFKR++R++L Y C+ G  +C++DK +RN+CQ CR +
Sbjct: 1   CKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNLLYTCKAGNGSCVVDKARRNQCQACRLK 60

Query: 117 KCLNMGMKREAVQ 129
           KCL + M ++AVQ
Sbjct: 61  KCLEVSMNKDAVQ 73

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

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

 Score =  112 bits (282), Expect = 2e-31
 Identities = 44/73 (60%), Positives = 60/73 (82%), Gaps = 1/73 (1%)

Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYA-CREGRNCIIDKRQRNRCQYCRYQ 116
           C +CGD+ASG HYGV+SCEGCKGFF+RT++ +L+Y  C  G  C+I ++ RNRCQYCR++
Sbjct: 1   CKVCGDKASGFHYGVHSCEGCKGFFRRTIQHNLTYRRCLNGGKCVIQRKNRNRCQYCRFK 60

Query: 117 KCLNMGMKREAVQ 129
           KCL++GM R AV+
Sbjct: 61  KCLSVGMSRNAVR 73

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

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

 Score =  112 bits (282), Expect = 3e-31
 Identities = 42/81 (51%), Positives = 58/81 (71%)

Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQK 117
           C +CGD+ASG HYGV SCEGCKGFF+R+++K + Y C     C I +  RNRCQYCR++K
Sbjct: 1   CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYRCLRDGKCEIIRLNRNRCQYCRFKK 60

Query: 118 CLNMGMKREAVQEERQRTKER 138
           CL  GM +++V+  R   ++R
Sbjct: 61  CLAAGMSKDSVRYGRIPNRQR 81

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

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

 Score =  111 bits (278), Expect = 1e-30
 Identities = 40/77 (51%), Positives = 57/77 (74%), Gaps = 2/77 (2%)

Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACRE--GRNCIIDKRQRNRCQYCRY 115
           C +CGDR+SGKHYG+Y+C+GC GFFKR++R++  Y C+      C +DK  RN+C+ CR 
Sbjct: 9   CKVCGDRSSGKHYGIYACDGCSGFFKRSIRRNRQYVCKSKGQGGCPVDKTHRNQCRACRL 68

Query: 116 QKCLNMGMKREAVQEER 132
           +KC  +GM ++AVQ ER
Sbjct: 69  KKCFEVGMNKDAVQHER 85

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

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

 Score =  110 bits (277), Expect = 2e-30
 Identities = 43/83 (51%), Positives = 62/83 (74%), Gaps = 1/83 (1%)

Query: 57  LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSY-ACREGRNCIIDKRQRNRCQYCRY 115
           LC +CGD+ASG HYGV++CEGCKGFF+R++++ + Y  C +   C I +  RNRCQYCR+
Sbjct: 5   LCKVCGDKASGFHYGVHACEGCKGFFRRSIQQKIQYRKCTKNETCSIMRINRNRCQYCRF 64

Query: 116 QKCLNMGMKREAVQEERQRTKER 138
           +KCL +GM R+AV+  R   +E+
Sbjct: 65  KKCLAVGMSRDAVRFGRIPKREK 87

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

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

 Score =  112 bits (283), Expect = 4e-30
 Identities = 51/163 (31%), Positives = 84/163 (51%), Gaps = 1/163 (0%)

Query: 183 TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGIL 242
            +  +     + ++V++AK IP F  L  EDQ+ LL+ G  E+L+   +      K+ + 
Sbjct: 5   DHFTEIMTVAIRRVVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATLYDPEKNSLT 64

Query: 243 LAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKS 302
              G    R      G G   + +  E   KM ++++D  E   L  I+LF+PD  GL+ 
Sbjct: 65  FGDGKGNSRDVLLNGGFGEFIEPLF-EFAEKMNKLQLDDNEYALLTAIVLFSPDRPGLQD 123

Query: 303 QQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
              VE L+E++  +L+ Y +VNH + P  FAKLL +L  LR++
Sbjct: 124 VDTVEKLQERLLEALQRYLKVNHPDAPQMFAKLLKKLTELRTL 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|132754 cd07069, NR_LBD_Lrh-1, The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,

 Score =  113 bits (285), Expect = 7e-30
 Identities = 68/202 (33%), Positives = 122/202 (60%), Gaps = 15/202 (7%)

Query: 154 PVERILEAEQRVDMKQEPADQDIVNEQQATN----ICKATDKQLFQLVDWAKHIPHFTTL 209
           P E  ++A+    ++QE A++   ++ +  +    +CK  D+ LF +V+WA+    F  L
Sbjct: 13  PDEPQVQAKIMAYLQQEQANR---SKHEKLSTFGLMCKMADQTLFSIVEWARSSIFFREL 69

Query: 210 PLEDQVLLLRAGWNELLIASFSHRSIS-VKDG-ILLAPGVTV-YRSSAHEAGVGGIFDRV 266
            ++DQ+ LL+  W+ELLI    +R +   K+G I L  G  V Y   A +AG     + +
Sbjct: 70  KVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQAGA--TLNNL 127

Query: 267 LT---ELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRV 323
           ++   ELV+K+R ++ D+ E  CL+ ++LF+ DV+ L++ Q+VE ++E+V  +L +YT  
Sbjct: 128 MSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMC 187

Query: 324 NHSEEPGRFAKLLLRLPSLRSI 345
           N+ ++  +F +LLLRLP +R+I
Sbjct: 188 NYPQQTEKFGQLLLRLPEIRAI 209

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

 Score =  106 bits (267), Expect = 4e-29
 Identities = 41/75 (54%), Positives = 53/75 (70%)

Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQK 117
           C +CGD ASG HYGV SCE CK FFKRT++ +L Y+C     C +DK++R  CQ CR QK
Sbjct: 1   CLVCGDIASGYHYGVASCEACKAFFKRTIQGNLGYSCPSTSECEVDKKRRKSCQACRLQK 60

Query: 118 CLNMGMKREAVQEER 132
           CL +GM +E V+ +R
Sbjct: 61  CLKVGMLKEGVRLDR 75

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

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

 Score =  108 bits (272), Expect = 4e-28
 Identities = 57/195 (29%), Positives = 100/195 (51%), Gaps = 4/195 (2%)

Query: 155 VERILEAE-QRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLED 213
           +  +L AE  ++    +PA  D   +   T +    D++L  ++ WAKHIP F++L L D
Sbjct: 2   LSHLLVAEPDKLFAMPDPALPDSDIKALTT-LSDLADRELVVIIGWAKHIPGFSSLSLND 60

Query: 214 QVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSK 273
           Q+ LL++ W E+L      RS+     ++ A    +    A EAG+  ++   L +LV +
Sbjct: 61  QMSLLQSAWMEILTLGVVFRSLPFNGELVFAEDFILDEELAREAGLLELYSACL-QLVRR 119

Query: 274 MREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHS-EEPGRF 332
           ++ ++++K E   L+ + L N D   ++  + V  LR+ +  +L +Y    H  E P R 
Sbjct: 120 LQRLRLEKEEYVLLKALALANSDSVHIEDVEAVRQLRDALLEALSDYEAGRHPGEAPRRA 179

Query: 333 AKLLLRLPSLRSIEV 347
            +LLL LP LR  + 
Sbjct: 180 GQLLLTLPLLRQTDG 194

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

 Score =  104 bits (260), Expect = 5e-28
 Identities = 33/71 (46%), Positives = 46/71 (64%)

Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQK 117
           C +CG ++SG H+G  +CEGCKGFF+RT     SY C  G+NC I    RN C+ CR+++
Sbjct: 1   CRVCGGKSSGFHFGALTCEGCKGFFRRTELSSNSYVCPGGQNCAITPATRNACKSCRFRR 60

Query: 118 CLNMGMKREAV 128
           CL +GM +   
Sbjct: 61  CLAVGMSKTGS 71

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

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

 Score =  103 bits (259), Expect = 6e-28
 Identities = 38/72 (52%), Positives = 49/72 (68%)

Query: 57  LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQ 116
            C +CGD+ASG HYGV SCEGCKGFF+R+V K   YAC+ G  C +D   R +CQ CR +
Sbjct: 1   NCVVCGDKASGFHYGVLSCEGCKGFFRRSVTKGAVYACKFGNKCEMDMYMRRKCQECRLR 60

Query: 117 KCLNMGMKREAV 128
           KC   GM+ + +
Sbjct: 61  KCKAAGMRPDCL 72

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

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

 Score =  104 bits (260), Expect = 8e-28
 Identities = 43/80 (53%), Positives = 55/80 (68%)

Query: 55  KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCR 114
           K LC +CGD ASG HYGV SCE CK FFKRT++ ++ Y+C     C I KR+R  CQ CR
Sbjct: 4   KRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACR 63

Query: 115 YQKCLNMGMKREAVQEERQR 134
           + KCL +GM +E V+ +R R
Sbjct: 64  FMKCLKVGMLKEGVRLDRVR 83

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

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

 Score =  102 bits (256), Expect = 2e-27
 Identities = 38/82 (46%), Positives = 51/82 (62%)

Query: 53  GSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQY 112
              H C++C D ASG HYGV+SCEGCK FFKR+++    Y C     C IDK +R  CQ 
Sbjct: 1   KDTHFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQA 60

Query: 113 CRYQKCLNMGMKREAVQEERQR 134
           CR +KC  +GM +  ++ ER+ 
Sbjct: 61  CRLRKCYEVGMMKGGIRRERRG 82

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

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

 Score =   99 bits (249), Expect = 2e-26
 Identities = 42/77 (54%), Positives = 53/77 (68%)

Query: 57  LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQ 116
           LC +CGDRASG HY   +CEGCKGFF+R+V K   Y C+ GR C +D   R +CQ CR +
Sbjct: 3   LCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYHCKYGRACEMDMYMRRKCQECRLK 62

Query: 117 KCLNMGMKREAVQEERQ 133
           KCL++GM+ E V  E Q
Sbjct: 63  KCLSVGMRPECVVPESQ 79

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

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

 Score =  103 bits (258), Expect = 5e-26
 Identities = 56/171 (32%), Positives = 88/171 (51%), Gaps = 11/171 (6%)

Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           IC++  + LF  + WA+ IP F  L  E Q  L+RA W EL     +  S  +    +LA
Sbjct: 26  ICESASRLLFLSIHWARSIPAFQALGAETQTSLVRACWPELFTLGLAQCSQQLSLPTILA 85

Query: 245 PGVTVYRSSAHEAGVGGIFDRV---------LTELVSKMREMKMDKTELGCLRTIILFNP 295
             +   ++S  +  +    D+V         L E V+ M+++ +D  E   L+ I+LF+P
Sbjct: 86  AIINHLQTSIQQDKLSA--DKVKQVMEHINKLQEFVNSMQKLDVDDHEYAYLKAIVLFSP 143

Query: 296 DVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIE 346
           D  G + +Q +E L+EK    L +Y    + E+  R +KLLLRLP LRS+ 
Sbjct: 144 DHPGQELRQQIEKLQEKALMELRDYVGKTYPEDEYRLSKLLLRLPPLRSLS 194

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

 Score = 98.6 bits (246), Expect = 5e-26
 Identities = 33/71 (46%), Positives = 49/71 (69%)

Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQK 117
           C +CGDRA+G H+   +CEGCKGFF+R++++   + C    +C I K  R  CQ CR +K
Sbjct: 1   CGVCGDRATGYHFNAMTCEGCKGFFRRSMKRKARFTCPFNGDCEITKDNRRHCQACRLKK 60

Query: 118 CLNMGMKREAV 128
           CL++GMK+E +
Sbjct: 61  CLDIGMKKEMI 71

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

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

 Score = 99.2 bits (247), Expect = 7e-26
 Identities = 40/82 (48%), Positives = 53/82 (64%)

Query: 57  LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQ 116
           +CS+CGD+ASG HY V SCEGCKGFF+R+V K   Y C+ G  C +D   R +CQ CR +
Sbjct: 20  VCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAQYVCKNGGKCQMDMYMRRKCQECRLR 79

Query: 117 KCLNMGMKREAVQEERQRTKER 138
           KC   GM+ + V  E Q   ++
Sbjct: 80  KCREAGMREQCVLSEEQIRLKK 101

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

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

 Score = 94.3 bits (234), Expect = 3e-24
 Identities = 40/82 (48%), Positives = 53/82 (64%)

Query: 57  LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQ 116
           LC +CGD+ASG HY   +CEGCKGFF+R++ K+  Y C+ G NC +D   R +CQ CR +
Sbjct: 3   LCVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCEMDMYMRRKCQECRLR 62

Query: 117 KCLNMGMKREAVQEERQRTKER 138
           KC  MGM  E +  E Q   +R
Sbjct: 63  KCKEMGMLAECLLTEIQCKSKR 84

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

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

 Score = 98.0 bits (244), Expect = 6e-24
 Identities = 58/187 (31%), Positives = 100/187 (53%), Gaps = 11/187 (5%)

Query: 161 AEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRA 220
           A+QRV +       D+    + + +     K + ++V++AK +P FTTL + DQ+ LL+A
Sbjct: 29  ADQRVRL-------DLGLWDKFSELST---KCIIKIVEFAKRLPGFTTLTIADQITLLKA 78

Query: 221 GWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMD 280
              ++LI     R    +D +  + G+T+ R+  H AG G + D V T   +++  ++MD
Sbjct: 79  ACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMHNAGFGPLTDLVFT-FANQLLPLEMD 137

Query: 281 KTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLP 340
            TE+G L  I L   D + L+    VE L+E +  +L+ Y R    ++P  F K+L+++ 
Sbjct: 138 DTEIGLLSAICLICGDRQDLEEPDRVEKLQEPLLEALKIYARKRRPDKPHMFPKMLMKIT 197

Query: 341 SLRSIEV 347
            LRSI  
Sbjct: 198 DLRSISA 204

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

 Score = 96.7 bits (241), Expect = 1e-23
 Identities = 51/166 (30%), Positives = 89/166 (53%), Gaps = 7/166 (4%)

Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +C+  D+ LF+ + W K +P FT L ++D   LL   W EL++ S    +     G LL 
Sbjct: 32  LCRLGDELLFRQIQWTKKLPFFTELSIKDHTHLLTTKWAELILLSTITVASLQNLG-LLQ 90

Query: 245 PGVTVYRSSAHE-----AGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRG 299
             ++ Y  S  E        G + +R+ T L++K R++K+   E  CL+ I   N D+ G
Sbjct: 91  DCLSKYLPSEDELERFGDEGGEVVERL-TYLLAKFRQLKVSNEEYVCLKVINFLNQDIDG 149

Query: 300 LKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           L +   +E L+++ +  L+++T +N+  +P RF+ LL  LP +R+ 
Sbjct: 150 LTNASQLESLQKRYWYVLQDFTELNYPNQPNRFSDLLSCLPEIRAA 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|132747 cd06949, NR_LBD_ER, Ligand binding domain of Estrogen receptor, which are activated by the hormone 17beta-estradiol (estrogen)

 Score = 95.2 bits (237), Expect = 5e-23
 Identities = 58/200 (29%), Positives = 98/200 (49%), Gaps = 10/200 (5%)

Query: 155 VERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQ 214
           +  +LEAE      +    +          +    D++L  +++WAK IP F  L L DQ
Sbjct: 7   ISALLEAEPPHIYSEYDPTRPFTEASLMMLLTNLADRELVHMINWAKKIPGFVDLSLHDQ 66

Query: 215 VLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRS-SAHEAGVGGIFDRVLTELVSK 273
           V LL + W ELL+     RS+     +L AP + + R+  +   G+  IFD +L    S+
Sbjct: 67  VHLLESAWLELLMLGLVWRSMEHPGKLLFAPDLLLDRNQGSCVEGMVEIFDMLL-ATASR 125

Query: 274 MREMKMDKTELGCLRTIILFNPDVRG-----LKSQQVVEMLREKVYTSLEEY---TRVNH 325
            RE+++ + E  CL+ IIL N  V       L+S++ V+ L +K+  +L        ++ 
Sbjct: 126 FRELQLQREEYVCLKAIILLNSSVYTFLLESLESRRQVQRLLDKITDALVHACSKRGLSL 185

Query: 326 SEEPGRFAKLLLRLPSLRSI 345
            ++  R A+LLL L  +R +
Sbjct: 186 QQQSRRLAQLLLILSHIRHV 205

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

 Score = 89.6 bits (222), Expect = 2e-22
 Identities = 35/82 (42%), Positives = 54/82 (65%)

Query: 57  LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQ 116
           +C +CGDRA+G H+   +CEGCKGFF+R ++++    C   + C+I K  R +CQ CR +
Sbjct: 1   ICRVCGDRATGYHFNAMTCEGCKGFFRRAMKRNARLCCPFQKGCVITKSNRRQCQACRLR 60

Query: 117 KCLNMGMKREAVQEERQRTKER 138
           KCL++GMK+E +  +    K R
Sbjct: 61  KCLSIGMKKELIMSDEAVEKRR 82

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

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

 Score = 89.1 bits (221), Expect = 3e-22
 Identities = 34/69 (49%), Positives = 43/69 (62%), Gaps = 2/69 (2%)

Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDL--SYACREGRNCIIDKRQRNRCQYCRY 115
           C +CG+ A+G H+G Y CE CK FF R+          C  G  CIIDK+ R +CQ CRY
Sbjct: 3   CQVCGEPAAGFHHGAYVCEACKKFFMRSSNAISFTISECPNGGKCIIDKKNRTKCQACRY 62

Query: 116 QKCLNMGMK 124
           +KCLN+GM 
Sbjct: 63  RKCLNVGMS 71

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

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

 Score = 87.3 bits (216), Expect = 2e-21
 Identities = 35/83 (42%), Positives = 55/83 (66%), Gaps = 2/83 (2%)

Query: 57  LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQ 116
           +C +CGDRA+G H+   +CEGCKGFF+R++++   + C    +C I K  R  CQ CR +
Sbjct: 8   ICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLK 67

Query: 117 KCLNMGMKREAV--QEERQRTKE 137
           +C+++GM +E +   EE QR +E
Sbjct: 68  RCVDIGMMKEFILTDEEVQRKRE 90

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

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

 Score = 86.0 bits (213), Expect = 3e-21
 Identities = 38/72 (52%), Positives = 44/72 (61%), Gaps = 2/72 (2%)

Query: 57  LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRN-CIIDKRQRNRCQYCRY 115
           +C +C D ASG HYGV +C  CK FFKR V    +Y C  GRN CIIDK +R  C  CR 
Sbjct: 4   ICLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLC-AGRNDCIIDKIRRKNCPACRL 62

Query: 116 QKCLNMGMKREA 127
           +KCL  GM   A
Sbjct: 63  RKCLQAGMNLGA 74

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

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

 Score = 90.0 bits (223), Expect = 5e-21
 Identities = 51/166 (30%), Positives = 90/166 (54%), Gaps = 6/166 (3%)

Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSI--SVKDGIL 242
           +C+  D+    +VDWA+    F  L + DQ+ LL+  W+ELL+    +R +    +  IL
Sbjct: 43  LCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQHGKEGSIL 102

Query: 243 LAPGVTVYRSSAHEAGVGGIFDRVL---TELVSKMREMKMDKTELGCLRTIILFNPDVRG 299
           L  G  V   S   A  G +   ++    ELV ++  +++D+ E  CL+ +ILF+ DV+ 
Sbjct: 103 LVTGQEV-ELSTVAAQAGSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILFSLDVKF 161

Query: 300 LKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           L +  +V+  +EK   +L +YT  ++     +F +LLLRL  +R++
Sbjct: 162 LNNHSLVKDAQEKANAALLDYTLCHYPHCGDKFQQLLLRLVEVRAL 207

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

 Score = 88.3 bits (219), Expect = 7e-21
 Identities = 46/151 (30%), Positives = 78/151 (51%), Gaps = 1/151 (0%)

Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++V++AK IP F  L   DQV LL+AG  E+L+  F+    + +  +    G        
Sbjct: 27  EVVEFAKRIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFDAKERSVTFLSGQKYSVDDL 86

Query: 255 HEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVY 314
           H  G G + + +  +   K+  +++   E+G    ++L + D  GL++  +VE L+E + 
Sbjct: 87  HSMGAGDLLNSMF-DFSEKLNSLQLSDEEMGLFTAVVLVSADRSGLENVNLVEALQETLI 145

Query: 315 TSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +L      NH  EP  F KLLL+LP LR++
Sbjct: 146 RALRTLIAKNHPNEPSIFTKLLLKLPDLRTL 176

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

 Score = 88.3 bits (219), Expect = 2e-20
 Identities = 43/150 (28%), Positives = 73/150 (48%)

Query: 196 LVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH 255
           +VD+AK +P F TL  EDQ+ LL+A   E+++   + R     + I         R    
Sbjct: 59  IVDFAKQLPGFLTLTREDQIALLKASTIEVMLLETARRYNPESEAITFLKDFPYSRDDFA 118

Query: 256 EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYT 315
            AG+   F   + E    MRE+++D  E   L  I +F+ D   ++    VE L+E    
Sbjct: 119 RAGLQVEFINPIFEFSKSMRELQLDDAEYALLIAINIFSADRPNVQDHHRVERLQETYVE 178

Query: 316 SLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +L  Y ++    +   F ++L++L SLR++
Sbjct: 179 ALHSYIKIKRPSDRLMFPRMLMKLVSLRTL 208

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

 Score = 81.1 bits (200), Expect = 2e-19
 Identities = 35/70 (50%), Positives = 40/70 (57%)

Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQK 117
           C ICGD ASG HYGV +C  CK FFKR      +Y C    +CIIDK +R  C  CR +K
Sbjct: 1   CLICGDEASGCHYGVLTCGSCKVFFKRAAEGQHNYLCAGRNDCIIDKIRRKNCPACRLRK 60

Query: 118 CLNMGMKREA 127
           C   GM   A
Sbjct: 61  CYQAGMTLGA 70

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

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

 Score = 81.7 bits (202), Expect = 2e-19
 Identities = 31/85 (36%), Positives = 48/85 (56%)

Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQK 117
           C +CGD+A G ++   +CE CK FF+R   K+  + C    +C I+   R  CQ CR  K
Sbjct: 3   CGVCGDKALGYNFNAITCESCKAFFRRNALKNKEFKCPFNESCEINVVTRRFCQKCRLDK 62

Query: 118 CLNMGMKREAVQEERQRTKERDSNE 142
           C  +GMK+E +  E  ++++R   E
Sbjct: 63  CFAIGMKKEWIMSEEDKSEKRQKIE 87

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

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

 Score = 80.5 bits (199), Expect = 2e-17
 Identities = 49/156 (31%), Positives = 79/156 (50%), Gaps = 10/156 (6%)

Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPG---VT--V 249
           +L ++AK +P F  L L DQV LL+ G +E++    +  S+  KDG+L   G   VT   
Sbjct: 78  ELTEFAKSLPGFRNLDLNDQVTLLKYGVHEVIFTMLA--SLYNKDGLLFPEGNGYVTREF 135

Query: 250 YRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEML 309
             S         I +    E   K   +++  +EL     +I+ +PD  GL +++ VE +
Sbjct: 136 LESL--RKPFCDIMEPKF-EFAEKFNALELTDSELALFCAVIILSPDRPGLINRKPVERI 192

Query: 310 REKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +E V  +LE   + NH + P  FAKLL ++  LR +
Sbjct: 193 QEHVLQALELQLKKNHPDSPQLFAKLLQKMVDLRQL 228

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

 Score = 77.9 bits (192), Expect = 8e-17
 Identities = 47/189 (24%), Positives = 77/189 (40%), Gaps = 15/189 (7%)

Query: 171 PADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASF 230
                 V       +C+A  + L + + + +++P FT LP +DQ+ LLR  W  LL+   
Sbjct: 10  CHQHRPVQLCAPQMVCRAASQVLLKTIRFVRNLPCFTYLPPDDQLRLLRRSWAPLLLLGL 69

Query: 231 SHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTE--------------LVSKMRE 276
           +   +      + AP +     +  E   GG     LT                + K   
Sbjct: 70  AQDKVPFDTVEVPAPSILCEILTGAEMHWGGTPPPTLTMPPCIPLADVQDIQQFLMKCWS 129

Query: 277 MKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLL 336
           + +D  E   L+  +LF P    L     +E L+++   +L E+T +    E  R A+LL
Sbjct: 130 LDLDCKEYAYLKGAVLFTPVPPLL-CPHYIEALQKEAQQALNEHTMMTRPLEQLRSARLL 188

Query: 337 LRLPSLRSI 345
           L L  LR I
Sbjct: 189 LMLSLLRGI 197

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

 Score = 77.9 bits (192), Expect = 1e-16
 Identities = 50/204 (24%), Positives = 92/204 (45%), Gaps = 2/204 (0%)

Query: 145 STSGTLIEMPVERILEAEQRVDMKQEPA-DQDIVNEQQATNICKATDKQLFQLVDWAKHI 203
           +T+        +R    E         A D D V+ +  ++  K     + ++VD+AK +
Sbjct: 16  ATNAQGSHWKQKRKFLPEDIGQAPIVSAPDGDKVDLEAFSHFTKIITPAITRVVDFAKKL 75

Query: 204 PHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIF 263
           P FT LP EDQ++LL+    E++    + R     + + L+  + V R      G+G + 
Sbjct: 76  PMFTELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLSGEMAVTREQLKNGGLGVVS 135

Query: 264 DRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRV 323
           D +  +L   +    +D TE+  L+ ++L + D  GL   + +E L++    + E Y   
Sbjct: 136 DAIF-DLGVSLSSFNLDDTEVALLQAVLLMSSDRPGLACVERIEKLQDSFLLAFEHYINY 194

Query: 324 NHSEEPGRFAKLLLRLPSLRSIEV 347
                P  + KLL+++  LR I  
Sbjct: 195 RKHHVPHFWPKLLMKVTDLRMIGA 218

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

 Score = 76.8 bits (189), Expect = 2e-16
 Identities = 50/200 (25%), Positives = 85/200 (42%), Gaps = 23/200 (11%)

Query: 169 QEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIA 228
                Q  V  +     CKA    L + + + K +P F  LPL+DQ++L+R+ W  LL+ 
Sbjct: 8   CSCGSQRRVTLKSPQVTCKAASAVLVKTLRFVKGVPCFQELPLDDQLVLVRSCWAPLLVL 67

Query: 229 SFSHRSI----------SVKDGIL-----------LAPGVTVYRSSAHEAG--VGGIFDR 265
             +   +          S+   IL                 + +    EA         R
Sbjct: 68  GLAQDGVDFETVETSEPSMLQRILTTRPPPTSGAEPGEPQALPQMPQAEASHLPSAADIR 127

Query: 266 VLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNH 325
            +   ++K   + +   E   L+  +LFNPD+ GL+  Q ++ L+ +   +L E+ R+ H
Sbjct: 128 AIKAFLAKCWSLDISTKEYAYLKGTVLFNPDLPGLQCVQYIQGLQWEAQQALNEHVRMIH 187

Query: 326 SEEPGRFAKLLLRLPSLRSI 345
             +  RFAKL + L  LR+I
Sbjct: 188 RGDQARFAKLNIALSLLRAI 207

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

 Score = 72.6 bits (178), Expect = 2e-16
 Identities = 32/66 (48%), Positives = 36/66 (54%)

Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQK 117
           C ICGD ASG HYG  +C  CK FFKR       Y C    +C IDK +R  C  CR +K
Sbjct: 6   CLICGDEASGCHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRK 65

Query: 118 CLNMGM 123
           C   GM
Sbjct: 66  CFEAGM 71

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

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

 Score = 75.1 bits (185), Expect = 9e-16
 Identities = 47/148 (31%), Positives = 76/148 (51%), Gaps = 4/148 (2%)

Query: 199 WAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG 258
           WA+ IP F  L  EDQ LLL + + EL +   ++RS  V   ++   G+ ++R      G
Sbjct: 60  WAEKIPGFKDLHREDQDLLLESAFLELFVLRLAYRSNPVDGKLVFCNGLVLHRLQC-VRG 118

Query: 259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLE 318
            G   D +L    S    +  D +   CL  ++L   +  GLK  + VE L+ K+ + L 
Sbjct: 119 FGEWLDSILAFSSSLQSLLLDDISAFCCLALLLLI-TERHGLKEPKKVEELQNKIISCLR 177

Query: 319 EYTRVNH--SEEPGRFAKLLLRLPSLRS 344
           ++   N+   ++P R +KLLL+LP LR+
Sbjct: 178 DHVTSNYPGQDKPNRLSKLLLKLPELRT 205

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|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 = 71.4 bits (175), Expect = 2e-14
 Identities = 46/150 (30%), Positives = 73/150 (48%), Gaps = 4/150 (2%)

Query: 196 LVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH 255
           LV++ K +P F TL  EDQ+ LL+    E +      RS  + +  L A    +      
Sbjct: 52  LVEFTKGLPGFETLDHEDQIALLKGSAVEAMFL----RSAQIYNKKLPAGHADLLEERIR 107

Query: 256 EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYT 315
            +G+   F   +      M E+KM + E   L  I +  PD   LK ++ VE L+E +  
Sbjct: 108 SSGISDEFITPMFNFYKSMGELKMTQEEYALLTAITILFPDRPYLKDKEAVEKLQEPLLD 167

Query: 316 SLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            L+++ ++ H E+P  FA LL RL  LR++
Sbjct: 168 LLQKFCKLYHPEDPQHFACLLGRLTELRTL 197

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

 Score = 71.4 bits (175), Expect = 2e-14
 Identities = 44/149 (29%), Positives = 77/149 (51%), Gaps = 5/149 (3%)

Query: 199 WAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG 258
           WA+ IP F+    EDQ LLL + + EL I   ++RS   +  ++   GV ++R+     G
Sbjct: 60  WAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNPEEGKLIFCNGVVLHRTQCVR-G 118

Query: 259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLE 318
            G   D +L E    +  M +D +   CL  +++   D  GLK  + VE L+ ++ + L+
Sbjct: 119 FGDWIDSIL-EFSQSLHRMNLDVSAFSCLAALVIIT-DRHGLKEPKRVEELQNRLISCLK 176

Query: 319 EY--TRVNHSEEPGRFAKLLLRLPSLRSI 345
           E+     +  + P   ++LL +LP LR++
Sbjct: 177 EHVSGSASEPQRPNCLSRLLGKLPELRTL 205

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

 Score = 70.1 bits (171), Expect = 7e-14
 Identities = 45/149 (30%), Positives = 77/149 (51%), Gaps = 5/149 (3%)

Query: 199 WAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG 258
           WA+ IP FT LP  DQ LL  + + EL +   ++RS  V+  ++   GV ++R      G
Sbjct: 60  WAEKIPGFTDLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIFCNGVVLHRLQCVR-G 118

Query: 259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLE 318
            G   D ++ E  S ++ M +D +   C+  + +   +  GLK  + VE L+ K+   L+
Sbjct: 119 FGEWIDSIV-EFSSNLQNMNIDISAFSCIAALAMVT-ERHGLKEPKRVEELQNKIVNCLK 176

Query: 319 EYTRVNHS--EEPGRFAKLLLRLPSLRSI 345
           ++   N+     P   +KLL +LP LR++
Sbjct: 177 DHVTFNNGGLNRPNYLSKLLGKLPELRTL 205

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

 Score = 67.9 bits (166), Expect = 2e-13
 Identities = 46/171 (26%), Positives = 78/171 (45%), Gaps = 11/171 (6%)

Query: 186 CKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSI---------- 235
           C+     L + V + +++P F  LP +DQ+LLL+  W  L +   +   +          
Sbjct: 25  CREASDVLVKTVAFMRNLPSFWQLPPQDQLLLLQNCWGPLFLLGLAQDRVTFEVAEAPVP 84

Query: 236 SVKDGILLAPGVTVYRSSAHE-AGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFN 294
           S+   ILL    +   S   +         + L   ++K   + +   E   L+  ILFN
Sbjct: 85  SMLKKILLEGQSSSGGSGQPDRPQPSLAAVQWLQCCLNKFWSLDLSPKEYAYLKGTILFN 144

Query: 295 PDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           PDV GL +   V  L+++   +L E     H ++ GRFA++LL   +L+SI
Sbjct: 145 PDVPGLTASSHVGHLQQEAQWALCEVLEPLHPQDQGRFARILLTASTLKSI 195

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

 Score = 67.8 bits (166), Expect = 4e-13
 Identities = 41/157 (26%), Positives = 81/157 (51%), Gaps = 15/157 (9%)

Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVK------DGILLAPGVT 248
            +V++AK IP F  L   DQ++LL+AG  E+++   S R+ +        DG      + 
Sbjct: 63  YVVEFAKRIPGFMELCQNDQIVLLKAGSLEVVLVRMS-RAFNPSNNTVLFDGKYA--PID 119

Query: 249 VYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEM 308
           +++S   +  +  +FD         + E+K+ + E+     ++L + D  GL+ ++ VE 
Sbjct: 120 LFKSLGCDDLISAVFD-----FAKSLCELKLTEDEIALFSALVLISADRPGLQEKRKVEK 174

Query: 309 LREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           L++K+  +L    + NH  +     KLL ++P+LR++
Sbjct: 175 LQQKIELALRHVLQKNHG-DDTILTKLLAKMPTLRAL 210

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

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

 Score = 66.7 bits (163), Expect = 1e-12
 Identities = 47/151 (31%), Positives = 73/151 (48%), Gaps = 3/151 (1%)

Query: 196 LVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH 255
           +V++AK +P F  L  EDQ+ LL+A  +E+++   + R  +  D I+ A      R S  
Sbjct: 55  IVEFAKRLPGFDKLSREDQITLLKACSSEVMMLRVARRYDAKTDSIVFANNQPYTRDSYR 114

Query: 256 EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYT 315
           +AG+G   +  L      M  MK+D  E   L  I++F+ D  GL   + VE ++E    
Sbjct: 115 KAGMGDSAE-DLFRFCRAMCSMKVDNAEYALLTAIVIFS-DRPGLLQPKKVEKIQEIYLE 172

Query: 316 SLEEYTRVNHSEEPG-RFAKLLLRLPSLRSI 345
           +L  Y            FAKLL  L  LR++
Sbjct: 173 ALRAYVDNRRPPSQRVIFAKLLSILTELRTL 203

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

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

 Score = 65.9 bits (161), Expect = 1e-12
 Identities = 44/155 (28%), Positives = 75/155 (48%), Gaps = 13/155 (8%)

Query: 197 VDWAKHIPHFTTLPLEDQVLLLRAGWNELLIA------SFSHRSISVKDGILLAPGVTVY 250
           V++AK IP F  L  +DQ+LL++AG+ E+ +       +    SI+  DGI ++      
Sbjct: 19  VEFAKRIPGFCDLSQDDQLLLIKAGFFEVWLVRISRLINSKSGSITFDDGISISRQQL-- 76

Query: 251 RSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLR 310
                +      F + L E       + +  TE+     ++L +PD  GL   + V +L+
Sbjct: 77  -----DIIYDSDFVKALFEFSDSFNSLGLSDTEVALFCAVVLLSPDRIGLSEPKKVAILQ 131

Query: 311 EKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           ++V  +L+     N   E   FA LL+++P LRSI
Sbjct: 132 DRVLEALKVQVSRNRPAEAQLFASLLMKIPELRSI 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|132757 cd07072, NR_LBD_DHR38_like, Ligand binding domain of DHR38_like proteins, members of the nuclear receptor superfamily

 Score = 59.5 bits (144), Expect = 3e-10
 Identities = 43/151 (28%), Positives = 73/151 (48%), Gaps = 5/151 (3%)

Query: 199 WAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG 258
           +A+ IP F  L  EDQ LL ++   EL +   ++R+      +    GV +++     + 
Sbjct: 61  FAEKIPGFPDLCKEDQELLFQSASLELFVLRLAYRTAPEDTKLTFCNGVVLHKQQCQRS- 119

Query: 259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLE 318
            G     +L E    +  M +D +   CL  + L   +  GLK    VE L+ K+ +SL 
Sbjct: 120 FGDWLHAIL-EFSKSLHAMDIDISAFACLCALTLIT-ERHGLKEPHKVEQLQMKIISSLR 177

Query: 319 EYTRVN--HSEEPGRFAKLLLRLPSLRSIEV 347
           ++   N    ++P  F++LL +LP LRS+ V
Sbjct: 178 DHVTYNAEAQKKPHYFSRLLGKLPELRSLSV 208

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|132732 cd06934, NR_LBD_PXR_like, The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive androstane receptor

 Score = 57.4 bits (139), Expect = 1e-09
 Identities = 43/157 (27%), Positives = 80/157 (50%), Gaps = 11/157 (7%)

Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           Q++ +AK +P+F +LP+EDQ+ LL+    E+    F+    + + G      +T     A
Sbjct: 50  QIIKFAKDLPYFRSLPIEDQISLLKGATFEICQIRFN-TVFNEETGTWECGPLTYCIEDA 108

Query: 255 HEAGVGGIFDRVLTELVSK----MREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLR 310
             AG    F ++L E + +    +R++++ + E   ++ + LF+PD  G+    V++ L+
Sbjct: 109 ARAG----FQQLLLEPLLRFHYTLRKLQLQEEEYVLMQAMSLFSPDRPGVTQHDVIDQLQ 164

Query: 311 EKVYTSLEEYTRVNHSEEPGRF--AKLLLRLPSLRSI 345
           EK+  +L+ Y          RF   K+L  L  LR+I
Sbjct: 165 EKMALTLKSYIDSKRPGPEKRFLYPKILACLTELRTI 201

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 these molecules from the cell. Constitutive androstane receptor (CAR) is a closest mammalian relative of PXR, which has also been proposed to function as a xenosensor. CAR is activated by some of the same ligands as PXR and regulates a subset of common genes. The sequence homology and functional similarity suggests that the CAR gene arose from a duplication of an ancestral PXR gene. Like other nuclear receptors, xenobiotic receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 226

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

 Score = 53.9 bits (130), Expect = 3e-08
 Identities = 32/126 (25%), Positives = 62/126 (49%), Gaps = 10/126 (7%)

Query: 191 KQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGVT 248
           +QL  +V WAK +P F  L L+DQ+ L++  W  L++ +   RS    +  +L  AP + 
Sbjct: 39  RQLVSVVKWAKALPGFRNLHLDDQMTLIQYSWMSLMVFALGWRSYKHVNSQMLYFAPDLV 98

Query: 249 VYRSSAHEAGVGGIFDRVLT--ELVSKMREMKMDKTELGCLRTIILFN--PDVRGLKSQQ 304
                 H++    ++   L   ++  +   +++   E  C++ ++L +  P   GLKSQ 
Sbjct: 99  FNEQRMHQS---AMYSLCLGMRQISQEFVRLQVTYEEFLCMKVLLLLSTIP-KDGLKSQA 154

Query: 305 VVEMLR 310
             + +R
Sbjct: 155 AFDEMR 160

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

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

 Score = 53.1 bits (127), Expect = 4e-08
 Identities = 39/156 (25%), Positives = 81/156 (51%), Gaps = 7/156 (4%)

Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           +++ +AK IP F  L  EDQ+ LL++   E+++   S++S S+ D +    G   ++   
Sbjct: 52  KVIGFAKMIPGFRDLTAEDQIALLKSSAIEVIMLR-SNQSFSLDD-MSWTCGSPDFKYKV 109

Query: 255 HEAGVGGIFDRVLTELVS---KMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
            +    G    +L  LV     ++++ + + E   L  I + +PD  G++   ++E +++
Sbjct: 110 SDVTKAGHSLELLEPLVKFQVGLKKLNLHEEEHVLLMAICILSPDRPGVQDHALIEAIQD 169

Query: 312 KVYTSLEEYTRVNHSEEPGR--FAKLLLRLPSLRSI 345
           ++  +L+ Y R  H     R  +AK++ +L  LRS+
Sbjct: 170 RLSDTLQTYIRCRHPPPGSRLLYAKMIQKLADLRSL 205

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

 Score = 51.9 bits (124), Expect = 1e-07
 Identities = 44/166 (26%), Positives = 82/166 (49%), Gaps = 17/166 (10%)

Query: 191 KQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGVT 248
           +Q+   V WAK IP F  L L+DQ+ LL+  W  L+  +   RS    +G LL  AP + 
Sbjct: 39  RQVVAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMAFALGWRSYRQSNGNLLCFAPDLI 98

Query: 249 VYRSSAHEAGVGGIFDRV--LTELVSKMREMKMDKTELGCLRTIILFNPDVR-GLKSQQV 305
           +         +  ++D+   +  + S++  +++   E  C++T++L +   + GLKSQ++
Sbjct: 99  INEQRMT---LPCMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSTVPKDGLKSQEL 155

Query: 306 VEMLREKVYTSLEEYTRV------NHSEEPGRFAKLLLRLPSLRSI 345
            + +R    T ++E  +       N S+   RF +L   L S+  +
Sbjct: 156 FDEIR---MTYIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEV 198

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

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

 Score = 49.9 bits (119), Expect = 5e-07
 Identities = 37/130 (28%), Positives = 59/130 (45%), Gaps = 18/130 (13%)

Query: 191 KQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGVT 248
           KQ+ Q+V WAK +P F  LPLEDQ+ L++  W  L   + S RS    +   L  AP + 
Sbjct: 39  KQMIQVVKWAKVLPGFRNLPLEDQITLIQYSWMCLSSFALSWRSYKHTNSQFLYFAPDLV 98

Query: 249 VYRSSAHEAGVGGIFDRVLTELVSKMRE-------MKMDKTELGCLRTIILFNPDV-RGL 300
                 H++         + EL   M +       +++   E   ++ ++L +     GL
Sbjct: 99  FNEERMHQSA--------MYELCQGMHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKDGL 150

Query: 301 KSQQVVEMLR 310
           KSQ   E +R
Sbjct: 151 KSQAAFEEMR 160

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

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

 Score = 49.2 bits (117), Expect = 9e-07
 Identities = 32/134 (23%), Positives = 68/134 (50%), Gaps = 8/134 (5%)

Query: 183 TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGIL 242
           T++ +  ++QL  +V W+K +P F  L ++DQ+ L++  W  L++     RS     G +
Sbjct: 31  TSLNQLCERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQM 90

Query: 243 L--APGVTVYRSSAHEAGVGGIFDRVLT--ELVSKMREMKMDKTELGCLRTIILFNP-DV 297
           L  AP + +      E+     +   LT  ++  +  ++++ + E  C++ ++L N   +
Sbjct: 91  LYFAPDLILNEQRMKES---SFYSLCLTMWQIPQEFVKLQVSQEEFLCMKALLLLNTIPL 147

Query: 298 RGLKSQQVVEMLRE 311
            GL+SQ   + +R 
Sbjct: 148 EGLRSQTQFDEMRS 161

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

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

 Score = 47.6 bits (113), Expect = 3e-06
 Identities = 44/171 (25%), Positives = 82/171 (47%), Gaps = 21/171 (12%)

Query: 190 DKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSIS-VKDGIL-LAPGV 247
           ++QL  +V WAK +P F  L ++DQ+ +++  W  L++ +   RS + V   +L  AP +
Sbjct: 38  ERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDL 97

Query: 248 TVYRSSAHEAGVGGIFDRVLTELVSKMRE-------MKMDKTELGCLRTIILFNP-DVRG 299
                  H++       R+ ++ V +MR        +++   E  C++ ++LF+   V G
Sbjct: 98  VFNEYRMHKS-------RMYSQCV-RMRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDG 149

Query: 300 LKSQQVVEMLREKVYTSLEE---YTRVNHSEEPGRFAKLLLRLPSLRSIEV 347
           LK+Q+  + LR      L+      R N +    RF +L   L S++ I  
Sbjct: 150 LKNQKFFDELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPIAR 200

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	347
KOG4215|consensus	432		100.0
KOG4217|consensus	605		100.0
KOG4216|consensus	479		100.0
KOG4218|consensus	475		100.0
KOG4846|consensus	538		100.0
cd06943	207	NR_LBD_RXR_like The ligand binding domain of the r	100.0
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
cd07160	101	NR_DBD_LXR DNA-binding domain of Liver X receptors	100.0
cd06956	77	NR_DBD_RXR DNA-binding domain of retinoid X recept	99.98
cd06944	237	NR_LBD_Ftz-F1_like The ligand binding domain of FT	99.98
cd06935	243	NR_LBD_TR The ligand binding domain of thyroid hor	99.98
cd06940	189	NR_LBD_REV_ERB The ligand binding domain of REV-ER	99.98
cd06961	85	NR_DBD_TR DNA-binding domain of thyroid hormone re	99.97
cd06947	246	NR_LBD_GR_Like Ligand binding domain of nuclear ho	99.97
cd07075	248	NR_LBD_MR Ligand binding domain of the mineralocor	99.97
cd06964	85	NR_DBD_RAR DNA-binding domain of retinoic acid rec	99.97
cd07170	97	NR_DBD_ERR DNA-binding domain of estrogen related	99.97
cd07171	82	NR_DBD_ER DNA-binding domain of estrogen receptors	99.97
cd07161	91	NR_DBD_EcR DNA-binding domain of Ecdysone receptor	99.97
cd07070	237	NR_LBD_SF-1 The ligand binding domain of nuclear r	99.97
cd06950	206	NR_LBD_Tlx_PNR_like The ligand binding domain of T	99.97
cd07073	246	NR_LBD_AR Ligand binding domain of the nuclear rec	99.97
cd06931	222	NR_LBD_HNF4_like The ligand binding domain of hept	99.97
cd07155	75	NR_DBD_ER_like DNA-binding domain of estrogen rece	99.97
cd07348	238	NR_LBD_NGFI-B The ligand binding domain of Nurr1,	99.97
cd07168	90	NR_DBD_DHR4_like DNA-binding domain of ecdysone-in	99.97
cd06962	84	NR_DBD_FXR DNA-binding domain of Farnesoid X recep	99.97
cd07068	221	NR_LBD_ER_like The ligand binding domain of estrog	99.97
cd06967	87	NR_DBD_TR2_like DNA-binding domain of the TR2 and	99.97
cd06970	92	NR_DBD_PNR DNA-binding domain of the photoreceptor	99.97
cd06929	174	NR_LBD_F1 Ligand-binding domain of nuclear recepto	99.97
cd07164	78	NR_DBD_PNR_like_1 DNA-binding domain of the photor	99.97
cd06930	165	NR_LBD_F2 Ligand-binding domain of nuclear recepto	99.97
cd06946	221	NR_LBD_ERR The ligand binding domain of estrogen r	99.97
cd07069	241	NR_LBD_Lrh-1 The ligand binding domain of the live	99.97
cd06957	82	NR_DBD_PNR_like_2 DNA-binding domain of the photor	99.97
cd07071	238	NR_LBD_Nurr1 The ligand binding domain of Nurr1, a	99.97
cd07163	92	NR_DBD_TLX DNA-binding domain of Tailless (TLX) is	99.97
cd06954	236	NR_LBD_LXR The ligand binding domain of Liver X re	99.97
cd07165	81	NR_DBD_DmE78_like DNA-binding domain of Drosophila	99.97
cd07166	89	NR_DBD_REV_ERB DNA-binding domain of REV-ERB recep	99.97
cd07167	93	NR_DBD_Lrh-1_like The DNA-binding domain of Lrh-1	99.97
cd07169	90	NR_DBD_GCNF_like DNA-binding domain of Germ cell n	99.97
cd06941	195	NR_LBD_DmE78_like The ligand binding domain of Dro	99.97
cd06966	94	NR_DBD_CAR DNA-binding domain of constitutive andr	99.97
cd06951	222	NR_LBD_Dax1_like The ligand binding domain of DAX1	99.97
cd06945	239	NR_LBD_Nurr1_like The ligand binding domain of Nur	99.97
cd06960	76	NR_DBD_HNF4A DNA-binding domain of heptocyte nucle	99.97
cd06959	73	NR_DBD_EcR_like The DNA-binding domain of Ecdysone	99.97
cd07074	248	NR_LBD_PR Ligand binding domain of the progesteron	99.97
cd06958	73	NR_DBD_COUP_TF DNA-binding domain of chicken ovalb	99.97
cd06969	75	NR_DBD_NGFI-B DNA-binding domain of the orphan nuc	99.97
cd07156	72	NR_DBD_VDR_like The DNA-binding domain of vitamin	99.97
cd06955	107	NR_DBD_VDR DNA-binding domain of vitamin D recepto	99.97
cd07162	87	NR_DBD_PXR DNA-binding domain of pregnane X recept	99.97
cd07173	82	NR_DBD_AR DNA-binding domain of androgen receptor	99.97
cd06948	236	NR_LBD_COUP-TF Ligand binding domain of chicken ov	99.97
cd07179	74	2DBD_NR_DBD2 The second DNA-binding domain (DBD) o	99.97
cd06968	95	NR_DBD_ROR DNA-binding domain of Retinoid-related	99.97
cd07349	222	NR_LBD_SHP The ligand binding domain of DAX1 prote	99.97
cd06963	73	NR_DBD_GR_like The DNA binding domain of GR_like n	99.97
cd07072	239	NR_LBD_DHR38_like Ligand binding domain of DHR38_l	99.97
cd07172	78	NR_DBD_GR_PR DNA-binding domain of glucocorticoid	99.97
cd07158	73	NR_DBD_Ppar_like The DNA-binding domain of peroxis	99.97
cd06934	226	NR_LBD_PXR_like The ligand binding domain of xenob	99.97
cd07154	73	NR_DBD_PNR_like The DNA-binding domain of the phot	99.97
cd07350	232	NR_LBD_Dax1 The ligand binding domain of DAX1 prot	99.97
cd06916	72	NR_DBD_like DNA-binding domain of nuclear receptor	99.97
cd06939	241	NR_LBD_ROR_like The ligand binding domain of Retin	99.96
cd06953	213	NR_LBD_DHR4_like The ligand binding domain of orph	99.96
cd07157	86	2DBD_NR_DBD1 The first DNA-binding domain (DBD) of	99.96
cd06965	84	NR_DBD_Ppar DNA-binding domain of peroxisome proli	99.96
cd06933	238	NR_LBD_VDR The ligand binding domain of vitamin D	99.96
cd06936	221	NR_LBD_Fxr The ligand binding domain of Farnesoid	99.96
cd06938	231	NR_LBD_EcR The ligand binding domain (LBD) of the	99.96
cd06932	259	NR_LBD_PPAR The ligand binding domain of peroxisom	99.96
smart00399	70	ZnF_C4 c4 zinc finger in nuclear hormone receptors	99.96
cd06942	191	NR_LBD_Sex_1_like The ligand binding domain of Cae	99.96
cd06952	222	NR_LBD_TR2_like The ligand binding domain of the o	99.96
PF00105	70	zf-C4: Zinc finger, C4 type (two domains); InterPr	99.95
cd06157	168	NR_LBD The ligand binding domain of nuclear recept	99.94
smart00430	163	HOLI Ligand binding domain of hormone receptors.	99.94
PF00104	203	Hormone_recep: Ligand-binding domain of nuclear ho	99.93
KOG3277|consensus	165		82.23
PF12760	46	Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int	80.7
PF01412	116	ArfGap: Putative GTPase activating protein for Arf	80.45

>KOG4215|consensus

Probab=100.00  E-value=3.6e-70  Score=474.63  Aligned_cols=289  Identities=41%  Similarity=0.776  Sum_probs=247.1

Q ss_pred             CCcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhh
Q psy3092          55 KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQR  134 (347)
Q Consensus        55 ~~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~  134 (347)
                      ...|.||||+|+|+||||.+|.||||||||+|+++..|.|+.+.+|.|||+.|+.||+|||+||+.+||++++||.+||+
T Consensus        19 ~~~CaICGDkaTGKHYGA~SCdGCKGFFRRSVrk~~~YtCRF~k~C~VDKdkRNaCRyCRfqKC~~aGMK~eAiQnERDr   98 (432)
T KOG4215|consen   19 AEFCAICGDKATGKHYGAISCDGCKGFFRRSVRKNHQYTCRFNKQCVVDKDKRNACRYCRFQKCVRAGMKREAIQNERDR   98 (432)
T ss_pred             cchhheeCCcccccccceeecCcchHHHHHHHHhcceeeeeccccccccchhhhhhhHhhHHHHHHhcccHHhhhccccc
Confidence            35799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhccccccccCCCCCCCCCcHHHHHHHHHhccCCCC------CCcc-c------cchhHHHhhhhHHHHHHHHHHHHHHh
Q psy3092         135 TKERDSNEVESTSGTLIEMPVERILEAEQRVDMKQE------PADQ-D------IVNEQQATNICKATDKQLFQLVDWAK  201 (347)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~------~~~~-~------~~~~~~~~~~~~~~~~~l~~~~~w~k  201 (347)
                      +..+.+....   +...+..++.++.++..+.....      +... +      .-......++++....++..+|||||
T Consensus        99 Ig~Rr~~~~~---~n~~~~~id~L~~aE~~~~q~~~srs~~~~~~~~d~r~~~~n~~~at~~Dv~eSm~qqLlllVEWAK  175 (432)
T KOG4215|consen   99 IGSRRPSYEA---GNENSPSIDALVQAEALVRQLRSSRSGGVPGIDGDIRQGPPNKKIATENDVCESMKQQLLLLVEWAK  175 (432)
T ss_pred             ccccCCCCCC---CCCCchhHHHHHhHHHHHhhhhccccccCcCcchhhhcCccccccccHHHHHHHHHHHHHHHHHHHH
Confidence            8775432211   11233345666666654432211      1000 0      11224567889999999999999999


Q ss_pred             hCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCchhhHHhhHHHHHHHHHhcCCCH
Q psy3092         202 HIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDK  281 (347)
Q Consensus       202 ~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~~~~~~~~~~~l~~~l~~L~l~~  281 (347)
                      .+|.|.+|+.+||+.|||+...+.+++..++|++..++..++.+...+..+..+......+..|+++|++.||++|++|+
T Consensus       176 ~i~~F~el~l~DqvaLLk~~a~~hllLg~a~RSm~l~~v~ll~N~~v~~~~~~~~~eis~v~~RIiDElv~Pmr~L~md~  255 (432)
T KOG4215|consen  176 YIPPFCELPLDDQVALLKAHAGQHLLLGAAFRSMHLKDVCLLNNTYVLHRHAPDLPEISRVAPRIIDELVNPMRRLQMDE  255 (432)
T ss_pred             hccchhcCCchhHHHHHHccchhhhhhhhhhccccccceEEecCceeeccCCCChHHHHHHHHHHHHHHhhHHHHhccch
Confidence            99999999999999999999999999999999999989888888887777666555566788899999999999999999


Q ss_pred             hHHHHHHHHHhhcCCCCCCCCH--HHHHHHHHHHHHHHHHHHHhcCC-CCchHHHHHHhhhhhhhccC
Q psy3092         282 TELGCLRTIILFNPDVRGLKSQ--QVVEMLREKVYTSLEEYTRVNHS-EEPGRFAKLLLRLPSLRSIE  346 (347)
Q Consensus       282 ~E~~lL~ai~l~~p~~~~l~~~--~~i~~~r~~~~~~L~~y~~~~~~-~~~~Rf~~LL~ll~~lr~i~  346 (347)
                      .||++||||+||+|+..||++.  ..|+++|++++..|+.|+..+.+ +.+.|||+||++||+|++|+
T Consensus       256 ~Ey~cLKAi~FfdP~akGis~~s~~~I~~aR~~vl~sLe~yi~d~q~~d~~~R~g~LLLllPsLqsIt  323 (432)
T KOG4215|consen  256 IEYVCLKAIAFFDPDAKGLSDPSQIRIREARNRVLKSLEAYISDRQPYDAPGRFGNLLLLLPSLQSIT  323 (432)
T ss_pred             HHHHHHHHHHhcCccccccCCchHhHHHHHHHHHHHHHHHHHhhcCccccccchhhHHHHHHHHHHHH
Confidence            9999999999999999999984  48999999999999999998875 78999999999999999874

>KOG4217|consensus

Probab=100.00  E-value=1.1e-52  Score=375.37  Aligned_cols=288  Identities=33%  Similarity=0.646  Sum_probs=229.2

Q ss_pred             CCcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhh
Q psy3092          55 KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQR  134 (347)
Q Consensus        55 ~~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~  134 (347)
                      ...|.||||.|.--||||.||+||||||+|+|+|+.+|.|-.+++|.|||..|++||+||||||++|||-+|.|+.+--+
T Consensus       269 e~~CAVCgDnAaCqHYGvRTCEGCKGFFKRTVQKnaKYvClanKnCPVDKRrRnRCQyCRfQKCL~VGMVKEVVRtdSLk  348 (605)
T KOG4217|consen  269 EGLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLAVGMVKEVVRTDSLK  348 (605)
T ss_pred             cceeeecCChHHhhhcCccccccchHHHHHHHhcCCeeEeecCCCCCcchhhhhhchhhhHhHHHHhhhhhhheeccccc
Confidence            56899999999999999999999999999999999999999999999999999999999999999999999999875322


Q ss_pred             hhc-cccccccCCCCCCCCCcHHHHHHHHHhccCCCCC--C------------ccccchhHHHhhhhHHHHHHHHHHHHH
Q psy3092         135 TKE-RDSNEVESTSGTLIEMPVERILEAEQRVDMKQEP--A------------DQDIVNEQQATNICKATDKQLFQLVDW  199 (347)
Q Consensus       135 ~~~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~--~------------~~~~~~~~~~~~~~~~~~~~l~~~~~w  199 (347)
                      .++ +-..+..+........|+. ++.+..+......+  .            .........+..+.+...-.+-.+-.|
T Consensus       349 GRRGRLpSKpKs~q~sppSpPi~-LltalvrAh~Dstp~~~~ldys~~q~~~~~~~~tdA~~vqqfy~lLtgsl~virk~  427 (605)
T KOG4217|consen  349 GRRGRLPSKPKSRQPSPPSPPIS-LLTALVRAHVDSTPSTMTLDYSRFQELVPHFSGTDALHVQQFYDLLTGSLEVIRKW  427 (605)
T ss_pred             cccCCCCCCCCCCCCCCCCCchH-HHHHHHHHhhcCCCCcchhhHHHhccccccccccHHHHHHHHHHHhhhhHHHHHHH
Confidence            111 1111111111122222332 22222211110110  0            001122344566667677777788899


Q ss_pred             HhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCchhhHHhhHHHHHHHHHhcCC
Q psy3092         200 AKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKM  279 (347)
Q Consensus       200 ~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~~~~~~~~~~~l~~~l~~L~l  279 (347)
                      |..+|+|.+|+.+||.+||.+.+.+++++++|||+...++.++|.+|..+.+-... .++++++|.++ ++...+..|.+
T Consensus       428 aekiPgf~el~paDq~lLlesaflelfvlRlAyRs~~~e~kliFcsG~vlhr~qC~-rgfgewidsi~-~FS~~l~~l~i  505 (605)
T KOG4217|consen  428 AEKIPGFAELPPADQDLLLESAFLELFVLRLAYRSNPSEDKLIFCSGLVLHRLQCL-RGFGEWIDSIR-EFSRSLHSLNI  505 (605)
T ss_pred             HHhCcCcccCChhhHHHHHHHHHHHHHHHHHHHhcCCCCCeEEEecchhhhHHHHH-HHHHHHHHHHH-HHHHHhhhchh
Confidence            99999999999999999999999999999999999999999999999999885543 45777777765 89999999999


Q ss_pred             CHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhc--CCCCchHHHHHHhhhhhhhccC
Q psy3092         280 DKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVN--HSEEPGRFAKLLLRLPSLRSIE  346 (347)
Q Consensus       280 ~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~--~~~~~~Rf~~LL~ll~~lr~i~  346 (347)
                      |..-|++|.|+.+.. ++.||.+...||++|++|.++|.+|+..+  ....+.++.++|-.|++||+|+
T Consensus       506 di~AfacL~aLa~iT-ErhGL~epkrVeelqnkIi~~LKDHvt~~~~~~~k~~~lSrllgklpeLr~l~  573 (605)
T KOG4217|consen  506 DISAFACLSALALIT-ERHGLKEPKRVEELQNKIINCLKDHVTGSAGKLAKPVYLSRLLGKLPELRTLC  573 (605)
T ss_pred             hHHHHHHHHHHHhhh-hhhcCCCcchHHHHHHHHHHHHHHHhhhcccccccchHHHHHhhhhHHHHHHH
Confidence            999999999999874 78999999999999999999999999654  3467899999999999999875

>KOG4216|consensus

Probab=100.00  E-value=8e-50  Score=349.71  Aligned_cols=286  Identities=31%  Similarity=0.588  Sum_probs=211.1

Q ss_pred             cCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhhh
Q psy3092          57 LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRTK  136 (347)
Q Consensus        57 ~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~~  136 (347)
                      +|.||||+++|.||||+||+||||||||+-+.+..|.|.+.++|.||...|++||+||+|||+++||.+++|.+.|..+|
T Consensus        48 PCKiCGDKSSGiHYGVITCEGCKGFFRRSQ~s~a~YsCpRqknC~iDRtnRNRCQ~CRLqKClaLGMSRDAVKFGRMSKK  127 (479)
T KOG4216|consen   48 PCKICGDKSSGIHYGVITCEGCKGFFRRSQQSNANYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSKK  127 (479)
T ss_pred             eeeeccCCCCcceeeeEeeccchHhhhhhhhccccccCCcccCCcccccccchhhHHHHHHHHHhccchhhHHhccccHh
Confidence            49999999999999999999999999999999999999999999999999999999999999999999999999886554


Q ss_pred             ccccc---------------ccc--------CCCC-------------------------C--------CCCC-------
Q psy3092         137 ERDSN---------------EVE--------STSG-------------------------T--------LIEM-------  153 (347)
Q Consensus       137 ~~~~~---------------~~~--------~~~~-------------------------~--------~~~~-------  153 (347)
                      .++..               +.+        ++++                         .        .++.       
T Consensus       128 QRdsl~aEVq~h~~q~q~q~~a~~~~~~y~~s~p~~~~~l~~~~s~y~~g~~p~~~k~~~s~Ys~~~q~tPdq~~~d~~g  207 (479)
T KOG4216|consen  128 QRDSLYAEVQKHRMQQQQQDEAEPLTPTYDISPPNGLTELHDDLSNYSDGHSPEGSKADSSFYSLDIQPTPDQSGLDING  207 (479)
T ss_pred             hHHHHHHHHHHHHHHHHhhhhcCCcccccccCCCCCccccccCcccccCCcCCCCCCCCCCcceeccccCCCccccccCC
Confidence            33210               000        0000                         0        0000       


Q ss_pred             --------------------------c---HH----HHHHHHHhc----------cCCCCCCcccc--chhHH----Hhh
Q psy3092         154 --------------------------P---VE----RILEAEQRV----------DMKQEPADQDI--VNEQQ----ATN  184 (347)
Q Consensus       154 --------------------------~---~~----~l~~~~~~~----------~~~~~~~~~~~--~~~~~----~~~  184 (347)
                                                +   ++    ++.++....          .+.... .+.+  ....+    |+.
T Consensus       208 ~~~d~t~~~~~~~~~s~~~~~~~p~~~~~e~d~laq~i~ksh~etq~~~e~lh~~~~~~~~-~e~I~~yq~k~~e~mWe~  286 (479)
T KOG4216|consen  208 PICDSTPGSGYFPYCSFTNGETSPTVSMAELDHLAQNIIKSHLETQYLLEELHQITWQTFD-QEEIENYQNKGREEMWEL  286 (479)
T ss_pred             CcccCCCCCCcccccccCCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCC-HHHHHHHHhhhHHHHHHH
Confidence                                      0   00    111111000          000000 0000  00001    112


Q ss_pred             hhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCchhhHH
Q psy3092         185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFD  264 (347)
Q Consensus       185 ~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~~~~~~  264 (347)
                      ........+..+|||||.+++|.+|+++||+.|||.+.+++.+..++.. ++..+..++..|.+....-+...+..++..
T Consensus       287 cA~~lt~~IQ~vVEFAK~I~GFM~L~Q~dQI~LLKaGsfEv~lvrm~r~-~~v~~ntV~~e~~~~g~~~f~a~~~~elis  365 (479)
T KOG4216|consen  287 CAIKLTPAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSFEVVLVRMCRA-FDVDNNTVYFEGKYAGPEVFYALGCEELIS  365 (479)
T ss_pred             HHHHHHHHHHHHHHHHHhhhHhhccCccceEEeeecCceeeeHHHHHHh-hcccccceeecccccchhheeccChHHHHH
Confidence            2222344677889999999999999999999999999999888877643 455555666666666655555555556667


Q ss_pred             hhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhhhhhhc
Q psy3092         265 RVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRS  344 (347)
Q Consensus       265 ~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll~~lr~  344 (347)
                      +++ ++...+..|++++.|++|+.|++|.++++.||.+..+|+++++++..+|++.+..+|... .-+.+|+-.+|.||.
T Consensus       366 ~vf-~~~ksL~~Lq~te~EiAL~~alVL~~~~r~gl~e~~ki~~lq~~~~~a~qhvl~knh~~~-~~l~kl~~k~~~~r~  443 (479)
T KOG4216|consen  366 RVF-EFGKSLCSLQLTEDEIALFSALVLMSADRSGLQEKVKIEKLQQKIQLALQHVLQKNHRED-GILTKLICKVSTLRA  443 (479)
T ss_pred             HHH-hhhHHHHhhccCcHHHHHHHHHHhhCCccccccchHHHHHHHHHHHHHHHHHHHhcCChh-hhHHHhhcccchHHH
Confidence            766 788999999999999999999999999999999999999999999999999998876533 478899999999987


Q ss_pred             cC
Q psy3092         345 IE  346 (347)
Q Consensus       345 i~  346 (347)
                      ++
T Consensus       444 ~~  445 (479)
T KOG4216|consen  444 LC  445 (479)
T ss_pred             HH
Confidence            64

>KOG4218|consensus

Probab=100.00  E-value=7.5e-47  Score=325.99  Aligned_cols=292  Identities=35%  Similarity=0.620  Sum_probs=219.1

Q ss_pred             CCcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhh
Q psy3092          55 KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQR  134 (347)
Q Consensus        55 ~~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~  134 (347)
                      .+.|.||||+.+|||||-.+|+.|||||+|+|+.++.|.|..+.+|.||+..|.+|.+||||||+.|||+-++|+-+|.+
T Consensus        15 ~ElCPVCGDkVSGYHYGLLTCESCKGFFKRTVQNnK~YtC~e~qnC~iDkTqRKRCP~CRFQKCLtvGMklEAVRADRMR   94 (475)
T KOG4218|consen   15 GELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKQYTCSEEQNCHIDKTQRKRCPSCRFQKCLTVGMKLEAVRADRMR   94 (475)
T ss_pred             ccccccccCccccceeeeeehhhhhhHHHHHhhcCcceecccccccccchHhhccCCchhHHHHhhhhhhHHHHHHhhhc
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999988764


Q ss_pred             hhcc--------c-------------------------cccccC-C--CCCC------------------CCCc--H---
Q psy3092         135 TKER--------D-------------------------SNEVES-T--SGTL------------------IEMP--V---  155 (347)
Q Consensus       135 ~~~~--------~-------------------------~~~~~~-~--~~~~------------------~~~~--~---  155 (347)
                      ....        +                         ....++ +  ++..                  ++.+  +   
T Consensus        95 GGRNKFGpmYKrDRAlkqQkkAqirAng~KlE~~~~~~~~~~psp~~~ss~~q~lh~~~~kgL~~~~aa~pp~~~~l~~f  174 (475)
T KOG4218|consen   95 GGRNKFGPMYKRDRALKQQKKAQIRANGIKLEYIKTEYDAHLPSPTLSSSTNQQLHVSDFKGLAVLLAATPPDPLQLNEF  174 (475)
T ss_pred             ccccccCchhhhhHHHHHHHHHHhhhcceeeeccccccCCCCCCCcccccccccccCCCcccchhhhccCCCCCcccccc
Confidence            2110        0                         000000 0  0000                  0000  0   


Q ss_pred             --------------------------HHHHHHHHhc---cCCC--------------CCC--------------------
Q psy3092         156 --------------------------ERILEAEQRV---DMKQ--------------EPA--------------------  172 (347)
Q Consensus       156 --------------------------~~l~~~~~~~---~~~~--------------~~~--------------------  172 (347)
                                                .+.+..+...   ...+              .+.                    
T Consensus       175 ~~~p~~ms~p~~HgsL~gY~tY~~fp~raikseyP~py~Sspqs~~~ygym~~~ss~sP~lP~lil~llk~epdE~qv~a  254 (475)
T KOG4218|consen  175 KQEPFDMSEPFIHGSLHGYPTYTSFPTRAIKSEYPMPYVSSPQSLVTYGYMTEASSTSPILPLLILPLLKTEPDEMQVTA  254 (475)
T ss_pred             cCCCccccCccCCCcccCCcccCCCcchhhhhcCCCCcCCCCcccccccccCccccCCCCccccchhhhccCChhhhhcc
Confidence                                      0000000000   0000              000                    


Q ss_pred             ------------ccccchhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccC--C
Q psy3092         173 ------------DQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISV--K  238 (347)
Q Consensus       173 ------------~~~~~~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~--~  238 (347)
                                  ......+..+.-.+++.+..+..+++||+.--.|.+|+.+||++||+++|.++++++..|+....  .
T Consensus       255 ~i~a~lq~~~ts~s~~~kp~~fgl~c~mAdqtl~sIV~WAr~~~~F~eL~vdDQM~LLQncWselli~DhiyrqV~hgke  334 (475)
T KOG4218|consen  255 PIDAQLQRIFTSVSGTSKPEKFGLSCQMADQTLKSIVIWARNDQLFSELSVDDQMILLQNCWSELLIVDHIYRQVHHGKE  334 (475)
T ss_pred             hhHHHHhhhhhcccCCCchhhhhhhhhhhHhHHHHHHHHHhhhhHHHhcchhhHHHHHHHhhHHHHHHHHHHHHHhcCcc
Confidence                        00001112334457788889999999999999999999999999999999999999998887644  3


Q ss_pred             CceEecCCccccccchhhcC--chhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHH
Q psy3092         239 DGILLAPGVTVYRSSAHEAG--VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTS  316 (347)
Q Consensus       239 ~~~~~~~g~~i~~~~~~~~~--~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~  316 (347)
                      ..+.+.+|..+.-.-.....  ...-+-....++|.+++.|++|..||++|+-|+||+-|...|...+.|+.+++....+
T Consensus       335 gsi~lvtGqeV~~~~vA~qags~l~tlvs~aqelV~~Lr~lqfd~~efvclkFl~LFsld~kfLenf~lv~~~qe~~naa  414 (475)
T KOG4218|consen  335 GSIKLVTGQEVPVGLVALQAGSLLQTLVSSAQELVIRLRNLQFDNFEFVCLKFLALFSLDMKFLENFELVRRLQEDSNAA  414 (475)
T ss_pred             cceEEecCCcccchhHhhhhhhHHHHHHHHHHHHHHHHHhcCCccchhhHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHH
Confidence            45667788776654332211  1112223346899999999999999999999999999998888899999999999999


Q ss_pred             HHHHHHhcCCCCchHHHHHHhhhhhhhccC
Q psy3092         317 LEEYTRVNHSEEPGRFAKLLLRLPSLRSIE  346 (347)
Q Consensus       317 L~~y~~~~~~~~~~Rf~~LL~ll~~lr~i~  346 (347)
                      |.+|....+++....|+++++.|+.||.++
T Consensus       415 Lldyt~c~yp~~~~kF~qllL~L~eiRa~s  444 (475)
T KOG4218|consen  415 LLDYTSCCYPNWEQKFPQLLLVLEEIRATS  444 (475)
T ss_pred             HHHhhccCCccHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999875

>KOG4846|consensus

Probab=100.00  E-value=6.6e-37  Score=270.38  Aligned_cols=82  Identities=50%  Similarity=1.160  Sum_probs=77.3

Q ss_pred             CCcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcc-cccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHh
Q psy3092          55 KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSY-ACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQ  133 (347)
Q Consensus        55 ~~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~-~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~  133 (347)
                      .-.|+||||.|+|+||||.+|+||||||||+|+.+..| .|-+..+|.|.++.|++||+|||+||+++||.+++|++.+.
T Consensus       132 ~~lCkVCgDkASGfHYGV~aCEGCKGFFRRSIQqkI~YrrClk~e~C~I~R~nRNRCQ~CRfKKCL~vGMSrDaVRFG~m  211 (538)
T KOG4846|consen  132 ISLCKVCGDKASGFHYGVTACEGCKGFFRRSIQQKIDYRRCLKQEVCEIKRENRNRCQYCRFKKCLDVGMSRDAVRFGQM  211 (538)
T ss_pred             eEeehhhccccccceeceeecccchHHHHHHHHHhhhHHHHhhhhceehhhhccchhhhhhHHHHHhcccchhhhhhccc
Confidence            45799999999999999999999999999999999999 79999999999999999999999999999999999998766


Q ss_pred             hhh
Q psy3092         134 RTK  136 (347)
Q Consensus       134 ~~~  136 (347)
                      +.+
T Consensus       212 ~~r  214 (538)
T KOG4846|consen  212 KFR  214 (538)
T ss_pred             ccc
Confidence            543

>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=1e-32  Score=237.91  Aligned_cols=168  Identities=75%  Similarity=1.222  Sum_probs=156.9

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV  259 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~  259 (347)
                      ...+.++++....+..+|+|+|++|+|..|+.+||+.|+|++|.+++++..+++++...+++++.+|..+.++.....++
T Consensus        30 ~~~~~~~~~~~~~l~~~Iewak~lp~F~~L~~~DQ~~LLk~~~~e~~~l~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~  109 (207)
T cd06943          30 DPVSNICQAADKQLFQLVEWAKRIPHFSELPLDDQVILLRAGWNELLIAAFAHRSIAVKDGILLATGLHLHRNSAHQAGV  109 (207)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHhCchhhccChhhhHHHHHHHHHHHHHHHHHHHccCCCCeeEecCCceeccchhhhccc
Confidence            34678999999999999999999999999999999999999999999999999999888999999998887776655666


Q ss_pred             hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhh
Q psy3092         260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRL  339 (347)
Q Consensus       260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll  339 (347)
                      ..++++++.+++.+|++|++|++||++|+||+|||||.+|+++...|+++|+++.++|++|+..++++++.||++||++|
T Consensus       110 ~~~~~~~~~~~~~~l~~L~ld~~E~~lLkaI~L~~pd~~~L~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LLl~L  189 (207)
T cd06943         110 GAIFDRILTELVVKMRDLKMDRTELGCLRAIILFNPDVKGLKSRQEVESLREKVYASLEEYCRQKHPEQPGRFAKLLLRL  189 (207)
T ss_pred             hHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHH
Confidence            77788888899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhccCC
Q psy3092         340 PSLRSIEV  347 (347)
Q Consensus       340 ~~lr~i~~  347 (347)
                      |+||+|+.
T Consensus       190 ~~lr~l~~  197 (207)
T cd06943         190 PALRSIGL  197 (207)
T ss_pred             HHHHhHhH
Confidence            99999873

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

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

Probab=100.00  E-value=2.4e-32  Score=237.75  Aligned_cols=168  Identities=23%  Similarity=0.371  Sum_probs=148.4

Q ss_pred             hhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCc--eEecCCccccccchh
Q psy3092         178 NEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDG--ILLAPGVTVYRSSAH  255 (347)
Q Consensus       178 ~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~--~~~~~g~~i~~~~~~  255 (347)
                      ...-.+.+++..+++++.+|+|||++|+|.+|+.+||+.|||++|.++++++.+||+++..+.  +++++|..+.++...
T Consensus        26 ~~~~~~~l~~la~r~L~~~VeWAK~IPgF~~L~l~DQi~LLk~sW~Ellvl~~a~rs~~~~~~~~l~fa~~~~~~~~~~~  105 (247)
T cd07076          26 TWRIMSTLNMLGGRQVVAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMAFALGWRSYRQSNGNLLCFAPDLIINEQRMT  105 (247)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHhccCCCCCceEEecCCeeecHHHHh
Confidence            345578899999999999999999999999999999999999999999999999999887654  577888888776654


Q ss_pred             hcCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcC-CCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCch---H
Q psy3092         256 EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNP-DVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPG---R  331 (347)
Q Consensus       256 ~~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p-~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~---R  331 (347)
                      ..+...+. +.+.+++.+|++|++|.+||+|||||+|||| |.+|+++...|+++|+++..+|.+|+..++++.+.   |
T Consensus       106 ~~~~~~~~-~~l~e~~~~~r~L~ld~~EfacLKAIvLfnp~d~~GL~~~~~Ve~lqe~~~~aL~~yi~~~~p~~~~~~~R  184 (247)
T cd07076         106 LPCMYDQC-KHMLYVSSELHRLQVSYEEYLCMKTLLLLSTVPKDGLKSQELFDEIRMTYIKELGKAIVKREGNSSQNWQR  184 (247)
T ss_pred             hhhHHHHH-HHHHHHHHHHHHcCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCcchhhhH
Confidence            44443333 3466899999999999999999999999999 99999999999999999999999999988876554   9


Q ss_pred             HHHHHhhhhhhhccC
Q psy3092         332 FAKLLLRLPSLRSIE  346 (347)
Q Consensus       332 f~~LL~ll~~lr~i~  346 (347)
                      ||+||++||+||+|+
T Consensus       185 F~kLLllLp~Lr~i~  199 (247)
T cd07076         185 FYQLTKLLDSMHEVV  199 (247)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999999986

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=1.5e-31  Score=233.65  Aligned_cols=170  Identities=32%  Similarity=0.550  Sum_probs=152.1

Q ss_pred             chhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchh-
Q psy3092         177 VNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH-  255 (347)
Q Consensus       177 ~~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~-  255 (347)
                      .....+..++++.++.++.+|+|||++|+|.+|+.+||+.|+|++|.++++++.++++....+.+.+.+|..+..+... 
T Consensus        29 ~~~~~~~~l~~la~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w~el~~L~~a~rs~~~~~~~~~~~~~~~~~~~~~~  108 (235)
T cd06949          29 TEASLMMLLTNLADRELVHMINWAKKIPGFVDLSLHDQVHLLESAWLELLMLGLVWRSMEHPGKLLFAPDLLLDRNQGSC  108 (235)
T ss_pred             ChHHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcCCCCeEEeeCCceecHHHhhh
Confidence            3455688899999999999999999999999999999999999999999999999999888888888888877766543 


Q ss_pred             hcCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCC-----CCCHHHHHHHHHHHHHHHHHHHHhcC---CC
Q psy3092         256 EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRG-----LKSQQVVEMLREKVYTSLEEYTRVNH---SE  327 (347)
Q Consensus       256 ~~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~-----l~~~~~i~~~r~~~~~~L~~y~~~~~---~~  327 (347)
                      ..++..+++.+. +++.+|++|++|++||++||||+|||||++|     +++...|+++|+++..+|++|+..++   ++
T Consensus       109 ~~~~~~~~~~~~-~~~~~l~~L~ld~~EyalLKAIvLfnpd~~g~~~~~l~~~~~Ve~lq~~~~~aL~~y~~~~~~~~p~  187 (235)
T cd06949         109 VEGMVEIFDMLL-ATASRFRELQLQREEYVCLKAIILLNSSVYTFLLESLESRRQVQRLLDKITDALVHACSKRGLSLQQ  187 (235)
T ss_pred             cccHHHHHHHHH-HHHHHHHHhCCCHHHHHHHHHHHHcCCCcCCcccccccCHHHHHHHHHHHHHHHHHHHHhcCCCCCC
Confidence            334455555544 8999999999999999999999999999999     88899999999999999999999888   88


Q ss_pred             CchHHHHHHhhhhhhhccCC
Q psy3092         328 EPGRFAKLLLRLPSLRSIEV  347 (347)
Q Consensus       328 ~~~Rf~~LL~ll~~lr~i~~  347 (347)
                      ++.||++||++||.||+|++
T Consensus       188 ~~~Rf~~LLl~Lp~LR~l~~  207 (235)
T cd06949         188 QSRRLAQLLLILSHIRHVSN  207 (235)
T ss_pred             cccHHHHHHHhchHHHHhhH
Confidence            99999999999999999863

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=1e-31  Score=234.13  Aligned_cols=166  Identities=31%  Similarity=0.540  Sum_probs=154.7

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV  259 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~  259 (347)
                      ..+..+++.....++.+|+|||.+|+|.+|+.+||+.|||++|.+++++..++++....+.+.+.+|..+.++.....++
T Consensus        38 ~~~~~l~e~~~~~l~~~V~wAK~iPgF~~L~~~DQi~LLk~~w~El~~L~~a~~~~~~~~~l~~~~~~~~~~~~~~~~~~  117 (231)
T cd06937          38 GLWDKFSELSTKCIIKIVEFAKRLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMHNAGF  117 (231)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEecCCceecHHHHhhcCh
Confidence            45778899999999999999999999999999999999999999999999999998888888898998888777766677


Q ss_pred             hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhh
Q psy3092         260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRL  339 (347)
Q Consensus       260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll  339 (347)
                      +.++++++ +++.+|++|++|++||+||+||+||+||++|+.+...|+++|+++..+|++|+..++|+.+.||++||++|
T Consensus       118 ~~~~~~~~-~~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~p~rf~kLLl~L  196 (231)
T cd06937         118 GPLTDLVF-TFANQLLPLEMDDTEIGLLSAICLICGDRQDLEEPDRVEKLQEPLLEALKIYARKRRPDKPHMFPKMLMKI  196 (231)
T ss_pred             HHHHHHHH-HHHHHHHHcCCCHHHHHHHHHHHHcCCCCccCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHh
Confidence            77777766 79999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhccC
Q psy3092         340 PSLRSIE  346 (347)
Q Consensus       340 ~~lr~i~  346 (347)
                      |+||+|+
T Consensus       197 p~LR~l~  203 (231)
T cd06937         197 TDLRSIS  203 (231)
T ss_pred             HHHHHHH
Confidence            9999986

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

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

Probab=100.00  E-value=1.4e-33  Score=209.97  Aligned_cols=82  Identities=49%  Similarity=1.031  Sum_probs=77.7

Q ss_pred             CCcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhh
Q psy3092          55 KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQR  134 (347)
Q Consensus        55 ~~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~  134 (347)
                      ...|.|||++++|+||||.+|+||++||||++.++..|.|..+++|.|+...|..||+|||+||+++||++++||.+|+.
T Consensus        18 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~~~   97 (101)
T cd07160          18 NEVCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAQYVCKNGGKCQMDMYMRRKCQECRLRKCREAGMREQCVLSEEQI   97 (101)
T ss_pred             CCCCeecCCcCcceEECcceehhhhhhhhhcccccCccccCCCCccccCCcccccCccchhHHHHHhCCCHHHhcChhhh
Confidence            35699999999999999999999999999999999999999999999999999999999999999999999999999886


Q ss_pred             hh
Q psy3092         135 TK  136 (347)
Q Consensus       135 ~~  136 (347)
                      ..
T Consensus        98 ~~   99 (101)
T cd07160          98 RL   99 (101)
T ss_pred             hh
Confidence            54

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

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

Probab=99.98  E-value=1.4e-33  Score=201.11  Aligned_cols=76  Identities=87%  Similarity=1.653  Sum_probs=73.3

Q ss_pred             cCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHH
Q psy3092          57 LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEER  132 (347)
Q Consensus        57 ~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r  132 (347)
                      +|.|||++++|+||||.+|+|||+||||++.++..|.|..+++|.+++..|..||+|||+||+++||++++||.+|
T Consensus         2 ~C~VC~~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r   77 (77)
T cd06956           2 ICAICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER   77 (77)
T ss_pred             CCcccCCcCcceEECceeehhHHHHHHHHhhCCCccccCCCCccccCCCccccCccchhHHHhHhCCCHHHhccCC
Confidence            5999999999999999999999999999999999999999999999999999999999999999999999999865

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

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

Probab=99.98  E-value=1.9e-31  Score=233.66  Aligned_cols=166  Identities=40%  Similarity=0.730  Sum_probs=150.2

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCC--CceEecCCccccccchhh-
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVK--DGILLAPGVTVYRSSAHE-  256 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~--~~~~~~~g~~i~~~~~~~-  256 (347)
                      ..+..++++.+..++.+|+|||++|+|..|+.+||+.|+|++|.+++++..+|+++..+  +.+.+++|..++++.... 
T Consensus        38 ~~~~~~~~~a~~~l~~~VewaK~lp~F~~L~~~DQi~LLk~~w~el~~L~~a~rs~~~~~~~~l~~~~g~~~~~~~~~~~  117 (237)
T cd06944          38 DTFGLMCKMADQTLFSIVEWARNSVFFKELKVDDQMKLLQNCWSELLVLDHIYRQVHHGKEDSILLVTGQEVDLSTLASQ  117 (237)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHhCCChhcCCHHHHHHHHHHHhHHHHHHHHHHHhcccCCCCceeecCCCccchhhhhhh
Confidence            45788999999999999999999999999999999999999999999999999998764  678889998887765432 


Q ss_pred             c--CchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHH
Q psy3092         257 A--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAK  334 (347)
Q Consensus       257 ~--~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~  334 (347)
                      .  +...+.++ +.+++.+|++|++|++||++|+||+|||||++|+++...|+++|+++.++|++|+..++++++.||++
T Consensus       118 ~~~~~~~~~~~-i~~~~~~l~~L~ld~~E~~lLkaIiL~npd~~gL~~~~~Ve~~q~~~~~aL~~y~~~~~~~~~~Rf~~  196 (237)
T cd06944         118 AGLGLSSLVDR-AQELVNKLRELQFDRQEFVCLKFLILFNPDVKGLENRQLVESVQEQVNAALLDYTLCNYPQQTDKFGQ  196 (237)
T ss_pred             ccccHHHHHHH-HHHHHHHHHHcCCCHHHHHHHHHHHHcCCCcCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccHHHH
Confidence            2  23445555 56899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhhhhhhccC
Q psy3092         335 LLLRLPSLRSIE  346 (347)
Q Consensus       335 LL~ll~~lr~i~  346 (347)
                      ||++||+||+|+
T Consensus       197 LL~~Lp~Lr~is  208 (237)
T cd06944         197 LLLRLPEIRAIS  208 (237)
T ss_pred             HHHHhHHHHHHH
Confidence            999999999987

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

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

Probab=99.98  E-value=1.4e-31  Score=235.07  Aligned_cols=167  Identities=26%  Similarity=0.449  Sum_probs=155.4

Q ss_pred             hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcC
Q psy3092         179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG  258 (347)
Q Consensus       179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~  258 (347)
                      ...+..+++.....+..+|+|||++|+|..|+.+||+.|||++|.++++++.++++....+.+.+++|..+.++.....+
T Consensus        51 ~~~~~~~~~~~~~~l~~iVefAK~iPgF~~L~~~DQi~LLk~~~~ElliL~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~  130 (243)
T cd06935          51 LEAFSHFTKIITPAITRVVDFAKKLPMFTELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLSGEMAVTREQLKNGG  130 (243)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCccccCChHHHHHHHHHhHHHHHHHHHHHHhCcCCCeEEeeCCeEeeHHHHHhcC
Confidence            44578889999999999999999999999999999999999999999999999998777888999999888877777777


Q ss_pred             chhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhh
Q psy3092         259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLR  338 (347)
Q Consensus       259 ~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~l  338 (347)
                      ++.+.+.++ +++.+|++|++|++||++|+||+||+||++|+++...|+++|+.+..+|++|+..++++.+.||++||++
T Consensus       131 ~~~~~~~i~-~f~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~rf~kLL~~  209 (243)
T cd06935         131 LGVVSDAIF-DLGVSLSSFNLDDTEVALLQAVLLMSSDRPGLACVERIEKLQDSFLLAFEHYINYRKHHVPHFWPKLLMK  209 (243)
T ss_pred             hHHHHHHHH-HHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccHHHHHHHH
Confidence            777777655 8999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhccC
Q psy3092         339 LPSLRSIE  346 (347)
Q Consensus       339 l~~lr~i~  346 (347)
                      ||.||+|+
T Consensus       210 L~~LR~i~  217 (243)
T cd06935         210 VTDLRMIG  217 (243)
T ss_pred             HHHHHHHH
Confidence            99999986

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

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

Probab=99.98  E-value=2.7e-31  Score=224.70  Aligned_cols=166  Identities=28%  Similarity=0.503  Sum_probs=152.7

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV  259 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~  259 (347)
                      ..+..+.+.....+..+|+|||++|+|.+|+.+||+.|||++|.++++++.++++....+.+.+.+|..+.++.....++
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            45778888889999999999999999999999999999999999999999999877777778888998887776666667


Q ss_pred             hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhh
Q psy3092         260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRL  339 (347)
Q Consensus       260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll  339 (347)
                      +.+.+.++ +++.+|++|++|++||++|+||+|||||++|+.+...|+++|+++..+|++|+..++|+.+.||++||++|
T Consensus        92 ~~~~~~~~-~~~~~l~~L~ld~~E~a~LkAivLf~pd~~~L~~~~~Ve~lq~~~~~aL~~~~~~~~p~~~~rf~kLL~~L  170 (189)
T cd06940          92 GDLLNSMF-DFSEKLNSLQLSDEEMGLFTAVVLVSADRSGLENVNLVEALQETLIRALRTLIAKNHPNEPSIFTKLLLKL  170 (189)
T ss_pred             HHHHHHHH-HHHHHHHhcCCCHHHHHHHHHHHHhCCCCcCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCccHHHHHHHHH
Confidence            77777765 89999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhccC
Q psy3092         340 PSLRSIE  346 (347)
Q Consensus       340 ~~lr~i~  346 (347)
                      |+||+|+
T Consensus       171 ~~LR~l~  177 (189)
T cd06940         171 PDLRTLN  177 (189)
T ss_pred             HHHHHHH
Confidence            9999986

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

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

Probab=99.97  E-value=2.1e-33  Score=203.70  Aligned_cols=81  Identities=52%  Similarity=1.164  Sum_probs=77.5

Q ss_pred             CcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhhhc
Q psy3092          58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRTKE  137 (347)
Q Consensus        58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~~~  137 (347)
                      |.|||++++|+||||.+|+||++||||++.++..|.|..+++|.++...|..|++|||+||+++||++++||.+|++..+
T Consensus         2 C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~~~   81 (85)
T cd06961           2 CVVCGDKATGYHYRCITCEGCKGFFRRTVQKKLSYSCKGEGKCEIDKVTRNQCQECRFKKCIAVGMAKDLVLDDRKRGAK   81 (85)
T ss_pred             CceeCCcCcceEEChhhhhhhhHhhHhhhccCCccccCCCCccccCccccccCccchhhhhhhccCCHHHcccccCcccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999988654


Q ss_pred             c
Q psy3092         138 R  138 (347)
Q Consensus       138 ~  138 (347)
                      +
T Consensus        82 ~   82 (85)
T cd06961          82 R   82 (85)
T ss_pred             c
Confidence            3

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

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

Probab=99.97  E-value=4.9e-31  Score=230.67  Aligned_cols=167  Identities=21%  Similarity=0.407  Sum_probs=145.8

Q ss_pred             hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCc--eEecCCccccccchhh
Q psy3092         179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDG--ILLAPGVTVYRSSAHE  256 (347)
Q Consensus       179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~--~~~~~g~~i~~~~~~~  256 (347)
                      ...+..++++.+++++.+|+|||++|+|.+|+.+||+.|||++|.++++++.+|+++...+.  +.+.+|..+.++....
T Consensus        27 ~~~~~~l~ela~~~L~~~VeWAK~iPgF~~L~~~DQi~LLk~~w~ElliL~~a~rs~~~~~~~~l~~~~~~~~~~~~~~~  106 (246)
T cd06947          27 ARLLSSLNRLGERQLVSVVKWAKALPGFRNLHLDDQMTLIQYSWMSLMVFALGWRSYKHVNSQMLYFAPDLVFNEQRMHQ  106 (246)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHhhccCCCCCeEEecCCeeecHHHhhh
Confidence            45578999999999999999999999999999999999999999999999999998876543  5667777776665544


Q ss_pred             cCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcC-CCCCCCCHHHHHHHHHHHHHHHHHHHHhcCC---CCchHH
Q psy3092         257 AGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNP-DVRGLKSQQVVEMLREKVYTSLEEYTRVNHS---EEPGRF  332 (347)
Q Consensus       257 ~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p-~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~---~~~~Rf  332 (347)
                      .+...+.. .+.+++.+|++|++|++||+||+||+|||| +++|+++...|+++|+++..+|.+|+..+++   +.+.||
T Consensus       107 ~~~~~~~~-~~~e~~~~l~~L~ld~~E~acLKAIvLfn~~d~~gL~~~~~Ve~lqe~i~~AL~~yi~~~~~~~~~~~~Rf  185 (246)
T cd06947         107 SAMYSLCL-GMRQISQEFVRLQVTYEEFLCMKVLLLLSTIPKDGLKSQAAFDEMRMNYIKELRKAIVKREKNSSQSWQRF  185 (246)
T ss_pred             ccHHHHHH-HHHHHHHHHHhcCCCHHHHHHHHHHHHcCCCccccccCHHHHHHHHHHHHHHHHHHHHHhCCCCcccchHH
Confidence            45554333 345899999999999999999999999999 7999999999999999999999999987764   558999


Q ss_pred             HHHHhhhhhhhccC
Q psy3092         333 AKLLLRLPSLRSIE  346 (347)
Q Consensus       333 ~~LL~ll~~lr~i~  346 (347)
                      |+||++||.||+|+
T Consensus       186 ~kLLllLp~Lr~i~  199 (246)
T cd06947         186 YQLTKLLDSMHDLV  199 (246)
T ss_pred             HHHHHhhhhHHHHH
Confidence            99999999999986

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

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

Probab=99.97  E-value=7.4e-31  Score=228.52  Aligned_cols=167  Identities=24%  Similarity=0.399  Sum_probs=147.4

Q ss_pred             hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCc--eEecCCccccccchhh
Q psy3092         179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDG--ILLAPGVTVYRSSAHE  256 (347)
Q Consensus       179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~--~~~~~g~~i~~~~~~~  256 (347)
                      ...+..+++..+++++.+|+|||++|+|.+|+.+||+.|||++|.+++++..+||+++..+.  +.+.+|..+..+....
T Consensus        27 ~~~~~~l~ela~~~L~~iVeWAK~IPgF~~L~~~DQi~LLk~~w~EllvL~~a~rs~~~~~~~~l~fa~~~~~~~~~~~~  106 (248)
T cd07075          27 ENLLSTLNRLAGKQMIQVVKWAKVLPGFRNLPLEDQITLIQYSWMCLSSFALSWRSYKHTNSQFLYFAPDLVFNEERMHQ  106 (248)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhccCCCCCceEEecCCccccHHHHhh
Confidence            34578999999999999999999999999999999999999999999999999999887543  7778888877776655


Q ss_pred             cCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCC-CCCCCCHHHHHHHHHHHHHHHHHHHHhcCC---CCchHH
Q psy3092         257 AGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD-VRGLKSQQVVEMLREKVYTSLEEYTRVNHS---EEPGRF  332 (347)
Q Consensus       257 ~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~-~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~---~~~~Rf  332 (347)
                      .+..++ .+.+.+++.+|++|++|++||+||+||+||||| ++||++...|+++|+++..+|++|+..+++   +.+.||
T Consensus       107 ~~~~~~-~~~~~e~~~~l~~L~Ld~~E~acLKAIvLfn~d~~~gL~~~~~Ve~lqe~~~~aL~~yi~~~~~~~~~~~~RF  185 (248)
T cd07075         107 SAMYEL-CQGMHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKDGLKSQAAFEEMRTNYIKELRKMVTKAPNNSGQSWQRF  185 (248)
T ss_pred             ccHHHH-HHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCCcccchhHH
Confidence            555553 344668999999999999999999999999996 799999999999999999999999996655   356999


Q ss_pred             HHHHhhhhhhhccC
Q psy3092         333 AKLLLRLPSLRSIE  346 (347)
Q Consensus       333 ~~LL~ll~~lr~i~  346 (347)
                      |+|+++||.||+|+
T Consensus       186 ~~LLllLp~Lr~i~  199 (248)
T cd07075         186 YQLTKLLDSMHDLV  199 (248)
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999999986

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

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

Probab=99.97  E-value=1.3e-33  Score=204.51  Aligned_cols=79  Identities=53%  Similarity=1.244  Sum_probs=75.9

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhh
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQR  134 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~  134 (347)
                      .+|.|||++++|+||||.+|+|||+||||++..+..|.|..+++|.+++..|..||+|||+||+++||++++||.+|++
T Consensus         5 ~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~R~~   83 (85)
T cd06964           5 KPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNK   83 (85)
T ss_pred             CCCcccCCcCcccEECcceeeeeeeEEeeeecCCCCeECCCCCccccCCcccccCccchhhhhhhhCCCHHHhhccccC
Confidence            4699999999999999999999999999999988999999999999999999999999999999999999999999876

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

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

Probab=99.97  E-value=3e-33  Score=206.82  Aligned_cols=81  Identities=52%  Similarity=1.073  Sum_probs=76.7

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhh
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRT  135 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~  135 (347)
                      ..|.|||++++|+||||.+|+|||+||||++..+..|.|..+++|.+++..|..||+|||+||+++||++++||.+|+..
T Consensus         5 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~vq~~r~~~   84 (97)
T cd07170           5 RLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRG   84 (97)
T ss_pred             CCCeecCCcCcceEECceeehhhhHHHHHHhccCCceeecCCCccccCcccCccCCccccchhhhcCCCHHHcccccCCC
Confidence            45999999999999999999999999999999999999999999999999999999999999999999999999988764


Q ss_pred             h
Q psy3092         136 K  136 (347)
Q Consensus       136 ~  136 (347)
                      .
T Consensus        85 ~   85 (97)
T cd07170          85 G   85 (97)
T ss_pred             C
Confidence            3

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

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

Probab=99.97  E-value=7.9e-33  Score=198.78  Aligned_cols=78  Identities=49%  Similarity=1.112  Sum_probs=74.4

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHh
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQ  133 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~  133 (347)
                      ..|.|||++++|+||||.+|+|||+||||++..+..|.|..+++|.++...|..||+|||+||+++||++++|+.+|.
T Consensus         4 ~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~~~   81 (82)
T cd07171           4 HFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRRERR   81 (82)
T ss_pred             CCCeecCCcCcceEECceeehhhHHhHHHHeeCCCceeCCCCCccccCCcccccCccchhHHHhHhcCCHHHHHHhhc
Confidence            459999999999999999999999999999998999999999999999999999999999999999999999998763

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

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

Probab=99.97  E-value=6e-33  Score=203.25  Aligned_cols=83  Identities=52%  Similarity=1.066  Sum_probs=77.6

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhh
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRT  135 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~  135 (347)
                      +.|.|||++++|+||||.+|+||++||||++.++..|.|..+++|.++...|..|++|||+||+++||++++||.+++-.
T Consensus         2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~~~   81 (91)
T cd07161           2 ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYHCKYGRACEMDMYMRRKCQECRLKKCLSVGMRPECVVPESQCA   81 (91)
T ss_pred             CCCeeCCCcCcceEECceeehhhHHHHHHHhccCCceecCCCCccccCccccccCccchhhHHhHcCCCHHHcCchhhhh
Confidence            35999999999999999999999999999999999999999999999999999999999999999999999999997765


Q ss_pred             hcc
Q psy3092         136 KER  138 (347)
Q Consensus       136 ~~~  138 (347)
                      .++
T Consensus        82 ~~~   84 (91)
T cd07161          82 IKR   84 (91)
T ss_pred             HHH
Confidence            443

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

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

Probab=99.97  E-value=7.8e-31  Score=229.41  Aligned_cols=167  Identities=31%  Similarity=0.526  Sum_probs=146.9

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccC--CCceEecCCccccccchhh-
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISV--KDGILLAPGVTVYRSSAHE-  256 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~--~~~~~~~~g~~i~~~~~~~-  256 (347)
                      ..+..++++.+..++.+|+|+|++|+|..|+.+||+.|||++|.+++++..+|+++..  .+.+.+++|..++.+.... 
T Consensus        38 ~~~~~l~~~a~~~L~~~VeWaK~lP~F~~L~~~DQi~LLk~~w~el~vL~~a~rs~~~~~~~~l~~~~g~~~~~~~~~~~  117 (237)
T cd07070          38 APFGLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQHGKEGSILLVTGQEVELSTVAAQ  117 (237)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHhCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCceeecCCCeechhHHHHH
Confidence            4578899999999999999999999999999999999999999999999999998754  4678888998887665422 


Q ss_pred             cCc--hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHH
Q psy3092         257 AGV--GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAK  334 (347)
Q Consensus       257 ~~~--~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~  334 (347)
                      .+.  .... ..+.+++.+|++|++|.+||++|+||+|||||.+|+++...|+++|+++..+|.+|+..++|+.+.||++
T Consensus       118 ~~~~~~~~~-~~~~e~~~kl~~L~ld~~Ey~~LkaIiLfnpd~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~Rf~k  196 (237)
T cd07070         118 AGSLLHSLV-LRAQELVLQLHALQLDRQEFVCLKFLILFSLDVKFLNNHSLVKDAQEKANAALLDYTLCHYPHCGDKFQQ  196 (237)
T ss_pred             HhHHHHHHH-HHHHHHHHHHHHhCCCHHHHHHHHHHHhcCCCccCCCCHHHHHHHHHHHHHHHHHHHHhcCCCcchHHHH
Confidence            221  1122 2246899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhhhhhhccCC
Q psy3092         335 LLLRLPSLRSIEV  347 (347)
Q Consensus       335 LL~ll~~lr~i~~  347 (347)
                      ||++||+||+|+.
T Consensus       197 LLl~Lp~LRsis~  209 (237)
T cd07070         197 LLLRLVEVRALSM  209 (237)
T ss_pred             HHHHhHHHHHhhH
Confidence            9999999999873

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

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

Probab=99.97  E-value=1.2e-30  Score=223.83  Aligned_cols=168  Identities=37%  Similarity=0.638  Sum_probs=143.1

Q ss_pred             hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcC
Q psy3092         179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG  258 (347)
Q Consensus       179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~  258 (347)
                      ....+.+++++.+.++.+|+|+|++|+|..|+.+||+.|+|++|.+++++..++++...++..++.++............
T Consensus        25 ~~~~~~~~~~a~~~L~~~VewaK~ip~F~~L~~~DQi~LLk~~w~el~iL~~a~~s~~~~~~~ll~~~~~~~~~~~~~~~  104 (206)
T cd06950          25 EVSPESVCESAARLLFMAVKWAKSIPAFSTLPFRDQLILLEESWSELFLLGAAQWSLPLDSCPLLAVPGLSPDNTEAERT  104 (206)
T ss_pred             ccCHHHHHHHHHHHHHHHHHHHHhCCccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCcceeecCCcccccccchhhH
Confidence            35678999999999999999999999999999999999999999999999999998877665555543332222211111


Q ss_pred             chhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhh
Q psy3092         259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLR  338 (347)
Q Consensus       259 ~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~l  338 (347)
                      +.... +.+.+++.+|++|++|++||++||||+|||||++|+++...|+++|+++..+|++|+..++++++.||++||++
T Consensus       105 ~~~~~-~~i~~~~~~~~~L~ld~~EyalLKai~L~npd~~~L~~~~~Ve~lq~~~~~aL~~y~~~~~~~~~~Rf~kLLl~  183 (206)
T cd06950         105 FLSEV-RALQETLSRFRQLRVDATEFACLKAIVLFKPETRGLKDPAQVEALQDQAQLMLNKHIRTRYPTQPARFGKLLLL  183 (206)
T ss_pred             HHHHH-HHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHH
Confidence            11222 44678999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhccCC
Q psy3092         339 LPSLRSIEV  347 (347)
Q Consensus       339 l~~lr~i~~  347 (347)
                      ||+||+++.
T Consensus       184 Lp~lr~ls~  192 (206)
T cd06950         184 LPSLRFISS  192 (206)
T ss_pred             HHHHHhhhH
Confidence            999999873

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

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

Probab=99.97  E-value=1.6e-30  Score=227.40  Aligned_cols=167  Identities=23%  Similarity=0.427  Sum_probs=144.7

Q ss_pred             hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccC-C-CceEecCCccccccchhh
Q psy3092         179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISV-K-DGILLAPGVTVYRSSAHE  256 (347)
Q Consensus       179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~-~-~~~~~~~g~~i~~~~~~~  256 (347)
                      ....+.++++.+++++.+|+|||++|+|.+|+.+||+.|||++|.++++++.+|+++.. + +.+.+.+|..+.......
T Consensus        27 ~~~~~~l~~la~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~w~ElliL~~a~rs~~~~~~~~l~~~~~~~l~~~~~~~  106 (246)
T cd07073          27 AALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHK  106 (246)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHcCCCccCCCHHHHHHHHHHHHHHHHHHHHHHhccccCCCCeEEecCCeeechhhhcc
Confidence            34577899999999999999999999999999999999999999999999999999876 3 347888887766554433


Q ss_pred             cCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcC-CCCCCCCHHHHHHHHHHHHHHHHHHHHhcCC---CCchHH
Q psy3092         257 AGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNP-DVRGLKSQQVVEMLREKVYTSLEEYTRVNHS---EEPGRF  332 (347)
Q Consensus       257 ~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p-~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~---~~~~Rf  332 (347)
                      .+......+ +.+++.+|++|++|.+||+|||||+|||| +.+|+++...|+++|+++..+|.+|+..+++   +.+.||
T Consensus       107 ~~~~~~~~~-l~~~~~~l~~L~ld~~EyacLKAIiLfnp~d~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~~~~~Rf  185 (246)
T cd07073         107 SRMYSQCVR-MRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFFDELRMNYIKELDRIIACKRKNPTSCSRRF  185 (246)
T ss_pred             ccHHHHHHH-HHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCcccccCHHHHHHHHHHHHHHHHHHHHhcCCCCcccchHH
Confidence            333344333 34899999999999999999999999999 8999999999999999999999999987642   568999


Q ss_pred             HHHHhhhhhhhccC
Q psy3092         333 AKLLLRLPSLRSIE  346 (347)
Q Consensus       333 ~~LL~ll~~lr~i~  346 (347)
                      ++||++||+||+|+
T Consensus       186 ~kLLl~Lp~LRsi~  199 (246)
T cd07073         186 YQLTKLLDSVQPIA  199 (246)
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999999986

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

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

Probab=99.97  E-value=2.5e-30  Score=225.37  Aligned_cols=167  Identities=39%  Similarity=0.690  Sum_probs=152.0

Q ss_pred             hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcC
Q psy3092         179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG  258 (347)
Q Consensus       179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~  258 (347)
                      ..+..+++..|..+++.+++|+|+||+|+.|+.+||+.|+|++|.+++++..+++++..++.+++++|..++.+... .+
T Consensus        31 ~~~~~~~~~~~~~~l~~~vewak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~s~~~~~~l~~~~g~~~~~~~~~-~~  109 (222)
T cd06931          31 IASINDVCESMKQQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGVARRSMPYKDILLLGNDLIIPRHCPE-PE  109 (222)
T ss_pred             cCCHHHHHHHHHHHHHHHHHHHHhCCccccCChHHHHHHHHHHHHHHHHHHHHHhccCCCCeeeeCCCccccccccc-ch
Confidence            35678999999999999999999999999999999999999999999999999999888888999999877665433 34


Q ss_pred             chhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhh
Q psy3092         259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLR  338 (347)
Q Consensus       259 ~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~l  338 (347)
                      +..+..+++.+++.+|++|++|++||++|+||++|+|+.+|+++...++++|+++.++|.+|+..++++++.||++||++
T Consensus       110 ~~~~~~~~~~~~~~~l~~L~l~~~E~~lLkaiil~~p~~~~ls~~~~i~~~r~~~~~aL~~y~~~~~~~~~~Rf~~LL~~  189 (222)
T cd06931         110 ISRVANRILDELVLPLRDLNIDDNEYACLKAIVFFDPDAKGLSDPQKIKRLRFQVQVSLEDYINDRQYDSRGRFGELLLL  189 (222)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCccCCCCHHHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHHHH
Confidence            45566777788999999999999999999999999999999999999999999999999999988888999999999999


Q ss_pred             hhhhhccC
Q psy3092         339 LPSLRSIE  346 (347)
Q Consensus       339 l~~lr~i~  346 (347)
                      +|.||+++
T Consensus       190 l~~lr~~~  197 (222)
T cd06931         190 LPTLQSIT  197 (222)
T ss_pred             HHHHHHHH
Confidence            99999875

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

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

Probab=99.97  E-value=6.7e-33  Score=196.76  Aligned_cols=75  Identities=55%  Similarity=1.140  Sum_probs=72.5

Q ss_pred             CcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHH
Q psy3092          58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEER  132 (347)
Q Consensus        58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r  132 (347)
                      |.|||++++|+||||.+|+|||+||||++..+..|.|..+++|.+++..|..||+|||+||+++||++++||.+|
T Consensus         1 C~VC~~~~~g~hygv~sC~aCk~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r   75 (75)
T cd07155           1 CLVCGDIASGYHYGVASCEACKAFFKRTIQGNLGYSCPSTSECEVDKKRRKSCQACRLQKCLKVGMLKEGVRLDR   75 (75)
T ss_pred             CcccCccCcceEEChhhhhhhHHHHHHHhhCCCceeCCcCCCcccCCcccccCccchhhhhhHhCCCHHHcccCC
Confidence            899999999999999999999999999999889999999999999999999999999999999999999999865

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

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

Probab=99.97  E-value=8.7e-31  Score=228.00  Aligned_cols=164  Identities=27%  Similarity=0.504  Sum_probs=150.4

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV  259 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~  259 (347)
                      ..+..+++.....+..+++|||++|+|.+|+.+||+.|||++|.++++++.++++....+.+++.+|..+.+... ..++
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            457888999999999999999999999999999999999999999999999999998888899999988876653 4566


Q ss_pred             hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhc--CCCCchHHHHHHh
Q psy3092         260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVN--HSEEPGRFAKLLL  337 (347)
Q Consensus       260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~--~~~~~~Rf~~LL~  337 (347)
                      +++.+.++ +++.+|++|++|.+||+||+||+|| ||++||++...|+++|+++..+|++|+..+  +++.+.||++||+
T Consensus       120 ~~~~~~i~-ef~~~l~~L~ld~~E~a~LkAIvLf-~Dr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~p~~p~rf~kLLl  197 (238)
T cd07348         120 GDWIDSIL-EFSQSLHRMNLDVSAFSCLAALVII-TDRHGLKEPKRVEELQNRLISCLKEHVSGSASEPQRPNCLSRLLG  197 (238)
T ss_pred             HHHHHHHH-HHHHHHHHcCCCHHHHHHHHHHHHc-CCCcCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccccHHHHHHH
Confidence            77777755 8999999999999999999999999 799999999999999999999999999875  4789999999999


Q ss_pred             hhhhhhccC
Q psy3092         338 RLPSLRSIE  346 (347)
Q Consensus       338 ll~~lr~i~  346 (347)
                      +||+||+|+
T Consensus       198 ~Lp~LRsl~  206 (238)
T cd07348         198 KLPELRTLC  206 (238)
T ss_pred             HHHHHHHHH
Confidence            999999986

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

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

Probab=99.97  E-value=1.3e-32  Score=201.58  Aligned_cols=80  Identities=56%  Similarity=1.145  Sum_probs=76.6

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhh
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRT  135 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~  135 (347)
                      ..|.|||++++|+||||.+|+|||+||||++..+..|.|..+++|.++...|..|++|||+||+++||++++||.+|++.
T Consensus         7 ~~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R~~~   86 (90)
T cd07168           7 KLCSICEDKATGLHYGIITCEGCKGFFKRTVQNKRVYTCVGDGRCEITKAQRNRCQYCRFRKCIRKGMMLAAVREDRMPG   86 (90)
T ss_pred             CCCcccCCcCcceEECceehhhhhHhhhhhhcCCCCccCCCCCCccccccccccccccchhhhhhcCCCHHHhhcccCCC
Confidence            46999999999999999999999999999999999999999999999999999999999999999999999999998864

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

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

Probab=99.97  E-value=6e-33  Score=200.35  Aligned_cols=80  Identities=49%  Similarity=1.053  Sum_probs=75.7

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhh
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRT  135 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~  135 (347)
                      ..|.|||++++|+||||.+|+|||+||||++.++..|.|..+++|.++...|..||+|||+||+++||++++|+.+++..
T Consensus         2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~~~   81 (84)
T cd06962           2 ELCVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCEMDMYMRRKCQECRLRKCKEMGMLAECLLTEIQCK   81 (84)
T ss_pred             CCCeecCCcCcceEECcceeecceeeeeeeeccCCceecCCCCcCccCccccccCccchhhHHHHhCCChHHccCHHHHh
Confidence            35999999999999999999999999999999999999999999999999999999999999999999999999887653

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

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

Probab=99.97  E-value=3.1e-30  Score=224.15  Aligned_cols=167  Identities=35%  Similarity=0.649  Sum_probs=150.6

Q ss_pred             hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcC
Q psy3092         179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG  258 (347)
Q Consensus       179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~  258 (347)
                      ...+..++++..+.++.+++|+|.+|+|..|+.+||+.|+|++|.+++++..|++++..++.+.+++|..+.++.....+
T Consensus        26 ~~~~~~~~~~a~~~l~~~vewaK~lp~F~~L~~~DQi~LLk~~~~~~~~l~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~  105 (221)
T cd07068          26 VSLLATLSDLADRELVHIISWAKHIPGFSDLSLNDQMHLLQSAWLEILMLGLVWRSLPHPGKLVFAPDLLLDREQARVEG  105 (221)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHhhHHHHHHHHHHhhcCCCCeEEeCCCceECHHHHhhcc
Confidence            45688999999999999999999999999999999999999999999999999999888887888888766655444445


Q ss_pred             chhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCC-CCchHHHHHHh
Q psy3092         259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHS-EEPGRFAKLLL  337 (347)
Q Consensus       259 ~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~-~~~~Rf~~LL~  337 (347)
                      ...+.+. +.+++.+|++|++|++||++|+||++||||++|+.+...|+++|+++.++|++|+..+++ +++.||++||+
T Consensus       106 ~~~~~~~-~~~~~~~l~~L~ld~~E~~lLkaIil~npd~~~L~~~~~V~~~q~~~~~aL~~y~~~~~~~~~~~Rf~~LL~  184 (221)
T cd07068         106 LLEIFDM-LLQLVRRFRELGLQREEYVCLKAIILANSDVRHLEDREAVQQLRDAILDALVDVEAKRHGSQQPRRLAQLLL  184 (221)
T ss_pred             HHHHHHH-HHHHHHHHHHcCCCHHHHHHHHHHHHcCCCccCccCHHHHHHHHHHHHHHHHHHHHHhCCCccccHHHHHHH
Confidence            5555554 468999999999999999999999999999999999999999999999999999999999 99999999999


Q ss_pred             hhhhhhccC
Q psy3092         338 RLPSLRSIE  346 (347)
Q Consensus       338 ll~~lr~i~  346 (347)
                      +++.||+++
T Consensus       185 ~l~~Lr~~~  193 (221)
T cd07068         185 LLPHLRQAS  193 (221)
T ss_pred             hccHHHHHH
Confidence            999999875

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

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

Probab=99.97  E-value=5.6e-33  Score=202.14  Aligned_cols=80  Identities=64%  Similarity=1.349  Sum_probs=76.6

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhh
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRT  135 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~  135 (347)
                      ..|.|||++++|+||||.+|+||++||||++.++..|.|..+++|.+++..|..|++|||+||+++||++++||.+|++.
T Consensus         4 ~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~R~~~   83 (87)
T cd06967           4 ELCVVCGDKASGRHYGAVSCEGCKGFFKRSIRKNLGYSCRGSKDCVINKHHRNRCQYCRLQKCLAMGMKSDSVQCERKPI   83 (87)
T ss_pred             CCCeecCCcCCcCEeCcceEeeeeeEeeeeeeCCCCcccCCCCccccCccccccCccchhhhhhHcCCCHHHhccccCCC
Confidence            45999999999999999999999999999999999999999999999999999999999999999999999999998864

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

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

Probab=99.97  E-value=5.2e-33  Score=203.74  Aligned_cols=79  Identities=58%  Similarity=1.262  Sum_probs=75.4

Q ss_pred             cCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCC-CCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhh
Q psy3092          57 LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREG-RNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRT  135 (347)
Q Consensus        57 ~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~-~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~  135 (347)
                      .|.|||++++|+||||.+|+|||+||||++.++..|.|..+ ++|.++...|..||+|||+||+++||++++||.+|++.
T Consensus         8 ~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R~~~   87 (92)
T cd06970           8 LCRVCGDTSSGKHYGIYACNGCSGFFKRSVRRKLIYRCQAGTGMCPVDKAHRNQCQACRLKKCLQAGMNKDAVQNERQPR   87 (92)
T ss_pred             CCeecCCcCcccEECccEEeeeeeEeeeeeecCCCceeecCCCcCccCCCccccCccchhhHhhHhCCCHHHcccccCcc
Confidence            49999999999999999999999999999999999999985 89999999999999999999999999999999998854

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

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

Probab=99.97  E-value=2e-30  Score=217.88  Aligned_cols=165  Identities=31%  Similarity=0.540  Sum_probs=148.9

Q ss_pred             HHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCch
Q psy3092         181 QATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVG  260 (347)
Q Consensus       181 ~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~~  260 (347)
                      .+..+++..+..+..+++|+|++|+|..|+.+||+.|+|++|.+++++..++++....+.+.+++|.....+.....+..
T Consensus         3 ~~~~~~~~~~~~l~~~v~~ak~ip~F~~L~~~Dq~~Llk~~~~~l~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (174)
T cd06929           3 KFDHFTEIMTVAIRRVVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATLYDPEKNSLTFGDGKGNSRDVLLNGGFG   82 (174)
T ss_pred             HHHHHHHHHHHHHHHHHhhccCCcCcccCChhHHHHHHHhcHHHHHHHHHHHHhcccCCeEEecCCceecHHHHHHcccH
Confidence            36788899999999999999999999999999999999999999999999997777677888889887655544444555


Q ss_pred             hhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhhh
Q psy3092         261 GIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLP  340 (347)
Q Consensus       261 ~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll~  340 (347)
                      .+.+++. +++.+|++|++|++||++|+||+||+|+.+|+++...+++.|+++..+|++|+..++++++.||++||++++
T Consensus        83 ~~~~~~~-~~~~~l~~L~l~~~E~~llkai~l~~pd~~~l~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~Ll~~l~  161 (174)
T cd06929          83 EFIEPLF-EFAEKMNKLQLDDNEYALLTAIVLFSPDRPGLQDVDTVEKLQERLLEALQRYLKVNHPDAPQMFAKLLKKLT  161 (174)
T ss_pred             HHHHHHH-HHHHHHHHcCCCHHHHHHHHHHHHhCCCcccCcCHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHHhH
Confidence            6666655 699999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhccC
Q psy3092         341 SLRSIE  346 (347)
Q Consensus       341 ~lr~i~  346 (347)
                      .||.++
T Consensus       162 ~lr~l~  167 (174)
T cd06929         162 ELRTLN  167 (174)
T ss_pred             HHHHHH
Confidence            999876

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).

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

Probab=99.97  E-value=1.6e-32  Score=196.35  Aligned_cols=77  Identities=58%  Similarity=1.316  Sum_probs=74.5

Q ss_pred             CcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhh
Q psy3092          58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQR  134 (347)
Q Consensus        58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~  134 (347)
                      |.|||++++|+||||.+|+|||+||||++.++..|.|..+++|.++...|..|++|||+||+++||++++||.+|++
T Consensus         1 C~VCg~~~~g~hyG~~~C~~C~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~   77 (78)
T cd07164           1 CRVCGDRASGKHYGVPSCDGCRGFFKRSIRRNLAYVCKENGSCVVDVARRNQCQACRFKKCLQVNMNRDAVQHERAP   77 (78)
T ss_pred             CcccCccCcceEECcchhhhhhhhhhhhccCCCCccCCCCCcccccCcccccCccchhhhhhHhcCCHHHhccCCCC
Confidence            89999999999999999999999999999988999999999999999999999999999999999999999998874

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

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

Probab=99.97  E-value=3.2e-30  Score=214.76  Aligned_cols=162  Identities=44%  Similarity=0.812  Sum_probs=144.1

Q ss_pred             hhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccC--CCceEecCCccccccchhhcCch
Q psy3092         183 TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISV--KDGILLAPGVTVYRSSAHEAGVG  260 (347)
Q Consensus       183 ~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~--~~~~~~~~g~~i~~~~~~~~~~~  260 (347)
                      +.++++..+.++.+++|+|.+|+|..|+.+||+.|+|++|.+++++..|++++..  .+.+.+++|..+..+.....+..
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            4678888999999999999999999999999999999999999999999999876  45677888887776654433334


Q ss_pred             hhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhhh
Q psy3092         261 GIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLP  340 (347)
Q Consensus       261 ~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll~  340 (347)
                      .+.+ .+.+++.+|++|++|++||++|+||++|+|+++|+++...+++.|+++.++|++|+..++++++.||++||+++|
T Consensus        82 ~~~~-~~~~~~~~l~~L~l~~~E~~lLkai~l~~p~~~~l~~~~~v~~~q~~~~~aL~~~~~~~~~~~~~R~~~ll~~l~  160 (165)
T cd06930          82 ELVQ-RLQELLSKLRSLQLDPKEYACLKAIVLFNPDLPGLKNQQQVEELQEKAQQALQEYIRKRYPQQPARFAKLLLRLP  160 (165)
T ss_pred             HHHH-HHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHHHHHHHHHHHhhCCCchhHHHHHHHHhH
Confidence            4444 456899999999999999999999999999999999999999999999999999999888899999999999999


Q ss_pred             hhhcc
Q psy3092         341 SLRSI  345 (347)
Q Consensus       341 ~lr~i  345 (347)
                      .||+|
T Consensus       161 ~lr~~  165 (165)
T cd06930         161 ELRSI  165 (165)
T ss_pred             hhccC
Confidence            99986

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).

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

Probab=99.97  E-value=3.9e-30  Score=223.71  Aligned_cols=167  Identities=30%  Similarity=0.555  Sum_probs=148.5

Q ss_pred             hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcC
Q psy3092         179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG  258 (347)
Q Consensus       179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~  258 (347)
                      ...+..++++..+.++.+++|+|++|+|..|+.+||+.|||++|.+++++..+++++..++.+++.+|....+......+
T Consensus        26 ~~~~~~~~~~~~~~l~~~Ve~aK~lp~F~~L~~~DQi~LLk~~~~el~lL~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~  105 (221)
T cd06946          26 IKALTTLSDLADRELVVIIGWAKHIPGFSSLSLNDQMSLLQSAWMEILTLGVVFRSLPFNGELVFAEDFILDEELAREAG  105 (221)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHccCCCCceeecCCeEEcHHHHhhcC
Confidence            35578899999999999999999999999999999999999999999999999999988888888777655544443344


Q ss_pred             chhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCC-CCchHHHHHHh
Q psy3092         259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHS-EEPGRFAKLLL  337 (347)
Q Consensus       259 ~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~-~~~~Rf~~LL~  337 (347)
                      ...+. +.+.+++.+|++|++|++||++|+||+||||+..++++.+.|+++|+++.++|.+||..+++ +++.||++||+
T Consensus       106 ~~~~~-~~~~~~~~~l~~L~l~~~E~~lLkai~L~npd~~~l~~~~~v~~~q~~~~~aL~~y~~~~~~~~~p~Rf~~LL~  184 (221)
T cd06946         106 LLELY-SACLQLVRRLQRLRLEKEEYVLLKALALANSDSVHIEDVEAVRQLRDALLEALSDYEAGRHPGEAPRRAGQLLL  184 (221)
T ss_pred             HHHHH-HHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcchhHHHHHHh
Confidence            44444 34568999999999999999999999999999999999999999999999999999998888 89999999999


Q ss_pred             hhhhhhccC
Q psy3092         338 RLPSLRSIE  346 (347)
Q Consensus       338 ll~~lr~i~  346 (347)
                      ++|.||+++
T Consensus       185 ~l~~Lr~~~  193 (221)
T cd06946         185 TLPLLRQTD  193 (221)
T ss_pred             hchhHHHHH
Confidence            999999875

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-

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

Probab=99.97  E-value=3.1e-30  Score=225.79  Aligned_cols=166  Identities=35%  Similarity=0.610  Sum_probs=145.2

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccC--CCceEecCCccccccchh--
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISV--KDGILLAPGVTVYRSSAH--  255 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~--~~~~~~~~g~~i~~~~~~--  255 (347)
                      ..+..++++.+..++.+|+|||++|+|.+|+.+||+.|||++|.++++++.++++...  .+.+.+.+|..++.....  
T Consensus        40 ~~~~~i~~~a~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~w~EllvL~~a~~s~~~~~~~~~ll~~~~~~~~~~~~~~  119 (241)
T cd07069          40 STFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQ  119 (241)
T ss_pred             chHHHHHHHHHHHHHHHHHHHhhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCeeEecCCCccCchhhhhh
Confidence            4578899999999999999999999999999999999999999999999999998754  355777788765543211  


Q ss_pred             -hcCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHH
Q psy3092         256 -EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAK  334 (347)
Q Consensus       256 -~~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~  334 (347)
                       ..++..+. +.+.+++.+|++|++|.+||++||||+|||||++|+++...|+++|+++..+|++|+..++|+.+.||++
T Consensus       120 ~~~~~~~~~-~~~~e~~~~lr~L~ld~~E~a~LKaivLfnpd~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~Rf~k  198 (241)
T cd07069         120 AGATLNNLM-SHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQ  198 (241)
T ss_pred             hhhHHHHHH-HHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCchhHHHH
Confidence             11233333 4467999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhhhhhhccC
Q psy3092         335 LLLRLPSLRSIE  346 (347)
Q Consensus       335 LL~ll~~lr~i~  346 (347)
                      ||++||+||+|+
T Consensus       199 LLl~Lp~LR~is  210 (241)
T cd07069         199 LLLRLPEIRAIS  210 (241)
T ss_pred             HHHHhHHHHHhh
Confidence            999999999986

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).

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

Probab=99.97  E-value=3.8e-33  Score=201.11  Aligned_cols=79  Identities=57%  Similarity=1.229  Sum_probs=74.9

Q ss_pred             CcccCCCCCCcccccccchhhHHHHHhhhcCCCccccc-CCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhhh
Q psy3092          58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACR-EGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRTK  136 (347)
Q Consensus        58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~-~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~~  136 (347)
                      |.|||++++|+||||.+|+|||+||||++.++..|.|. .+++|.++...|..||+|||+||+++||++++||.+|++.+
T Consensus         1 C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~p~~   80 (82)
T cd06957           1 CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKGIIYTCIAGNGNCVVDKARRNWCPFCRLQKCFAVGMNRAAVQEERGPRK   80 (82)
T ss_pred             CCccCccCcceEECcceEeeeeeEEEEeecCCCceEccCccCCCccCCCccCcccCcchhhcccccCCHHHhccccCcCC
Confidence            89999999999999999999999999999999999999 56899999999999999999999999999999999887654

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

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

Probab=99.97  E-value=3e-30  Score=224.87  Aligned_cols=164  Identities=28%  Similarity=0.508  Sum_probs=149.4

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV  259 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~  259 (347)
                      ..+..+++.....+..+|+|||++|+|.+|+.+||+.|||++|.++++++.++++....+.+++.+|..+.+... ..++
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            457788899999999999999999999999999999999999999999999999988888899999988776553 3566


Q ss_pred             hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcC--CCCchHHHHHHh
Q psy3092         260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNH--SEEPGRFAKLLL  337 (347)
Q Consensus       260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~--~~~~~Rf~~LL~  337 (347)
                      +.+++.+ .+++.+|++|++|++||+||+||+|| +|++|+.+...|+++|+++..+|++|+..++  ++.+.||++||+
T Consensus       120 ~~~~~~i-~ef~~~l~~L~ld~~E~alLkAIvLf-~D~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~p~~~~rf~kLLl  197 (238)
T cd07071         120 GEWIDSI-VEFSSNLQNMNIDISAFSCIAALAMV-TERHGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLG  197 (238)
T ss_pred             HHHHHHH-HHHHHHHHhcCCCHHHHHHHHHHHHc-CCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCCcccHHHHHHH
Confidence            7777776 48999999999999999999999999 5999999999999999999999999998764  589999999999


Q ss_pred             hhhhhhccC
Q psy3092         338 RLPSLRSIE  346 (347)
Q Consensus       338 ll~~lr~i~  346 (347)
                      +||+||+|+
T Consensus       198 ~Lp~LRsl~  206 (238)
T cd07071         198 KLPELRTLC  206 (238)
T ss_pred             HhHHHHHHH
Confidence            999999986

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).

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

Probab=99.97  E-value=8.3e-33  Score=203.43  Aligned_cols=80  Identities=50%  Similarity=1.198  Sum_probs=75.5

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccC--CCCcccccccccCchhhhhHHHHhcCcchhHHHHHHh
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACRE--GRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQ  133 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~--~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~  133 (347)
                      ..|.|||++++|+||||.+|+|||+||||++..+..|.|..  +++|.+++..|..||+|||+||+++||++++||.+|+
T Consensus         7 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~r~   86 (92)
T cd07163           7 IPCKVCGDRSSGKHYGIYACDGCSGFFKRSIRRNRQYVCKSKGQGGCPVDKTHRNQCRACRLKKCFEVGMNKDAVQHERG   86 (92)
T ss_pred             CCCcccCCcCcccEECceeeeeeeeEEeeeecCCCCcCCCCCCCCCCccCCCccccCccchhhhhhhhcCCHHHhhcccC
Confidence            45999999999999999999999999999999999999997  4799999999999999999999999999999999888


Q ss_pred             hh
Q psy3092         134 RT  135 (347)
Q Consensus       134 ~~  135 (347)
                      +.
T Consensus        87 p~   88 (92)
T cd07163          87 PR   88 (92)
T ss_pred             cC
Confidence            64

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

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

Probab=99.97  E-value=2.6e-30  Score=227.05  Aligned_cols=167  Identities=26%  Similarity=0.407  Sum_probs=149.6

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV  259 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~  259 (347)
                      ..+..++++....+..+|+|||.+|+|..|+.+||+.|||++|.+++++..++++....+.+.+++|..+.++.....+.
T Consensus        43 ~~~~~~~~~~~~~i~~~VefaK~lP~F~~L~~~DQi~LLK~~~~el~iL~~a~~~~~~~~~~~~~~g~~~~~~~~~~~~~  122 (236)
T cd06954          43 QRFAHFTELAILSVQEIVDFAKQLPGFLTLTREDQIALLKASTIEVMLLETARRYNPESEAITFLKDFPYSRDDFARAGL  122 (236)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCCCcccCChHHHHHHHHHhHHHHHHHHHHHHhcCCCCeEEeeCCccccHHHHHHhcC
Confidence            45677788888899999999999999999999999999999999999999999987778888999998877766543443


Q ss_pred             hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhh
Q psy3092         260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRL  339 (347)
Q Consensus       260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll  339 (347)
                      ...+.+.+.+++.+|++|++|++||++|+||+|||||++|+++...|+++|+++..+|++|+..++|+.+.||++||++|
T Consensus       123 ~~~~~~~i~~~~~~l~~L~ld~~E~~lL~aivLf~pd~~gL~~~~~V~~lQ~~~~~aL~~y~~~~~p~~~~rf~klL~~L  202 (236)
T cd06954         123 QVEFINPIFEFSKSMRELQLDDAEYALLIAINIFSADRPNVQDHHRVERLQETYVEALHSYIKIKRPSDRLMFPRMLMKL  202 (236)
T ss_pred             hHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhhccCCcccCCCHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHH
Confidence            33333445589999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhccC
Q psy3092         340 PSLRSIE  346 (347)
Q Consensus       340 ~~lr~i~  346 (347)
                      ++||+|+
T Consensus       203 ~~Lr~l~  209 (236)
T cd06954         203 VSLRTLS  209 (236)
T ss_pred             HHHHHHH
Confidence            9999986

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

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

Probab=99.97  E-value=1.9e-32  Score=197.20  Aligned_cols=79  Identities=52%  Similarity=1.170  Sum_probs=75.9

Q ss_pred             CcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhhh
Q psy3092          58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRTK  136 (347)
Q Consensus        58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~~  136 (347)
                      |.|||++++|+||||.+|+||++||||++.++..|.|..+++|.+++..|..|++|||+||+++||++++||.+|++.+
T Consensus         1 C~VCg~~~~g~hyG~~sC~aC~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~V~~~r~~~~   79 (81)
T cd07165           1 CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYRCLRDGKCEIIRLNRNRCQYCRFKKCLAAGMSKDSVRYGRIPNR   79 (81)
T ss_pred             CCccCccCcceEECchhhhhHHHHHHhHhccCCceeCCCCCCccccccccccccchhhhhcccccCCHHHcccCCCCcc
Confidence            8999999999999999999999999999998999999999999999999999999999999999999999999988754

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

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

Probab=99.97  E-value=9.7e-33  Score=201.78  Aligned_cols=82  Identities=52%  Similarity=1.171  Sum_probs=77.0

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcc-cccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhh
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSY-ACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQR  134 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~-~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~  134 (347)
                      .+|.|||++++|+||||.+|+||++||||++..+..| .|..+++|.+++..|..|++|||+||+++||++++||.+|++
T Consensus         4 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~~   83 (89)
T cd07166           4 VLCKVCGDKASGFHYGVHACEGCKGFFRRSIQQKIQYRKCTKNETCSIMRINRNRCQYCRFKKCLAVGMSRDAVRFGRIP   83 (89)
T ss_pred             CCCcccCccCcceEEChhhhhhHhhEecceeEcCCcchhhccCCcccccccccccccchhhhhcccccCCHHHhcCCCCC
Confidence            4699999999999999999999999999999988999 599999999999999999999999999999999999999887


Q ss_pred             hhc
Q psy3092         135 TKE  137 (347)
Q Consensus       135 ~~~  137 (347)
                      .++
T Consensus        84 ~~~   86 (89)
T cd07166          84 KRE   86 (89)
T ss_pred             Ccc
Confidence            543

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

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

Probab=99.97  E-value=2.8e-32  Score=200.06  Aligned_cols=78  Identities=60%  Similarity=1.255  Sum_probs=75.1

Q ss_pred             CcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhh
Q psy3092          58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRT  135 (347)
Q Consensus        58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~  135 (347)
                      |.|||++++|+||||.+|+|||+||||++..+..|.|..+++|.++...|..|++|||+||+++||++++||.+|.+.
T Consensus         1 C~VCg~~a~g~hyGv~sC~aCk~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~Vq~~r~~~   78 (93)
T cd07167           1 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMRG   78 (93)
T ss_pred             CcccCccCcceEECchhhhhHHHHHHHHeeCCCccccCCCCccccCccccCcCCCcccchhhhccCCHHHhhhcccCC
Confidence            899999999999999999999999999999999999999999999999999999999999999999999999988753

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

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

Probab=99.97  E-value=2.8e-32  Score=199.53  Aligned_cols=80  Identities=55%  Similarity=1.220  Sum_probs=76.2

Q ss_pred             CCcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhh
Q psy3092          55 KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQR  134 (347)
Q Consensus        55 ~~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~  134 (347)
                      ...|.|||++++|+||||.+|+|||+||||++..+..|.|..+++|.++...|..|++|||+||+++||++++||.+|.+
T Consensus         6 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~   85 (90)
T cd07169           6 QRTCLICGDRATGLHYGIISCEGCKGFFKRSICNKRVYRCSRDKNCVMSRKQRNRCQYCRLLKCLQMGMNRKAIREDGMP   85 (90)
T ss_pred             CCCCeecCCcCcceEECcceehhhHHHHHHHhcCCCceecCCCCcccccccccccccccchhhhccccCCHHHhccccCC
Confidence            45699999999999999999999999999999999999999999999999999999999999999999999999998764

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

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

Probab=99.97  E-value=4.1e-30  Score=219.35  Aligned_cols=164  Identities=27%  Similarity=0.447  Sum_probs=145.6

Q ss_pred             HhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCchh
Q psy3092         182 ATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGG  261 (347)
Q Consensus       182 ~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~~~  261 (347)
                      +..+.+..+..+..+|+|||++|+|+.|+.+||+.|+|++|.+++++..++++....+.+.+.+|..+..+.........
T Consensus         4 w~~~~~~~~~~l~~iI~waK~iP~F~~L~~~DQi~LLk~~~~el~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (195)
T cd06941           4 WQQLSEALTPSVQRVVEFAKRIPGFCDLSQDDQLLLIKAGFFEVWLVRISRLINSKSGSITFDDGISISRQQLDIIYDSD   83 (195)
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHcCCCCeEEecCCeEeeHHHHHhccchH
Confidence            56778888999999999999999999999999999999999999999999877666678888898887765543222223


Q ss_pred             hHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhhhh
Q psy3092         262 IFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPS  341 (347)
Q Consensus       262 ~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll~~  341 (347)
                      +.+ .+.+++.+|++|++|++||++|+||+||+||++|+++...|+++|+++..+|++|+..++++.+.||++||++||+
T Consensus        84 ~~~-~~~~~~~~l~~L~ld~~E~allkAi~Lf~pd~~gl~~~~~Ve~lq~~~~~aL~~~i~~~~p~~~~rf~~Ll~~Lp~  162 (195)
T cd06941          84 FVK-ALFEFSDSFNSLGLSDTEVALFCAVVLLSPDRIGLSEPKKVAILQDRVLEALKVQVSRNRPAEAQLFASLLMKIPE  162 (195)
T ss_pred             HHH-HHHHHHHHHHhcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHhHH
Confidence            444 4568999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhccC
Q psy3092         342 LRSIE  346 (347)
Q Consensus       342 lr~i~  346 (347)
                      ||+|+
T Consensus       163 Lr~l~  167 (195)
T cd06941         163 LRSIG  167 (195)
T ss_pred             HHHHH
Confidence            99886

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

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

Probab=99.97  E-value=1.5e-32  Score=202.67  Aligned_cols=82  Identities=37%  Similarity=0.891  Sum_probs=77.8

Q ss_pred             cCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhhh
Q psy3092          57 LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRTK  136 (347)
Q Consensus        57 ~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~~  136 (347)
                      .|.|||++++|+||||.+|+||++||||++..+..|.|..+++|.++...|..|++|||+||+++||++++||.+|+...
T Consensus         2 ~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~r~~~~   81 (94)
T cd06966           2 ICGVCGDKALGYNFNAITCESCKAFFRRNALKNKEFKCPFNESCEINVVTRRFCQKCRLDKCFAIGMKKEWIMSEEDKSE   81 (94)
T ss_pred             CCeeCCCcCcceEECcceeeeehheehhcccCCCccccCCCCccccCccccccCccchhhhCcccCCCHHHccchhhhhH
Confidence            49999999999999999999999999999999999999999999999999999999999999999999999999988765


Q ss_pred             cc
Q psy3092         137 ER  138 (347)
Q Consensus       137 ~~  138 (347)
                      ++
T Consensus        82 ~r   83 (94)
T cd06966          82 KR   83 (94)
T ss_pred             HH
Confidence            44

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

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

Probab=99.97  E-value=4.3e-30  Score=222.35  Aligned_cols=167  Identities=24%  Similarity=0.356  Sum_probs=139.3

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCce----------EecCCccc
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGI----------LLAPGVTV  249 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~----------~~~~g~~i  249 (347)
                      .+...+++...+.++.+|+|||++|+|..|+.+||+.|||++|.++++++.++++...++..          +..++...
T Consensus        19 ~~~~~~ce~a~~~L~~~V~wAK~iP~F~~L~~~DQi~LLk~~w~El~iL~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~   98 (222)
T cd06951          19 CAPQMVCRAASQVLLKTIRFVRNLPCFTYLPPDDQLRLLRRSWAPLLLLGLAQDKVPFDTVEVPAPSILCEILTGAEMHW   98 (222)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHhCCCcccCChHHHHHHHHHHhHHHHHHHHHHHhccccccccccchHHHHHHhcccccc
Confidence            45788999999999999999999999999999999999999999999999999987665432          22222222


Q ss_pred             cccch--hhcCc--hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcC
Q psy3092         250 YRSSA--HEAGV--GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNH  325 (347)
Q Consensus       250 ~~~~~--~~~~~--~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~  325 (347)
                      .....  ...+.  ...+.+.+.+++.+|++|++|++||++|+||+|||||++|+ +...|+++|+++..+|++|+..++
T Consensus        99 ~~~~~~~~~~~~~~~~~~~~~l~e~~~~l~~L~ld~~Eya~LkAivLfnpD~~gl-~~~~Ve~lQe~~~~aL~~yi~~~~  177 (222)
T cd06951          99 GGTPPPTLTMPPCIPLADVQDIQQFLMKCWSLDLDCKEYAYLKGAVLFTPVPPLL-CPHYIEALQKEAQQALNEHTMMTR  177 (222)
T ss_pred             ccccccccccchhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCcc-CHHHHHHHHHHHHHHHHHHHHhhC
Confidence            21110  00111  11233557799999999999999999999999999999999 999999999999999999999999


Q ss_pred             CCCchHHHHHHhhhhhhhccCC
Q psy3092         326 SEEPGRFAKLLLRLPSLRSIEV  347 (347)
Q Consensus       326 ~~~~~Rf~~LL~ll~~lr~i~~  347 (347)
                      ++.+.||++||++||+||+|++
T Consensus       178 p~~~~Rf~kLLl~Lp~LRsl~~  199 (222)
T cd06951         178 PLEQLRSARLLLMLSLLRGIKT  199 (222)
T ss_pred             CCcccHHHHHHHHhHHhhcCCH
Confidence            9999999999999999999973

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.

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

Probab=99.97  E-value=5.1e-30  Score=224.35  Aligned_cols=165  Identities=29%  Similarity=0.502  Sum_probs=152.0

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV  259 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~  259 (347)
                      ..+..+++.....+..+++|||++|+|.+|+.+||+.|||++|.++++++.++++....+.+++++|..+.++.. ..++
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            457888899999999999999999999999999999999999999999999999988888889999988777653 3456


Q ss_pred             hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCC--CCchHHHHHHh
Q psy3092         260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHS--EEPGRFAKLLL  337 (347)
Q Consensus       260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~--~~~~Rf~~LL~  337 (347)
                      +.+++.++ +++.+|++|++|++||++|+||+||+||++|+++...|+++|+++..+|++|+..+++  +.+.||++||+
T Consensus       120 ~~~~~~i~-~f~~~l~~L~ld~~E~~~LkaivL~~pD~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~~~rf~kLLl  198 (239)
T cd06945         120 GEWLDSIL-AFSSSLQSLLLDDISAFCCLALLLLITERHGLKEPKKVEELQNKIISCLRDHVTSNYPGQDKPNRLSKLLL  198 (239)
T ss_pred             HHHHHHHH-HHHHHHHHHhCChHHHHHHHHHHHhCCCccccCCHHHHHHHHHHHHHHHHHHHHHhCCCcccccHHHHHHH
Confidence            66777755 7999999999999999999999999999999999999999999999999999999998  89999999999


Q ss_pred             hhhhhhccC
Q psy3092         338 RLPSLRSIE  346 (347)
Q Consensus       338 ll~~lr~i~  346 (347)
                      +||+||+|+
T Consensus       199 ~Lp~LR~ls  207 (239)
T cd06945         199 KLPELRTLS  207 (239)
T ss_pred             HhHHHHHHH
Confidence            999999986

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

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

Probab=99.97  E-value=2.1e-32  Score=195.11  Aligned_cols=76  Identities=64%  Similarity=1.406  Sum_probs=73.4

Q ss_pred             CcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHh
Q psy3092          58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQ  133 (347)
Q Consensus        58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~  133 (347)
                      |.|||++++|+||||.+|+||++||||++.++..|.|..+++|.++...|..|++|||+||+++||++++||.+||
T Consensus         1 C~vCg~~~~~~hygv~~C~aC~~FFrR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~   76 (76)
T cd06960           1 CAVCGDRATGKHYGVLSCNGCKGFFRRSVRKNRTYTCRFGGNCVVDKDKRNACRYCRFKKCLEVGMDPEAVQNERD   76 (76)
T ss_pred             CCccCccCcccEECcceeeeehheeCccccCCCceeCCCCCcccccCcccccCccchhhhhhhcCCCHHHcccCCC
Confidence            8999999999999999999999999999998889999999999999999999999999999999999999998775

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

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

Probab=99.97  E-value=5.9e-32  Score=190.88  Aligned_cols=73  Identities=52%  Similarity=1.116  Sum_probs=69.9

Q ss_pred             cCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHH
Q psy3092          57 LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQ  129 (347)
Q Consensus        57 ~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq  129 (347)
                      +|.|||++++|+||||.+|+|||+||||++.++..|.|..+++|.+++..|..||+|||+||+++||+++.|+
T Consensus         1 ~C~vCg~~~~~~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~   73 (73)
T cd06959           1 NCVVCGDKASGFHYGVLSCEGCKGFFRRSVTKGAVYACKFGNKCEMDMYMRRKCQECRLRKCKAAGMRPDCLL   73 (73)
T ss_pred             CCceeCCcCcceEECceeehhhHHHHHHhhcCCCCccCCCCCcCCcCCcccccCccchhHHHHHhCCChhhcC
Confidence            4999999999999999999999999999999899999999999999999999999999999999999998763

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

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

Probab=99.97  E-value=1.6e-29  Score=219.91  Aligned_cols=167  Identities=19%  Similarity=0.419  Sum_probs=141.1

Q ss_pred             hhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCC-C-ceEecCCccccccchh
Q psy3092         178 NEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVK-D-GILLAPGVTVYRSSAH  255 (347)
Q Consensus       178 ~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~-~-~~~~~~g~~i~~~~~~  255 (347)
                      .......+++..+++++.+|+|||++|+|.+|+.+||+.|+|++|.+++++..+|+++... + .+.+.+|..+.++...
T Consensus        26 ~~~~~~~l~~la~r~L~~vVeWAK~lPgF~~L~~~DQi~LLk~sw~ellvL~~a~rS~~~~~~~~l~fa~d~~~~~~~~~  105 (248)
T cd07074          26 PSSLLTSLNQLCERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMK  105 (248)
T ss_pred             chhhHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCeEEecCCcccchhhhh
Confidence            3345788899999999999999999999999999999999999999999999999998764 3 3556677777766543


Q ss_pred             hcCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcC-CCCCCCCHHHHHHHHHHHHHHHHHHHHhc-C--CCCchH
Q psy3092         256 EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNP-DVRGLKSQQVVEMLREKVYTSLEEYTRVN-H--SEEPGR  331 (347)
Q Consensus       256 ~~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p-~~~~l~~~~~i~~~r~~~~~~L~~y~~~~-~--~~~~~R  331 (347)
                      ..++.... ..+.+++.+|++|++|.+||+|||||+|||| +.+||+++..|+++|++|.++|.+|+..+ +  .+++.|
T Consensus       106 ~~~~~~~~-~~m~e~~~~~~~L~ld~~Ey~cLKAIvLfnp~d~~gL~~q~~Ve~lR~~y~~aL~~yi~~~~~~~~~~~~R  184 (248)
T cd07074         106 ESSFYSLC-LTMWQIPQEFVKLQVSQEEFLCMKALLLLNTIPLEGLRSQTQFDEMRSSYIRELIKAIGLRQKGVVASSQR  184 (248)
T ss_pred             hccHHHHH-HHHHHHHHHHHHcCCCHHHHHHHHHHHHCCCCcCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCCCccCcHH
Confidence            33333322 2345789999999999999999999999999 79999999999999999999999996554 3  378999


Q ss_pred             HHHHHhhhhhhhcc
Q psy3092         332 FAKLLLRLPSLRSI  345 (347)
Q Consensus       332 f~~LL~ll~~lr~i  345 (347)
                      |++|+++++.|+++
T Consensus       185 F~~Ll~ll~~l~~~  198 (248)
T cd07074         185 FYQLTKLMDNMHDL  198 (248)
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999999853

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

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

Probab=99.97  E-value=5.5e-32  Score=191.00  Aligned_cols=72  Identities=65%  Similarity=1.438  Sum_probs=70.1

Q ss_pred             CcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHH
Q psy3092          58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQ  129 (347)
Q Consensus        58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq  129 (347)
                      |.|||++++|+||||.+|+|||+||||++.++..|.|..+++|.+++..|..|++|||+||+++||++++||
T Consensus         1 C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   72 (73)
T cd06958           1 CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRGNRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQ   72 (73)
T ss_pred             CCccCccCcceEEChhhhhhhhhhhhhhhcCCCceeCCCCCcCccCCcccccCccchhhHhhHhCCCHHHcc
Confidence            899999999999999999999999999999999999999999999999999999999999999999999987

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

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

Probab=99.97  E-value=2e-32  Score=194.12  Aligned_cols=74  Identities=62%  Similarity=1.334  Sum_probs=71.2

Q ss_pred             cCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHH
Q psy3092          57 LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQE  130 (347)
Q Consensus        57 ~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~  130 (347)
                      +|.|||++++|+||||.+|+|||+||||++.++..|.|..+++|.+++..|..||+|||+||+++||++++||+
T Consensus         2 ~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~   75 (75)
T cd06969           2 LCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLQVGMVKEVVRT   75 (75)
T ss_pred             CCeecCCcCcceEECcceeeeeeeeeeeeeecCCcccCCcCCccccCCcccccCcccHhHHHHHhCCCHHHccC
Confidence            49999999999999999999999999999998899999999999999999999999999999999999999873

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

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

Probab=99.97  E-value=6.6e-32  Score=190.09  Aligned_cols=71  Identities=46%  Similarity=1.161  Sum_probs=69.0

Q ss_pred             CcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHH
Q psy3092          58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAV  128 (347)
Q Consensus        58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~v  128 (347)
                      |.|||++++|+||||.+|+|||+||||++.++..|.|..+++|.+++..|..||+|||+||+++||++++|
T Consensus         1 C~VC~~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v   71 (72)
T cd07156           1 CGVCGDRATGYHFNAMTCEGCKGFFRRSMKRKARFTCPFNGDCEITKDNRRHCQACRLKKCLDIGMKKEMI   71 (72)
T ss_pred             CCccCccCcccEECcceehhhhhhhchhccCcCccccCCCCccccCCcccccCccchhHHHHHhCCCHHHc
Confidence            89999999999999999999999999999988999999999999999999999999999999999999987

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

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

Probab=99.97  E-value=4e-32  Score=204.00  Aligned_cols=76  Identities=39%  Similarity=1.053  Sum_probs=71.6

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHH
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEE  131 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~  131 (347)
                      ..|.|||++++|+||||.+|+|||+||||++..+..|.|..+++|.++...|..|++|||+||+++||++++|+.+
T Consensus         7 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~   82 (107)
T cd06955           7 RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTD   82 (107)
T ss_pred             CCCeecCCcCcccEECcceeeeecceecceeccCCccccCCCCccccccCCccccccchhHHHHHcCCCchhccCH
Confidence            5699999999999999999999999999999999999999999999999999999999999999999998766654

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

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

Probab=99.97  E-value=8.2e-32  Score=196.46  Aligned_cols=80  Identities=43%  Similarity=1.058  Sum_probs=74.7

Q ss_pred             cCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhhh
Q psy3092          57 LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRTK  136 (347)
Q Consensus        57 ~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~~  136 (347)
                      +|.|||++++|+||||.+|+||++||||++.++..|.|..+++|.++...|..|++|||+||+++||++++||.+++-.+
T Consensus         1 ~C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~~~~~   80 (87)
T cd07162           1 ICRVCGDRATGYHFNAMTCEGCKGFFRRAMKRNARLCCPFQKGCVITKSNRRQCQACRLRKCLSIGMKKELIMSDEAVEK   80 (87)
T ss_pred             CCcccCCcCcceEECcceehhhHHHHHhhhccCceeEcCCCCceecCCcccccCccchhhHHhHhCCCHHHccCHHHHHH
Confidence            39999999999999999999999999999999999999999999999999999999999999999999999988755433

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

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

Probab=99.97  E-value=1.5e-31  Score=191.94  Aligned_cols=76  Identities=43%  Similarity=0.912  Sum_probs=71.3

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHH
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEE  131 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~  131 (347)
                      ..|.|||++++|+||||.+|+||++||||++..+..|.|..+++|.+++..|..||+|||+||+++||+++....+
T Consensus         4 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~~~~~   79 (82)
T cd07173           4 KTCLICGDEASGCHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCFEAGMTLGARKLK   79 (82)
T ss_pred             CCCeecCCcCcceEECcchhhhHHHHHHHHhcCCCceecCCCCccccCCCccCcCcchhhhhhhhcCCCcChHHhh
Confidence            4599999999999999999999999999999999999999999999999999999999999999999998766543

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

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

Probab=99.97  E-value=1.4e-29  Score=221.90  Aligned_cols=166  Identities=39%  Similarity=0.699  Sum_probs=143.8

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCc-eEecCCccccccchhhcC
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDG-ILLAPGVTVYRSSAHEAG  258 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~-~~~~~g~~i~~~~~~~~~  258 (347)
                      ...+.++++..+.++.+|+|+|.+|+|.+|+.+||+.|||++|.+++++..++++...... +++++|..+......  .
T Consensus        30 ~~~~~l~~~a~~~L~~~VewaK~lp~F~~L~~~DQi~LLk~~w~el~lL~~a~~s~~~~~~~~~~~~g~~~~~~~~~--~  107 (236)
T cd06948          30 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLSWSELFVLNAAQCCMPLHVAPLLAAAGLHASPMSAD--R  107 (236)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHhhHHHHHHHHHHHcccccchhhhhccccccCccchh--h
Confidence            4578999999999999999999999999999999999999999999999999998776544 455667665443321  1


Q ss_pred             chhhHH--hhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHH
Q psy3092         259 VGGIFD--RVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLL  336 (347)
Q Consensus       259 ~~~~~~--~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL  336 (347)
                      ...+.+  +.+.+++.+|++|++|++||++|+||+|||||.+|+++.+.|+++|+++..+|++|+..++++++.||++||
T Consensus       108 ~~~~~~~~~~~~~l~~~l~~L~ld~~E~~lLkaiiL~npd~~~L~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LL  187 (236)
T cd06948         108 VVAFMDHIRIFQEQVEKLKALHVDSAEFSCLKAIVLFTSDACGLSDPAHIESLQEKSQCALEEYVRTQYPNQPTRFGKLL  187 (236)
T ss_pred             HhHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCcccccccCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHH
Confidence            222222  345689999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhhccCC
Q psy3092         337 LRLPSLRSIEV  347 (347)
Q Consensus       337 ~ll~~lr~i~~  347 (347)
                      ++||.||+|+.
T Consensus       188 l~Lp~Lr~is~  198 (236)
T cd06948         188 LRLPSLRTVSS  198 (236)
T ss_pred             HHHHHHHhccH
Confidence            99999999873

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

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

Probab=99.97  E-value=1e-31  Score=190.00  Aligned_cols=73  Identities=45%  Similarity=1.095  Sum_probs=70.3

Q ss_pred             CcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHH
Q psy3092          58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQE  130 (347)
Q Consensus        58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~  130 (347)
                      |.|||++++|+||||.+|+|||+||||++.++..|.|..+++|.+++..|..|++|||+||+++||++++|+.
T Consensus         1 C~VCg~~~~g~hygv~sC~aC~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~   73 (74)
T cd07179           1 CRVCGGKSSGFHFGALTCEGCKGFFRRTELSSNSYVCPGGQNCAITPATRNACKSCRFRRCLAVGMSKTGSRI   73 (74)
T ss_pred             CcccCccCcceEECceeehhHHHHHHHHhhCCCcccCCCCCccccCCcccccCccchhHHHHHhCCCHhHeeC
Confidence            8999999999999999999999999999999999999999999999999999999999999999999999864

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

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

Probab=99.97  E-value=5.3e-32  Score=199.89  Aligned_cols=83  Identities=55%  Similarity=1.175  Sum_probs=77.7

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhh
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRT  135 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~  135 (347)
                      ..|.|||++++|+||||.+|+||++||||++.++..|.|..+++|.++...|..|++|||+||+++||++++||.+|.+.
T Consensus         6 ~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~V~~~r~~~   85 (95)
T cd06968           6 IPCKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVSYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSK   85 (95)
T ss_pred             cCCcccCCcCcceEECceeehhhHHhhHHheeCCCceecCCCcccccccCCceeccccchhhcccccCChhhcccCcCCh
Confidence            45999999999999999999999999999999999999999999999999999999999999999999999999987765


Q ss_pred             hcc
Q psy3092         136 KER  138 (347)
Q Consensus       136 ~~~  138 (347)
                      +.+
T Consensus        86 ~~~   88 (95)
T cd06968          86 KQR   88 (95)
T ss_pred             hhh
Confidence            543

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

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

Probab=99.97  E-value=1e-29  Score=219.42  Aligned_cols=168  Identities=26%  Similarity=0.435  Sum_probs=138.4

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCce---------EecCCcccc
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGI---------LLAPGVTVY  250 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~---------~~~~g~~i~  250 (347)
                      ..++.+++...+.++.+|+|+|++|+|..|+.+||+.|||++|.++++++.++++.......         ++..|....
T Consensus        19 ~~~~~ice~a~~~L~~~V~WAK~iP~F~~L~~~DQi~LLk~~W~EL~iL~laq~s~~~~~~~~~~~~~~~~~l~~~~~~~   98 (222)
T cd07349          19 CTPHRTCREASDVLVKTVAFMRNLPSFWQLPPQDQLLLLQNCWGPLFLLGLAQDRVTFEVAEAPVPSMLKKILLEGQSSS   98 (222)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHhcCCCcccCChHHHHHHHHHccHHHHHHHHHHHccccccccccchhHHHHHHhcccccc
Confidence            34778899999999999999999999999999999999999999999999999986654321         112222111


Q ss_pred             ccc-h-hhcCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCC
Q psy3092         251 RSS-A-HEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEE  328 (347)
Q Consensus       251 ~~~-~-~~~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~  328 (347)
                      ... . ...+......+.+.+++.+|++|++|.+||++|+||+|||||++|+++...|+.+|+++..+|++|+..++++.
T Consensus        99 ~~~~~~~~~~~~~~~~~~l~e~~~~l~~L~ld~~Eya~LkaivLf~pd~~gl~~~~~V~~lqe~~~~aL~~~~~~~~p~~  178 (222)
T cd07349          99 GGSGQPDRPQPSLAAVQWLQCCLNKFWSLDLSPKEYAYLKGTILFNPDVPGLTASSHVGHLQQEAQWALCEVLEPLHPQD  178 (222)
T ss_pred             cccchhhhhhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCcccCCCHHHHHHHHHHHHHHHHHHHHHHCCCc
Confidence            111 0 01111111224467899999999999999999999999999999999999999999999999999999999999


Q ss_pred             chHHHHHHhhhhhhhccCC
Q psy3092         329 PGRFAKLLLRLPSLRSIEV  347 (347)
Q Consensus       329 ~~Rf~~LL~ll~~lr~i~~  347 (347)
                      +.||++||++||.||+|+.
T Consensus       179 ~~r~~kLLl~Lp~LR~i~~  197 (222)
T cd07349         179 QGRFARILLTASTLKSIPP  197 (222)
T ss_pred             ccHHHHHHHHhHHHhcCCH
Confidence            9999999999999999873

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.

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

Probab=99.97  E-value=1.4e-31  Score=188.53  Aligned_cols=72  Identities=49%  Similarity=1.001  Sum_probs=69.3

Q ss_pred             CcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHH
Q psy3092          58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQ  129 (347)
Q Consensus        58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq  129 (347)
                      |.|||++++|+||||.+|+|||+||||++..+..|.|..+++|.|++..|..||+|||+||+++||+++++.
T Consensus         1 C~VCg~~a~~~hygv~sC~aCk~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~a~~   72 (73)
T cd06963           1 CLICGDEASGCHYGVLTCGSCKVFFKRAAEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCYQAGMTLGARK   72 (73)
T ss_pred             CcccCccCcceEECceeehhhhHhHHHhhcCCCceeCCCCCccccCCcccccCccchhhHHHHcCCChhhcc
Confidence            899999999999999999999999999999999999999999999999999999999999999999998763

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

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

Probab=99.97  E-value=2.4e-29  Score=219.06  Aligned_cols=166  Identities=25%  Similarity=0.436  Sum_probs=148.6

Q ss_pred             hhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhc
Q psy3092         178 NEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEA  257 (347)
Q Consensus       178 ~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~  257 (347)
                      ....+..+++.....+..+++|||++|+|.+|+.+||+.|||++|.++++++.++++....+.+.+.+|..+.+..... 
T Consensus        40 ~~~~~~~~~~l~t~~i~~iv~wAK~IPgF~~L~~~DQi~LLk~~w~Ell~L~~a~r~~~~~~~l~~~~g~~~~~~~~~~-  118 (239)
T cd07072          40 EAEKVQQFYSLLTSSIDVIKTFAEKIPGFPDLCKEDQELLFQSASLELFVLRLAYRTAPEDTKLTFCNGVVLHKQQCQR-  118 (239)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHHHHHHhHHHHHHHHHHHHccCCCCeEEeeCCeeecHHHHHh-
Confidence            3456788888899999999999999999999999999999999999999999999998888888899998877765433 


Q ss_pred             CchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCC--CCchHHHHH
Q psy3092         258 GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHS--EEPGRFAKL  335 (347)
Q Consensus       258 ~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~--~~~~Rf~~L  335 (347)
                      +++.+.+. +.+++.+|++|++|++||+||+||+||+ |++|+.+...|+++|+++..+|++|+..+++  +.+.||++|
T Consensus       119 ~~~~~~~~-i~ef~~~l~~L~ld~~E~a~LkAivLf~-dr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~~~~rf~kL  196 (239)
T cd07072         119 SFGDWLHA-ILEFSKSLHAMDIDISAFACLCALTLIT-ERHGLKEPHKVEQLQMKIISSLRDHVTYNAEAQKKPHYFSRL  196 (239)
T ss_pred             hHHHHHHH-HHHHHHHHHHcCCCHHHHHHHHHHHHhC-CCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcccccHHHHH
Confidence            56665554 4599999999999999999999999995 9999999999999999999999999987544  678999999


Q ss_pred             HhhhhhhhccC
Q psy3092         336 LLRLPSLRSIE  346 (347)
Q Consensus       336 L~ll~~lr~i~  346 (347)
                      |++||.||+|+
T Consensus       197 Ll~Lp~LRsl~  207 (239)
T cd07072         197 LGKLPELRSLS  207 (239)
T ss_pred             HHHhHHHHhhH
Confidence            99999999986

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).

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

Probab=99.97  E-value=1.5e-31  Score=190.47  Aligned_cols=74  Identities=47%  Similarity=0.994  Sum_probs=70.2

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHH
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQ  129 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq  129 (347)
                      ..|.|||++++|+||||.+|+||++||||++..+..|.|..+++|.++...|..||+|||+||+++||+..++.
T Consensus         3 ~~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~   76 (78)
T cd07172           3 KICLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCLQAGMNLGARK   76 (78)
T ss_pred             CCCeecCCcCcceEECceeehhhHHhHHHHeeCCCceeCCCCCccccCCcccccCccchhHHHHHhCCCccccc
Confidence            35999999999999999999999999999999999999999999999999999999999999999999987763

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

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

Probab=99.97  E-value=1.6e-31  Score=189.03  Aligned_cols=72  Identities=61%  Similarity=1.406  Sum_probs=69.5

Q ss_pred             CcccCCCCCCcccccccchhhHHHHHhhhcCCCcc-cccCCCCcccccccccCchhhhhHHHHhcCcchhHHH
Q psy3092          58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSY-ACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQ  129 (347)
Q Consensus        58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~-~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq  129 (347)
                      |.|||++++|+||||.+|+||++||||++..+..| .|..+++|.+++..|..|++|||+||+++||++++|+
T Consensus         1 C~VCg~~~~g~hyGv~~C~aC~~FFRR~v~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   73 (73)
T cd07158           1 CKVCGDKASGFHYGVHSCEGCKGFFRRTIQHNLTYRRCLNGGKCVIQRKNRNRCQYCRFKKCLSVGMSRNAVR   73 (73)
T ss_pred             CcccCccCcceEECcchhhHHHHHHhhhhcCCCCcccCCCCCCcCCCccccccCccchhhhhhHccCChHHcC
Confidence            89999999999999999999999999999999999 8999999999999999999999999999999999874

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

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

Probab=99.97  E-value=1.8e-29  Score=219.19  Aligned_cols=166  Identities=23%  Similarity=0.361  Sum_probs=141.4

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV  259 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~  259 (347)
                      ..+..+++.....+..+|+|||++|+|.+|+.+||+.|||++|.+++++.+++++....+ .++.+|..+...+....++
T Consensus        35 ~~~~~~~~~~~~~l~~iV~wAK~iPgF~~L~~~DQi~LLk~~~~Ellil~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~  113 (226)
T cd06934          35 SLLPHFADLTTYMIKQIIKFAKDLPYFRSLPIEDQISLLKGATFEICQIRFNTVFNEETG-TWECGPLTYCIEDAARAGF  113 (226)
T ss_pred             hHHHHHHHHHHHHHHHHHHHhcCCcccccCCcchHHHHHHHhHHHHHHHHHHHHhcccCC-eEeeCCEeecHHHHHHccc
Confidence            346677888888999999999999999999999999999999999999998877655444 4455555544444444555


Q ss_pred             hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCc--hHHHHHHh
Q psy3092         260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEP--GRFAKLLL  337 (347)
Q Consensus       260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~--~Rf~~LL~  337 (347)
                      ...+.+.+.+++.+|++|++|++||+||+||+||+||++||++...|+++|+++..+|++|+..+++..+  .||++||+
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            5555556678999999999999999999999999999999999999999999999999999998887544  45999999


Q ss_pred             hhhhhhccC
Q psy3092         338 RLPSLRSIE  346 (347)
Q Consensus       338 ll~~lr~i~  346 (347)
                      +||+||+|+
T Consensus       194 ~L~~LRsl~  202 (226)
T cd06934         194 CLTELRTIN  202 (226)
T ss_pred             HhHHHhcch
Confidence            999999997

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

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

Probab=99.97  E-value=6e-32  Score=191.02  Aligned_cols=72  Identities=57%  Similarity=1.359  Sum_probs=69.4

Q ss_pred             CcccCCCCCCcccccccchhhHHHHHhhhcCCCccccc-CCCCcccccccccCchhhhhHHHHhcCcchhHHH
Q psy3092          58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACR-EGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQ  129 (347)
Q Consensus        58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~-~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq  129 (347)
                      |.|||++++|+||||.+|+|||+||||++..+..|.|. .+++|.++...|..||+|||+||+++||++++||
T Consensus         1 C~vCg~~~~~~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~vq   73 (73)
T cd07154           1 CKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNLLYTCKAGNGSCVVDKARRNQCQACRLKKCLEVSMNKDAVQ   73 (73)
T ss_pred             CcccCccCcceEECcceeeeeeeEeeeeecCCCCcccCCCCCCCccCCcccccCccchhhHhhHhCCChHHCC
Confidence            89999999999999999999999999999999999999 6789999999999999999999999999999886

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

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

Probab=99.97  E-value=2.2e-29  Score=218.55  Aligned_cols=167  Identities=27%  Similarity=0.454  Sum_probs=138.5

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEe---------cCCcccc
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL---------APGVTVY  250 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~---------~~g~~i~  250 (347)
                      ..++.+++...+.++.+|+|||++|+|.+|+.+||+.|||++|.++++++.++++++.+....+         .++....
T Consensus        19 ~~~~~~ce~a~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~W~El~iL~~a~~s~~~~~~~~~~~~~~~~~l~~~~~~~   98 (232)
T cd07350          19 KSPQVTCKAASAVLVKTLRFVKGVPCFQELPLDDQLVLVRSCWAPLLVLGLAQDGVDFETVETSEPSMLQRILTTRPPPT   98 (232)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHhCcCcccCChHHHHHHHHHhhHHHHHHHHHHHcCCCccccccchhHHHHHHhcccccc
Confidence            4578889999999999999999999999999999999999999999999999998776543222         1111110


Q ss_pred             ccc------------hhhcCc--hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHH
Q psy3092         251 RSS------------AHEAGV--GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTS  316 (347)
Q Consensus       251 ~~~------------~~~~~~--~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~  316 (347)
                      ...            ....+.  .....+.+.+++.+|++|+||++||++|+||+|||||++|+++...|+++|+++..+
T Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~e~~~~l~~L~ld~~E~a~LkAivLf~pD~~~L~~~~~Ve~lQe~~~~a  178 (232)
T cd07350          99 SGAEPGEPQALPQMPQAEASHLPSAADIRAIKAFLAKCWSLDISTKEYAYLKGTVLFNPDLPGLQCVQYIQGLQWEAQQA  178 (232)
T ss_pred             cccccccccccccccchhhccccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcccCCCHHHHHHHHHHHHHH
Confidence            000            000011  111224577999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcCCCCchHHHHHHhhhhhhhccC
Q psy3092         317 LEEYTRVNHSEEPGRFAKLLLRLPSLRSIE  346 (347)
Q Consensus       317 L~~y~~~~~~~~~~Rf~~LL~ll~~lr~i~  346 (347)
                      |++|+..++++.+.||++||++||.||+|+
T Consensus       179 L~~yi~~~~p~~~~rf~kLLl~Lp~LRsi~  208 (232)
T cd07350         179 LNEHVRMIHRGDQARFAKLNIALSLLRAIN  208 (232)
T ss_pred             HHHHHHhhCCChhhHHHHHHHHhHHHHccC
Confidence            999999999999999999999999999986

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.

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

Probab=99.97  E-value=7.4e-32  Score=190.02  Aligned_cols=72  Identities=65%  Similarity=1.429  Sum_probs=69.8

Q ss_pred             CcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHH
Q psy3092          58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQ  129 (347)
Q Consensus        58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq  129 (347)
                      |.|||++++|+||||.+|+|||+||||++..+..|.|..+++|.++...|..|++|||+||+++||++++||
T Consensus         1 C~vC~~~~~~~hygv~sC~aC~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   72 (72)
T cd06916           1 CAVCGDKASGYHYGVLTCEGCKGFFRRSVRRNLEYTCPAGGNCVIDKRNRNRCQACRLKKCLAVGMRKEAVR   72 (72)
T ss_pred             CCccCccCcccEECcceeeeeeeeEeEeecCCCCccCCCCCccccCCcccccCccchhhHhhHhCCChHHcC
Confidence            899999999999999999999999999999999999999999999999999999999999999999999886

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

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

Probab=99.96  E-value=3.7e-29  Score=219.02  Aligned_cols=164  Identities=24%  Similarity=0.385  Sum_probs=142.6

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV  259 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~  259 (347)
                      ..+..+.+.....+..+|+|||++|+|.+|+.+||+.|||++|.+++++.+++++.. .+..++.+|....++.....+.
T Consensus        48 ~~~~~~~~~~t~~i~~vVefAK~IPgF~~L~~~DQi~LLk~~~~Ellll~~a~~~~~-~~~~~~~~~~~~~~~~~~~~~~  126 (241)
T cd06939          48 EMWQLCAEKITEAIQYVVEFAKRIPGFMELCQNDQIVLLKAGSLEVVLVRMSRAFNP-SNNTVLFDGKYAPIDLFKSLGC  126 (241)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhCC-CCCEEEECCccccHHHHHHcCc
Confidence            457777788888999999999999999999999999999999999999999965544 4444555666555555455566


Q ss_pred             hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhh
Q psy3092         260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRL  339 (347)
Q Consensus       260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll  339 (347)
                      +++.+.+ .+++.+|++|++|++||++|+||+||+||++||.+...|+++|+++..+|+.|+..++ +.+.||++||++|
T Consensus       127 ~~~~~~~-~~f~~~l~~L~ld~~E~all~AivL~~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~-~~~~rf~kLL~~L  204 (241)
T cd06939         127 DDLISAV-FDFAKSLCELKLTEDEIALFSALVLISADRPGLQEKRKVEKLQQKIELALRHVLQKNH-GDDTILTKLLAKM  204 (241)
T ss_pred             HHHHHHH-HHHHHHHHhcCCCHHHHHHHHHHHHhcCCCcCCCCHHHHHHHHHHHHHHHHHHHHHhC-CCccHHHHHHHHH
Confidence            6666554 4899999999999999999999999999999999999999999999999999999888 8899999999999


Q ss_pred             hhhhccC
Q psy3092         340 PSLRSIE  346 (347)
Q Consensus       340 ~~lr~i~  346 (347)
                      |.||+|+
T Consensus       205 p~LR~l~  211 (241)
T cd06939         205 PTLRALC  211 (241)
T ss_pred             HHHHHHH
Confidence            9999986

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

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

Probab=99.96  E-value=2.8e-29  Score=216.35  Aligned_cols=167  Identities=28%  Similarity=0.511  Sum_probs=139.3

Q ss_pred             hhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCce-----EecCCcccccc
Q psy3092         178 NEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGI-----LLAPGVTVYRS  252 (347)
Q Consensus       178 ~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~-----~~~~g~~i~~~  252 (347)
                      ....+..+++..++.++.+|+|+|.+|+|.+|+.+||+.|||++|.+++++..+++++......     ..+.|......
T Consensus        25 ~~~~~~~l~~la~~~l~~~I~waK~lp~F~~L~~~DQi~LLk~~w~el~iL~~a~~s~~~~~~~l~~~~~~~~~~~~~~~  104 (213)
T cd06953          25 QAELFALLCRLGDELLFRQIQWTKKLPFFTELSIKDHTHLLTTKWAELILLSTITVASLQNLGLLQDCLSKYLPSEDELE  104 (213)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHhcCCchhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHhhhccCCchhhHH
Confidence            3456788999999999999999999999999999999999999999999999999987643211     11111111000


Q ss_pred             chhhcCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHH
Q psy3092         253 SAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRF  332 (347)
Q Consensus       253 ~~~~~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf  332 (347)
                      .. .....++.+++ .+++.+|++|++|++||++|+||+|||||++|+++.+.|+++|+++.++|++|+..++++++.||
T Consensus       105 ~~-~~~~~~~~~~i-~~l~~~l~~L~ld~eEy~lLkAIvLfnpd~~gLs~~~~Ve~lQ~~~~~aL~~y~~~~~~~~p~Rf  182 (213)
T cd06953         105 RF-GDEGGEVVERL-TYLLAKFRQLKVSNEEYVCLKVINFLNQDIDGLTNASQLESLQKRYWYVLQDFTELNYPNQPNRF  182 (213)
T ss_pred             HH-HhhHHHHHHHH-HHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcchHH
Confidence            00 11234556664 58999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhhhhhhccC
Q psy3092         333 AKLLLRLPSLRSIE  346 (347)
Q Consensus       333 ~~LL~ll~~lr~i~  346 (347)
                      ++||+++|.||+|+
T Consensus       183 ~~LL~~L~~Lr~l~  196 (213)
T cd06953         183 SDLLSCLPEIRAAA  196 (213)
T ss_pred             HHHHHHhHHHHHHH
Confidence            99999999999986

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).

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

Probab=99.96  E-value=1.2e-31  Score=194.71  Aligned_cols=78  Identities=45%  Similarity=0.955  Sum_probs=72.7

Q ss_pred             cCcccCCCCCCcccccccchhhHHHHHhhhcCCC--cccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhh
Q psy3092          57 LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDL--SYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQR  134 (347)
Q Consensus        57 ~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~--~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~  134 (347)
                      .|.|||++++|+||||.+|+|||+||||++..+.  .|.|..+++|.++...|..||+|||+||+++||+++.++.+|+.
T Consensus         2 ~C~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~~~~~~   81 (86)
T cd07157           2 TCQVCGEPAAGFHHGAYVCEACKKFFMRSSNAISFTISECPNGGKCIIDKKNRTKCQACRYRKCLNVGMSLGGPRYGRRS   81 (86)
T ss_pred             CCcccCCcCcccEECcceeeEeeeEEecceecCCCccccCCCCCccccCccccccCccchhhHHhHcCCCcccccccccc
Confidence            4999999999999999999999999999987654  89999999999999999999999999999999999999887664

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

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

Probab=99.96  E-value=1.6e-31  Score=193.36  Aligned_cols=78  Identities=58%  Similarity=1.209  Sum_probs=72.6

Q ss_pred             CcccCCCCCCcccccccchhhHHHHHhhhcCCCccc-ccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhhh
Q psy3092          58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYA-CREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRTK  136 (347)
Q Consensus        58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~-C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~~  136 (347)
                      |.|||++++|+||||.+|+||++||||++..+..|. |..+  |.+++..|..|++|||+||+++||++++||.+|++..
T Consensus         2 C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~~C~~~--C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~~~~   79 (84)
T cd06965           2 CRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLVYKPCDLS--CKIHKKSRNKCQYCRFQKCLNVGMSHNAIRFGRMPRV   79 (84)
T ss_pred             CcccCccCcceEEChhhhhhhhhheeeeeecCCCccccccC--CCcCccccccccchhhhhhhhccCCHHHcccCCCCch
Confidence            999999999999999999999999999999888995 9754  9999999999999999999999999999999888644


Q ss_pred             c
Q psy3092         137 E  137 (347)
Q Consensus       137 ~  137 (347)
                      +
T Consensus        80 ~   80 (84)
T cd06965          80 E   80 (84)
T ss_pred             h
Confidence            3

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

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

Probab=99.96  E-value=1e-28  Score=216.24  Aligned_cols=166  Identities=21%  Similarity=0.359  Sum_probs=136.8

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCc-eEecCC-ccccccchhhc
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDG-ILLAPG-VTVYRSSAHEA  257 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~-~~~~~g-~~i~~~~~~~~  257 (347)
                      .-+..+++.....+..+|+|||++|+|.+|+.+||+.|||++|.++++++.++. +...+. +.+.++ ..+..+.....
T Consensus        37 ~l~~~l~~l~~~~l~~iI~wAK~iPgF~~L~~~DQi~LLk~~~~ElliL~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~  115 (238)
T cd06933          37 SMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEVIMLRSNQS-FSLDDMSWTCGSPDFKYKVSDVTKA  115 (238)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCCccccCChHHHHHHHHHhHHHHHHHHHHHh-cCcCCCeeEecCCceeecHHHHHHc
Confidence            345677888889999999999999999999999999999999999999998764 444443 443332 22333333333


Q ss_pred             CchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCC--CCchHHHHH
Q psy3092         258 GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHS--EEPGRFAKL  335 (347)
Q Consensus       258 ~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~--~~~~Rf~~L  335 (347)
                      +....+.+.+.++..+|++|++|++||+||+||+|||||++|+.+...|+++|+++..+|.+|+..+++  +.+.||++|
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            333233345668999999999999999999999999999999999999999999999999999998877  456789999


Q ss_pred             HhhhhhhhccC
Q psy3092         336 LLRLPSLRSIE  346 (347)
Q Consensus       336 L~ll~~lr~i~  346 (347)
                      |++||+||+|+
T Consensus       196 Ll~L~~LRsi~  206 (238)
T cd06933         196 IQKLADLRSLN  206 (238)
T ss_pred             HHHhHHHHhhh
Confidence            99999999987

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

>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=99.96  E-value=9.9e-29  Score=214.03  Aligned_cols=162  Identities=28%  Similarity=0.431  Sum_probs=137.3

Q ss_pred             hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccc-cchhhc
Q psy3092         179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYR-SSAHEA  257 (347)
Q Consensus       179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~-~~~~~~  257 (347)
                      +..+..+++|....++.+|+|+|++|+|..|+.+||+.|||++|.+++++..++++ ..+    ++.|..+.. +.....
T Consensus        35 ~~~~~~~~e~a~~~l~~~IefaK~iP~F~~L~~~DQi~LLk~~~~el~iL~~a~~~-~~~----~~~~~~~~~~~~~~~~  109 (221)
T cd06936          35 EENFLILTEMATSHVQVLVEFTKGLPGFETLDHEDQIALLKGSAVEAMFLRSAQIY-NKK----LPAGHADLLEERIRSS  109 (221)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHhCCCchhhCChhHHHHHHHHhHHHHHHHHHHHHh-ccc----ccCCCchhhHHHHHhc
Confidence            45688899999999999999999999999999999999999999999999988543 211    344442222 222222


Q ss_pred             Cc-hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHH
Q psy3092         258 GV-GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLL  336 (347)
Q Consensus       258 ~~-~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL  336 (347)
                      +. ..+.+.+. +++.+|++|++|++||+||+||+|||||++||++...|+.+|+++.++|++|+..++++.+.||++||
T Consensus       110 ~~~~e~~~~i~-~~~~kl~~L~l~~~E~~lLkaIvL~npd~~gL~~~~~Ve~~Q~~~~~aL~~y~~~~~p~~p~rf~~LL  188 (221)
T cd06936         110 GISDEFITPMF-NFYKSMGELKMTQEEYALLTAITILFPDRPYLKDKEAVEKLQEPLLDLLQKFCKLYHPEDPQHFACLL  188 (221)
T ss_pred             cchHHHHHHHH-HHHHHHHHcCCCHHHHHHHHHHHHhcCCCcCCCCHHHHHHHHHHHHHHHHHHHHhhCCCchhHHHHHH
Confidence            32 24555554 79999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhhccC
Q psy3092         337 LRLPSLRSIE  346 (347)
Q Consensus       337 ~ll~~lr~i~  346 (347)
                      ++||.||+|+
T Consensus       189 ~~L~~LR~l~  198 (221)
T cd06936         189 GRLTELRTLN  198 (221)
T ss_pred             HHhHHHHHHH
Confidence            9999999986

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=99.96  E-value=1.2e-28  Score=215.46  Aligned_cols=165  Identities=30%  Similarity=0.413  Sum_probs=147.5

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV  259 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~  259 (347)
                      ..+..++++....+..+|+|+|++|+|..|+.+||+.|+|++|.+++++..++++....+.+.+++|..+.++.....+.
T Consensus        39 ~~~~~~~~~~~~~i~~iIefaK~lp~F~~L~~~DQi~LLK~~~~el~~L~~a~~~~~~~~~~~f~~g~~~~~~~~~~~~~  118 (231)
T cd06938          39 MRFRHITEMTILTVQLIVEFAKRLPGFDKLSREDQITLLKACSSEVMMLRVARRYDAKTDSIVFANNQPYTRDSYRKAGM  118 (231)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhcCCccccCChhHHHHHHHHHHHHHHHHHHHHHhCCCCCeEEeeCCEEecHHHHhhcCH
Confidence            45778888888999999999999999999999999999999999999999999877777888999998877766555555


Q ss_pred             hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCC-CchHHHHHHhh
Q psy3092         260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSE-EPGRFAKLLLR  338 (347)
Q Consensus       260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~-~~~Rf~~LL~l  338 (347)
                      +.+.+. +.+++.+|++|++|++||++|+||+||+ +++|+++...|+++|+++..+|+.|+..+++. ++.||++||++
T Consensus       119 ~~~~~~-l~~~~~~l~~L~ld~~E~~lL~AI~Lf~-d~~~L~~~~~Ve~~Q~~~~~aL~~y~~~~~~~~~~~rf~kLL~~  196 (231)
T cd06938         119 GDSAED-LFRFCRAMCSMKVDNAEYALLTAIVIFS-DRPGLLQPKKVEKIQEIYLEALRAYVDNRRPPSQRVIFAKLLSI  196 (231)
T ss_pred             HHHHHH-HHHHHHHHHHcCCCHHHHHHHHHHHHcc-CCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCcccHHHHHHHH
Confidence            555554 4479999999999999999999999997 67899999999999999999999999999886 89999999999


Q ss_pred             hhhhhccC
Q psy3092         339 LPSLRSIE  346 (347)
Q Consensus       339 l~~lr~i~  346 (347)
                      |+.||+|+
T Consensus       197 L~~Lr~l~  204 (231)
T cd06938         197 LTELRTLG  204 (231)
T ss_pred             HHHHHHHH
Confidence            99999986

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=99.96  E-value=2.7e-28  Score=215.69  Aligned_cols=163  Identities=29%  Similarity=0.458  Sum_probs=139.0

Q ss_pred             HHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCc-cccccchhhcC-
Q psy3092         181 QATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGV-TVYRSSAHEAG-  258 (347)
Q Consensus       181 ~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~-~i~~~~~~~~~-  258 (347)
                      -+..+.......+..+++|||++|+|.+|+.+||+.|||++|.+++++.++.+.  ..++.++++|. ++.++.....+ 
T Consensus        64 ~~~~~~~~~~~~i~~vVewAK~IPgF~~L~~~DQi~LLk~~~~Ellil~~a~~~--~~~~~~~~~~~~~~~~~~~~~~~~  141 (259)
T cd06932          64 LFQRCQVRSVETIRELTEFAKSLPGFRNLDLNDQVTLLKYGVHEVIFTMLASLY--NKDGLLFPEGNGYVTREFLESLRK  141 (259)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCcccCChhHHHHHHHHhhHHHHHHHHHHhc--CCCCeEEeCCCEEeeHHHHHHhcc
Confidence            345555566678999999999999999999999999999999999999888653  34567777653 34444433332 


Q ss_pred             -chhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHh
Q psy3092         259 -VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLL  337 (347)
Q Consensus       259 -~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~  337 (347)
                       ...+++.++ +++.+|++|+||++||+||+||+||+||++||.+...|+++|+++..+|+.|+..++|+.+.||++||+
T Consensus       142 ~~~~~~~~~~-e~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~~i~~~~p~~~~rf~kLLl  220 (259)
T cd06932         142 PFCDIMEPKF-EFAEKFNALELTDSELALFCAVIILSPDRPGLINRKPVERIQEHVLQALELQLKKNHPDSPQLFAKLLQ  220 (259)
T ss_pred             cHHHHHHHHH-HHHHHHHHcCCCHHHHHHHHHHHHhCCCcccCcCHHHHHHHHHHHHHHHHHHHhhhCCCcccHHHHHHH
Confidence             245566654 899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhccC
Q psy3092         338 RLPSLRSIE  346 (347)
Q Consensus       338 ll~~lr~i~  346 (347)
                      +||.||+|+
T Consensus       221 ~L~~LRsl~  229 (259)
T cd06932         221 KMVDLRQLV  229 (259)
T ss_pred             HHHHHHHHH
Confidence            999999986

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

>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors

Probab=99.96  E-value=3.5e-30  Score=180.98  Aligned_cols=69  Identities=54%  Similarity=1.141  Sum_probs=66.7

Q ss_pred             CcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchh
Q psy3092          58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKRE  126 (347)
Q Consensus        58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~  126 (347)
                      |.|||++++|+||||.+|+||++||||++..+..|.|..+++|.+++..|..|++|||+||+++||+++
T Consensus         2 C~vC~~~~~~~hygv~~C~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~   70 (70)
T smart00399        2 CCVCGDHASGFHFGVCSCRACKAFFRRTVNLRYKYRCDRKNNCSINKRYRCRCRACRLKKCLGVGMDPE   70 (70)
T ss_pred             CeEeCCcCcccEeCCcEechhhhhhhhheeCCCCeecCCCcccccCCCccccCccCcChhHhhccCcCC
Confidence            999999999999999999999999999999888999999999999999999999999999999999874

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

Probab=99.96  E-value=5.9e-28  Score=205.15  Aligned_cols=163  Identities=20%  Similarity=0.272  Sum_probs=143.4

Q ss_pred             HHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchh-hcCc
Q psy3092         181 QATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH-EAGV  259 (347)
Q Consensus       181 ~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~-~~~~  259 (347)
                      .+..+.+.....+..+|+|+|++|+|..|+.+||+.|+|++|.+++++..++ ++... ..++++|..+.++... ....
T Consensus         3 ~w~~~~~~~~~~i~~~IefaK~iPgF~~L~~~DQi~LLk~~~~e~~ll~~~~-~~~~~-~~~~~~g~~~~~~~~~~~~~~   80 (191)
T cd06942           3 AWGHFAHEFEMHIQEIVQFVKSIPGFNQLSGEDRAQLLKGNMFPLYLLRLSR-DYNNE-GTVLCDFRPVEFASLLSQLLH   80 (191)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCcccCChhHHHHHHHHHHHHHHHHHHHH-HhCcC-CeEEeCCccccHHHHHHhcch
Confidence            4677888889999999999999999999999999999999999999998775 44444 6788888888765432 2233


Q ss_pred             hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCC--CCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHh
Q psy3092         260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD--VRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLL  337 (347)
Q Consensus       260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~--~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~  337 (347)
                      ..+.+++ .+++.+|++|++|++||++|+||+||+||  ++++++...++++|+.+..+|.+|+..++++.+.||++||+
T Consensus        81 ~~~~~~~-~~~~~~l~~L~l~~~E~~lL~Aivl~~pd~~~~~l~~~~~v~~~q~~l~~~L~~~~~~~~~~~~~rf~kLL~  159 (191)
T cd06942          81 GKLIDEM-LQFANKILTLNLTNAELALLCAAELLQPDSLGIQLEETAKSNLQLSVLFQFLKSVLFKDGEDTEQRLQKLFD  159 (191)
T ss_pred             HHHHHHH-HHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCCccchHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHH
Confidence            4566664 58999999999999999999999999999  99999999999999999999999999999988899999999


Q ss_pred             hhhhhhccC
Q psy3092         338 RLPSLRSIE  346 (347)
Q Consensus       338 ll~~lr~i~  346 (347)
                      +++.||+++
T Consensus       160 ~l~~Lr~~~  168 (191)
T cd06942         160 ILNRLRNMN  168 (191)
T ss_pred             HHHHHHHHH
Confidence            999999875

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).

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

Probab=99.96  E-value=7.4e-28  Score=209.64  Aligned_cols=167  Identities=32%  Similarity=0.553  Sum_probs=136.8

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecC-Cccc----cccch
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAP-GVTV----YRSSA  254 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~-g~~i----~~~~~  254 (347)
                      .....+++.+.+++..+++|+|++|+|..|+.+||+.|+|++|.+++++..++++.......+++. +...    ..+..
T Consensus        21 ~~~~~~~~~a~~~l~~~v~wak~iP~F~~L~~~DQ~~LLk~~w~el~lL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  100 (222)
T cd06952          21 LNVHYICESASRLLFLSIHWARSIPAFQALGAETQTSLVRACWPELFTLGLAQCSQQLSLPTILAAIINHLQTSIQQDKL  100 (222)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHhCCchhhCChHHHHHHHHHHhHHHHHHHHHHHhcccCchHHhhhhhhhhhhhHhcCCC
Confidence            347788999999999999999999999999999999999999999999988877654443333322 1111    11111


Q ss_pred             hhcCchhhHHhh--HHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHH
Q psy3092         255 HEAGVGGIFDRV--LTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRF  332 (347)
Q Consensus       255 ~~~~~~~~~~~~--~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf  332 (347)
                      .......+++.+  +.+++.+|++|++|++||++|+||+||+||++|+++.+.|+++|+++.++|.+|+..++++.+.||
T Consensus       101 ~~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~~~LkaiiLf~~d~~~l~~~~~v~~lq~~i~~aL~~y~~~~~p~~~~R~  180 (222)
T cd06952         101 SADKVKQVMEHINKLQEFVNSMQKLDVDDHEYAYLKAIVLFSPDHPGQELRQQIEKLQEKALMELRDYVGKTYPEDEYRL  180 (222)
T ss_pred             chhhhHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCcCCcCHHHHHHHHHHHHHHHHHHHHHhCCCcccHH
Confidence            111222333322  458999999999999999999999999999999999999999999999999999998889999999


Q ss_pred             HHHHhhhhhhhccC
Q psy3092         333 AKLLLRLPSLRSIE  346 (347)
Q Consensus       333 ~~LL~ll~~lr~i~  346 (347)
                      ++||++||.||+++
T Consensus       181 ~klLl~Lp~Lr~~~  194 (222)
T cd06952         181 SKLLLRLPPLRSLS  194 (222)
T ss_pred             HHHHHHhHHhhhcC
Confidence            99999999999986

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

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

Probab=99.95  E-value=3.6e-29  Score=176.39  Aligned_cols=69  Identities=55%  Similarity=1.222  Sum_probs=62.6

Q ss_pred             cCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcch
Q psy3092          57 LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKR  125 (347)
Q Consensus        57 ~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~  125 (347)
                      .|.|||++++|+||||.+|++|++||||++.++..|.|..+++|.+++..+..|++|||+||+++||++
T Consensus         2 ~C~VCg~~~~~~~ygv~sC~~C~~FFrR~~~~~~~~~C~~~~~C~i~~~~~~~C~~CRf~KCl~~GM~k   70 (70)
T PF00105_consen    2 KCKVCGDPASGYHYGVLSCNACKMFFRRSVKKKKPYKCKKNGNCKIDKDNRRKCRSCRFQKCLEVGMKK   70 (70)
T ss_dssp             BSTTTSSBESEEETTEEEEHHHHHHHHHHHHTTCG-STSSSST---STTTTTTSHHHHHHHHHHTTBSG
T ss_pred             CCeECCCccCcccccccccccceeeeeecccccccccccccccccccccCCCEeCcchHHHHHHHCCcC
Confidence            599999999999999999999999999999999999999999999999999999999999999999974

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

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

Probab=99.94  E-value=4.7e-26  Score=189.71  Aligned_cols=162  Identities=39%  Similarity=0.682  Sum_probs=137.6

Q ss_pred             hhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceE-ecCCcccc--ccchhhcCch
Q psy3092         184 NICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGIL-LAPGVTVY--RSSAHEAGVG  260 (347)
Q Consensus       184 ~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~-~~~g~~i~--~~~~~~~~~~  260 (347)
                      .++.++..++..+++|++++|+|+.|+.+||+.|+|++|.+++++..++++........ .+++....  ........+.
T Consensus         2 ~~~~~~~~~~~~~i~~~~~~~~f~~L~~~dq~~Llk~~~~~~~~L~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (168)
T cd06157           2 LLCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLLLAPNGGHTDDDKEDEMKLLLK   81 (168)
T ss_pred             cHHHHHHHHHHHHHHHHHcCCchhcCChHHHHHHHHHHhHHHHHHHHHHHHHhcCCCcEEeecccccccCchHHHHHhHH
Confidence            46788999999999999999999999999999999999999999999999887765443 34443321  1111122334


Q ss_pred             hhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCC-CCCCHHHHHHHHHHHHHHHHHHHHhcCC-CCchHHHHHHhh
Q psy3092         261 GIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVR-GLKSQQVVEMLREKVYTSLEEYTRVNHS-EEPGRFAKLLLR  338 (347)
Q Consensus       261 ~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~-~l~~~~~i~~~r~~~~~~L~~y~~~~~~-~~~~Rf~~LL~l  338 (347)
                      ..+.+.+.+++.+|.+|++|++||++|+||++|+|+.+ +..+.+.+++.|+++..+|+.|+..+++ +++.||++||++
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            56777888999999999999999999999999999998 5667999999999999999999998887 899999999999


Q ss_pred             hhhhhcc
Q psy3092         339 LPSLRSI  345 (347)
Q Consensus       339 l~~lr~i  345 (347)
                      +++||++
T Consensus       162 l~~l~~~  168 (168)
T cd06157         162 LPSLRKL  168 (168)
T ss_pred             chhcccC
Confidence            9999975

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

>smart00430 HOLI Ligand binding domain of hormone receptors

Probab=99.94  E-value=8.2e-26  Score=187.32  Aligned_cols=156  Identities=36%  Similarity=0.630  Sum_probs=134.7

Q ss_pred             HHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCce-EecCCccccccchh--hcCchhhHHhh
Q psy3092         190 DKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGI-LLAPGVTVYRSSAH--EAGVGGIFDRV  266 (347)
Q Consensus       190 ~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~-~~~~g~~i~~~~~~--~~~~~~~~~~~  266 (347)
                      ...+..+++|++++|+|+.|+.+||..|+|++|.+++++..++++....... ..++|..+..+...  ...+...+.+.
T Consensus         2 ~~~~~~~~~~~~~~~~f~~L~~~dq~~Llk~~~~~~~~l~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (163)
T smart00430        2 ERDLLLAVEWAKTFPFFRELSQEDKLILLKHFWFEWLLLESAYRSAKMKKSLLLLPDGTFIDNDKVDLLRKLFSPFLDRI   81 (163)
T ss_pred             hhHHHHHHHHHHhChhHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEeCCCcccCcchhHHHHHHHHHHHHHH
Confidence            4678899999999999999999999999999999999999999988776644 44555555544322  13344566778


Q ss_pred             HHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCH--HHHHHHHHHHHHHHHHHHHhcCC-CCchHHHHHHhhhhhhh
Q psy3092         267 LTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ--QVVEMLREKVYTSLEEYTRVNHS-EEPGRFAKLLLRLPSLR  343 (347)
Q Consensus       267 ~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~--~~i~~~r~~~~~~L~~y~~~~~~-~~~~Rf~~LL~ll~~lr  343 (347)
                      +.+++.+|++|++|++||++|+||++|+|+..++++.  +.++++|+.+.++|+.|+..+.+ +++.||++||+++++|+
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            8899999999999999999999999999999999885  89999999999999999998877 78999999999999998


Q ss_pred             cc
Q psy3092         344 SI  345 (347)
Q Consensus       344 ~i  345 (347)
                      ++
T Consensus       162 ~~  163 (163)
T smart00430      162 KI  163 (163)
T ss_pred             cC
Confidence            74

>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=7.4e-25  Score=188.27  Aligned_cols=169  Identities=33%  Similarity=0.629  Sum_probs=144.2

Q ss_pred             chhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccc-cCCCceEecCCccccccchh
Q psy3092         177 VNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSI-SVKDGILLAPGVTVYRSSAH  255 (347)
Q Consensus       177 ~~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~-~~~~~~~~~~g~~i~~~~~~  255 (347)
                      .....++.+++++...+..+++|++.||+|..|+.+||+.|+|++|.+++++..++++. ...+.+.+++|..++.....
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            45567899999999999999999999999999999999999999999999999999988 56678899999988766554


Q ss_pred             hc---CchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCC-C-HHHHHHHHHHHHHHHHHHH-HhcCC-CC
Q psy3092         256 EA---GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLK-S-QQVVEMLREKVYTSLEEYT-RVNHS-EE  328 (347)
Q Consensus       256 ~~---~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~-~-~~~i~~~r~~~~~~L~~y~-~~~~~-~~  328 (347)
                      ..   ...+.+ +.+.+++.+|.++++|++||++|+|+++|+|+.++++ + .+.++++|+++..+|++|+ ...++ ++
T Consensus        94 ~~~~~~~~~~~-~~~~~~~~~~~~l~l~~~E~~~l~~l~l~~~~~~~~~~~~~~~~~~~r~~~~~~L~~y~~~~~~~~~~  172 (203)
T PF00104_consen   94 DFITGIFSEFI-QYMNEVLRPFRRLKLDEEEFALLKALILFNPDYPGLSEETREIVEELRDRIIQALHSYYNQSKGPEDY  172 (203)
T ss_dssp             HTSTTTHHHHH-HHHHHHHHHHHHTT-BHHHHHHHHHHHHSSTTSTTHS-SHHHHHHHHHHHHHHHHHHHHHHHHSTTTH
T ss_pred             cccccccccch-hHHHHHHHHHHHhhhhhHHHHHHHHHhhhcccccccccchhHHHHHHHHHHHHHHHHHHhccCCCccH
Confidence            33   122333 3556889999999999999999999999999999998 5 4559999999999999999 65555 66


Q ss_pred             chHHHHHHhhhhhhhccC
Q psy3092         329 PGRFAKLLLRLPSLRSIE  346 (347)
Q Consensus       329 ~~Rf~~LL~ll~~lr~i~  346 (347)
                      +.||++||++++.|+.++
T Consensus       173 ~~R~~~ll~ll~~l~~~~  190 (203)
T PF00104_consen  173 AQRFGKLLLLLPSLRKIS  190 (203)
T ss_dssp             TTHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            899999999999999864

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 ....

>KOG3277|consensus

Probab=82.23  E-value=0.91  Score=36.21  Aligned_cols=26  Identities=35%  Similarity=0.865  Sum_probs=19.5

Q ss_pred             CcCcccCCCC------CCccccc--ccchhhHHH
Q psy3092          56 HLCSICGDRA------SGKHYGV--YSCEGCKGF   81 (347)
Q Consensus        56 ~~C~VCg~~a------~g~HyGv--~sC~~Ck~F   81 (347)
                      -.|.||+.+.      ..||=|+  ++|.||+.+
T Consensus        80 yTCkvCntRs~ktisk~AY~~GvVivqC~gC~~~  113 (165)
T KOG3277|consen   80 YTCKVCNTRSTKTISKQAYEKGVVIVQCPGCKNH  113 (165)
T ss_pred             EEeeccCCccccccChhhhhCceEEEECCCCccc
Confidence            3699999865      3467786  479999865

>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc

Probab=80.70  E-value=0.93  Score=28.53  Aligned_cols=40  Identities=30%  Similarity=0.735  Sum_probs=26.5

Q ss_pred             hhhHHHHHhhhcCCCcccccC-C--CCcccccccccCchhhhhH
Q psy3092          76 EGCKGFFKRTVRKDLSYACRE-G--RNCIIDKRQRNRCQYCRYQ  116 (347)
Q Consensus        76 ~~Ck~FFRR~v~~~~~~~C~~-~--~~C~~~~~~r~~Cr~CR~~  116 (347)
                      ++|..||+..-..+- +.|.. +  .-..+...+++.|+.||.|
T Consensus         4 ~~c~~~l~~~RW~~g-~~CP~Cg~~~~~~~~~~~~~~C~~C~~q   46 (46)
T PF12760_consen    4 EACREYLEEIRWPDG-FVCPHCGSTKHYRLKTRGRYRCKACRKQ   46 (46)
T ss_pred             HHHHHHHHHhcCCCC-CCCCCCCCeeeEEeCCCCeEECCCCCCc
Confidence            468888888765555 45653 2  2334455688999999864

It may be a zinc-binding beta ribbon domain that could bind DNA.

>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []

Probab=80.45  E-value=1.1  Score=34.45  Aligned_cols=31  Identities=26%  Similarity=0.808  Sum_probs=21.5

Q ss_pred             CCcCcccCCCCCC---cccccccchhhHHHHHhh
Q psy3092          55 KHLCSICGDRASG---KHYGVYSCEGCKGFFKRT   85 (347)
Q Consensus        55 ~~~C~VCg~~a~g---~HyGv~sC~~Ck~FFRR~   85 (347)
                      ++.|.-||.+...   ..||+..|..|++.-|-.
T Consensus        13 N~~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~l   46 (116)
T PF01412_consen   13 NKVCADCGAPNPTWASLNYGIFLCLECAGIHRSL   46 (116)
T ss_dssp             CTB-TTT-SBS--EEETTTTEEE-HHHHHHHHHH
T ss_pred             cCcCCCCCCCCCCEEEeecChhhhHHHHHHHHHh
Confidence            4679999977643   589999999999996653

The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	347
3dzu_A	467	Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp		1e-114
1z5x_U	262	Hemipteran Ecdysone Receptor Ligand-Binding Domain		2e-88
1lbd_A	282	Ligand-Binding Domain Of The Human Nuclear Receptor		2e-84
1xiu_A	230	Crystal Structure Of The Agonist-Bound Ligand-Bindi		7e-77
2gl8_A	241	Human Retinoic Acid Receptor Rxr-Gamma Ligand-Bindi		8e-75
3eyb_A	219	Structural And Functional Insights Into The Ligand		2e-74
1mv9_A	240	Crystal Structure Of The Human Rxr Alpha Ligand Bin		4e-74
3e94_A	244	Crystal Structure Of Rxralpha Ligand Binding Domain		4e-74
3uvv_B	244	Crystal Structure Of The Ligand Binding Domains Of		5e-74
1fby_A	239	Crystal Structure Of The Human Rxr Alpha Ligand Bin		6e-74
1fm6_A	238	The 2.1 Angstrom Resolution Crystal Structure Of Th		6e-74
1rdt_A	242	Crystal Structure Of A New Rexinoid Bound To The Rx		6e-74
3a9e_A	240	Crystal Structure Of A Mixed Agonist-Bound Rar-Alph		7e-74
3pcu_A	230	Crystal Structure Of Human Retinoic X Receptor Alph		8e-74
1xls_A	232	Crystal Structure Of The Mouse CarRXR LBD HETERODIM		9e-74
3oap_A	231	Crystal Structure Of Human Retinoid X Receptor Alph		9e-74
1xv9_A	236	Crystal Structure Of CarRXR HETERODIMER BOUND WITH		9e-74
3h0a_A	228	Crystal Structure Of Peroxisome Proliferator-Activa		9e-74
1xdk_A	238	Crystal Structure Of The RarbetaRXRALPHA LIGAND BIN		1e-73
2nxx_A	235	Crystal Structure Of The Ligand-Binding Domains Of		4e-73
1uhl_A	236	Crystal Structure Of The Lxralfa-Rxrbeta Lbd Hetero		9e-73
1dkf_A	233	Crystal Structure Of A Heterodimeric Complex Of Rar		1e-72
1h9u_A	224	The Structure Of The Human Retinoid-X-Receptor Beta		3e-72
2q60_A	258	Crystal Structure Of The Ligand Binding Domain Of P		2e-71
1hg4_A	279	Ultraspiracle Ligand Binding Domain From Drosophila		5e-44
1g2n_A	264	Crystal Structure Of The Ligand Binding Domain Of T		1e-38
1r1k_A	263	Crystal Structure Of The Ligand-Binding Domains Of		1e-38
1r0o_A	86	Crystal Structure Of The Heterodimeric Ecdysone Rec		4e-33
2han_A	93	Structural Basis Of Heterodimeric Ecdysteroid Recep		6e-33
1ynw_B	99	Crystal Structure Of Vitamin D Receptor And 9-Cis R		1e-32
1dsz_B	85	Structure Of The RxrRAR DNA-Binding Domain Heterodi		6e-28
1rxr_A	83	High Resolution Solution Structure Of The Retinoid		7e-28
1lv2_A	229	Hepatocyte Nuclear Factor 4 Is A Transcription Fact		2e-27
3cjw_A	244	Crystal Structure Of The Human Coup-Tfii Ligand Bin		3e-27
1by4_A	82	Structure And Mechanism Of The Homodimeric Assembly		9e-27
1m7w_A	250	Hnf4a Ligand Binding Domain With Bound Fatty Acid L		2e-26
3fs1_A	230	Crystal Structure Of Hnf4a Lbd In Complex With The		7e-26
1pzl_A	237	Crystal Structure Of Hnf4a Lbd In Complex With The		8e-26
1r0n_A	81	Crystal Structure Of Heterodimeric Ecdsyone Recepto		2e-25
4dos_A	242	Human Nuclear Receptor Liver Receptor Homologue-1,		3e-24
1yuc_A	255	Human Nuclear Receptor Liver Receptor Homologue-1,		4e-24
1vjb_A	251	Crystal Structure Of The Ligand-Binding Domain Of T		4e-24
1s9q_A	251	Crystal Structure Of The Ligand-Binding Domain Of T		4e-24
1s9p_A	227	Crystal Structure Of The Ligand-Binding Domain Of T		4e-24
2e2r_A	244	Crystal Structure Of Human Estrogen-Related Recepto		4e-24
2ewp_A	226	Crystal Structure Of Estrogen Related Receptor-3 (E		4e-24
1kv6_A	230	X-Ray Structure Of The Orphan Nuclear Receptor Err3		4e-24
1zdu_A	245	The Crystal Structure Of Human Liver Receptor Homol		4e-24
3plz_A	257	Human Lrh1 Lbd Bound To Gr470 Length = 257		5e-24
1yok_A	256	Crystal Structure Of Human Lrh-1 Bound With Tif-2 P		5e-24
3dzu_D	419	Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp		6e-24
3tx7_B	352	Crystal Structure Of Lrh-1BETA-Catenin Complex Leng		8e-24
1pk5_A	248	Crystal Structure Of The Orphan Nuclear Receptor Lr		9e-24
1zh7_A	243	Structural And Biochemical Basis For Selective Repr		2e-23
2nll_A	66	Retinoid X Receptor-Thyroid Hormone Receptor Dna-Bi		4e-20
3cbb_A	78	Crystal Structure Of Hepatocyte Nuclear Factor 4alp		5e-19
3a9e_B	269	Crystal Structure Of A Mixed Agonist-Bound Rar-Alph		1e-18
3p0u_A	249	Crystal Structure Of The Ligand Binding Domain Of H		2e-18
1dkf_B	235	Crystal Structure Of A Heterodimeric Complex Of Rar		2e-18
3kmr_A	266	Crystal Structure Of Raralpha Ligand Binding Domain		2e-18
4dqm_A	234	Revealing A Marine Natural Product As A Novel Agoni		2e-18
1xdk_B	303	Crystal Structure Of The RarbetaRXRALPHA LIGAND BIN		2e-18
1ymt_A	246	Mouse Sf-1 Lbd Length = 246		5e-18
1xap_A	267	Structure Of The Ligand Binding Domain Of The Retin		5e-18
1yp0_A	239	Structure Of The Steroidogenic Factor-1 Ligand Bind		2e-17
2ebl_A	89	Solution Structure Of The Zinc Finger, C4-type Doma		3e-17
3f7d_A	244	Sf-1 Lbd Bound By Phosphatidylcholine Length = 244		1e-16
3d24_A	253	Crystal Structure Of Ligand-Binding Domain Of Estro		1e-15
3k6p_A	248	Estrogen Related Receptor Alpha In Complex With An		1e-15
1xb7_A	247	X-Ray Structure Of Erralpha Lbd In Complex With A P		1e-15
3n00_A	245	Crystal Structure Of A Deletion Mutant Of Human Rev		3e-15
1dsz_A	86	Structure Of The RxrRAR DNA-Binding Domain Heterodi		4e-15
2a66_A	113	Human Liver Receptor Homologue Dna-Binding Domain (		1e-14
2xhs_A	245	Crystal Structure Of The Ligand Binding Domain Of F		1e-14
2pjl_A	247	Crystal Structure Of Human Estrogen-Related Recepto		2e-14
1exa_A	246	Enantiomer Discrimination Illustrated By Crystal St		6e-14
2ff0_A	102	Solution Structure Of Steroidogenic Factor 1 Dna Bi		6e-14
1fcx_A	235	Isotype Selectivity Of The Human Retinoic Acid Nucl		6e-14
2lbd_A	267	Ligand-Binding Domain Of The Human Retinoic Acid Re		6e-14
1fcy_A	236	Isotype Selectivity Of The Human Retinoic Acid Nucl		6e-14
3m9e_A	105	Thyroid Hormone Beta Dna Binding Domain Homodimer W		9e-14
1r0n_B	109	Crystal Structure Of Heterodimeric Ecdsyone Recepto		1e-13
2acl_B	244	Liver X-Receptor Alpha Ligand Binding Domain With S		1e-13
3fc6_B	266	Hrxralpha & Mlxralpha With An Indole Pharmacophore,		1e-13
2han_B	119	Structural Basis Of Heterodimeric Ecdysteroid Recep		2e-13
1hra_A	80	The Solution Structure Of The Human Retinoic Acid R		2e-13
1qkn_A	255	Rat Oestrogen Receptor Beta Ligand-Binding Domain I		2e-13
2j7x_A	255	Structure Of Estradiol-bound Estrogen Receptor Beta		2e-13
2fsz_A	246	A Second Binding Site For Hydroxytamoxifen Within T		2e-13
1p8d_A	250	X-Ray Crystal Structure Of Lxr Ligand Binding Domai		2e-13
1pq6_A	253	Human Lxr Beta Hormone Receptor / Gw3965 Complex Le		2e-13
1upv_A	257	Crystal Structure Of The Human Liver X Receptor Bet		2e-13
1nav_A	263	Thyroid Receptor Alpha In Complex With An Agonist S		3e-13
4dk8_A	247	Crystal Structure Of Lxr Ligand Binding Domain In C		3e-13
2h77_A	269	Crystal Structure Of Human Tr Alpha Bound T3 In Mon		4e-13
3hzf_A	269	Structure Of Tr-alfa Bound To Selective Thyromimeti		4e-13
2h79_A	269	Crystal Structure Of Human Tr Alpha Bound T3 In Ort		4e-13
3jzb_A	267	Crystal Structure Of Tr-Alfa Bound To The Selective		4e-13
3cqv_A	199	Crystal Structure Of Reverb Beta In Complex With He		5e-13
1cit_A	89	Dna-Binding Mechanism Of The Monomeric Orphan Nucle		5e-13
1yy4_A	268	Crystal Structure Of Estrogen Receptor Beta Complex		5e-13
2v0v_A	194	Crystal Structure Of Rev-Erb Beta Length = 194		5e-13
1hlz_A	94	Crystal Structure Of The Orphan Nuclear Receptor Re		5e-13
2v7c_A	194	Crystal Structure Of Rev-Erb Beta Length = 194		6e-13
2yat_A	252	Crystal Structure Of Estradiol Derived Metal Chelat		6e-13
1uom_A	254	The Structure Of Estrogen Receptor In Complex With		6e-13
1qkt_A	248	Mutant Estrogen Nuclear Receptor Ligand Binding Dom		7e-13
1pcg_A	244	Helix-Stabilized Cyclic Peptides As Selective Inhib		7e-13
3ltx_A	243	Crystal Structure Of The Pacific Oyster Estrogen Re		7e-13
1l2j_A	271	Human Estrogen Receptor Beta Ligand-Binding Domain		7e-13
2i0g_A	257	Benzopyrans Are Selective Estrogen Receptor Beta Ag		8e-13
2ocf_A	298	Human Estrogen Receptor Alpha Ligand-Binding Domain		8e-13
1qkm_A	255	Human Oestrogen Receptor Beta Ligand-Binding Domain		8e-13
2nll_B	103	Retinoid X Receptor-Thyroid Hormone Receptor Dna-Bi		9e-13
2jfa_B	252	Estrogen Receptor Alpha Lbd In Complex With An Affi		9e-13
1nde_A	255	Estrogen Receptor Beta With Selective Triazine Modu		9e-13
1u9e_A	241	Crystal Structure Of Estrogen Receptor Beta Complex		9e-13
1x76_A	240	Crystal Structure Of Estrogen Receptor Beta Complex		9e-13
2nv7_A	238	Crystal Structure Of Estrogen Receptor Beta Complex		1e-12
1l2i_A	261	Human Estrogen Receptor Alpha Ligand-Binding Domain		1e-12
2giu_A	241	Human Estrogen Receptor Beta Ligand-Binding Domain		1e-12
3q95_B	260	Crystal Structure Of Human Estrogen Receptor Alpha		1e-12
3uu7_A	251	Crystal Structure Of Hera-Lbd (Y537s) In Complex Wi		1e-12
3l0e_A	253	X-Ray Crystal Structure Of A Potent Liver X Recepto		1e-12
2yly_A	240	Sulfonamides As Selective Estrogen Receptor Beta Ag		1e-12
3q97_A	260	Crystal Structure Of Human Estrogen Receptor Alpha		1e-12
3oll_A	240	Crystal Structure Of Phosphorylated Estrogen Recept		1e-12
1zky_A	257	Human Estrogen Receptor Alpha Ligand-Binding Domain		1e-12
3uvv_A	265	Crystal Structure Of The Ligand Binding Domains Of		1e-12
3uu7_B	251	Crystal Structure Of Hera-Lbd (Y537s) In Complex Wi		1e-12
3hm1_A	253	Crystal Structure Of Human Estrogen Receptor Alpha		1e-12
1zaf_A	238	Crystal Structure Of Estrogen Receptor Beta Complex		1e-12
2bj4_A	252	Estrogen Receptor Alpha Lbd In Complex With A Phage		1e-12
3hlv_A	253	Crystal Structure Of Human Estrogen Receptor Alpha		2e-12
3dt3_A	255	Human Estrogen Receptor Alpha Lbd With Gw368 Length		2e-12
1gwq_A	248	Human Oestrogen Receptor Alpha Ligand-Binding Domai		2e-12
1g50_A	247	Crystal Structure Of A Wild Type Her Alpha Lbd At 2		2e-12
3q95_A	260	Crystal Structure Of Human Estrogen Receptor Alpha		2e-12
2qa8_B	258	Crystal Structure Of The Estrogen Receptor Alpha Li		2e-12
3erd_A	261	Human Estrogen Receptor Alpha Ligand-Binding Domain		2e-12
3uua_A	251	Crystal Structure Of Hera-Lbd (Y537s) In Complex Wi		2e-12
2p15_A	258	Crystal Structure Of The Er Alpha Ligand Binding Do		2e-12
2qxs_A	258	Crystal Structure Of Antagonizing Mutant 536s Of Th		2e-12
1ere_A	253	Human Estrogen Receptor Ligand-Binding Domain In Co		2e-12
1sj0_A	248	Human Estrogen Receptor Alpha Ligand-binding Domain		2e-12
2iok_A	254	Human Estrogen Receptor Alpha Ligand-binding Domain		2e-12
2iog_A	246	Human Estrogen Receptor Alpha Ligand-Binding Domain		2e-12
1err_A	253	Human Estrogen Receptor Ligand-Binding Domain In Co		2e-12
3uuc_A	251	Crystal Structure Of Hera-Lbd (Wt) In Complex With		2e-12
2qa8_A	258	Crystal Structure Of The Estrogen Receptor Alpha Li		2e-12
1gwr_A	245	Human Oestrogen Receptor Alpha Ligand-Binding Domai		2e-12
3l03_A	253	Crystal Structure Of Human Estrogen Receptor Alpha		2e-12
1qku_A	250	Wild Type Estrogen Nuclear Receptor Ligand Binding		2e-12
2qzo_B	258	Crystal Structure Of The Estrogen Receptor Alpha Li		2e-12
4dma_A	247	Crystal Structure Of Era Lbd In Complex With Ru1001		2e-12
3uua_B	251	Crystal Structure Of Hera-Lbd (Y537s) In Complex Wi		2e-12
1a52_A	258	Estrogen Receptor Alpha Ligand-Binding Domain Compl		3e-12
1x7e_A	245	Crystal Structure Of Estrogen Receptor Alpha Comple		3e-12
3os8_A	258	Estrogen Receptor Length = 258		6e-12
1lo1_A	98	Estrogen Related Receptor 2 Dna Binding Domain In C		1e-11
3os8_C	258	Estrogen Receptor Length = 258		1e-11
2env_A	88	Solution Sturcture Of The C4-Type Zinc Finger Domai		1e-11
1uhl_B	242	Crystal Structure Of The Lxralfa-Rxrbeta Lbd Hetero		1e-11
1ovl_A	271	Crystal Structure Of Nurr1 Lbd Length = 271		1e-11
1ovl_B	271	Crystal Structure Of Nurr1 Lbd Length = 271		1e-11
3ipq_A	283	X-Ray Structure Of Gw3965 Synthetic Agonist Bound T		1e-11
1zdt_A	241	The Crystal Structure Of Human Steroidogenic Factor		2e-11
1hcq_A	84	The Crystal Structure Of The Estrogen Receptor Dna-		2e-11
1i7i_A	292	Crystal Structure Of The Ligand Binding Domain Of H		2e-11
1nyx_A	276	Ligand Binding Domain Of The Human Peroxisome Proli		2e-11
3s9s_A	284	Ligand Binding Domain Of Ppargamma Complexed With A		2e-11
2om9_A	278	Ajulemic Acid, A Synthetic Cannabinoid Bound To Ppa		2e-11
4dk7_A	247	Crystal Structure Of Lxr Ligand Binding Domain In C		2e-11
2i4j_A	286	Crystal Structure Of The Complex Between Ppargamma		2e-11
2vsr_A	276	Hppargamma Ligand Binding Domain In Complex With 9-		2e-11
1rdt_D	284	Crystal Structure Of A New Rexinoid Bound To The Rx		2e-11
3osi_A	285	Crystal Structure Of Ppargamma Ligand Binding Domai		2e-11
3ads_A	287	Human Ppargamma Ligand-Binding Domain In Complex Wi		2e-11
3lmp_A	283	Crystal Structure Of The Ppargamma-Lbd Complexed Wi		2e-11
1yow_A	242	Human Steroidogenic Factor 1 Lbd With Bound Co-Fact		2e-11
1k74_D	283	The 2.3 Angstrom Resolution Crystal Structure Of Th		2e-11
1wm0_X	292	Ppargamma In Complex With A 2-Baba Compound Length		2e-11
3vn2_A	285	Crystal Structure Of Ppargamma Complexed With Telmi		2e-11
1zeo_A	277	Crystal Structure Of Human Ppar-Gamma Ligand Bindin		2e-11
3bc5_A	296	X-Ray Crystal Structure Of Human Ppar Gamma With 2-		2e-11
2vv1_B	276	Hppargamma Ligand Binding Domain In Complex With 4-		2e-11
3b0q_A	274	Human Ppar Gamma Ligand Binding Domain In Complex W		2e-11
3cs8_A	275	Structural And Biochemical Basis For The Binding Se		2e-11
2q59_B	274	Crystal Structure Of Ppargamma Lbd Bound To Full Ag		2e-11
3pba_A	286	Crystal Structure Of Ppargamma Ligand Binding Domai		2e-11
3et3_A	292	Structure Of Ppargamma With 3-[5-Methoxy-1-(4-Metho		2e-11
3r8a_A	282	X-Ray Crystal Structure Of The Nuclear Hormone Rece		2e-11
2vv4_B	276	Hppargamma Ligand Binding Domain In Complex With 6-		2e-11
4prg_A	270	0072 Partial Agonist Ppar Gamma Cocrystal Length =		2e-11
3prg_A	278	Ligand Binding Domain Of Human Peroxisome Prolifera		2e-11
2zvt_A	286	Cys285ser Mutant Ppargamma Ligand-Binding Domain Co		2e-11
1fm6_D	272	The 2.1 Angstrom Resolution Crystal Structure Of Th		2e-11
3cwd_A	270	Molecular Recognition Of Nitro-Fatty Acids By Ppar		2e-11
2prg_A	271	Ligand-Binding Domain Of The Human Peroxisome Proli		2e-11
2hfp_A	282	Crystal Structure Of Ppar Gamma With N-Sulfonyl-2-I		2e-11
1knu_A	274	Ligand Binding Domain Of The Human Peroxisome Proli		2e-11
3t03_A	284	Crystal Structure Of Ppar Gamma Ligand Binding Doma		2e-11
3u9q_A	269	Ligand Binding Domain Of Ppargamma Complexed With D		2e-11
2q59_A	274	Crystal Structure Of Ppargamma Lbd Bound To Full Ag		3e-11
3et0_A	292	Structure Of Ppargamma With 3-(5-Methoxy-1h-Indol-3		3e-11
4aa6_E	71	The Oestrogen Receptor Recognizes An Imperfectly Pa		9e-11
4aa6_A	71	The Oestrogen Receptor Recognizes An Imperfectly Pa		9e-11
2j4a_A	253	Human Thyroid Hormone Receptor Beta Ligand Binding		9e-11
1hcp_A	76	Dna Recognition By The Oestrogen Receptor: From Sol		9e-11
3hc6_A	232	Fxr With Src1 And Gsk088 Length = 232		1e-10
3gd2_A	229	Isoxazole Ligand Bound To Farnesoid X Receptor (Fxr		1e-10
1lat_A	82	Glucocorticoid Receptor MutantDNA COMPLEX Length =		1e-10
2b50_A	272	Human Nuclear Receptor-Ligand Complex 2 Length = 27		1e-10
3p88_A	229	Fxr Bound To Isoquinolinecarboxylic Acid Length = 2		1e-10
2q5g_A	283	Ligand Binding Domain Of Ppar Delta Receptor In Com		2e-10
2awh_A	268	Human Nuclear Receptor-Ligand Complex 1 Length = 26		2e-10
3p89_A	229	Fxr Bound To A Quinolinecarboxylic Acid Length = 22		2e-10
3et2_A	287	Structure Of Ppardelta With 3-[5-Methoxy-1-(4-Metho		2e-10
2j14_A	285	3,4,5-Trisubstituted Isoxazoles As Novel Ppardelta		2e-10
1osv_A	230	Structural Basis For Bile Acid Binding And Activati		2e-10
2gwx_A	267	Molecular Recognition Of Fatty Acids By Peroxisome		2e-10
1nuo_A	261	Two Rth Mutants With Impaired Hormone Binding Lengt		2e-10
1ot7_A	229	Structural Basis For 3-Deoxy-Cdca Binding And Activ		2e-10
3sp9_A	281	Structural Basis For Iloprost As A Dual PparalphaDE		2e-10
2xyj_A	288	Novel Sulfonylthiadiazoles With An Unusual Binding		2e-10
2znp_A	276	Human Pprr Delta Ligand Binding Domain In Complex W		2e-10
1y0s_A	272	Crystal Structure Of Ppar Delta Complexed With Gw23		2e-10
1gwx_A	271	Molecular Recognition Of Fatty Acids By Peroxisome		2e-10
3dct_A	235	Fxr With Src1 And Gw4064 Length = 235		2e-10
1q4x_A	253	Crystal Structure Of Human Thyroid Hormone Receptor		2e-10
1r6g_A	259	Crystal Structure Of The Thyroid Hormone Receptor B		2e-10
3fxv_A	233	Identification Of An N-Oxide Pyridine Gw4064 Analog		2e-10
1bsx_A	260	Structure And Specificity Of Nuclear Receptor-Coact		2e-10
1xzx_X	281	Thyroxine-Thyroid Hormone Receptor Interactions Len		2e-10
3tkm_A	275	Crystal Structure Ppar Delta Binding Gw0742 Length		2e-10
3bej_A	238	Structure Of Human Fxr In Complex With Mfa-1 And Co		2e-10
3g9p_B	90	Gr Dna Binding Domain:sgk 16bp Complex-7 Length = 9		2e-10
1nq0_A	263	Tr Receptor Mutations Conferring Hormone Resistance		2e-10
1nax_A	252	Thyroid Receptor Beta1 In Complex With A Beta-Selec		2e-10
1n46_A	258	Crystal Structure Of Human Tr Beta Ligand-Binding D		2e-10
1nq1_A	263	Tr Receptor Mutations Conferring Hormone Resistance		2e-10
3l1b_A	233	Complex Structure Of Fxr Ligand-Binding Domain With		3e-10
1osh_A	232	A Chemical, Genetic, And Structural Analysis Of The		3e-10
3fli_A	231	Discovery Of Xl335, A Highly Potent, Selective And		3e-10
3hc5_A	232	Fxr With Src1 And Gsk826 Length = 232		3e-10
1nq2_A	264	Two Rth Mutants With Impaired Hormone Binding Lengt		3e-10
3jzc_A	263	Crystal Structure Of Tr-Beta Bound To The Selective		3e-10
3imy_A	261	Structure Of Tr-Beta Bound To Selective Thyromimeti		3e-10
3gws_X	259	Crystal Structure Of T3-Bound Thyroid Hormone Recep		3e-10
3rut_A	229	Fxr With Src1 And Gsk359 Length = 229		3e-10
3d57_A	266	Tr Variant D355r Length = 266		3e-10
2pin_A	253	Thyroid Receptor Beta In Complex With Inhibitor Len		4e-10
1ynw_A	110	Crystal Structure Of Vitamin D Receptor And 9-Cis R		8e-10
3gz9_A	269	Crystal Structure Of Peroxisome Proliferator-Activa		1e-09
4hn6_A	114	Gr Dna Binding Domain R460d/d462r - Tslp Ngre Compl		1e-09
2nxx_E	248	Crystal Structure Of The Ligand-Binding Domains Of		2e-09
3g6t_A	91	Gr Gamma Dna-Binding Domain:fkbp5 16bp Complex-34 L		2e-09
1kb2_A	110	Crystal Structure Of Vdr Dna-Binding Domain Bound T		3e-09
1z5x_E	310	Hemipteran Ecdysone Receptor Ligand-Binding Domain		3e-09
1gdc_A	72	Refined Solution Structure Of The Glucocorticoid Re		3e-09
2gda_A	72	Refined Solution Structure Of The Glucocorticoid Re		4e-09
1r4o_A	92	Crystallographic Analysis Of The Interaction Of The		4e-09
1r4r_B	92	Crystallographic Analysis Of The Interaction Of The		4e-09
1yje_A	264	Crystal Structure Of The Rngfi-B Ligand-Binding Dom		5e-09
3v3e_B	257	Crystal Structure Of The Human Nur77 Ligand-Binding		5e-09
2qw4_A	273	Human Nr4a1 Ligand-Binding Domain Length = 273		6e-09
2c7a_A	78	Structure Of The Progesterone Receptor-Dna Complex		1e-08
1rgd_A	71	Structure Refinement Of The Glucocorticoid Receptor		1e-08
4hn5_A	117	Gr Dna Binding Domain - Tslp Ngre Complex Length =		1e-08
1glu_A	81	Crystallographic Analysis Of The Interaction Of The		1e-08
1r20_D	265	Crystal Structure Of The Ligand-Binding Domains Of		2e-08
3vhu_A	294	Mineralocorticoid Receptor Ligand-Binding Domain Wi		4e-08
3vhv_A	260	Mineralocorticoid Receptor Ligand-Binding Domain Wi		4e-08
2aa6_A	275	Mineralocorticoid Receptor S810l Mutant With Bound		4e-08
1i7g_A	287	Crystal Structure Of The Ligand Binding Domain From		7e-08
1r1k_D	266	Crystal Structure Of The Ligand-Binding Domains Of		7e-08
2znn_A	273	Human Pprr Alpha Ligand Binding Domain In Complex W		8e-08
2rew_A	277	Crystal Structure Of Pparalpha Ligand Binding Domai		8e-08
1r4i_A	105	Crystal Structure Of Androgen Receptor Dna-Binding		8e-08
3sp6_A	285	Structural Basis For Iloprost As A Dual PparalphaDE		9e-08
3et1_A	291	Structure Of Pparalpha With 3-[5-Methoxy-1-(4-Metho		9e-08
1k7l_A	288	The 2.5 Angstrom Resolution Crystal Structure Of Th		9e-08
2p54_A	267	A Crystal Structure Of Ppar Alpha Bound With Src1 P		9e-08
2npa_A	270	The Crystal Structure Of The Human Pparaplpha Ligan		9e-08
3g8i_A	270	Aleglitazar, A New, Potent, And Balanced Ppar Alpha		1e-07
1kkq_A	269	Crystal Structure Of The Human Ppar-Alpha Ligand-Bi		1e-07
1n4h_A	259	Characterization Of Ligands For The Orphan Nuclear		1e-07
2hbh_A	302	Crystal Structure Of Vitamin D Nuclear Receptor Lig		1e-07
1y9r_A	255	Crystal Structure Of The Human Mineralocorticoid Re		1e-07
2oax_A	256	Crystal Structure Of The S810l Mutant Mineralocorti		1e-07
1ilg_A	316	Crystal Structure Of Apo Human Pregnane X Receptor		2e-07
4fhh_A	300	Development Of Synthetically Accessible Non-Secoste		2e-07
1k4w_A	252	X-Ray Structure Of The Orphan Nuclear Receptor Ror		2e-07
1skx_A	313	Structural Disorder In The Complex Of Human Pxr And		2e-07
1nq7_A	244	Characterization Of Ligands For The Orphan Nuclear		2e-07
3ctb_A	344	Tethered Pxr-LbdSRC-1p Apoprotein Length = 344		2e-07
3mno_A	261	Crystal Structure Of The Agonist Form Of Mouse Gluc		2e-07
2o9i_A	293	Crystal Structure Of The Human Pregnane X Receptor		3e-07
3e7c_A	257	Glucocorticoid Receptor Lbd Bound To Gsk866 Length		3e-07
3cld_A	259	Ligand Binding Domain Of The Glucocorticoid Recepto		3e-07
1xv9_B	246	Crystal Structure Of CarRXR HETERODIMER BOUND WITH		3e-07
2aa2_A	275	Mineralocorticoid Receptor With Bound Aldosterone L		3e-07
2a3i_A	253	Structural And Biochemical Mechanisms For The Speci		3e-07
3mnp_A	261	Crystal Structure Of The Agonist Form Of Mouse Gluc		4e-07
3f5c_B	268	Structure Of Dax-1:lrh-1 Complex Length = 268		4e-07
3mne_A	261	Crystal Structure Of The Agonist Form Of Mouse Gluc		6e-07
1i38_A	260	Crystal Structure Of The Rat Androgen Receptor Liga		7e-07
1i37_A	260	Crystal Structure Of The Rat Androgen Receptor Liga		7e-07
3g8o_A	263	Progesterone Receptor With Bound Pyrrolidine 1 Leng		7e-07
1e3k_A	258	Human Progesteron Receptor Ligand Binding Domain In		7e-07
1sr7_A	259	Progesterone Receptor Hormone Binding Domain With B		8e-07
2q7k_A	257	The Androgen Receptor Prostate Cancer Mutant H874y		8e-07
1a28_A	256	Hormone-Bound Human Progesterone Receptor Ligand-Bi		8e-07
2ax6_A	256	Crystal Structure Of The Androgen Receptor Ligand B		8e-07
1xj7_A	257	Complex Androgen Receptor Lbd And Rac3 Peptide Leng		8e-07
1t73_A	269	Crystal Structure Of The Androgen Receptor Ligand B		8e-07
3h52_A	254	Crystal Structure Of The Antagonist Form Of Human G		8e-07
2am9_A	266	Crystal Structure Of Human Androgen Receptor Ligand		8e-07
1t5z_A	251	Crystal Structure Of The Androgen Receptor Ligand B		8e-07
2ax9_A	256	Crystal Structure Of The Androgen Receptor Ligand B		8e-07
1e3g_A	263	Human Androgen Receptor Ligand Binding In Complex W		8e-07
1pdu_A	244	Ligand-Binding Domain Of Drosophila Orphan Nuclear		9e-07
2w8y_A	260	Ru486 Bound To The Progesterone Receptor In A Desta		9e-07
2hvc_A	250	The Crystal Structure Of Ligand-Binding Domain (Lbd		9e-07
1sqn_A	261	Progesterone Receptor Ligand Binding Domain With Bo		9e-07
1nhz_A	280	Crystal Structure Of The Antagonist Form Of Glucoco		9e-07
2abi_A	256	Crystal Structure Of The Human Mineralocorticoid Re		9e-07
3a2i_A	263	Crystal Structure Of The Human Vitamin D Receptor (		1e-06
3a2j_A	263	Crystal Structure Of The Human Vitamin D Receptor (		1e-06
3kba_A	253	Progesterone Receptor Bound To Sulfonamide Pyrrolid		1e-06
1gs4_A	248	Structural Basis For The Glucocorticoid Response In		1e-06
2z4j_A	248	Crystal Structure Of Ar Lbd With Shp Peptide Nr Box		1e-06
3rlj_A	247	Crystal Structure Of The Androgen Receptor Ligand B		1e-06
2oz7_A	249	Crystal Structure Of The Human Androgen Receptor T8		1e-06
1xow_A	249	Crystal Structure Of The Human Androgen Receptor Li		1e-06
3rll_A	247	Crystal Structure Of The T877a Androgen Receptor Li		1e-06
3l3x_A	250	Crystal Structure Of Dht-Bound Androgen Receptor In		1e-06
1n83_A	270	Crystal Structure Of The Complex Between The Orphan		1e-06
3bqd_A	255	Doubling The Size Of The Glucocorticoid Receptor Li		1e-06
1m2z_A	257	Crystal Structure Of A Dimer Complex Of The Human G		2e-06
3m7r_A	253	Crystal Structure Of Vdr H305q Mutant Length = 253		2e-06
2zl9_A	271	2-Substituted-16-Ene-22-Thia-1alpha,25-Dihydroxy-26		2e-06
1db1_A	259	Crystal Structure Of The Nuclear Receptor For Vitam		2e-06
4e2j_A	250	X-Ray Crystal Structure Of The Ancestral Glucocorti		2e-06
1s0z_A	263	Crystal Structure Of The Vdr Lbd Complexed To Seoca		2e-06
3gn8_A	249	X-Ray Crystal Structure Of Ancgr2 In Complex With D		2e-06
3p8x_A	280	Synthesis, Structure, And Biological Activity Of De		2e-06
2zfx_A	265	Crystal Structure Of The Rat Vitamin D Receptor Lig		3e-06
1rjk_A	292	Crystal Structure Of The Rat Vitamin D Receptor Lig		3e-06
3b0t_A	254	Human Vdr Ligand Binding Domain In Complex With Max		3e-06
3az1_A	253	Crystal Structure Analysis Of Vitamin D Receptor Le		3e-06
4fne_A	254	X-Ray Crystal Structure Of The Ancestral 3-Keto Ste		5e-06
2q3y_A	249	Ancestral Corticiod Receptor In Complex With Doc Le		8e-06
1xnx_A	256	Crystal Structure Of Constitutive Androstane Recept		9e-06
2q1h_A	250	Ancestral Corticoid Receptor In Complex With Aldost		9e-06
1xls_E	242	Crystal Structure Of The Mouse CarRXR LBD HETERODIM		1e-05
3ry9_A	250	Crystal Structure Of The Resurrected Ancestral Gluc		2e-05
2ax8_A	256	Crystal Structure Of The Androgen Receptor Ligand B		4e-05
1z95_A	246	Crystal Structure Of The Androgen Receptor Ligand-B		5e-05

>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 =  409 bits (1050), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 203/309 (65%), Positives = 236/309 (76%), Gaps = 10/309 (3%)
Query: 47  PNHP----LCGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCII 102
           P HP       +KH+C+ICGDR+SGKHYGVYSCEGCKGFFKRTVRKDL+Y CR+ ++C+I
Sbjct: 125 PAHPSGNMASFTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLI 184
Query: 103 DXXXXXXXXXXXXXXXLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAE 162
           D               L MGMKREAVQEERQR K+R+ NEVESTS    +MPVERILEAE
Sbjct: 185 DKRQRNRCQYCRYQKCLAMGMKREAVQEERQRGKDRNENEVESTSSANEDMPVERILEAE 244
Query: 163 QRVDMKQEPADQDIVN------EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVL 216
             V+ K E   +  +           TNIC+A DKQLF LV+WAK IPHF+ LPL+DQV+
Sbjct: 245 LAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVI 304
Query: 217 LLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMRE 276
           LLRAGWNELLIASFSHRSI+VKDGILLA G+ V+R+SAH AGVG IFDRVLTELVSKMR+
Sbjct: 305 LLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRD 364
Query: 277 MKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLL 336
           M+MDKTELGCLR I+LFNPD +GL +   VE LREKVY SLE Y +  + E+PGRFAKLL
Sbjct: 365 MQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLL 424
Query: 337 LRLPSLRSI 345
           LRLP+LRSI
Sbjct: 425 LRLPALRSI 433

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

Iteration: 1
 Score =  322 bits (825), Expect = 2e-88,   Method: Compositional matrix adjust.
 Identities = 155/224 (69%), Positives = 188/224 (83%), Gaps = 4/224 (1%)
Query: 122 GMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQRVDMKQEPADQDIVNEQQ 181
           G KREAVQEERQR KE+  NEVESTS +  +MP+ERILEAE RV    EP ++DI +   
Sbjct: 10  GPKREAVQEERQRNKEKSENEVESTSNSQNDMPIERILEAELRV----EPKNEDIDSRDP 65
Query: 182 ATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGI 241
            ++IC+A D+QL+QL++WAKHIPHFT LP+EDQV+LL++GWNELLIA FSHRS+SVKDGI
Sbjct: 66  VSDICQAADRQLYQLIEWAKHIPHFTELPVEDQVILLKSGWNELLIAGFSHRSMSVKDGI 125
Query: 242 LLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLK 301
           +LA G+ V+R+ AH+AGVG IFDRVLTELV+KMREMKMDKTELGCLR+I+LFNP+ +GLK
Sbjct: 126 MLATGLVVHRNCAHQAGVGAIFDRVLTELVAKMREMKMDKTELGCLRSIVLFNPEAKGLK 185
Query: 302 SQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           S Q VE LREKVY  LEEY R  + ++ GRFAKLLLRLP+LRSI
Sbjct: 186 STQQVENLREKVYAILEEYCRQTYPDQSGRFAKLLLRLPALRSI 229

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

Iteration: 1
 Score =  308 bits (790), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 157/228 (68%), Positives = 181/228 (79%), Gaps = 6/228 (2%)
Query: 124 KREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQRVDMKQEPADQDIVN----- 178
           KREAVQEERQR K+R+ NEVESTS    +MPVERILEAE  V+ K E   +  +      
Sbjct: 21  KREAVQEERQRGKDRNENEVESTSSANEDMPVERILEAELAVEPKTETYVEANMGLNPSS 80
Query: 179 -EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISV 237
                TNIC+A DKQLF LV+WAK IPHF+ LPL+DQV+LLRAGWNELLIASFSHRSI+V
Sbjct: 81  PNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAV 140
Query: 238 KDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDV 297
           KDGILLA G+ V+R+SAH AGVG IFDRVLTELVSKMR+M+MDKTELGCLR I+LFNPD 
Sbjct: 141 KDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDS 200
Query: 298 RGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +GL +   VE LREKVY SLE Y +  + E+PGRFAKLLLRLP+LRSI
Sbjct: 201 KGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSI 248

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

Iteration: 1
 Score =  283 bits (725), Expect = 7e-77,   Method: Compositional matrix adjust.
 Identities = 141/196 (71%), Positives = 161/196 (82%), Gaps = 6/196 (3%)
Query: 152 EMPVERILEAEQRVDMKQEPADQDIVNEQQ--ATNICKATDKQLFQLVDWAKHIPHFTTL 209
           +MPVE+ILEAE  VD    P     ++ Q+   TNIC+A DKQLF LV+WAK IPHFT L
Sbjct: 5   DMPVEQILEAELAVD----PKIDTYIDAQKDPVTNICQAADKQLFTLVEWAKRIPHFTEL 60
Query: 210 PLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTE 269
           PLEDQV+LLRAGWNELLIA FSHRSI  KDGILLA G+ V+RSSAH+AGVG IFDRVLTE
Sbjct: 61  PLEDQVILLRAGWNELLIAGFSHRSIMAKDGILLATGLHVHRSSAHQAGVGTIFDRVLTE 120
Query: 270 LVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEP 329
           LV+KMR+MKMDKTELGCLR ++LFNPD +GL + Q VE LREKVY SLEEYT+  + EEP
Sbjct: 121 LVAKMRDMKMDKTELGCLRAVVLFNPDAKGLTAVQEVEQLREKVYASLEEYTKSRYPEEP 180
Query: 330 GRFAKLLLRLPSLRSI 345
           GRFAKLLLRLP+LRSI
Sbjct: 181 GRFAKLLLRLPALRSI 196

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

Iteration: 1
 Score =  276 bits (707), Expect = 8e-75,   Method: Compositional matrix adjust.
 Identities = 137/197 (69%), Positives = 160/197 (81%), Gaps = 3/197 (1%)
Query: 152 EMPVERILEAEQRVDMKQEP-ADQDIVNEQQ--ATNICKATDKQLFQLVDWAKHIPHFTT 208
           +MPVERILEAE  V+ K E   D ++ N      TNIC A DKQLF LV+WAK IPHF+ 
Sbjct: 11  DMPVERILEAELAVEPKTESYGDMNMENSTNDPVTNICHAADKQLFTLVEWAKRIPHFSD 70
Query: 209 LPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLT 268
           L LEDQV+LLRAGWNELLIASFSHRS+SV+DGILLA G+ V+RSSAH AGVG IFDRVLT
Sbjct: 71  LTLEDQVILLRAGWNELLIASFSHRSVSVQDGILLATGLHVHRSSAHSAGVGSIFDRVLT 130
Query: 269 ELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEE 328
           ELVSKM++M+MDK+ELGCLR I+LFNPD +GL +   VE LREKVY +LE YT+  + E+
Sbjct: 131 ELVSKMKDMQMDKSELGCLRAIVLFNPDAKGLSNPSEVETLREKVYATLEAYTKQKYPEQ 190
Query: 329 PGRFAKLLLRLPSLRSI 345
           PGRFAKLLLRLP+LRSI
Sbjct: 191 PGRFAKLLLRLPALRSI 207

>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 =  276 bits (705), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 136/196 (69%), Positives = 160/196 (81%), Gaps = 6/196 (3%)
Query: 152 EMPVERILEAEQRVDMKQEPADQDIVNEQQ--ATNICKATDKQLFQLVDWAKHIPHFTTL 209
           +MPVE+I EAE    M  EP D ++V +     TNIC+A DKQL  LV+WAK IPHF+ L
Sbjct: 1   DMPVEKIQEAE----MAVEPKDGNMVEQPNDPVTNICQAADKQLVTLVEWAKRIPHFSDL 56
Query: 210 PLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTE 269
           P++DQV+LLRAGWNELLIA+FSHRSI VKDGILLA G+ V+RSSAH+AGVG IFDRVLTE
Sbjct: 57  PIDDQVILLRAGWNELLIAAFSHRSIDVKDGILLASGLHVHRSSAHQAGVGTIFDRVLTE 116
Query: 270 LVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEP 329
           LV+KMR+MKMDKTELGCLR I+LFNPD +GL    +VE LREKVY SLEEY +  + E+P
Sbjct: 117 LVAKMRDMKMDKTELGCLRAIVLFNPDAKGLTDPSLVESLREKVYASLEEYCKQQYPEQP 176
Query: 330 GRFAKLLLRLPSLRSI 345
           GRFAKLLLRLP+LRSI
Sbjct: 177 GRFAKLLLRLPALRSI 192

>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 =  274 bits (701), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 139/206 (67%), Positives = 161/206 (78%), Gaps = 6/206 (2%)
Query: 146 TSGTLIEMPVERILEAEQRVDMKQEPADQDIVN------EQQATNICKATDKQLFQLVDW 199
           TS    +MPVERILEAE  V+ K E   +  +           TNIC+A DKQLF LV+W
Sbjct: 1   TSSANEDMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEW 60
Query: 200 AKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV 259
           AK IPHF+ LPL+DQV+LLRAGWNELLIASFSHRSI+VKDGILLA G+ V+R+SAH AGV
Sbjct: 61  AKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGV 120
Query: 260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEE 319
           G IFDRVLTELVSKMR+M+MDKTELGCLR I+LFNPD +GL +   VE LREKVY SLE 
Sbjct: 121 GAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEA 180
Query: 320 YTRVNHSEEPGRFAKLLLRLPSLRSI 345
           Y +  + E+PGRFAKLLLRLP+LRSI
Sbjct: 181 YCKHKYPEQPGRFAKLLLRLPALRSI 206

>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 =  274 bits (701), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 139/206 (67%), Positives = 161/206 (78%), Gaps = 6/206 (2%)
Query: 146 TSGTLIEMPVERILEAEQRVDMKQEPADQDIVN------EQQATNICKATDKQLFQLVDW 199
           TS    +MPVERILEAE  V+ K E   +  +           TNIC+A DKQLF LV+W
Sbjct: 5   TSSANEDMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEW 64
Query: 200 AKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV 259
           AK IPHF+ LPL+DQV+LLRAGWNELLIASFSHRSI+VKDGILLA G+ V+R+SAH AGV
Sbjct: 65  AKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGV 124
Query: 260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEE 319
           G IFDRVLTELVSKMR+M+MDKTELGCLR I+LFNPD +GL +   VE LREKVY SLE 
Sbjct: 125 GAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEA 184
Query: 320 YTRVNHSEEPGRFAKLLLRLPSLRSI 345
           Y +  + E+PGRFAKLLLRLP+LRSI
Sbjct: 185 YCKHKYPEQPGRFAKLLLRLPALRSI 210

>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 =  274 bits (701), Expect = 5e-74,   Method: Compositional matrix adjust.
 Identities = 137/200 (68%), Positives = 159/200 (79%), Gaps = 6/200 (3%)
Query: 152 EMPVERILEAEQRVDMKQEPADQDIVN------EQQATNICKATDKQLFQLVDWAKHIPH 205
           +MPVERILEAE  V+ K E   +  +           TNIC+A DKQLF LV+WAK IPH
Sbjct: 9   DMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPH 68
Query: 206 FTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDR 265
           F+ LPL+DQV+LLRAGWNELLIASFSHRSI+VKDGILLA G+ V+R+SAH AGVG IFDR
Sbjct: 69  FSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDR 128
Query: 266 VLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNH 325
           VLTELVSKMR+M+MDKTELGCLR I+LFNPD +GL +   VE LREKVY SLE Y +  +
Sbjct: 129 VLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKY 188
Query: 326 SEEPGRFAKLLLRLPSLRSI 345
            E+PGRFAKLLLRLP+LRSI
Sbjct: 189 PEQPGRFAKLLLRLPALRSI 208

>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 =  274 bits (700), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 137/200 (68%), Positives = 159/200 (79%), Gaps = 6/200 (3%)
Query: 152 EMPVERILEAEQRVDMKQEPADQDIVN------EQQATNICKATDKQLFQLVDWAKHIPH 205
           +MPVERILEAE  V+ K E   +  +           TNIC+A DKQLF LV+WAK IPH
Sbjct: 6   DMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPH 65
Query: 206 FTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDR 265
           F+ LPL+DQV+LLRAGWNELLIASFSHRSI+VKDGILLA G+ V+R+SAH AGVG IFDR
Sbjct: 66  FSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDR 125
Query: 266 VLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNH 325
           VLTELVSKMR+M+MDKTELGCLR I+LFNPD +GL +   VE LREKVY SLE Y +  +
Sbjct: 126 VLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKY 185
Query: 326 SEEPGRFAKLLLRLPSLRSI 345
            E+PGRFAKLLLRLP+LRSI
Sbjct: 186 PEQPGRFAKLLLRLPALRSI 205

>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 =  274 bits (700), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 137/200 (68%), Positives = 159/200 (79%), Gaps = 6/200 (3%)
Query: 152 EMPVERILEAEQRVDMKQEPADQDIVN------EQQATNICKATDKQLFQLVDWAKHIPH 205
           +MPVERILEAE  V+ K E   +  +           TNIC+A DKQLF LV+WAK IPH
Sbjct: 5   DMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPH 64
Query: 206 FTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDR 265
           F+ LPL+DQV+LLRAGWNELLIASFSHRSI+VKDGILLA G+ V+R+SAH AGVG IFDR
Sbjct: 65  FSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDR 124
Query: 266 VLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNH 325
           VLTELVSKMR+M+MDKTELGCLR I+LFNPD +GL +   VE LREKVY SLE Y +  +
Sbjct: 125 VLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKY 184
Query: 326 SEEPGRFAKLLLRLPSLRSI 345
            E+PGRFAKLLLRLP+LRSI
Sbjct: 185 PEQPGRFAKLLLRLPALRSI 204

>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 =  274 bits (700), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 137/200 (68%), Positives = 159/200 (79%), Gaps = 6/200 (3%)
Query: 152 EMPVERILEAEQRVDMKQEPADQDIVN------EQQATNICKATDKQLFQLVDWAKHIPH 205
           +MPVERILEAE  V+ K E   +  +           TNIC+A DKQLF LV+WAK IPH
Sbjct: 9   DMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPH 68
Query: 206 FTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDR 265
           F+ LPL+DQV+LLRAGWNELLIASFSHRSI+VKDGILLA G+ V+R+SAH AGVG IFDR
Sbjct: 69  FSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDR 128
Query: 266 VLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNH 325
           VLTELVSKMR+M+MDKTELGCLR I+LFNPD +GL +   VE LREKVY SLE Y +  +
Sbjct: 129 VLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKY 188
Query: 326 SEEPGRFAKLLLRLPSLRSI 345
            E+PGRFAKLLLRLP+LRSI
Sbjct: 189 PEQPGRFAKLLLRLPALRSI 208

>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 =  273 bits (699), Expect = 7e-74,   Method: Compositional matrix adjust.
 Identities = 138/206 (66%), Positives = 161/206 (78%), Gaps = 6/206 (2%)
Query: 146 TSGTLIEMPVERILEAEQRVDMKQEPADQDIVN------EQQATNICKATDKQLFQLVDW 199
           TS    +MPVE+ILEAE  V+ K E   +  +           TNIC+A DKQLF LV+W
Sbjct: 1   TSSANEDMPVEKILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEW 60
Query: 200 AKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV 259
           AK IPHF+ LPL+DQV+LLRAGWNELLIASFSHRSI+VKDGILLA G+ V+R+SAH AGV
Sbjct: 61  AKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGV 120
Query: 260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEE 319
           G IFDRVLTELVSKMR+M+MDKTELGCLR I+LFNPD +GL +   VE LREKVY SLE 
Sbjct: 121 GAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEA 180
Query: 320 YTRVNHSEEPGRFAKLLLRLPSLRSI 345
           Y +  + E+PGRFAKLLLRLP+LRSI
Sbjct: 181 YCKHKYPEQPGRFAKLLLRLPALRSI 206

>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 =  273 bits (699), Expect = 8e-74,   Method: Compositional matrix adjust.
 Identities = 137/200 (68%), Positives = 159/200 (79%), Gaps = 6/200 (3%)
Query: 152 EMPVERILEAEQRVDMKQEPADQDIVN------EQQATNICKATDKQLFQLVDWAKHIPH 205
           +MPVERILEAE  V+ K E   +  +           TNIC+A DKQLF LV+WAK IPH
Sbjct: 1   DMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPH 60
Query: 206 FTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDR 265
           F+ LPL+DQV+LLRAGWNELLIASFSHRSI+VKDGILLA G+ V+R+SAH AGVG IFDR
Sbjct: 61  FSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDR 120
Query: 266 VLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNH 325
           VLTELVSKMR+M+MDKTELGCLR I+LFNPD +GL +   VE LREKVY SLE Y +  +
Sbjct: 121 VLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKY 180
Query: 326 SEEPGRFAKLLLRLPSLRSI 345
            E+PGRFAKLLLRLP+LRSI
Sbjct: 181 PEQPGRFAKLLLRLPALRSI 200

>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 =  273 bits (699), Expect = 9e-74,   Method: Compositional matrix adjust.
 Identities = 137/200 (68%), Positives = 159/200 (79%), Gaps = 6/200 (3%)
Query: 152 EMPVERILEAEQRVDMKQEPADQDIVN------EQQATNICKATDKQLFQLVDWAKHIPH 205
           +MPVERILEAE  V+ K E   +  +           TNIC+A DKQLF LV+WAK IPH
Sbjct: 3   DMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPH 62
Query: 206 FTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDR 265
           F+ LPL+DQV+LLRAGWNELLIASFSHRSI+VKDGILLA G+ V+R+SAH AGVG IFDR
Sbjct: 63  FSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDR 122
Query: 266 VLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNH 325
           VLTELVSKMR+M+MDKTELGCLR I+LFNPD +GL +   VE LREKVY SLE Y +  +
Sbjct: 123 VLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKY 182
Query: 326 SEEPGRFAKLLLRLPSLRSI 345
            E+PGRFAKLLLRLP+LRSI
Sbjct: 183 PEQPGRFAKLLLRLPALRSI 202

>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 =  273 bits (699), Expect = 9e-74,   Method: Compositional matrix adjust.
 Identities = 137/200 (68%), Positives = 159/200 (79%), Gaps = 6/200 (3%)
Query: 152 EMPVERILEAEQRVDMKQEPADQDIVN------EQQATNICKATDKQLFQLVDWAKHIPH 205
           +MPVERILEAE  V+ K E   +  +           TNIC+A DKQLF LV+WAK IPH
Sbjct: 2   DMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPH 61
Query: 206 FTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDR 265
           F+ LPL+DQV+LLRAGWNELLIASFSHRSI+VKDGILLA G+ V+R+SAH AGVG IFDR
Sbjct: 62  FSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDR 121
Query: 266 VLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNH 325
           VLTELVSKMR+M+MDKTELGCLR I+LFNPD +GL +   VE LREKVY SLE Y +  +
Sbjct: 122 VLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKY 181
Query: 326 SEEPGRFAKLLLRLPSLRSI 345
            E+PGRFAKLLLRLP+LRSI
Sbjct: 182 PEQPGRFAKLLLRLPALRSI 201

>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 =  273 bits (699), Expect = 9e-74,   Method: Compositional matrix adjust.
 Identities = 137/200 (68%), Positives = 159/200 (79%), Gaps = 6/200 (3%)
Query: 152 EMPVERILEAEQRVDMKQEPADQDIVN------EQQATNICKATDKQLFQLVDWAKHIPH 205
           +MPVERILEAE  V+ K E   +  +           TNIC+A DKQLF LV+WAK IPH
Sbjct: 3   DMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPH 62
Query: 206 FTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDR 265
           F+ LPL+DQV+LLRAGWNELLIASFSHRSI+VKDGILLA G+ V+R+SAH AGVG IFDR
Sbjct: 63  FSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDR 122
Query: 266 VLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNH 325
           VLTELVSKMR+M+MDKTELGCLR I+LFNPD +GL +   VE LREKVY SLE Y +  +
Sbjct: 123 VLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKY 182
Query: 326 SEEPGRFAKLLLRLPSLRSI 345
            E+PGRFAKLLLRLP+LRSI
Sbjct: 183 PEQPGRFAKLLLRLPALRSI 202

>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 =  273 bits (698), Expect = 9e-74,   Method: Compositional matrix adjust.
 Identities = 137/200 (68%), Positives = 159/200 (79%), Gaps = 6/200 (3%)
Query: 152 EMPVERILEAEQRVDMKQEPADQDIVN------EQQATNICKATDKQLFQLVDWAKHIPH 205
           +MPVERILEAE  V+ K E   +  +           TNIC+A DKQLF LV+WAK IPH
Sbjct: 2   DMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPH 61
Query: 206 FTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDR 265
           F+ LPL+DQV+LLRAGWNELLIASFSHRSI+VKDGILLA G+ V+R+SAH AGVG IFDR
Sbjct: 62  FSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDR 121
Query: 266 VLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNH 325
           VLTELVSKMR+M+MDKTELGCLR I+LFNPD +GL +   VE LREKVY SLE Y +  +
Sbjct: 122 VLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKY 181
Query: 326 SEEPGRFAKLLLRLPSLRSI 345
            E+PGRFAKLLLRLP+LRSI
Sbjct: 182 PEQPGRFAKLLLRLPALRSI 201

>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 =  273 bits (697), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 136/200 (68%), Positives = 159/200 (79%), Gaps = 6/200 (3%)
Query: 152 EMPVERILEAEQRVDMKQEPADQDIVN------EQQATNICKATDKQLFQLVDWAKHIPH 205
           +MPVE+ILEAE  V+ K E   +  +           TNIC+A DKQLF LV+WAK IPH
Sbjct: 5   DMPVEKILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPH 64
Query: 206 FTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDR 265
           F+ LPL+DQV+LLRAGWNELLIASFSHRSI+VKDGILLA G+ V+R+SAH AGVG IFDR
Sbjct: 65  FSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDR 124
Query: 266 VLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNH 325
           VLTELVSKMR+M+MDKTELGCLR I+LFNPD +GL +   VE LREKVY SLE Y +  +
Sbjct: 125 VLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKY 184
Query: 326 SEEPGRFAKLLLRLPSLRSI 345
            E+PGRFAKLLLRLP+LRSI
Sbjct: 185 PEQPGRFAKLLLRLPALRSI 204

>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 =  271 bits (693), Expect = 4e-73,   Method: Compositional matrix adjust.
 Identities = 137/202 (67%), Positives = 161/202 (79%), Gaps = 3/202 (1%)
Query: 146 TSGTLIEMPVERILEAEQRVDMKQEP--ADQDIVNEQQATNICKATDKQLFQLVDWAKHI 203
           TS    +MP+ERI+EAE+RV+   +P  A     N     NIC+AT KQLFQLV WAK +
Sbjct: 2   TSNLQADMPLERIIEAEKRVEC-NDPLVALVVNENNTTVNNICQATHKQLFQLVQWAKLV 60
Query: 204 PHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIF 263
           PHFT+LPL DQV LLRAGWNELLIA+FSHRS+  +D I+LA G+TV +S+AH  GVG I+
Sbjct: 61  PHFTSLPLTDQVQLLRAGWNELLIAAFSHRSMQAQDAIVLATGLTVNKSTAHAVGVGNIY 120
Query: 264 DRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRV 323
           DRVL+ELV+KM+EMKMDKTELGCLR IIL+NPDVRG+KS Q VEMLREK+Y  LEEYTR 
Sbjct: 121 DRVLSELVNKMKEMKMDKTELGCLRAIILYNPDVRGIKSVQEVEMLREKIYGVLEEYTRT 180
Query: 324 NHSEEPGRFAKLLLRLPSLRSI 345
            H  EPGRFAKLLLRLP+LRSI
Sbjct: 181 THPNEPGRFAKLLLRLPALRSI 202

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

Iteration: 1
 Score =  270 bits (690), Expect = 9e-73,   Method: Compositional matrix adjust.
 Identities = 135/202 (66%), Positives = 158/202 (78%), Gaps = 8/202 (3%)
Query: 152 EMPVERILEAEQRVDMKQEPADQDIVN--------EQQATNICKATDKQLFQLVDWAKHI 203
           EMPV+RILEAE  V+ K +   +                TNIC+A DKQLF LV+WAK I
Sbjct: 1   EMPVDRILEAELAVEQKSDQGVEGPGGTGGSGSSPNDPVTNICQAADKQLFTLVEWAKRI 60
Query: 204 PHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIF 263
           PHF++LPL+DQV+LLRAGWNELLIASFSHRSI V+DGILLA G+ V+R+SAH AGVG IF
Sbjct: 61  PHFSSLPLDDQVILLRAGWNELLIASFSHRSIDVRDGILLATGLHVHRNSAHSAGVGAIF 120
Query: 264 DRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRV 323
           DRVLTELVSKMR+M+MDKTELGCLR IILFNPD +GL +   VE+LREKVY SLE Y + 
Sbjct: 121 DRVLTELVSKMRDMRMDKTELGCLRAIILFNPDAKGLSNPSEVEVLREKVYASLETYCKQ 180
Query: 324 NHSEEPGRFAKLLLRLPSLRSI 345
            + E+ GRFAKLLLRLP+LRSI
Sbjct: 181 KYPEQQGRFAKLLLRLPALRSI 202

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

Iteration: 1
 Score =  269 bits (688), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 135/200 (67%), Positives = 158/200 (79%), Gaps = 6/200 (3%)
Query: 152 EMPVERILEAEQRVDMKQEPADQDIVN------EQQATNICKATDKQLFQLVDWAKHIPH 205
           +MPVE+ILEAE  V+ K E   +  +           TNIC+A DKQLF LV+WAK IPH
Sbjct: 5   DMPVEKILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPH 64
Query: 206 FTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDR 265
           F+ LPL+DQV+LLRAGWNELLIAS SHRSI+VKDGILLA G+ V+R+SAH AGVG IFDR
Sbjct: 65  FSELPLDDQVILLRAGWNELLIASASHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDR 124
Query: 266 VLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNH 325
           VLTELVSKMR+M+MDKTELGCLR I+LFNPD +GL +   VE LREKVY SLE Y +  +
Sbjct: 125 VLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKY 184
Query: 326 SEEPGRFAKLLLRLPSLRSI 345
            E+PGRFAKLLLRLP+LRSI
Sbjct: 185 PEQPGRFAKLLLRLPALRSI 204

>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 =  268 bits (686), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 134/201 (66%), Positives = 157/201 (78%), Gaps = 8/201 (3%)
Query: 153 MPVERILEAEQRVDMKQEPADQDIVN--------EQQATNICKATDKQLFQLVDWAKHIP 204
           MPV+RILEAE  V+ K +   +                TNIC+A DKQLF LV+WAK IP
Sbjct: 1   MPVDRILEAELAVEQKSDQGVEGPGGTGGSGSSPNDPVTNICQAADKQLFTLVEWAKRIP 60
Query: 205 HFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFD 264
           HF++LPL+DQV+LLRAGWNELLIASFSHRSI V+DGILLA G+ V+R+SAH AGVG IFD
Sbjct: 61  HFSSLPLDDQVILLRAGWNELLIASFSHRSIDVRDGILLATGLHVHRNSAHSAGVGAIFD 120
Query: 265 RVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVN 324
           RVLTELVSKMR+M+MDKTELGCLR IILFNPD +GL +   VE+LREKVY SLE Y +  
Sbjct: 121 RVLTELVSKMRDMRMDKTELGCLRAIILFNPDAKGLSNPSEVEVLREKVYASLETYCKQK 180
Query: 325 HSEEPGRFAKLLLRLPSLRSI 345
           + E+ GRFAKLLLRLP+LRSI
Sbjct: 181 YPEQQGRFAKLLLRLPALRSI 201

>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 =  266 bits (679), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 135/198 (68%), Positives = 157/198 (79%), Gaps = 6/198 (3%)
Query: 152 EMPVERILEAEQRVDMKQE---PADQDIVNEQQ-ATNICKATDKQLFQLVDWAKHIPHFT 207
           +MPV++ILEAE   D K E   P +Q  VNE    +NICKA D+QL  LV+WAK IPHF+
Sbjct: 28  DMPVDKILEAELISDPKVEQVVPFEQ--VNENDPVSNICKAADRQLVTLVEWAKRIPHFS 85
Query: 208 TLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVL 267
           +LPLEDQV+LLRAGWNELLIASFSHRSI VKD ILLA G+ V+R SAH+AGVG IFDRVL
Sbjct: 86  SLPLEDQVILLRAGWNELLIASFSHRSIDVKDSILLASGLHVHRHSAHQAGVGPIFDRVL 145
Query: 268 TELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSE 327
           TELVSKMR+M MDKTELGCLR ++LFNPDV+       +E LREKVY SLE Y R  + +
Sbjct: 146 TELVSKMRDMMMDKTELGCLRAVVLFNPDVKNPSDSAHIESLREKVYASLEAYCRSKYPD 205
Query: 328 EPGRFAKLLLRLPSLRSI 345
           +PGRFAKLLLRLP+LRSI
Sbjct: 206 QPGRFAKLLLRLPALRSI 223

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

Iteration: 1
 Score =  174 bits (442), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 95/234 (40%), Positives = 142/234 (60%), Gaps = 38/234 (16%)
Query: 152 EMPVERILEAEQRVD----------MKQEPADQDIVNEQQATN-ICKATDKQLFQLVDWA 200
           +  +ERI+EAEQR +          ++  P      + + A + +C+  +KQLFQ+V++A
Sbjct: 8   DFSIERIIEAEQRAETQCGDRALTFLRVGPYSTVQPDYKGAVSALCQVVNKQLFQMVEYA 67
Query: 201 KHIPHFTTLPLEDQVLLLRAGWNELLIA--------------------------SFSHRS 234
           + +PHF  +PL+DQV+LL+A W ELLIA                          SF  RS
Sbjct: 68  RMMPHFAQVPLDDQVILLKAAWIELLIANVAWCSIVSLDDGGAGGGGGGLGHDGSFERRS 127
Query: 235 ISVK-DGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILF 293
             ++   + L    + +R+SA +AGV  IFDR+L+EL  KM+ + +D+ EL CL+ IIL+
Sbjct: 128 PGLQPQQLFLNQSFSYHRNSAIKAGVSAIFDRILSELSVKMKRLNLDRRELSCLKAIILY 187
Query: 294 NPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIEV 347
           NPD+RG+KS+  +EM REKVY  L+E+ R+ H  + GRFA+LLLRLP+LRSI +
Sbjct: 188 NPDIRGIKSRAEIEMCREKVYACLDEHCRLEHPGDDGRFAQLLLRLPALRSISL 241

>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 =  156 bits (395), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 87/208 (41%), Positives = 131/208 (62%), Gaps = 27/208 (12%)
Query: 152 EMPVERILEAEQRVDMKQEP-------ADQDIVNEQQA--TNICKATDKQLFQLVDWAKH 202
           E+ +ER+LE E  V    E         D ++  + +A  +++C+  +KQ+  LV WA+ 
Sbjct: 5   ELSIERLLEMESLVADPSEEFQFLRVGPDSNVPPKFRAPVSSLCQIGNKQIAALVVWARD 64
Query: 203 IPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISV----KDGI--------------LLA 244
           IPHF+ L +EDQ+LL++  WNELL+ + + RS+      +DG+               L 
Sbjct: 65  IPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLTEERDGVDGTGNRTTSPPQLMCLM 124
Query: 245 PGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQ 304
           PG+T++R+SA +AGVG IFDRVL+EL  KMR +++D+ E   L+ IIL NPDV+GLK++Q
Sbjct: 125 PGMTLHRNSALQAGVGQIFDRVLSELSLKMRTLRVDQAEYVALKAIILLNPDVKGLKNRQ 184
Query: 305 VVEMLREKVYTSLEEYTRVNHSEEPGRF 332
            VE+LREK++  L+EY R + S E GRF
Sbjct: 185 EVEVLREKMFLCLDEYCRRSRSSEEGRF 212

>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 =  156 bits (395), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 87/208 (41%), Positives = 131/208 (62%), Gaps = 27/208 (12%)
Query: 152 EMPVERILEAEQRVDMKQEP-------ADQDIVNEQQA--TNICKATDKQLFQLVDWAKH 202
           E+ +ER+LE E  V    E         D ++  + +A  +++C+  +KQ+  LV WA+ 
Sbjct: 4   ELSIERLLEMESLVADPSEEFQFLRVGPDSNVPPKFRAPVSSLCQIGNKQIAALVVWARD 63
Query: 203 IPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISV----KDGI--------------LLA 244
           IPHF+ L +EDQ+LL++  WNELL+ + + RS+      +DG+               L 
Sbjct: 64  IPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLTEERDGVDGTGNRTTSPPQLMCLM 123
Query: 245 PGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQ 304
           PG+T++R+SA +AGVG IFDRVL+EL  KMR +++D+ E   L+ IIL NPDV+GLK++Q
Sbjct: 124 PGMTLHRNSALQAGVGQIFDRVLSELSLKMRTLRVDQAEYVALKAIILLNPDVKGLKNRQ 183
Query: 305 VVEMLREKVYTSLEEYTRVNHSEEPGRF 332
            VE+LREK++  L+EY R + S E GRF
Sbjct: 184 EVEVLREKMFLCLDEYCRRSRSSEEGRF 211

>pdb|1R0O|A Chain A, Crystal Structure Of The Heterodimeric Ecdysone Receptor Dna-Binding Complex Length = 86

Iteration: 1
 Score =  138 bits (348), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 66/86 (76%), Positives = 67/86 (77%)
Query: 48  NHPLCGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXX 107
           NHPL GSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDL+YACRE RNCIID    
Sbjct: 1   NHPLSGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYACRENRNCIIDKRQR 60
Query: 108 XXXXXXXXXXXLNMGMKREAVQEERQ 133
                      L  GMKREAVQEERQ
Sbjct: 61  NRCQYCRYQKCLTCGMKREAVQEERQ 86

>pdb|2HAN|A Chain A, Structural Basis Of Heterodimeric Ecdysteroid Receptor Interaction With Natural Response Element Hsp27 Gene Promoter Length = 93

Iteration: 1
 Score =  138 bits (347), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 66/87 (75%), Positives = 67/87 (77%)
Query: 47  PNHPLCGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXX 106
            NHPL GSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDL+YACRE RNCIID   
Sbjct: 2   SNHPLSGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYACRENRNCIIDKRQ 61
Query: 107 XXXXXXXXXXXXLNMGMKREAVQEERQ 133
                       L  GMKREAVQEERQ
Sbjct: 62  RNRCQYCRYQKCLTCGMKREAVQEERQ 88

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

Iteration: 1
 Score =  137 bits (345), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 63/94 (67%), Positives = 74/94 (78%)
Query: 54  SKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXXXXXXXX 113
           +KH+C+ICGDR+SGKHYGVYSCEGCKGFFKRTVRKDL+Y CR+ ++C+ID          
Sbjct: 2   TKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYC 61
Query: 114 XXXXXLNMGMKREAVQEERQRTKERDSNEVESTS 147
                L MGMKREAVQEERQR K+R+ NEVESTS
Sbjct: 62  RYQKCLAMGMKREAVQEERQRGKDRNENEVESTS 95

>pdb|1DSZ|B Chain B, Structure Of The RxrRAR DNA-Binding Domain Heterodimer In Complex With The Retinoic Acid Response Element Dr1 Length = 85

Iteration: 1
 Score =  121 bits (303), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 54/81 (66%), Positives = 63/81 (77%)
Query: 54  SKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXXXXXXXX 113
           +KH+C+ICGDR+SGKHYGVYSCEGCKGFFKRTVRKDL+Y CR+ ++C+ID          
Sbjct: 4   TKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYC 63
Query: 114 XXXXXLNMGMKREAVQEERQR 134
                L MGMKREAVQEERQR
Sbjct: 64  RYQKCLAMGMKREAVQEERQR 84

>pdb|1RXR|A Chain A, High Resolution Solution Structure Of The Retinoid X Receptor Dna Binding Domain, Nmr, 20 Structure Length = 83

Iteration: 1
 Score =  121 bits (303), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 54/81 (66%), Positives = 63/81 (77%)
Query: 54  SKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXXXXXXXX 113
           +KH+C+ICGDR+SGKHYGVYSCEGCKGFFKRTVRKDL+Y CR+ ++C+ID          
Sbjct: 2   TKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYC 61
Query: 114 XXXXXLNMGMKREAVQEERQR 134
                L MGMKREAVQEERQR
Sbjct: 62  RYQKALAMGMKREAVQEERQR 82

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

Iteration: 1
 Score =  119 bits (299), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 65/162 (40%), Positives = 100/162 (61%), Gaps = 1/162 (0%)
Query: 184 NICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL 243
           ++C++  +QL  LV+WAK+IP F  LPL+DQV LLRA   E L+   + RS+  KD +LL
Sbjct: 39  DVCESMKQQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMMYKDILLL 98
Query: 244 APGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
                ++R+S  E  +  + +RVL ELV   +E+++D  E  CL+ I+ F+PD +GL   
Sbjct: 99  GNNYVIHRNSC-EVEISRVANRVLDELVRPFQEIQIDDNEYACLKAIVFFDPDAKGLSDP 157
Query: 304 QVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
             ++ +R +V   LE+Y      +  GRF +LLL LP+L+SI
Sbjct: 158 VKIKNMRFQVQIGLEDYINDRQYDSRGRFGELLLLLPTLQSI 199

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

Iteration: 1
 Score =  119 bits (297), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 65/164 (39%), Positives = 92/164 (56%), Gaps = 3/164 (1%)
Query: 184 NICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL 243
           NIC+   + LF  V+WA++IP F  L + DQV LLR  W+EL + + +  S+ +    LL
Sbjct: 41  NICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHVAPLL 100
Query: 244 APGVTVYRSSAHEAGVGGIFD--RVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLK 301
           A    ++ S      V    D  R+  E V K++ + +D  E  CL+ I+LF  D  GL 
Sbjct: 101 A-AAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDACGLS 159
Query: 302 SQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
               VE L+EK   +LEEY R  +  +P RF KLLLRLPSLR++
Sbjct: 160 DVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTV 203

>pdb|1BY4|A Chain A, Structure And Mechanism Of The Homodimeric Assembly Of The Rxr On Dna Length = 82

Iteration: 1
 Score =  117 bits (293), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 52/79 (65%), Positives = 61/79 (77%)
Query: 54  SKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXXXXXXXX 113
           +KH+C+ICGDR+SGKHYGVYSCEGCKGFFKRTVRKDL+Y CR+ ++C+ID          
Sbjct: 4   TKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYC 63
Query: 114 XXXXXLNMGMKREAVQEER 132
                L MGMKREAVQEER
Sbjct: 64  RYQKCLAMGMKREAVQEER 82

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

Iteration: 1
 Score =  116 bits (291), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 67/163 (41%), Positives = 97/163 (59%)
Query: 183 TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGIL 242
           T++C++  +QL  LV+WAK+IP F  L L+DQV LLRA   E L+   + RS+  KD +L
Sbjct: 44  TDVCESMKEQLLVLVEWAKYIPAFCELLLDDQVALLRAHAGEHLLLGATKRSMVFKDVLL 103
Query: 243 LAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKS 302
           L     V R     A +  +  R+L ELV   +E+++D  E  CL+ II F+PD +GL  
Sbjct: 104 LGNDYIVPRHCPELAEMSRVSIRILDELVLPFQELQIDDNEYACLKAIIFFDPDAKGLSD 163
Query: 303 QQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
              ++ LR +V  SLE+Y      +  GRF +LLL LP+L+SI
Sbjct: 164 PGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSI 206

>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 =  114 bits (285), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 66/163 (40%), Positives = 96/163 (58%)
Query: 183 TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGIL 242
            ++C++  +QL  LV+WAK+IP F  LPL+DQV LLRA   E L+   + RS+  KD +L
Sbjct: 38  ADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVLL 97
Query: 243 LAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKS 302
           L     V R     A +  +  R+L ELV   +E+++D  E   L+ II F+PD +GL  
Sbjct: 98  LGNDYIVPRHCPELAEMSRVSIRILDELVLPFQELQIDDNEYAYLKAIIFFDPDAKGLSD 157
Query: 303 QQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
              ++ LR +V  SLE+Y      +  GRF +LLL LP+L+SI
Sbjct: 158 PGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSI 200

>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 =  114 bits (285), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 66/163 (40%), Positives = 96/163 (58%)
Query: 183 TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGIL 242
            ++C++  +QL  LV+WAK+IP F  LPL+DQV LLRA   E L+   + RS+  KD +L
Sbjct: 44  ADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVLL 103
Query: 243 LAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKS 302
           L     V R     A +  +  R+L ELV   +E+++D  E   L+ II F+PD +GL  
Sbjct: 104 LGNDYIVPRHCPELAEMSRVSIRILDELVLPFQELQIDDNEYAYLKAIIFFDPDAKGLSD 163
Query: 303 QQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
              ++ LR +V  SLE+Y      +  GRF +LLL LP+L+SI
Sbjct: 164 PGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSI 206

>pdb|1R0N|A Chain A, Crystal Structure Of Heterodimeric Ecdsyone Receptor Dna Binding Complex Length = 81

Iteration: 1
 Score =  113 bits (282), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 49/76 (64%), Positives = 58/76 (76%)
Query: 54  SKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXXXXXXXX 113
           +KH+C+ICGDR+SGKHYGVYSCEGCKGFFKRTVRKDL+Y CR+ ++C+ID          
Sbjct: 2   TKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYC 61
Query: 114 XXXXXLNMGMKREAVQ 129
                L MGMKREAVQ
Sbjct: 62  RYQKCLAMGMKREAVQ 77

>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 =  108 bits (271), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 62/169 (36%), Positives = 106/169 (62%), Gaps = 8/169 (4%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSI-SVKDG-IL 242
           +CK  D+ LF +V+WA+    F  L ++DQ+ LL+  W+ELLI    +R +   K+G I 
Sbjct: 49  MCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIF 108
Query: 243 LAPGVTV-YRSSAHEAGVGGIFDRVLT---ELVSKMREMKMDKTELGCLRTIILFNPDVR 298
           L  G  V Y   A +AG     + +++   ELV+K+R ++ D+ E  CL+ ++LF+ DV+
Sbjct: 109 LVTGQQVDYSIIASQAG--ATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVK 166
Query: 299 GLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIEV 347
            L++ Q+VE ++E+V  +L +YT  N+ ++  +F +LLLRLP +R+I +
Sbjct: 167 NLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISM 215

>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 =  108 bits (271), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 62/169 (36%), Positives = 106/169 (62%), Gaps = 8/169 (4%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSI-SVKDG-IL 242
           +CK  D+ LF +V+WA+    F  L ++DQ+ LL+  W+ELLI    +R +   K+G I 
Sbjct: 59  MCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIF 118
Query: 243 LAPGVTV-YRSSAHEAGVGGIFDRVLT---ELVSKMREMKMDKTELGCLRTIILFNPDVR 298
           L  G  V Y   A +AG     + +++   ELV+K+R ++ D+ E  CL+ ++LF+ DV+
Sbjct: 119 LVTGQQVDYSIIASQAG--ATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVK 176
Query: 299 GLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIEV 347
            L++ Q+VE ++E+V  +L +YT  N+ ++  +F +LLLRLP +R+I +
Sbjct: 177 NLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISM 225

>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 =  108 bits (270), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 59/171 (34%), Positives = 100/171 (58%), Gaps = 4/171 (2%)
Query: 173 DQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSH 232
           D DI   +  T +C   D++L  ++ WAKHIP F+TL L DQ+ LL++ W E+LI    +
Sbjct: 52  DSDI---KALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVY 108
Query: 233 RSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIIL 292
           RS+S +D ++ A    +    +  AG+  + + +L +LV K + MK++K E   L+ I L
Sbjct: 109 RSLSFEDELVYADDYIMDEDQSKLAGLLDLNNAIL-QLVKKYKSMKLEKEEFVTLKAIAL 167
Query: 293 FNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLR 343
            N D   ++  + V+ L++ ++ +L++Y    H E+P R  K+L+ LP LR
Sbjct: 168 ANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLR 218

>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 =  108 bits (270), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 59/171 (34%), Positives = 100/171 (58%), Gaps = 4/171 (2%)
Query: 173 DQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSH 232
           D DI   +  T +C   D++L  ++ WAKHIP F+TL L DQ+ LL++ W E+LI    +
Sbjct: 52  DSDI---KALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVY 108
Query: 233 RSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIIL 292
           RS+S +D ++ A    +    +  AG+  + + +L +LV K + MK++K E   L+ I L
Sbjct: 109 RSLSFEDELVYADDYIMDEDQSKLAGLLDLNNAIL-QLVKKYKSMKLEKEEFVTLKAIAL 167
Query: 293 FNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLR 343
            N D   ++  + V+ L++ ++ +L++Y    H E+P R  K+L+ LP LR
Sbjct: 168 ANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLR 218

>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 =  108 bits (270), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 59/171 (34%), Positives = 100/171 (58%), Gaps = 4/171 (2%)
Query: 173 DQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSH 232
           D DI   +  T +C   D++L  ++ WAKHIP F+TL L DQ+ LL++ W E+LI    +
Sbjct: 28  DSDI---KALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVY 84
Query: 233 RSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIIL 292
           RS+S +D ++ A    +    +  AG+  + + +L +LV K + MK++K E   L+ I L
Sbjct: 85  RSLSFEDELVYADDYIMDEDQSKLAGLLDLNNAIL-QLVKKYKSMKLEKEEFVTLKAIAL 143
Query: 293 FNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLR 343
            N D   ++  + V+ L++ ++ +L++Y    H E+P R  K+L+ LP LR
Sbjct: 144 ANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLR 194

>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 =  108 bits (270), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 59/171 (34%), Positives = 100/171 (58%), Gaps = 4/171 (2%)
Query: 173 DQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSH 232
           D DI   +  T +C   D++L  ++ WAKHIP F+TL L DQ+ LL++ W E+LI    +
Sbjct: 44  DSDI---KALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVY 100
Query: 233 RSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIIL 292
           RS+S +D ++ A    +    +  AG+  + + +L +LV K + MK++K E   L+ I L
Sbjct: 101 RSLSFEDELVYADDYIMDEDQSKLAGLLDLNNAIL-QLVKKYKSMKLEKEEFVTLKAIAL 159
Query: 293 FNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLR 343
            N D   ++  + V+ L++ ++ +L++Y    H E+P R  K+L+ LP LR
Sbjct: 160 ANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLR 210

>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 =  108 bits (270), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 59/171 (34%), Positives = 100/171 (58%), Gaps = 4/171 (2%)
Query: 173 DQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSH 232
           D DI   +  T +C   D++L  ++ WAKHIP F+TL L DQ+ LL++ W E+LI    +
Sbjct: 27  DSDI---KALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVY 83
Query: 233 RSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIIL 292
           RS+S +D ++ A    +    +  AG+  + + +L +LV K + MK++K E   L+ I L
Sbjct: 84  RSLSFEDELVYADDYIMDEDQSKLAGLLDLNNAIL-QLVKKYKSMKLEKEEFVTLKAIAL 142
Query: 293 FNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLR 343
            N D   ++  + V+ L++ ++ +L++Y    H E+P R  K+L+ LP LR
Sbjct: 143 ANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLR 193

>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 =  108 bits (270), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 59/171 (34%), Positives = 100/171 (58%), Gaps = 4/171 (2%)
Query: 173 DQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSH 232
           D DI   +  T +C   D++L  ++ WAKHIP F+TL L DQ+ LL++ W E+LI    +
Sbjct: 31  DSDI---KALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVY 87
Query: 233 RSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIIL 292
           RS+S +D ++ A    +    +  AG+  + + +L +LV K + MK++K E   L+ I L
Sbjct: 88  RSLSFEDELVYADDYIMDEDQSKLAGLLDLNNAIL-QLVKKYKSMKLEKEEFVTLKAIAL 146
Query: 293 FNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLR 343
            N D   ++  + V+ L++ ++ +L++Y    H E+P R  K+L+ LP LR
Sbjct: 147 ANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLR 197

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

Iteration: 1
 Score =  108 bits (270), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 62/169 (36%), Positives = 106/169 (62%), Gaps = 8/169 (4%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSI-SVKDG-IL 242
           +CK  D+ LF +V+WA+    F  L ++DQ+ LL+  W+ELLI    +R +   K+G I 
Sbjct: 49  MCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIF 108
Query: 243 LAPGVTV-YRSSAHEAGVGGIFDRVLT---ELVSKMREMKMDKTELGCLRTIILFNPDVR 298
           L  G  V Y   A +AG     + +++   ELV+K+R ++ D+ E  CL+ ++LF+ DV+
Sbjct: 109 LVTGQQVDYSIIASQAG--ATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVK 166
Query: 299 GLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIEV 347
            L++ Q+VE ++E+V  +L +YT  N+ ++  +F +LLLRLP +R+I +
Sbjct: 167 NLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISM 215

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

Iteration: 1
 Score =  108 bits (270), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 62/169 (36%), Positives = 106/169 (62%), Gaps = 8/169 (4%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSI-SVKDG-IL 242
           +CK  D+ LF +V+WA+    F  L ++DQ+ LL+  W+ELLI    +R +   K+G I 
Sbjct: 61  MCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIF 120
Query: 243 LAPGVTV-YRSSAHEAGVGGIFDRVLT---ELVSKMREMKMDKTELGCLRTIILFNPDVR 298
           L  G  V Y   A +AG     + +++   ELV+K+R ++ D+ E  CL+ ++LF+ DV+
Sbjct: 121 LVTGQQVDYSIIASQAG--ATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVK 178
Query: 299 GLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIEV 347
            L++ Q+VE ++E+V  +L +YT  N+ ++  +F +LLLRLP +R+I +
Sbjct: 179 NLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISM 227

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

Iteration: 1
 Score =  108 bits (270), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 62/169 (36%), Positives = 106/169 (62%), Gaps = 8/169 (4%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSI-SVKDG-IL 242
           +CK  D+ LF +V+WA+    F  L ++DQ+ LL+  W+ELLI    +R +   K+G I 
Sbjct: 60  MCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIF 119
Query: 243 LAPGVTV-YRSSAHEAGVGGIFDRVLT---ELVSKMREMKMDKTELGCLRTIILFNPDVR 298
           L  G  V Y   A +AG     + +++   ELV+K+R ++ D+ E  CL+ ++LF+ DV+
Sbjct: 120 LVTGQQVDYSIIASQAG--ATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVK 177
Query: 299 GLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIEV 347
            L++ Q+VE ++E+V  +L +YT  N+ ++  +F +LLLRLP +R+I +
Sbjct: 178 NLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISM 226

>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 =  108 bits (269), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 93/338 (27%), Positives = 146/338 (43%), Gaps = 53/338 (15%)
Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXXXXXXXXXXXX 117
           C +CGD+ASG HYGV++CEGCKGFF+RT+R  L Y  R   NC I               
Sbjct: 53  CRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLIYD-RCDLNCRIHKKSRNKCQYCRFQK 111
Query: 118 XLNMGMKREAVQEER--QRTKERDSNEVES------------------------TSGTLI 151
            L +GM   A++  R  Q  KE+   E+ S                         S  L 
Sbjct: 112 CLAVGMSHNAIRFGRMPQAEKEKLLAEISSDIDQLNPESADLRALAKHLYDSYIKSFPLT 171
Query: 152 EMPVERILEAEQR-------VDMKQEPADQDIVNEQQATNI---CKATDKQLFQ------ 195
           +     IL  +          DM      +D +  +  T +    K    ++FQ      
Sbjct: 172 KAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRS 231
Query: 196 ------LVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTV 249
                 + ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G   
Sbjct: 232 VEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGF 289
Query: 250 YRSSAHEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVE 307
                 ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E
Sbjct: 290 MTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIE 349
Query: 308 MLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +++ +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 350 DIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 387

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

Iteration: 1
 Score =  107 bits (268), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 70/202 (34%), Positives = 124/202 (61%), Gaps = 11/202 (5%)
Query: 154 PVERILEAEQRVDMKQEPADQDIVNEQQATN--ICKATDKQLFQLVDWAKHIPHFTTLPL 211
           P E  ++A+    ++QE A++   +E+ +T   +CK  D+ LF +V+WA+    F  L +
Sbjct: 124 PDEPQVQAKIMAYLQQEQANRS-KHEKLSTFGLMCKMADQTLFSIVEWARSSIFFRELKV 182
Query: 212 EDQVLLLRAGWNELLIASFSHRSI-SVKDG-ILLAPGVTV-YRSSAHEAGVGGIFDRVLT 268
           +DQ+ LL+  W+ELLI    +R +   K+G I L  G  V Y   A +AG     + +++
Sbjct: 183 DDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQAG--ATLNNLMS 240
Query: 269 ---ELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNH 325
              ELV+K+R ++ D+ E  CL+ ++LF+ DV+ L++ Q+VE ++E+V  +L +YT  N+
Sbjct: 241 HAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNY 300
Query: 326 SEEPGRFAKLLLRLPSLRSIEV 347
            ++  +F +LLLRLP +R+I +
Sbjct: 301 PQQTEKFGQLLLRLPEIRAISM 322

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

Iteration: 1
 Score =  107 bits (267), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 62/167 (37%), Positives = 104/167 (62%), Gaps = 8/167 (4%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISV-KDG-IL 242
           +CK  D+ LF +V+WA+    F  L ++DQ+ LL+  W+ELLI    +R ++  K+G I 
Sbjct: 52  LCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVAHGKEGTIF 111
Query: 243 LAPGVTV-YRSSAHEAGVGGIFDRVLT---ELVSKMREMKMDKTELGCLRTIILFNPDVR 298
           L  G  V Y +      V   F+ +L+   ELV ++R ++ D+ E  CL+ ++LF+ DV+
Sbjct: 112 LVTGEHVDYSTIISHTEVA--FNNLLSLAQELVVRLRSLQFDQREFVCLKFLVLFSSDVK 169
Query: 299 GLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            L++ Q+VE ++E+V  +L +YT  N+ ++  +F +LLLRLP LR+I
Sbjct: 170 NLENLQLVEGVQEQVNAALLDYTVCNYPQQTEKFGQLLLRLPELRAI 216

>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 =  106 bits (264), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 61/167 (36%), Positives = 104/167 (62%), Gaps = 8/167 (4%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISV-KDG-IL 242
           +CK  D+ LF +V+WA+    F  L ++DQ+ LL+  W+ELLI    +R ++  K+G I 
Sbjct: 47  LCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVAHGKEGTIF 106
Query: 243 LAPGVTV-YRSSAHEAGVGGIFDRVLT---ELVSKMREMKMDKTELGCLRTIILFNPDVR 298
           L  G  V Y +      V   F+ +L+   ELV ++R ++ D+ E  CL+ ++LF+ DV+
Sbjct: 107 LVTGEHVDYSTIISHTEVA--FNNLLSLAQELVVRLRSLQFDQREFVCLKFLVLFSSDVK 164
Query: 299 GLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            L++ Q+VE ++E+V  +L +YT  N+ ++  +F +LLLRLP +R+I
Sbjct: 165 NLENLQLVEGVQEQVNAALLDYTVCNYPQQTEKFGQLLLRLPEIRAI 211

>pdb|2NLL|A Chain A, Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding Domain Heterodimer Bound To Thyroid Response Element Dna Length = 66

Iteration: 1
 Score = 95.5 bits (236), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 41/66 (62%), Positives = 48/66 (72%)
Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXXXXXXXXXXXX 117
           C+ICGDR+SGKHYGVYSCEGCKGFFKRTVRKDL+Y CR+ ++C+ID              
Sbjct: 1   CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQK 60
Query: 118 XLNMGM 123
            L MGM
Sbjct: 61  CLAMGM 66

>pdb|3CBB|A Chain A, Crystal Structure Of Hepatocyte Nuclear Factor 4alpha In Complex With Dna: Diabetes Gene Product Length = 78

Iteration: 1
 Score = 91.7 bits (226), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 40/76 (52%), Positives = 50/76 (65%)
Query: 57  LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXXXXXXXXXXX 116
           LC+ICGDRA+GKHYG  SC+GCKGFF+R+VRK+  Y+CR  R C++D             
Sbjct: 2   LCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLK 61
Query: 117 XXLNMGMKREAVQEER 132
                GMK+EAVQ ER
Sbjct: 62  KCFRAGMKKEAVQNER 77

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

Iteration: 1
 Score = 90.5 bits (223), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 51/155 (32%), Positives = 84/155 (54%), Gaps = 1/155 (0%)
Query: 191 KQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVY 250
           K + + V++AK +P FTTL + DQ+ LL+A   ++LI     R    +D +  + G+T+ 
Sbjct: 82  KCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLN 141
Query: 251 RSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLR 310
           R+  H AG G + D V     +++  ++MD  E G L  I L   D + L+    V+ML+
Sbjct: 142 RTQMHNAGFGPLTDLVFA-FANQLLPLEMDDAETGLLSAICLICGDRQDLEQPDRVDMLQ 200
Query: 311 EKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           E +  +L+ Y R      P  F K+L+++  LRSI
Sbjct: 201 EPLLEALKVYVRKRRPSRPHMFPKMLMKITDLRSI 235

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

Iteration: 1
 Score = 90.1 bits (222), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 53/168 (31%), Positives = 86/168 (51%), Gaps = 11/168 (6%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           IC++  + LF  + WA+ IP F  L  +    L+RA WNEL     +  +  +    +LA
Sbjct: 39  ICESASRLLFLSMHWARSIPAFQALGQDCNTSLVRACWNELFTLGLAQCAQVMSLSTILA 98
Query: 245 PGVTVYRSSAHEAGVGGIFDRV---------LTELVSKMREMKMDKTELGCLRTIILFNP 295
             V   ++S  E  + G  DR+         L E  + M ++ +D  E   L+ I+LF+P
Sbjct: 99  AIVNHLQNSIQEDKLSG--DRIKQVMEHIWKLQEFCNSMAKLDIDGYEYAYLKAIVLFSP 156
Query: 296 DVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLR 343
           D  GL S   +E  +E     L++Y +  +SE+  R A++L+RLP+LR
Sbjct: 157 DHPGLTSTSQIEKFQEAAQMELQDYVQATYSEDTYRLARILVRLPALR 204

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

Iteration: 1
 Score = 90.1 bits (222), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 51/155 (32%), Positives = 84/155 (54%), Gaps = 1/155 (0%)
Query: 191 KQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVY 250
           K + + V++AK +P FTTL + DQ+ LL+A   ++LI     R    +D +  + G+T+ 
Sbjct: 53  KCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLN 112
Query: 251 RSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLR 310
           R+  H AG G + D V     +++  ++MD  E G L  I L   D + L+    V+ML+
Sbjct: 113 RTQMHNAGFGPLTDLVFA-FANQLLPLEMDDAETGLLSAICLICGDRQDLEQPDRVDMLQ 171
Query: 311 EKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           E +  +L+ Y R      P  F K+L+++  LRSI
Sbjct: 172 EPLLEALKVYVRKRRPSRPHMFPKMLMKITDLRSI 206

>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 = 90.1 bits (222), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 51/155 (32%), Positives = 84/155 (54%), Gaps = 1/155 (0%)
Query: 191 KQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVY 250
           K + + V++AK +P FTTL + DQ+ LL+A   ++LI     R    +D +  + G+T+ 
Sbjct: 79  KCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLN 138
Query: 251 RSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLR 310
           R+  H AG G + D V     +++  ++MD  E G L  I L   D + L+    V+ML+
Sbjct: 139 RTQMHNAGFGPLTDLVFA-FANQLLPLEMDDAETGLLSAICLICGDRQDLEQPDRVDMLQ 197
Query: 311 EKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           E +  +L+ Y R      P  F K+L+++  LRSI
Sbjct: 198 EPLLEALKVYVRKRRPSRPHMFPKMLMKITDLRSI 232

>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 = 89.7 bits (221), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 51/155 (32%), Positives = 84/155 (54%), Gaps = 1/155 (0%)
Query: 191 KQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVY 250
           K + + V++AK +P FTTL + DQ+ LL+A   ++LI     R    +D +  + G+T+ 
Sbjct: 53  KCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLN 112
Query: 251 RSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLR 310
           R+  H AG G + D V     +++  ++MD  E G L  I L   D + L+    V+ML+
Sbjct: 113 RTQMHNAGFGPLTDLVFA-FANQLLPLEMDDAETGLLSAICLICGDRQDLEQPDRVDMLQ 171
Query: 311 EKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           E +  +L+ Y R      P  F K+L+++  LRSI
Sbjct: 172 EPLLEALKVYVRKRRPSRPHMFPKMLMKITDLRSI 206

>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 = 89.7 bits (221), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 51/155 (32%), Positives = 86/155 (55%), Gaps = 1/155 (0%)
Query: 191 KQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVY 250
           K + ++V++AK +P FT L + DQ+ LL+A   ++LI     R    +D +  + G+T+ 
Sbjct: 82  KCIIKIVEFAKRLPGFTGLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLN 141
Query: 251 RSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLR 310
           R+  H AG G + D V T   +++  ++MD TE G L  I L   D + L+    V+ L+
Sbjct: 142 RTQMHNAGFGPLTDLVFT-FANQLLPLEMDDTETGLLSAICLICGDRQDLEEPTKVDKLQ 200
Query: 311 EKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           E +  +L+ Y R     +P  F K+L+++  LRSI
Sbjct: 201 EPLLEALKIYIRKRRPSKPHMFPKILMKITDLRSI 235

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

Iteration: 1
 Score = 88.6 bits (218), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 55/183 (30%), Positives = 95/183 (51%), Gaps = 4/183 (2%)
Query: 169 QEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIA 228
           QEPA          + +C+  D+    +VDWA+    F  L + DQ+ LL+  W+ELL+ 
Sbjct: 34  QEPAKSRSDQPAPFSLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNSWSELLVL 93
Query: 229 SFSHRSISV--KDGILLAPGVTVYRSSAHEAGVGGIFDRVL--TELVSKMREMKMDKTEL 284
              +R +    +D ILL  G  V  S+        +   VL   ELV ++  +++D+ E 
Sbjct: 94  DHIYRQVQYGKEDSILLVTGQEVELSTVAVQAGSLLHSLVLRAQELVLQLHALQLDRQEF 153
Query: 285 GCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRS 344
            CL+ +ILF+ DV+ L +  +V+  +EK   +L +YT  ++     +F +LLL L  +R+
Sbjct: 154 VCLKFLILFSLDVKFLNNHSLVKDAQEKANAALLDYTLSHYPHSGDKFQQLLLSLVEVRA 213
Query: 345 IEV 347
           + +
Sbjct: 214 LSM 216

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

Iteration: 1
 Score = 88.6 bits (218), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 51/155 (32%), Positives = 86/155 (55%), Gaps = 1/155 (0%)
Query: 191 KQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVY 250
           K + ++V++AK +P FT L + DQ+ LL+A   ++LI     R    +D +  + G+T+ 
Sbjct: 80  KCIIKIVEFAKRLPGFTGLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLN 139
Query: 251 RSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLR 310
           R+  H AG G + D V T   +++  ++MD TE G L  I L   D + L+    V+ L+
Sbjct: 140 RTQMHNAGFGPLTDLVFT-FANQLLPLEMDDTETGLLSAICLICGDRQDLEEPTKVDKLQ 198
Query: 311 EKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           E +  +L+ Y R     +P  F K+L+++  LRSI
Sbjct: 199 EPLLEALKIYIRKRRPSKPHMFPKILMKITDLRSI 233

>pdb|1YP0|A Chain A, Structure Of The Steroidogenic Factor-1 Ligand Binding Domain Bound To Phospholipid And A Shp Peptide Motif Length = 239

Iteration: 1
 Score = 86.7 bits (213), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 55/183 (30%), Positives = 95/183 (51%), Gaps = 4/183 (2%)
Query: 169 QEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIA 228
           QEPA          + +C+  D+    +VDWA+    F  L + DQ+ LL+  W+ELL+ 
Sbjct: 28  QEPAKSRSDQPAPFSLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVL 87
Query: 229 SFSHRSISV--KDGILLAPGVTVYRSSAHEAGVGGIFDRVL--TELVSKMREMKMDKTEL 284
              +R +    +D ILL  G  V  S+        +   VL   ELV ++  +++D+ E 
Sbjct: 88  DHIYRQVQYGKEDSILLVTGQEVELSTVAVQAGSLLHSLVLRAQELVLQLHALQLDRQEF 147
Query: 285 GCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRS 344
            CL+ +ILF+ DV+ L +  +V+  +EK   +L +YT  ++     +F +LLL L  +R+
Sbjct: 148 VCLKFLILFSLDVKFLNNHSLVKDAQEKANAALLDYTLCHYPHCGDKFQQLLLCLVEVRA 207
Query: 345 IEV 347
           + +
Sbjct: 208 LSM 210

>pdb|2EBL|A Chain A, Solution Structure Of The Zinc Finger, C4-type Domain Of Human Coup Transcription Factor 1 Length = 89

Iteration: 1
 Score = 85.9 bits (211), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 38/72 (52%), Positives = 49/72 (68%)
Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXXXXXXXXXXXX 117
           C +CGD++SGKHYG ++CEGCK FFKR+VR++L+Y CR  RNC ID              
Sbjct: 10  CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRANRNCPIDQHHRNQCQYCRLKK 69
Query: 118 XLNMGMKREAVQ 129
            L +GM+REAVQ
Sbjct: 70  CLKVGMRREAVQ 81

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

Iteration: 1
 Score = 84.0 bits (206), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 54/183 (29%), Positives = 94/183 (51%), Gaps = 4/183 (2%)
Query: 169 QEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIA 228
           QEPA          + + +  D+    +VDWA+    F  L + DQ+ LL+  W+ELL+ 
Sbjct: 32  QEPAKSRSDQPAPFSLLXRMADQTFISIVDWARRCMVFKELEVADQMTLLQNSWSELLVL 91
Query: 229 SFSHRSISV--KDGILLAPGVTVYRSSAHEAGVGGIFDRVL--TELVSKMREMKMDKTEL 284
              +R +    +D ILL  G  V  S+        +   VL   ELV ++  +++D+ E 
Sbjct: 92  DHIYRQVQYGKEDSILLVTGQEVELSTVAVQAGSLLHSLVLRAQELVLQLHALQLDRQEF 151
Query: 285 GCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRS 344
            CL+ +ILF+ DV+ L +  +V+  +EK   +L +YT  ++     +F +LLL L  +R+
Sbjct: 152 VCLKFLILFSLDVKFLNNHSLVKDAQEKANAALLDYTLSHYPHSGDKFQQLLLSLVEVRA 211
Query: 345 IEV 347
           + +
Sbjct: 212 LSM 214

>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 = 80.9 bits (198), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 40/138 (28%), Positives = 79/138 (57%), Gaps = 1/138 (0%)
Query: 183 TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGIL 242
             +C   D+++   + WAK IP F++L L DQ+ +L++ W E+L+   + RS+ ++D + 
Sbjct: 56  ATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQDELA 115
Query: 243 LAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKS 302
            A  + +    A  AG+G +    L +LV +++ +++++ E   L+ + L N D   ++ 
Sbjct: 116 FAEDLVLDEEGARAAGLGEL-GAALLQLVRRLQALRLEREEYVLLKALALANSDSVHIED 174
Query: 303 QQVVEMLREKVYTSLEEY 320
            + VE LRE ++ +L EY
Sbjct: 175 AEAVEQLREALHEALLEY 192

>pdb|3K6P|A Chain A, Estrogen Related Receptor Alpha In Complex With An Ether Based Ligand Length = 248

Iteration: 1
 Score = 80.5 bits (197), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 40/138 (28%), Positives = 79/138 (57%), Gaps = 1/138 (0%)
Query: 183 TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGIL 242
             +C   D+++   + WAK IP F++L L DQ+ +L++ W E+L+   + RS+ ++D + 
Sbjct: 51  ATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQDELA 110
Query: 243 LAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKS 302
            A  + +    A  AG+G +    L +LV +++ +++++ E   L+ + L N D   ++ 
Sbjct: 111 FAEDLVLDEEGARAAGLGEL-GAALLQLVRRLQALRLEREEYVLLKALALANSDSVHIED 169
Query: 303 QQVVEMLREKVYTSLEEY 320
            + VE LRE ++ +L EY
Sbjct: 170 AEAVEQLREALHEALLEY 187

>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 = 80.5 bits (197), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 40/138 (28%), Positives = 79/138 (57%), Gaps = 1/138 (0%)
Query: 183 TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGIL 242
             +C   D+++   + WAK IP F++L L DQ+ +L++ W E+L+   + RS+ ++D + 
Sbjct: 50  ATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQDELA 109
Query: 243 LAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKS 302
            A  + +    A  AG+G +    L +LV +++ +++++ E   L+ + L N D   ++ 
Sbjct: 110 FAEDLVLDEEGARAAGLGEL-GAALLQLVRRLQALRLEREEYVLLKALALANSDSVHIED 168
Query: 303 QQVVEMLREKVYTSLEEY 320
            + VE LRE ++ +L EY
Sbjct: 169 AEAVEQLREALHEALLEY 186

>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 = 79.3 bits (194), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 52/153 (33%), Positives = 82/153 (53%), Gaps = 5/153 (3%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++V++AKHIP F  L   DQV LL+AG  E+L+  F+    +VKD  ++    T Y  S 
Sbjct: 80  EVVEFAKHIPGFRDLSQHDQVTLLKAGTFEVLMVRFASL-FNVKDQTVMFLSRTTY--SL 136
Query: 255 HEAGVGGIFD--RVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            E G  G+ D    + +   K+  + + + ELG    ++L + D  G+++   VE L+E 
Sbjct: 137 QELGAMGMGDLLSAMFDFSEKLNSLALTEEELGLFTAVVLVSADRSGMENSASVEQLQET 196
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +L      N   E  RF KLLL+LP LR++
Sbjct: 197 LLRALRALVLKNRPLETSRFTKLLLKLPDLRTL 229

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

Iteration: 1
 Score = 79.0 bits (193), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 31/80 (38%), Positives = 50/80 (62%)
Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXXXXXXXXXXXX 117
           C +C D++SG HYGV +CEGCKGFF+R+++K++ Y C   +NCII+              
Sbjct: 7   CFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQK 66
Query: 118 XLNMGMKREAVQEERQRTKE 137
              +GM +E+V+ +R + K+
Sbjct: 67  CFEVGMSKESVRNDRNKKKK 86

>pdb|2A66|A Chain A, Human Liver Receptor Homologue Dna-Binding Domain (Hlrh-1 Dbd) In Complex With Dsdna From The Hcyp7a1 Promoter Length = 113

Iteration: 1
 Score = 77.4 bits (189), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 37/78 (47%), Positives = 48/78 (61%)
Query: 57  LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXXXXXXXXXXX 116
           LC +CGD+ SG HYG+ +CE CKGFFKRTV+ +  Y C E +NC ID             
Sbjct: 11  LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQNCQIDKTQRKRCPYCRFQ 70
Query: 117 XXLNMGMKREAVQEERQR 134
             L++GMK EAV+ +R R
Sbjct: 71  KCLSVGMKLEAVRADRMR 88

>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 = 77.4 bits (189), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 49/164 (29%), Positives = 80/164 (48%), Gaps = 3/164 (1%)
Query: 186 CKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSI--SVKDGILL 243
           CK  D+ LF  VDWA++   F  L ++DQ  LL+  W++ L+    H  I   + D   L
Sbjct: 52  CKVLDQNLFSQVDWARNTVFFKDLKVDDQXKLLQHSWSDXLVLDHLHHRIHNGLPDETQL 111
Query: 244 APGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
             G      S    GV  + D    EL +K++++K D  +  C + +IL NP VRG+ ++
Sbjct: 112 NNGQVFNLXSLGLLGVPQLGD-YFNELQNKLQDLKFDXGDYVCXKFLILLNPSVRGIVNR 170
Query: 304 QVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIEV 347
           + V    + V  +L +YT   +     +F  L+  LP + +  V
Sbjct: 171 KTVSEGHDNVQAALLDYTLTCYPSVNDKFRGLVNILPEIHAXAV 214

>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 = 77.0 bits (188), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 39/131 (29%), Positives = 77/131 (58%), Gaps = 1/131 (0%)
Query: 190 DKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTV 249
           D+++   + WAK IP F++L L DQ+ +L++ W E+L+   + RS+ ++D +  A  + +
Sbjct: 57  DREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQDELAFAEDLVL 116
Query: 250 YRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEML 309
               A  AG+G +    L +LV +++ +++++ E   L+ + L N D   ++  + VE L
Sbjct: 117 DEEGARAAGLGEL-GAALLQLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQL 175
Query: 310 REKVYTSLEEY 320
           RE ++ +L EY
Sbjct: 176 REALHEALLEY 186

>pdb|1EXA|A Chain A, Enantiomer Discrimination Illustrated By Crystal Structures Of The Human Retinoic Acid Receptor Hrargamma Ligand Binding Domain: The Complex With The Active R-Enantiomer Bms270394. Length = 246

Iteration: 1
 Score = 75.1 bits (183), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 47/155 (30%), Positives = 82/155 (52%), Gaps = 1/155 (0%)
Query: 191 KQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVY 250
           K + ++V++AK +P FT L + DQ+ LL+A   ++L+     R    +D +  + G+T+ 
Sbjct: 59  KCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMTFSDGLTLN 118
Query: 251 RSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLR 310
           R+  H AG G + D V      ++  ++MD TE G L  I L   D   L+  + V+ L+
Sbjct: 119 RTQMHNAGFGPLTDLVFA-FAGQLLPLEMDDTETGLLSAICLICGDRMDLEEPEKVDKLQ 177
Query: 311 EKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           E +  +L  Y R     +P  F ++L+++  LR I
Sbjct: 178 EPLLEALRLYARRRRPSQPYMFPRMLMKITDLRGI 212

>pdb|2FF0|A Chain A, Solution Structure Of Steroidogenic Factor 1 Dna Binding Domain Bound To Its Target Sequence In The Inhibin Alpha- Subunit Promoter Length = 102

Iteration: 1
 Score = 75.1 bits (183), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 35/78 (44%), Positives = 47/78 (60%)
Query: 57  LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXXXXXXXXXXX 116
           LC +CGD+ SG HYG+ +CE CKGFFKRTV+ +  Y C E ++C ID             
Sbjct: 3   LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKHYTCTESQSCKIDKTQRKRCPFCRFQ 62
Query: 117 XXLNMGMKREAVQEERQR 134
             L +GM+ EAV+ +R R
Sbjct: 63  KCLTVGMRLEAVRADRMR 80

>pdb|1FCX|A Chain A, Isotype Selectivity Of The Human Retinoic Acid Nuclear Receptor Hrar: The Complex With The Rargamma-Selective Retinoid Bms184394 Length = 235

Iteration: 1
 Score = 75.1 bits (183), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 47/155 (30%), Positives = 82/155 (52%), Gaps = 1/155 (0%)
Query: 191 KQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVY 250
           K + ++V++AK +P FT L + DQ+ LL+A   ++L+     R    +D +  + G+T+ 
Sbjct: 54  KCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMTFSDGLTLN 113
Query: 251 RSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLR 310
           R+  H AG G + D V      ++  ++MD TE G L  I L   D   L+  + V+ L+
Sbjct: 114 RTQMHNAGFGPLTDLVFA-FAGQLLPLEMDDTETGLLSAICLICGDRMDLEEPEKVDKLQ 172
Query: 311 EKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           E +  +L  Y R     +P  F ++L+++  LR I
Sbjct: 173 EPLLEALRLYARRRRPSQPYMFPRMLMKITDLRGI 207

>pdb|2LBD|A Chain A, Ligand-Binding Domain Of The Human Retinoic Acid Receptor Gamma Bound To All-Trans Retinoic Acid Length = 267

Iteration: 1
 Score = 74.7 bits (182), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 47/155 (30%), Positives = 82/155 (52%), Gaps = 1/155 (0%)
Query: 191 KQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVY 250
           K + ++V++AK +P FT L + DQ+ LL+A   ++L+     R    +D +  + G+T+ 
Sbjct: 80  KCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMTFSDGLTLN 139
Query: 251 RSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLR 310
           R+  H AG G + D V      ++  ++MD TE G L  I L   D   L+  + V+ L+
Sbjct: 140 RTQMHNAGFGPLTDLVFA-FAGQLLPLEMDDTETGLLSAICLICGDRMDLEEPEKVDKLQ 198
Query: 311 EKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           E +  +L  Y R     +P  F ++L+++  LR I
Sbjct: 199 EPLLEALRLYARRRRPSQPYMFPRMLMKITDLRGI 233

>pdb|1FCY|A Chain A, Isotype Selectivity Of The Human Retinoic Acid Nuclear Receptor Hrar: The Complex With The RarbetaGAMMA- Selective Retinoid Cd564 Length = 236

Iteration: 1
 Score = 74.7 bits (182), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 47/155 (30%), Positives = 82/155 (52%), Gaps = 1/155 (0%)
Query: 191 KQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVY 250
           K + ++V++AK +P FT L + DQ+ LL+A   ++L+     R    +D +  + G+T+ 
Sbjct: 55  KCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMTFSDGLTLN 114
Query: 251 RSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLR 310
           R+  H AG G + D V      ++  ++MD TE G L  I L   D   L+  + V+ L+
Sbjct: 115 RTQMHNAGFGPLTDLVFA-FAGQLLPLEMDDTETGLLSAICLICGDRMDLEEPEKVDKLQ 173
Query: 311 EKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           E +  +L  Y R     +P  F ++L+++  LR I
Sbjct: 174 EPLLEALRLYARRRRPSQPYMFPRMLMKITDLRGI 208

>pdb|3M9E|A Chain A, Thyroid Hormone Beta Dna Binding Domain Homodimer With Inverted Palindrome Tre Length = 105

Iteration: 1
 Score = 74.3 bits (181), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 35/88 (39%), Positives = 51/88 (57%), Gaps = 2/88 (2%)
Query: 53  GSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDL--SYACREGRNCIIDXXXXXXX 110
           GS  LC +CGD+A+G HY   +CEGCKGFF+RT++K L  SY+C+    CIID       
Sbjct: 1   GSDELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKSLHPSYSCKYEGKCIIDKVTRNQC 60
Query: 111 XXXXXXXXLNMGMKREAVQEERQRTKER 138
                   + +GM  + V ++ +R  +R
Sbjct: 61  QECRFKKCIYVGMATDLVLDDSKRLAKR 88

>pdb|1R0N|B Chain B, Crystal Structure Of Heterodimeric Ecdsyone Receptor Dna Binding Complex Length = 109

Iteration: 1
 Score = 73.9 bits (180), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 37/98 (37%), Positives = 49/98 (50%)
Query: 57  LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXXXXXXXXXXX 116
           LC +CGDRASG HY   +CEGCKGFF+R+V K   Y C+ GR C +D             
Sbjct: 8   LCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECRLK 67
Query: 117 XXLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMP 154
             L +GM+ E V  E Q   +R   + +     +   P
Sbjct: 68  KCLAVGMRPECVVPENQCAMKRREKKAQKEKDKMTTSP 105

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

Iteration: 1
 Score = 73.6 bits (179), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 43/151 (28%), Positives = 75/151 (49%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++VD+AK +P F  L  EDQ+ LL+    E+++   S R     + I      +  R   
Sbjct: 64  EIVDFAKQLPGFLQLSREDQIALLKTSAIEVMLLETSRRYNPGSESITFLKDFSYNREDF 123
Query: 255 HEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVY 314
            +AG+   F   + E    M E++++  E   L  I +F+ D   ++ Q  VE L+    
Sbjct: 124 AKAGLQVEFINPIFEFSRAMNELQLNDAEFALLIAISIFSADRPNVQDQLQVERLQHTYV 183
Query: 315 TSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +L  Y  +NH  +P  F ++L++L SLR++
Sbjct: 184 EALHAYVSINHPHDPLMFPRMLMKLVSLRTL 214

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

Iteration: 1
 Score = 73.6 bits (179), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 43/151 (28%), Positives = 75/151 (49%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++VD+AK +P F  L  EDQ+ LL+    E+++   S R     + I      +  R   
Sbjct: 86  EIVDFAKQLPGFLQLSREDQIALLKTSAIEVMLLETSRRYNPGSESITFLKDFSYNREDF 145
Query: 255 HEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVY 314
            +AG+   F   + E    M E++++  E   L  I +F+ D   ++ Q  VE L+    
Sbjct: 146 AKAGLQVEFINPIFEFSRAMNELQLNDAEFALLIAISIFSADRPNVQDQLQVERLQHTYV 205
Query: 315 TSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +L  Y  +NH  +P  F ++L++L SLR++
Sbjct: 206 EALHAYVSINHPHDPLMFPRMLMKLVSLRTL 236

>pdb|2HAN|B Chain B, Structural Basis Of Heterodimeric Ecdysteroid Receptor Interaction With Natural Response Element Hsp27 Gene Promoter Length = 119

Iteration: 1
 Score = 73.6 bits (179), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 37/98 (37%), Positives = 49/98 (50%)
Query: 57  LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXXXXXXXXXXX 116
           LC +CGDRASG HY   +CEGCKGFF+R+V K   Y C+ GR C +D             
Sbjct: 10  LCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECRLK 69
Query: 117 XXLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMP 154
             L +GM+ E V  E Q   +R   + +     +   P
Sbjct: 70  KCLAVGMRPECVVPENQCAMKRREKKAQKEKDKMTTSP 107

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

Iteration: 1
 Score = 73.2 bits (178), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 28/72 (38%), Positives = 45/72 (62%)
Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXXXXXXXXXXXX 117
           C +C D++SG HYGV +CEGCKGFF+R+++K++ Y C   +NC+I+              
Sbjct: 8   CFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMIYTCHRDKNCVINKVTRNRCQYCRLQK 67
Query: 118 XLNMGMKREAVQ 129
              +GM +E+V+
Sbjct: 68  CFEVGMSKESVR 79

>pdb|1QKN|A Chain A, Rat Oestrogen Receptor Beta Ligand-Binding Domain In Complex With Antagonist Raloxifene Length = 255

Iteration: 1
 Score = 73.2 bits (178), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 49/152 (32%), Positives = 73/152 (48%), Gaps = 3/152 (1%)
Query: 152 EMPVERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPL 211
           E  V  +LEAE    +   P+           ++ K  DK+L  ++ WAK IP F  L L
Sbjct: 12  EQLVLTLLEAEPPNVLVSRPS-MPFTEASMMMSLTKLADKELVHMIGWAKKIPGFVELSL 70
Query: 212 EDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH-EAGVGGIFDRVLTEL 270
            DQV LL + W E+L+     RSI     ++ AP + + R       G+  IFD +L   
Sbjct: 71  LDQVRLLESCWMEVLMVGLMWRSIDHPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLAT- 129
Query: 271 VSKMREMKMDKTELGCLRTIILFNPDVRGLKS 302
            S+ RE+K+   E  C++ +IL N  +  L S
Sbjct: 130 TSRFRELKLQHKEYLCVKAMILLNSSMYPLAS 161

>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 = 73.2 bits (178), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 49/152 (32%), Positives = 73/152 (48%), Gaps = 3/152 (1%)
Query: 152 EMPVERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPL 211
           E  V  +LEAE    +   P+           ++ K  DK+L  ++ WAK IP F  L L
Sbjct: 12  EQLVLTLLEAEPPNVLVSRPS-MPFTEASMMMSLTKLADKELVHMIGWAKKIPGFVELSL 70
Query: 212 EDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH-EAGVGGIFDRVLTEL 270
            DQV LL + W E+L+     RSI     ++ AP + + R       G+  IFD +L   
Sbjct: 71  LDQVRLLESCWMEVLMVGLMWRSIDHPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLAT- 129
Query: 271 VSKMREMKMDKTELGCLRTIILFNPDVRGLKS 302
            S+ RE+K+   E  C++ +IL N  +  L S
Sbjct: 130 TSRFRELKLQHKEYLCVKAMILLNSSMYPLAS 161

>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 = 73.2 bits (178), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 41/118 (34%), Positives = 62/118 (52%), Gaps = 2/118 (1%)
Query: 184 NICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL 243
           ++ K  DK+L  ++ WAK IP F  L L DQV LL + W E+L+     RSI     ++ 
Sbjct: 41  SLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESSWMEVLMMGLMWRSIDHPGKLIF 100
Query: 244 APGVTVYRSSAHEA-GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGL 300
           AP + + R       G+  IFD +L    S+ RE+K+   E  C++ +IL N  +  L
Sbjct: 101 APDLVLDRDEGKSVEGILEIFDMLLAT-TSRFRELKLQHKEYLCVKAMILLNSSMYPL 157

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

Iteration: 1
 Score = 73.2 bits (178), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 44/151 (29%), Positives = 76/151 (50%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++VD+AK +P F  L  EDQ+ LL+A   E+++   + R     + I      T  +   
Sbjct: 70  EIVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETARRYNHETECITFLKDFTYSKDDF 129
Query: 255 HEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVY 314
           H AG+   F   + E    MR + +D  E   L  I +F+ D   ++    VE L++   
Sbjct: 130 HRAGLQVEFINPIFEFSRAMRRLGLDDAEYALLIAINIFSADRPNVQEPGRVEALQQPYV 189
Query: 315 TSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +L  YTR+   ++  RF ++L++L SLR++
Sbjct: 190 EALLSYTRIKRPQDQLRFPRMLMKLVSLRTL 220

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

Iteration: 1
 Score = 72.8 bits (177), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 44/151 (29%), Positives = 76/151 (50%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++VD+AK +P F  L  EDQ+ LL+A   E+++   + R     + I      T  +   
Sbjct: 73  EIVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETARRYNHETECITFLKDFTYSKDDF 132
Query: 255 HEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVY 314
           H AG+   F   + E    MR + +D  E   L  I +F+ D   ++    VE L++   
Sbjct: 133 HRAGLQVEFINPIFEFSRAMRRLGLDDAEYALLIAINIFSADRPNVQEPGRVEALQQPYV 192
Query: 315 TSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +L  YTR+   ++  RF ++L++L SLR++
Sbjct: 193 EALLSYTRIKRPQDQLRFPRMLMKLVSLRTL 223

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

Iteration: 1
 Score = 72.8 bits (177), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 44/151 (29%), Positives = 76/151 (50%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++VD+AK +P F  L  EDQ+ LL+A   E+++   + R     + I      T  +   
Sbjct: 77  EIVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETARRYNHETECITFLKDFTYSKDDF 136
Query: 255 HEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVY 314
           H AG+   F   + E    MR + +D  E   L  I +F+ D   ++    VE L++   
Sbjct: 137 HRAGLQVEFINPIFEFSRAMRRLGLDDAEYALLIAINIFSADRPNVQEPGRVEALQQPYV 196
Query: 315 TSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +L  YTR+   ++  RF ++L++L SLR++
Sbjct: 197 EALLSYTRIKRPQDQLRFPRMLMKLVSLRTL 227

>pdb|1NAV|A Chain A, Thyroid Receptor Alpha In Complex With An Agonist Selective For Thyroid Receptor Beta1 Length = 263

Iteration: 1
 Score = 72.8 bits (177), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 53/186 (28%), Positives = 90/186 (48%), Gaps = 9/186 (4%)
Query: 166 DMKQEP----ADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAG 221
           D+ Q P     D D V+ +  +   K     + ++VD+AK +P F+ LP EDQ++LL+  
Sbjct: 50  DIGQSPIVSMPDGDKVDLEAFSEFTKIITPAITRVVDFAKKLPMFSELPCEDQIILLKGC 109
Query: 222 WNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDK 281
             E++    + R     D + L+  + V R      G+G + D +  EL   +    +D 
Sbjct: 110 CMEIMSLRAAVRYDPESDTLTLSGEMAVKREQLKNGGLGVVSDAIF-ELGKSLSAFNLDD 168
Query: 282 TELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEE--PGRFAKLLLRL 339
           TE+  L+ ++L + D  GL     +E  +E    + E Y  VNH +   P  + KLL+++
Sbjct: 169 TEVALLQAVLLMSTDRSGLLCVDKIEKSQEAYLLAFEHY--VNHRKHNIPHFWPKLLMKV 226
Query: 340 PSLRSI 345
             LR I
Sbjct: 227 TDLRMI 232

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

Iteration: 1
 Score = 72.8 bits (177), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 44/151 (29%), Positives = 76/151 (50%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++VD+AK +P F  L  EDQ+ LL+A   E+++   + R     + I      T  +   
Sbjct: 67  EIVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETARRYNHETECITFLKDFTYSKDDF 126
Query: 255 HEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVY 314
           H AG+   F   + E    MR + +D  E   L  I +F+ D   ++    VE L++   
Sbjct: 127 HRAGLQVEFINPIFEFSRAMRRLGLDDAEYALLIAINIFSADRPNVQEPGRVEALQQPYV 186
Query: 315 TSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +L  YTR+   ++  RF ++L++L SLR++
Sbjct: 187 EALLSYTRIKRPQDQLRFPRMLMKLVSLRTL 217

>pdb|2H77|A Chain A, Crystal Structure Of Human Tr Alpha Bound T3 In Monoclinic Space Group Length = 269

Iteration: 1
 Score = 72.4 bits (176), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 53/186 (28%), Positives = 90/186 (48%), Gaps = 9/186 (4%)
Query: 166 DMKQEP----ADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAG 221
           D+ Q P     D D V+ +  +   K     + ++VD+AK +P F+ LP EDQ++LL+  
Sbjct: 54  DIGQSPIVSMPDGDKVDLEAFSEFTKIITPAITRVVDFAKKLPMFSELPCEDQIILLKGC 113
Query: 222 WNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDK 281
             E++    + R     D + L+  + V R      G+G + D +  EL   +    +D 
Sbjct: 114 CMEIMSLRAAVRYDPESDTLTLSGEMAVKREQLKNGGLGVVSDAIF-ELGKSLSAFNLDD 172
Query: 282 TELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEE--PGRFAKLLLRL 339
           TE+  L+ ++L + D  GL     +E  +E    + E Y  VNH +   P  + KLL+++
Sbjct: 173 TEVALLQAVLLMSTDRSGLLXVDKIEKSQEAYLLAFEHY--VNHRKHNIPHFWPKLLMKV 230
Query: 340 PSLRSI 345
             LR I
Sbjct: 231 TDLRMI 236

>pdb|3HZF|A Chain A, Structure Of Tr-alfa Bound To Selective Thyromimetic Gc-1 In C2 Space Group Length = 269

Iteration: 1
 Score = 72.4 bits (176), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 53/186 (28%), Positives = 90/186 (48%), Gaps = 9/186 (4%)
Query: 166 DMKQEP----ADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAG 221
           D+ Q P     D D V+ +  +   K     + ++VD+AK +P F+ LP EDQ++LL+  
Sbjct: 54  DIGQSPIVSMPDGDKVDLEAFSEFTKIITPAITRVVDFAKKLPMFSELPXEDQIILLKGC 113
Query: 222 WNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDK 281
             E++    + R     D + L+  + V R      G+G + D +  EL   +    +D 
Sbjct: 114 CMEIMSLRAAVRYDPESDTLTLSGEMAVKREQLKNGGLGVVSDAIF-ELGKSLSAFNLDD 172
Query: 282 TELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEE--PGRFAKLLLRL 339
           TE+  L+ ++L + D  GL     +E  +E    + E Y  VNH +   P  + KLL+++
Sbjct: 173 TEVALLQAVLLMSTDRSGLLXVDKIEKSQEAYLLAFEHY--VNHRKHNIPHFWPKLLMKV 230
Query: 340 PSLRSI 345
             LR I
Sbjct: 231 TDLRMI 236

>pdb|2H79|A Chain A, Crystal Structure Of Human Tr Alpha Bound T3 In Orthorhombic Space Group Length = 269

Iteration: 1
 Score = 72.0 bits (175), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 53/186 (28%), Positives = 90/186 (48%), Gaps = 9/186 (4%)
Query: 166 DMKQEP----ADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAG 221
           D+ Q P     D D V+ +  +   K     + ++VD+AK +P F+ LP EDQ++LL+  
Sbjct: 54  DIGQSPIVSMPDGDKVDLEAFSEFTKIITPAITRVVDFAKKLPMFSELPXEDQIILLKGC 113
Query: 222 WNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDK 281
             E++    + R     D + L+  + V R      G+G + D +  EL   +    +D 
Sbjct: 114 CMEIMSLRAAVRYDPESDTLTLSGEMAVKREQLKNGGLGVVSDAIF-ELGKSLSAFNLDD 172
Query: 282 TELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEE--PGRFAKLLLRL 339
           TE+  L+ ++L + D  GL     +E  +E    + E Y  VNH +   P  + KLL+++
Sbjct: 173 TEVALLQAVLLMSTDRSGLLXVDKIEKSQEAYLLAFEHY--VNHRKHNIPHFWPKLLMKV 230
Query: 340 PSLRSI 345
             LR I
Sbjct: 231 TDLRMI 236

>pdb|3JZB|A Chain A, Crystal Structure Of Tr-Alfa Bound To The Selective Thyromimetic Triac Length = 267

Iteration: 1
 Score = 72.0 bits (175), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 53/186 (28%), Positives = 90/186 (48%), Gaps = 9/186 (4%)
Query: 166 DMKQEP----ADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAG 221
           D+ Q P     D D V+ +  +   K     + ++VD+AK +P F+ LP EDQ++LL+  
Sbjct: 52  DIGQSPIVSMPDGDKVDLEAFSEFTKIITPAITRVVDFAKKLPMFSELPXEDQIILLKGC 111
Query: 222 WNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDK 281
             E++    + R     D + L+  + V R      G+G + D +  EL   +    +D 
Sbjct: 112 CMEIMSLRAAVRYDPESDTLTLSGEMAVKREQLKNGGLGVVSDAIF-ELGKSLSAFNLDD 170
Query: 282 TELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEE--PGRFAKLLLRL 339
           TE+  L+ ++L + D  GL     +E  +E    + E Y  VNH +   P  + KLL+++
Sbjct: 171 TEVALLQAVLLMSTDRSGLLXVDKIEKSQEAYLLAFEHY--VNHRKHNIPHFWPKLLMKV 228
Query: 340 PSLRSI 345
             LR I
Sbjct: 229 TDLRMI 234

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

Iteration: 1
 Score = 72.0 bits (175), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 45/151 (29%), Positives = 72/151 (47%), Gaps = 1/151 (0%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++V++AK IP F  L   DQV LL+AG  E+L   F+    + +  +    G        
Sbjct: 35  EVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLXVRFASLFDAKERTVTFLSGKKYSVDDL 94
Query: 255 HEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVY 314
           H  G G + +    E   K+  +++   E      ++L + D  G+++   VE L+E + 
Sbjct: 95  HSXGAGDLLNSXF-EFSEKLNALQLSDEEXSLFTAVVLVSADRSGIENVNSVEALQETLI 153
Query: 315 TSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +L      NH  E   F KLLL+LP LRS+
Sbjct: 154 RALRTLIXKNHPNEASIFTKLLLKLPDLRSL 184

>pdb|1CIT|A Chain A, Dna-Binding Mechanism Of The Monomeric Orphan Nuclear Receptor Ngfi-B Length = 89

Iteration: 1
 Score = 72.0 bits (175), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 32/74 (43%), Positives = 44/74 (59%)
Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXXXXXXXXXXXX 117
           C++CGD AS +HYGV +CEGCKGFFKRTV+K   Y C   ++C +D              
Sbjct: 3   CAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQK 62
Query: 118 XLNMGMKREAVQEE 131
            L +GM +E V+ +
Sbjct: 63  CLAVGMVKEVVRTD 76

>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 = 72.0 bits (175), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 48/150 (32%), Positives = 72/150 (48%), Gaps = 3/150 (2%)
Query: 152 EMPVERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPL 211
           E  V  +LEAE    +   P+           ++ K  DK+L  ++ WAK IP F  L L
Sbjct: 4   EQLVLTLLEAEPPHVLISRPS-APFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSL 62
Query: 212 EDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH-EAGVGGIFDRVLTEL 270
            DQV LL + W E+L+     RSI     ++ AP + + R       G+  IFD +L   
Sbjct: 63  FDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLAT- 121
Query: 271 VSKMREMKMDKTELGCLRTIILFNPDVRGL 300
            S+ RE+K+   E  C++ +IL N  +  L
Sbjct: 122 TSRFRELKLQHKEYLCVKAMILLNSSMYPL 151

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

Iteration: 1
 Score = 71.6 bits (174), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 47/152 (30%), Positives = 76/152 (50%), Gaps = 3/152 (1%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYR-SS 253
           ++V++AK IP F  L   DQV LL+AG  E+L+  F+      K+  +   G   Y    
Sbjct: 30  EVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASL-FDAKERTVTFLGSKKYSVDD 88
Query: 254 AHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKV 313
            H  G G + + +  E   K+  +++   E+     ++L + D  G+++   VE L+E +
Sbjct: 89  LHSMGAGDLLNSMF-EFSEKLNALQLSDEEMSLFTAVVLVSADRSGIENVNSVEALQETL 147
Query: 314 YTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
             +L      NH  E   F KLLL+LP LRS+
Sbjct: 148 IRALRTLIMKNHPNEASIFTKLLLKLPDLRSL 179

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

Iteration: 1
 Score = 71.6 bits (174), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 38/91 (41%), Positives = 54/91 (59%), Gaps = 3/91 (3%)
Query: 51  LCGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYA-CREGRNCIIDXXXXXX 109
           L G   LC +CGD ASG HYGV +CEGCKGFF+R++++++ Y  C +  NC I       
Sbjct: 3   LNGMVLLCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRNR 62
Query: 110 XXXXXXXXXLNMGMKREAVQEER--QRTKER 138
                    L++GM R+AV+  R  +R K+R
Sbjct: 63  CQQCRFKKCLSVGMSRDAVRFGRIPKREKQR 93

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

Iteration: 1
 Score = 71.6 bits (174), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 45/151 (29%), Positives = 72/151 (47%), Gaps = 1/151 (0%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++V++AK IP F  L   DQV LL+AG  E+L   F+    + +  +    G        
Sbjct: 30  EVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLXVRFASLFDAKERTVTFLSGKKYSVDDL 89
Query: 255 HEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVY 314
           H  G G + +    E   K+  +++   E      ++L + D  G+++   VE L+E + 
Sbjct: 90  HSXGAGDLLNSXF-EFSEKLNALQLSDEEXSLFTAVVLVSADRSGIENVNSVEALQETLI 148
Query: 315 TSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +L      NH  E   F KLLL+LP LRS+
Sbjct: 149 RALRTLIXKNHPNEASIFTKLLLKLPDLRSL 179

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

Iteration: 1
 Score = 71.6 bits (174), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 85/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL + W E+L+     RS+     +L A
Sbjct: 47  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLESAWLEILMIGLVWRSMEHPGKLLFA 106
Query: 245 PGVTVYRSSAHEA-GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 107 PNLLLDRNQGKSVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 164
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 165 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 218

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

Iteration: 1
 Score = 71.6 bits (174), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 85/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL + W E+L+     RS+     +L A
Sbjct: 47  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLESAWLEILMIGLVWRSMEHPGKLLFA 106
Query: 245 PGVTVYRSSAHEA-GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 107 PNLLLDRNQGKSVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 164
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 165 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 218

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

Iteration: 1
 Score = 71.6 bits (174), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 85/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL + W E+L+     RS+     +L A
Sbjct: 43  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLESAWLEILMIGLVWRSMEHPGKLLFA 102
Query: 245 PGVTVYRSSAHEA-GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 103 PNLLLDRNQGKSVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 160
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 161 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 214

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

Iteration: 1
 Score = 71.6 bits (174), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 85/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL + W E+L+     RS+     +L A
Sbjct: 43  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLESAWLEILMIGLVWRSMEHPGKLLFA 102
Query: 245 PGVTVYRSSAHEA-GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 103 PNLLLDRNQGKSVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 160
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 161 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 214

>pdb|3LTX|A Chain A, Crystal Structure Of The Pacific Oyster Estrogen Receptor Ligand Binding Domain Length = 243

Iteration: 1
 Score = 71.2 bits (173), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 45/162 (27%), Positives = 85/162 (52%), Gaps = 2/162 (1%)
Query: 183 TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISV-KDGI 241
            ++ K  +++L  L++WAK++P +T L L DQV L+   W ELL+ + + RSI      +
Sbjct: 39  NSLVKLAERELVHLINWAKNVPGYTDLSLSDQVHLIECCWMELLLLNCAFRSIEHGGKSL 98
Query: 242 LLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLK 301
             AP + + RSS     +  IF++V   +  +M +  + K EL  L+ ++L N +VR L 
Sbjct: 99  AFAPDLVLDRSSWSTVEMTEIFEQV-AAVSEQMMQNHLHKDELLLLQAMVLVNAEVRRLA 157
Query: 302 SQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLR 343
           S   +  +++ +  ++ +  +  H +       +LL L  +R
Sbjct: 158 SYNQIFNMQQSLLDAIVDTAQKYHPDNVRHVPAVLLLLTHIR 199

>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 = 71.2 bits (173), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 48/150 (32%), Positives = 72/150 (48%), Gaps = 3/150 (2%)
Query: 152 EMPVERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPL 211
           E  V  +LEAE    +   P+           ++ K  DK+L  ++ WAK IP F  L L
Sbjct: 32  EQLVLTLLEAEPPHVLISRPS-APFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSL 90
Query: 212 EDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH-EAGVGGIFDRVLTEL 270
            DQV LL + W E+L+     RSI     ++ AP + + R       G+  IFD +L   
Sbjct: 91  FDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLAT- 149
Query: 271 VSKMREMKMDKTELGCLRTIILFNPDVRGL 300
            S+ RE+K+   E  C++ +IL N  +  L
Sbjct: 150 TSRFRELKLQHKEYLCVKAMILLNSSMYPL 179

>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 = 71.2 bits (173), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 48/150 (32%), Positives = 72/150 (48%), Gaps = 3/150 (2%)
Query: 152 EMPVERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPL 211
           E  V  +LEAE    +   P+           ++ K  DK+L  ++ WAK IP F  L L
Sbjct: 18  EQLVLTLLEAEPPHVLISRPS-APFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSL 76
Query: 212 EDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH-EAGVGGIFDRVLTEL 270
            DQV LL + W E+L+     RSI     ++ AP + + R       G+  IFD +L   
Sbjct: 77  FDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLAT- 135
Query: 271 VSKMREMKMDKTELGCLRTIILFNPDVRGL 300
            S+ RE+K+   E  C++ +IL N  +  L
Sbjct: 136 TSRFRELKLQHKEYLCVKAMILLNSSMYPL 165

>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 = 71.2 bits (173), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 49  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFA 108
Query: 245 PGVTVYRSSAHEA-GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 109 PNLLLDRNQGKXVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 166
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 167 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 220

>pdb|1QKM|A Chain A, Human Oestrogen Receptor Beta Ligand-Binding Domain In Complex With Partial Agonist Genistein Length = 255

Iteration: 1
 Score = 71.2 bits (173), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 48/150 (32%), Positives = 72/150 (48%), Gaps = 3/150 (2%)
Query: 152 EMPVERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPL 211
           E  V  +LEAE    +   P+           ++ K  DK+L  ++ WAK IP F  L L
Sbjct: 12  EQLVLTLLEAEPPHVLISRPS-APFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSL 70
Query: 212 EDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH-EAGVGGIFDRVLTEL 270
            DQV LL + W E+L+     RSI     ++ AP + + R       G+  IFD +L   
Sbjct: 71  FDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLAT- 129
Query: 271 VSKMREMKMDKTELGCLRTIILFNPDVRGL 300
            S+ RE+K+   E  C++ +IL N  +  L
Sbjct: 130 TSRFRELKLQHKEYLCVKAMILLNSSMYPL 159

>pdb|2NLL|B Chain B, Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding Domain Heterodimer Bound To Thyroid Response Element Dna Length = 103

Iteration: 1
 Score = 71.2 bits (173), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 32/84 (38%), Positives = 50/84 (59%), Gaps = 2/84 (2%)
Query: 57  LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDL--SYACREGRNCIIDXXXXXXXXXXX 114
           LC +CGD+A+G HY   +CEGCKGFF+RT++K+L  SY+C+    C+ID           
Sbjct: 3   LCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQECR 62
Query: 115 XXXXLNMGMKREAVQEERQRTKER 138
               + +GM  + V ++ +R  +R
Sbjct: 63  FKKCIYVGMATDLVLDDSKRLAKR 86

>pdb|2JFA|B Chain B, Estrogen Receptor Alpha Lbd In Complex With An Affinity- Selected Corepressor Peptide Length = 252

Iteration: 1
 Score = 71.2 bits (173), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 65  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFA 124
Query: 245 PGVTVYRSSAHEA-GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 125 PNLLLDRNQGKXVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 182
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 183 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 236

>pdb|1NDE|A Chain A, Estrogen Receptor Beta With Selective Triazine Modulator Length = 255

Iteration: 1
 Score = 70.9 bits (172), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 48/150 (32%), Positives = 72/150 (48%), Gaps = 3/150 (2%)
Query: 152 EMPVERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPL 211
           E  V  +LEAE    +   P+           ++ K  DK+L  ++ WAK IP F  L L
Sbjct: 20  EQLVLTLLEAEPPHVLISRPS-APFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSL 78
Query: 212 EDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH-EAGVGGIFDRVLTEL 270
            DQV LL + W E+L+     RSI     ++ AP + + R       G+  IFD +L   
Sbjct: 79  FDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLAT- 137
Query: 271 VSKMREMKMDKTELGCLRTIILFNPDVRGL 300
            S+ RE+K+   E  C++ +IL N  +  L
Sbjct: 138 TSRFRELKLQHKEYLCVKAMILLNSSMYPL 167

>pdb|1U9E|A Chain A, Crystal Structure Of Estrogen Receptor Beta Complexed With Way-397 Length = 241

Iteration: 1
 Score = 70.9 bits (172), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 48/150 (32%), Positives = 72/150 (48%), Gaps = 3/150 (2%)
Query: 152 EMPVERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPL 211
           E  V  +LEAE    +   P+           ++ K  DK+L  ++ WAK IP F  L L
Sbjct: 6   EQLVLTLLEAEPPHVLISRPS-APFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSL 64
Query: 212 EDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH-EAGVGGIFDRVLTEL 270
            DQV LL + W E+L+     RSI     ++ AP + + R       G+  IFD +L   
Sbjct: 65  FDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLAT- 123
Query: 271 VSKMREMKMDKTELGCLRTIILFNPDVRGL 300
            S+ RE+K+   E  C++ +IL N  +  L
Sbjct: 124 TSRFRELKLQHKEYLCVKAMILLNSSMYPL 153

>pdb|1X76|A Chain A, Crystal Structure Of Estrogen Receptor Beta Complexed With Way-697 Length = 240

Iteration: 1
 Score = 70.9 bits (172), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 48/150 (32%), Positives = 72/150 (48%), Gaps = 3/150 (2%)
Query: 152 EMPVERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPL 211
           E  V  +LEAE    +   P+           ++ K  DK+L  ++ WAK IP F  L L
Sbjct: 6   EQLVLTLLEAEPPHVLISRPS-APFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSL 64
Query: 212 EDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH-EAGVGGIFDRVLTEL 270
            DQV LL + W E+L+     RSI     ++ AP + + R       G+  IFD +L   
Sbjct: 65  FDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLAT- 123
Query: 271 VSKMREMKMDKTELGCLRTIILFNPDVRGL 300
            S+ RE+K+   E  C++ +IL N  +  L
Sbjct: 124 TSRFRELKLQHKEYLCVKAMILLNSSMYPL 153

>pdb|2NV7|A Chain A, Crystal Structure Of Estrogen Receptor Beta Complexed With Way-555 Length = 238

Iteration: 1
 Score = 70.9 bits (172), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 48/150 (32%), Positives = 72/150 (48%), Gaps = 3/150 (2%)
Query: 152 EMPVERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPL 211
           E  V  +LEAE    +   P+           ++ K  DK+L  ++ WAK IP F  L L
Sbjct: 4   EQLVLTLLEAEPPHVLISRPS-APFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSL 62
Query: 212 EDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH-EAGVGGIFDRVLTEL 270
            DQV LL + W E+L+     RSI     ++ AP + + R       G+  IFD +L   
Sbjct: 63  FDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLAT- 121
Query: 271 VSKMREMKMDKTELGCLRTIILFNPDVRGL 300
            S+ RE+K+   E  C++ +IL N  +  L
Sbjct: 122 TSRFRELKLQHKEYLCVKAMILLNSSMYPL 151

>pdb|1L2I|A Chain A, Human Estrogen Receptor Alpha Ligand-Binding Domain In Complex With (R,R)-5,11-Cis-Diethyl-5,6,11,12- Tetrahydrochrysene-2,8-Diol And A Glucocorticoid Receptor Interacting Protein 1 Nr Box Ii Peptide Length = 261

Iteration: 1
 Score = 70.9 bits (172), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 53  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFA 112
Query: 245 PGVTVYRSSAHEA-GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 113 PNLLLDRNQGKXVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 170
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 171 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 224

>pdb|2GIU|A Chain A, Human Estrogen Receptor Beta Ligand-Binding Domain In Complex With Compound 45 Length = 241

Iteration: 1
 Score = 70.9 bits (172), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 48/150 (32%), Positives = 72/150 (48%), Gaps = 3/150 (2%)
Query: 152 EMPVERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPL 211
           E  V  +LEAE    +   P+           ++ K  DK+L  ++ WAK IP F  L L
Sbjct: 7   EQLVLTLLEAEPPHVLISRPS-APFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSL 65
Query: 212 EDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH-EAGVGGIFDRVLTEL 270
            DQV LL + W E+L+     RSI     ++ AP + + R       G+  IFD +L   
Sbjct: 66  FDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLAT- 124
Query: 271 VSKMREMKMDKTELGCLRTIILFNPDVRGL 300
            S+ RE+K+   E  C++ +IL N  +  L
Sbjct: 125 TSRFRELKLQHKEYLCVKAMILLNSSMYPL 154

>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 = 70.9 bits (172), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 52  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFA 111
Query: 245 PGVTVYRSSAHEA-GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 112 PNLLLDRNQGKXVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 169
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 170 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 223

>pdb|3UU7|A Chain A, Crystal Structure Of Hera-Lbd (Y537s) In Complex With Bisphenol-A Length = 251

Iteration: 1
 Score = 70.9 bits (172), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 45  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFA 104
Query: 245 PGVTVYRSSAHEA-GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 105 PNLLLDRNQGKXVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 162
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 163 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 216

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

Iteration: 1
 Score = 70.9 bits (172), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 43/151 (28%), Positives = 75/151 (49%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++VD+AK +P F  L  EDQ+ LL+A   E+++   + R     + I      T  +   
Sbjct: 73  EIVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETARRYNHETESITFLKDFTYSKDDF 132
Query: 255 HEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVY 314
           H AG+   F   + E    M  + +D  E   L  I +F+ D   ++    VE L++   
Sbjct: 133 HRAGLQVEFINPIFEFSRAMSSLGLDDAEYALLIAINIFSADRPNVQEPGRVEALQQPYV 192
Query: 315 TSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +L  YTR+   ++  RF ++L++L SLR++
Sbjct: 193 EALLSYTRIKRPQDQLRFPRMLMKLVSLRTL 223

>pdb|2YLY|A Chain A, Sulfonamides As Selective Estrogen Receptor Beta Agonists. Length = 240

Iteration: 1
 Score = 70.9 bits (172), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 48/150 (32%), Positives = 72/150 (48%), Gaps = 3/150 (2%)
Query: 152 EMPVERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPL 211
           E  V  +LEAE    +   P+           ++ K  DK+L  ++ WAK IP F  L L
Sbjct: 7   EQLVLTLLEAEPPHVLISRPS-APFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSL 65
Query: 212 EDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH-EAGVGGIFDRVLTEL 270
            DQV LL + W E+L+     RSI     ++ AP + + R       G+  IFD +L   
Sbjct: 66  FDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLAT- 124
Query: 271 VSKMREMKMDKTELGCLRTIILFNPDVRGL 300
            S+ RE+K+   E  C++ +IL N  +  L
Sbjct: 125 TSRFRELKLQHKEYLCVKAMILLNSSMYPL 154

>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 = 70.9 bits (172), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 52  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFA 111
Query: 245 PGVTVYRSSAHEA-GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 112 PNLLLDRNQGKXVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 169
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 170 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 223

>pdb|3OLL|A Chain A, Crystal Structure Of Phosphorylated Estrogen Receptor Beta Ligand Binding Domain Length = 240

Iteration: 1
 Score = 70.9 bits (172), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 48/150 (32%), Positives = 72/150 (48%), Gaps = 3/150 (2%)
Query: 152 EMPVERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPL 211
           E  V  +LEAE    +   P+           ++ K  DK+L  ++ WAK IP F  L L
Sbjct: 6   EQLVLTLLEAEPPHVLISRPS-APFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSL 64
Query: 212 EDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH-EAGVGGIFDRVLTEL 270
            DQV LL + W E+L+     RSI     ++ AP + + R       G+  IFD +L   
Sbjct: 65  FDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLAT- 123
Query: 271 VSKMREMKMDKTELGCLRTIILFNPDVRGL 300
            S+ RE+K+   E  C++ +IL N  +  L
Sbjct: 124 TSRFRELKLQHKEYLCVKAMILLNSSMYPL 153

>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 = 70.9 bits (172), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 49  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFA 108
Query: 245 PGVTVYRSSAHEA-GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 109 PNLLLDRNQGKXVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 166
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 167 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 220

>pdb|3UVV|A Chain A, Crystal Structure Of The Ligand Binding Domains Of The Thyroid Receptor:retinoid X Receptor Complexed With 3,3',5 Triiodo-L- Thyronine And 9-Cis Retinoic Acid Length = 265

Iteration: 1
 Score = 70.9 bits (172), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 48/184 (26%), Positives = 86/184 (46%), Gaps = 5/184 (2%)
Query: 166 DMKQEP----ADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAG 221
           D+ Q P     D D V+ +  +   K     + ++VD+AK +P F+ LP EDQ++LL+  
Sbjct: 50  DIGQSPMASMPDGDKVDLEAFSEFTKIITPAITRVVDFAKKLPMFSELPCEDQIILLKGC 109
Query: 222 WNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDK 281
             E++    + R     + + L+  + V R      G+G + D +  +L   +    +D 
Sbjct: 110 CMEIMSLRAAVRYDPESETLTLSGEMAVKREQLKNGGLGVVSDAIF-DLGKSLSAFNLDD 168
Query: 282 TELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPS 341
           TE+  L+ ++L + D  GL     +E  +E    + E Y        P  + KLL+++  
Sbjct: 169 TEVALLQAVLLMSSDRTGLICVDKIEKCQETYLLAFEHYINYRKHNIPHFWPKLLMKVTD 228
Query: 342 LRSI 345
           LR I
Sbjct: 229 LRMI 232

>pdb|3UU7|B Chain B, Crystal Structure Of Hera-Lbd (Y537s) In Complex With Bisphenol-A Length = 251

Iteration: 1
 Score = 70.5 bits (171), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 45  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFA 104
Query: 245 PGVTVYRSSAHEA-GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 105 PNLLLDRNQGKXVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 162
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 163 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 216

>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 = 70.5 bits (171), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 49  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFA 108
Query: 245 PGVTVYRSSAHEA-GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 109 PNLLLDRNQGKXVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 166
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 167 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 220

>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 = 70.5 bits (171), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 47/144 (32%), Positives = 70/144 (48%), Gaps = 3/144 (2%)
Query: 152 EMPVERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPL 211
           E  V  +LEAE    +   P+           ++ K  DK+L  ++ WAK IP F  L L
Sbjct: 4   EQLVLTLLEAEPPHVLISRPS-APFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSL 62
Query: 212 EDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH-EAGVGGIFDRVLTEL 270
            DQV LL + W E+L+     RSI     ++ AP + + R       G+  IFD +L   
Sbjct: 63  FDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLAT- 121
Query: 271 VSKMREMKMDKTELGCLRTIILFN 294
            S+ RE+K+   E  C++ +IL N
Sbjct: 122 TSRFRELKLQHKEYLCVKAMILLN 145

>pdb|2BJ4|A Chain A, Estrogen Receptor Alpha Lbd In Complex With A Phage-Display Derived Peptide Antagonist Length = 252

Iteration: 1
 Score = 70.5 bits (171), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 65  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFA 124
Query: 245 PGVTVYRSSAH-EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 125 PNLLLDRNQGKCVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 182
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 183 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 236

>pdb|3HLV|A Chain A, Crystal Structure Of Human Estrogen Receptor Alpha Ligand-Bi Domain In Complex With A Glucocorticoid Receptor Interactin 1 Nr Box Ii Peptide And 16-Alpha-Hydroxy-Estrone ((8s,9r,13 16r)-3,16-Dihydroxy-13-Methyl-7,8,9,11,12,14,15, 16-Octahyd Cyclopenta[a]phenanthren-17-One Length = 253

Iteration: 1
 Score = 70.1 bits (170), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 49  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFA 108
Query: 245 PGVTVYRSSAH-EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 109 PNLLLDRNQGKCVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 166
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 167 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 220

>pdb|3DT3|A Chain A, Human Estrogen Receptor Alpha Lbd With Gw368 Length = 255

Iteration: 1
 Score = 70.1 bits (170), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 50  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFA 109
Query: 245 PGVTVYRSSAH-EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 110 PNLLLDRNQGKCVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 167
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 168 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 221

>pdb|1GWQ|A Chain A, Human Oestrogen Receptor Alpha Ligand-Binding Domain In Complex With Raloxifene Core And Tif2 Nrbox2 Peptide Length = 248

Iteration: 1
 Score = 70.1 bits (170), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 46  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFA 105
Query: 245 PGVTVYRSSAH-EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 106 PNLLLDRNQGKCVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 163
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 164 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 217

>pdb|1G50|A Chain A, Crystal Structure Of A Wild Type Her Alpha Lbd At 2.9 Angstrom Resolution Length = 247

Iteration: 1
 Score = 70.1 bits (170), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 43  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFA 102
Query: 245 PGVTVYRSSAH-EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 103 PNLLLDRNQGKCVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 160
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 161 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 214

>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 = 70.1 bits (170), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 52  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFA 111
Query: 245 PGVTVYRSSAH-EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 112 PNLLLDRNQGKCVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 169
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 170 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 223

>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 = 70.1 bits (170), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 50  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFA 109
Query: 245 PGVTVYRSSAH-EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 110 PNLLLDRNQGKCVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 167
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 168 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 221

>pdb|3ERD|A Chain A, Human Estrogen Receptor Alpha Ligand-Binding Domain In Complex With Diethylstilbestrol And A Glucocorticoid Receptor Interacting Protein 1 Nr Box Ii Peptide Length = 261

Iteration: 1
 Score = 70.1 bits (170), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 53  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFA 112
Query: 245 PGVTVYRSSAH-EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 113 PNLLLDRNQGKCVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 170
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 171 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 224

>pdb|3UUA|A Chain A, Crystal Structure Of Hera-Lbd (Y537s) In Complex With Bisphenol-Af Length = 251

Iteration: 1
 Score = 69.7 bits (169), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 45  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFA 104
Query: 245 PGVTVYRSSAH-EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 105 PNLLLDRNQGKCVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 162
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 163 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 216

>pdb|2P15|A Chain A, Crystal Structure Of The Er Alpha Ligand Binding Domain With The Agonist Ortho-Trifluoromethylphenylvinyl Estradiol Length = 258

Iteration: 1
 Score = 69.7 bits (169), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 50  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFA 109
Query: 245 PGVTVYRSSAH-EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 110 PNLLLDRNQGKCVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 167
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 168 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 221

>pdb|2QXS|A Chain A, Crystal Structure Of Antagonizing Mutant 536s Of The Estrogen Receptor Alpha Ligand Binding Domain Complexed To Raloxifene Length = 258

Iteration: 1
 Score = 69.7 bits (169), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 50  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFA 109
Query: 245 PGVTVYRSSAH-EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 110 PNLLLDRNQGKCVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 167
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 168 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 221

>pdb|1ERE|A Chain A, Human Estrogen Receptor Ligand-Binding Domain In Complex With 17beta-Estradiol Length = 253

Iteration: 1
 Score = 69.7 bits (169), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 46  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFA 105
Query: 245 PGVTVYRSSAH-EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 106 PNLLLDRNQGKCVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 163
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 164 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 217

>pdb|1SJ0|A Chain A, Human Estrogen Receptor Alpha Ligand-binding Domain In Complex With The Antagonist Ligand 4-d Length = 248

Iteration: 1
 Score = 69.7 bits (169), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 40  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFA 99
Query: 245 PGVTVYRSSAH-EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 100 PNLLLDRNQGKCVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 157
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 158 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 211

>pdb|2IOK|A Chain A, Human Estrogen Receptor Alpha Ligand-binding Domain In Complex With Compound 1d Length = 254

Iteration: 1
 Score = 69.7 bits (169), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 46  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFA 105
Query: 245 PGVTVYRSSAH-EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 106 PNLLLDRNQGKCVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 163
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 164 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 217

>pdb|2IOG|A Chain A, Human Estrogen Receptor Alpha Ligand-Binding Domain In Complex With Compound 11f Length = 246

Iteration: 1
 Score = 69.7 bits (169), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 38  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFA 97
Query: 245 PGVTVYRSSAH-EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 98  PNLLLDRNQGKCVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 155
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 156 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 209

>pdb|1ERR|A Chain A, Human Estrogen Receptor Ligand-Binding Domain In Complex With Raloxifene Length = 253

Iteration: 1
 Score = 69.7 bits (169), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 46  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFA 105
Query: 245 PGVTVYRSSAH-EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 106 PNLLLDRNQGKCVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 163
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 164 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 217

>pdb|3UUC|A Chain A, Crystal Structure Of Hera-Lbd (Wt) In Complex With Bisphenol-C Length = 251

Iteration: 1
 Score = 69.7 bits (169), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 45  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFA 104
Query: 245 PGVTVYRSSAH-EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 105 PNLLLDRNQGKCVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 162
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 163 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 216

>pdb|2QA8|A Chain A, Crystal Structure Of The Estrogen Receptor Alpha Ligand Binding Domain Mutant 537s Complexed With Genistein Length = 258

Iteration: 1
 Score = 69.7 bits (169), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 50  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFA 109
Query: 245 PGVTVYRSSAH-EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 110 PNLLLDRNQGKCVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 167
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 168 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 221

>pdb|1GWR|A Chain A, Human Oestrogen Receptor Alpha Ligand-Binding Domain In Complex With 17beta-Oestradiol And Tif2 Nrbox3 Peptide Length = 245

Iteration: 1
 Score = 69.7 bits (169), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 42  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFA 101
Query: 245 PGVTVYRSSAH-EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 102 PNLLLDRNQGKCVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 159
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 160 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 213

>pdb|3L03|A Chain A, Crystal Structure Of Human Estrogen Receptor Alpha Ligand-Binding Domain In Complex With A Glucocorticoid Receptor Interacting Protein 1 Nr Box Ii Peptide And Estetrol (Estra-1,3,5(10)-Triene-3,15 Alpha, 16alpha,17beta-Tetrol) Length = 253

Iteration: 1
 Score = 69.7 bits (169), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 49  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFA 108
Query: 245 PGVTVYRSSAH-EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 109 PNLLLDRNQGKCVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 166
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 167 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 220

>pdb|1QKU|A Chain A, Wild Type Estrogen Nuclear Receptor Ligand Binding Domain Complexed With Estradiol Length = 250

Iteration: 1
 Score = 69.7 bits (169), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 46  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFA 105
Query: 245 PGVTVYRSSAH-EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 106 PNLLLDRNQGKCVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 163
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 164 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 217

>pdb|2QZO|B Chain B, Crystal Structure Of The Estrogen Receptor Alpha Ligand Binding Domain Complexed With Way-169916 Length = 258

Iteration: 1
 Score = 69.7 bits (169), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 50  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFA 109
Query: 245 PGVTVYRSSAH-EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 110 PNLLLDRNQGKCVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 167
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 168 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 221

>pdb|4DMA|A Chain A, Crystal Structure Of Era Lbd In Complex With Ru100132 Length = 247

Iteration: 1
 Score = 69.7 bits (169), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 44  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFA 103
Query: 245 PGVTVYRSSAH-EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 104 PNLLLDRNQGKCVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 161
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 162 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 215

>pdb|3UUA|B Chain B, Crystal Structure Of Hera-Lbd (Y537s) In Complex With Bisphenol-Af Length = 251

Iteration: 1
 Score = 69.7 bits (169), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 45  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFA 104
Query: 245 PGVTVYRSSAH-EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 105 PNLLLDRNQGKCVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 162
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 163 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 216

>pdb|1A52|A Chain A, Estrogen Receptor Alpha Ligand-Binding Domain Complexed To Estradiol Length = 258

Iteration: 1
 Score = 69.3 bits (168), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 50  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFA 109
Query: 245 PGVTVYRSSAH-EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 110 PNLLLDRNQGKCVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 167
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 168 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHERLAQLLLILSHIRHM 221

>pdb|1X7E|A Chain A, Crystal Structure Of Estrogen Receptor Alpha Complexed With Way-244 Length = 245

Iteration: 1
 Score = 68.9 bits (167), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 84/174 (48%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L L DQV LL   W E+L+     RS+     +L A
Sbjct: 42  LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPVKLLFA 101
Query: 245 PGVTVYRSSAH-EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 102 PNLLLDRNQGKCVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 159
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 160 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 213

>pdb|3OS8|A Chain A, Estrogen Receptor Length = 258

Iteration: 1
 Score = 68.2 bits (165), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 51/174 (29%), Positives = 83/174 (47%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L   DQV LL   W E+L+     RS+     +L A
Sbjct: 51  LTNLADRELVHMINWAKRVPGFVDLTRHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFA 110
Query: 245 PGVTVYRSSAHEA-GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 111 PNLLLDRNQGKXVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 168
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 169 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 222

>pdb|1LO1|A Chain A, Estrogen Related Receptor 2 Dna Binding Domain In Complex With Dna Length = 98

Iteration: 1
 Score = 67.8 bits (164), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 34/80 (42%), Positives = 44/80 (55%)
Query: 55  KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXXXXXXXXX 114
           K LC +CGD ASG HYGV SCE CK FFKRT++ ++ Y+C     C I            
Sbjct: 4   KRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACR 63
Query: 115 XXXXLNMGMKREAVQEERQR 134
               L +GM +E V+ +R R
Sbjct: 64  FMKALKVGMLKEGVRLDRVR 83

>pdb|3OS8|C Chain C, Estrogen Receptor Length = 258

Iteration: 1
 Score = 67.4 bits (163), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 51/174 (29%), Positives = 83/174 (47%), Gaps = 15/174 (8%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLA 244
           +    D++L  +++WAK +P F  L   DQV LL   W E+L+     RS+     +L A
Sbjct: 51  LTNLADRELVHMINWAKRVPGFVDLTRHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFA 110
Query: 245 PGVTVYRSSAH-EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
           P + + R+      G+  IFD +L    S+ R M +   E  CL++IIL N  V    S 
Sbjct: 111 PNLLLDRNQGKCVEGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLS- 168
Query: 304 QVVEMLREK--VYTSLEEYTR----------VNHSEEPGRFAKLLLRLPSLRSI 345
             ++ L EK  ++  L++ T           +   ++  R A+LLL L  +R +
Sbjct: 169 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 222

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

Iteration: 1
 Score = 67.4 bits (163), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 32/72 (44%), Positives = 42/72 (58%), Gaps = 1/72 (1%)
Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXXXXXXXXXXXX 117
           C +CGD+ASG HYGV++CEGCKGFF+RT+R  L Y   E R+C I               
Sbjct: 10  CRVCGDKASGFHYGVHACEGCKGFFRRTIRMKLEYEKCE-RSCKIQKKNRNKCQYCRFQK 68
Query: 118 XLNMGMKREAVQ 129
            L +GM   A++
Sbjct: 69  CLALGMSHNAIR 80

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

Iteration: 1
 Score = 67.4 bits (163), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 41/151 (27%), Positives = 74/151 (49%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++VD+AK +P F  L  EDQ+ LL+    E+++   S R     + I      +  R   
Sbjct: 62  EIVDFAKQLPGFLQLSREDQIALLKTSAIEVMLLETSRRYNPGSESITFLKDFSYNREDF 121
Query: 255 HEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVY 314
            +AG+   F   + E    M E++++  E   L  I +F+ D   ++ Q  VE L+    
Sbjct: 122 AKAGLQVEFINPIFEFSRAMNELQLNDAEFALLIAISIFSADRPNVQDQLQVERLQHTYV 181
Query: 315 TSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +L  Y  ++H  +   F ++L++L SLR++
Sbjct: 182 EALHAYVSIHHPHDRLMFPRMLMKLVSLRTL 212

>pdb|1OVL|A Chain A, Crystal Structure Of Nurr1 Lbd Length = 271

Iteration: 1
 Score = 67.0 bits (162), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 43/149 (28%), Positives = 74/149 (49%), Gaps = 5/149 (3%)
Query: 199 WAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG 258
           WA+ IP F  LP  DQ LL  + + EL +   ++RS  V+  ++   GV ++R      G
Sbjct: 93  WAEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIFCNGVVLHRLQCVR-G 151
Query: 259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLE 318
            G   D ++ E  S ++   +D +   C+  +     +  GLK  + VE L+ K+   L+
Sbjct: 152 FGEWIDSIV-EFSSNLQNXNIDISAFSCIAALAXVT-ERHGLKEPKRVEELQNKIVNCLK 209
Query: 319 EYTRVNHS--EEPGRFAKLLLRLPSLRSI 345
           ++   N+     P   +KLL +LP LR++
Sbjct: 210 DHVTFNNGGLNRPNYLSKLLGKLPELRTL 238

>pdb|1OVL|B Chain B, Crystal Structure Of Nurr1 Lbd Length = 271

Iteration: 1
 Score = 67.0 bits (162), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 43/149 (28%), Positives = 74/149 (49%), Gaps = 5/149 (3%)
Query: 199 WAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG 258
           WA+ IP F  LP  DQ LL  + + EL +   ++RS  V+  ++   GV ++R      G
Sbjct: 93  WAEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIFCNGVVLHRLQCVR-G 151
Query: 259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLE 318
            G   D ++ E  S ++   +D +   C+  +     +  GLK  + VE L+ K+   L+
Sbjct: 152 FGEWIDSIV-EFSSNLQNXNIDISAFSCIAALAXVT-ERHGLKEPKRVEELQNKIVNCLK 209
Query: 319 EYTRVNHS--EEPGRFAKLLLRLPSLRSI 345
           ++   N+     P   +KLL +LP LR++
Sbjct: 210 DHVTFNNGGLNRPNYLSKLLGKLPELRTL 238

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

Iteration: 1
 Score = 67.0 bits (162), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 41/151 (27%), Positives = 74/151 (49%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++VD+AK +P F  L  EDQ+ LL+    E+++   S R     + I      +  R   
Sbjct: 103 EIVDFAKQLPGFLQLSREDQIALLKTSAIEVMLLETSRRYNPGSESITFLKDFSYNREDF 162
Query: 255 HEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVY 314
            +AG+   F   + E    M E++++  E   L  I +F+ D   ++ Q  VE L+    
Sbjct: 163 AKAGLQVEFINPIFEFSRAMNELQLNDAEFALLIAISIFSADRPNVQDQLQVERLQHTYV 222
Query: 315 TSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +L  Y  ++H  +   F ++L++L SLR++
Sbjct: 223 EALHAYVSIHHPHDRLMFPRMLMKLVSLRTL 253

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

Iteration: 1
 Score = 67.0 bits (162), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 51/167 (30%), Positives = 91/167 (54%), Gaps = 4/167 (2%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISV-KDG-IL 242
           +C+  D+    +VDWA+    F  L + DQ+ LL+  W+ELL+    +R +   K+G IL
Sbjct: 45  LCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQHGKEGSIL 104
Query: 243 LAPGVTVYRSSAHEAGVGGIFDRVL--TELVSKMREMKMDKTELGCLRTIILFNPDVRGL 300
           L  G  V  ++        +   VL   ELV ++  +++D+ E  CL+ IILF+ D++ L
Sbjct: 105 LVTGQEVELTTVATQAGSLLHSLVLRAQELVLQLLALQLDRQEFVCLKFIILFSLDLKFL 164
Query: 301 KSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIEV 347
            +  +V+  +EK   +L +YT  ++     +F +LLL L  +R++ +
Sbjct: 165 NNHILVKDAQEKANAALLDYTLCHYPHSGDKFQQLLLCLVEVRALSM 211

>pdb|1HCQ|A Chain A, The Crystal Structure Of The Estrogen Receptor Dna-Binding Domain Bound To Dna: How Receptors Discriminate Between Their Response Elements Length = 84

Iteration: 1
 Score = 67.0 bits (162), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 28/76 (36%), Positives = 41/76 (53%)
Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXXXXXXXXXXXX 117
           C++C D ASG HYGV+SCEGCK FFKR+++    Y C     C ID              
Sbjct: 7   CAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRK 66
Query: 118 XLNMGMKREAVQEERQ 133
              +GM +  ++++R+
Sbjct: 67  CYEVGMMKGGIRKDRR 82

>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 = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 110 EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 167
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 168 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 227
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 228 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 260

>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 = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 94  EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 151
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 152 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 211
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 212 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 244

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

Iteration: 1
 Score = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 102 EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 159
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 160 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 219
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 220 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 252

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

Iteration: 1
 Score = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 96  EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 153
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 154 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 213
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 214 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 246

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

Iteration: 1
 Score = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 43/151 (28%), Positives = 72/151 (47%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++VD+AK +P F  L  EDQ+ LL+A   E+ +   + R     + I      T  +   
Sbjct: 67  EIVDFAKQVPGFLQLGREDQIALLKASTIEIXLLETARRYNHETECITFLKDFTYSKDDF 126
Query: 255 HEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVY 314
           H AG+   F   + E     R + +D  E   L  I +F+ D   ++    VE L++   
Sbjct: 127 HRAGLQVEFINPIFEFSRAXRRLGLDDAEYALLIAINIFSADRPNVQEPGRVEALQQPYV 186
Query: 315 TSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +L  YTR+   ++  RF + L +L SLR++
Sbjct: 187 EALLSYTRIKRPQDQLRFPRXLXKLVSLRTL 217

>pdb|2I4J|A Chain A, Crystal Structure Of The Complex Between Ppargamma And The Agonist Lt160 (Ureidofibrate Derivative) Length = 286

Iteration: 1
 Score = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 105 EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 162
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 163 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 222
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 223 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 255

>pdb|2VSR|A Chain A, Hppargamma Ligand Binding Domain In Complex With 9-(S)-Hode Length = 276

Iteration: 1
 Score = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 94  EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 151
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 152 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 211
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 212 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 244

>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 = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 102 EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 159
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 160 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 219
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 220 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 252

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

Iteration: 1
 Score = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 104 EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 161
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 162 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 221
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 222 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 254

>pdb|3ADS|A Chain A, Human Ppargamma Ligand-Binding Domain In Complex With Indomethacin Length = 287

Iteration: 1
 Score = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 105 EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 162
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 163 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 222
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 223 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 255

>pdb|3LMP|A Chain A, Crystal Structure Of The Ppargamma-Lbd Complexed With A Cercosporamide Derivative Modulator Length = 283

Iteration: 1
 Score = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 101 EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 158
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 159 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 218
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 219 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 251

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

Iteration: 1
 Score = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 51/167 (30%), Positives = 91/167 (54%), Gaps = 4/167 (2%)
Query: 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISV-KDG-IL 242
           +C+  D+    +VDWA+    F  L + DQ+ LL+  W+ELL+    +R +   K+G IL
Sbjct: 46  LCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQHGKEGSIL 105
Query: 243 LAPGVTVYRSSAHEAGVGGIFDRVL--TELVSKMREMKMDKTELGCLRTIILFNPDVRGL 300
           L  G  V  ++        +   VL   ELV ++  +++D+ E  CL+ IILF+ D++ L
Sbjct: 106 LVTGQEVELTTVATQAGSLLHSLVLRAQELVLQLLALQLDRQEFVCLKFIILFSLDLKFL 165
Query: 301 KSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIEV 347
            +  +V+  +EK   +L +YT  ++     +F +LLL L  +R++ +
Sbjct: 166 NNHILVKDAQEKANAALLDYTLCHYPHCGDKFQQLLLCLVEVRALSM 212

>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 = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 101 EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 158
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 159 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 218
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 219 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 251

>pdb|1WM0|X Chain X, Ppargamma In Complex With A 2-Baba Compound Length = 292

Iteration: 1
 Score = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 110 EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 167
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 168 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 227
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 228 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 260

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

Iteration: 1
 Score = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 103 EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 160
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 161 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 220
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 221 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 253

>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 = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 95  EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 152
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 153 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 212
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 213 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 245

>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 = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 114 EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 171
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 172 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 231
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 232 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 264

>pdb|2VV1|B Chain B, Hppargamma Ligand Binding Domain In Complex With 4-Hdha Length = 276

Iteration: 1
 Score = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 94  EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 151
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 152 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 211
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 212 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 244

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

Iteration: 1
 Score = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 93  EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 150
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 151 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 210
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 211 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 243

>pdb|3CS8|A Chain A, Structural And Biochemical Basis For The Binding Selectivity Of Pparg To Pgc-1a Length = 275

Iteration: 1
 Score = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 94  EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 151
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 152 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 211
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 212 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 244

>pdb|2Q59|B Chain B, Crystal Structure Of Ppargamma Lbd Bound To Full Agonist Mrl20 Length = 274

Iteration: 1
 Score = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 92  EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 149
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 150 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 209
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 210 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 242

>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 = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 104 EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 161
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 162 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 221
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 222 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 254

>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 = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 110 EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 167
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 168 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 227
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 228 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 260

>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 = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 100 EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 157
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 158 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 217
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 218 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 250

>pdb|2VV4|B Chain B, Hppargamma Ligand Binding Domain In Complex With 6-Oxoote Length = 276

Iteration: 1
 Score = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 94  EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 151
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 152 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 211
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 212 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 244

>pdb|4PRG|A Chain A, 0072 Partial Agonist Ppar Gamma Cocrystal Length = 270

Iteration: 1
 Score = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 89  EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 146
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 147 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 206
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 207 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 239

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

Iteration: 1
 Score = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 96  EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 153
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 154 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 213
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 214 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 246

>pdb|2ZVT|A Chain A, Cys285ser Mutant Ppargamma Ligand-Binding Domain Complexed With 15-Deoxy-Delta12,14-Prostaglandin J2 Length = 286

Iteration: 1
 Score = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 105 EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 162
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 163 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 222
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 223 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 255

>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 = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 90  EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 147
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 148 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 207
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 208 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 240

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

Iteration: 1
 Score = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 88  EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 145
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 146 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 205
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 206 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 238

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

Iteration: 1
 Score = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 89  EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 146
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 147 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 206
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 207 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 239

>pdb|2HFP|A Chain A, Crystal Structure Of Ppar Gamma With N-Sulfonyl-2-Indole Carboxamide Ligands Length = 282

Iteration: 1
 Score = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 100 EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 157
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 158 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 217
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 218 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 250

>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 = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 92  EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 149
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 150 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 209
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 210 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 242

>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 = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 102 EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 159
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 160 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 219
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 220 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 252

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

Iteration: 1
 Score = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 88  EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 145
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 146 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 205
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 206 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 238

>pdb|2Q59|A Chain A, Crystal Structure Of Ppargamma Lbd Bound To Full Agonist Mrl20 Length = 274

Iteration: 1
 Score = 66.2 bits (160), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 92  EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 149
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 150 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 209
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 210 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 242

>pdb|3ET0|A Chain A, Structure Of Ppargamma With 3-(5-Methoxy-1h-Indol-3-Yl)- Propionic Acid Length = 292

Iteration: 1
 Score = 66.2 bits (160), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 79/153 (51%), Gaps = 4/153 (2%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           ++ ++AK IP F  L L DQV LL+ G +E++    +  S+  KDG+L++ G        
Sbjct: 110 EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREF 167
Query: 255 HEA--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
            ++     G F     E   K   +++D ++L     +I+ + D  GL + + +E +++ 
Sbjct: 168 LKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDN 227
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 228 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 260

>pdb|4AA6|E Chain E, The Oestrogen Receptor Recognizes An Imperfectly Palindromic Response Element Through An Alternative Side- Chain Conformation Length = 71

Iteration: 1
 Score = 64.3 bits (155), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 25/46 (54%), Positives = 31/46 (67%)
Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIID 103
           C++C D ASG HYGV+SCEGCK FFKR+++    Y C     C ID
Sbjct: 4   CAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTID 49

>pdb|4AA6|A Chain A, The Oestrogen Receptor Recognizes An Imperfectly Palindromic Response Element Through An Alternative Side- Chain Conformation Length = 71

Iteration: 1
 Score = 64.3 bits (155), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 25/46 (54%), Positives = 31/46 (67%)
Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIID 103
           C++C D ASG HYGV+SCEGCK FFKR+++    Y C     C ID
Sbjct: 4   CAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTID 49

>pdb|2J4A|A Chain A, Human Thyroid Hormone Receptor Beta Ligand Binding Domain In Complex With Kb131084 Length = 253

Iteration: 1
 Score = 64.3 bits (155), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 41/169 (24%), Positives = 80/169 (47%), Gaps = 1/169 (0%)
Query: 177 VNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSIS 236
           V+ +  ++  K     + ++VD+AK +P F  LP EDQ++LL+    E++    + R   
Sbjct: 56  VDLEAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDP 115
Query: 237 VKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD 296
             + + L+  + V R      G+G + D +  +L   +    +D TE+  L+ ++L + D
Sbjct: 116 ESETLTLSGEMAVTRGQLKNGGLGVVSDAIF-DLGMSLSSFNLDDTEVALLQAVLLMSSD 174
Query: 297 VRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
             GL   + +E  ++    + E Y           + KLL+++  LR I
Sbjct: 175 RPGLACVERIEKYQDSFLLAFEHYINYRKHHVTHFWPKLLMKVTDLRMI 223

>pdb|1HCP|A Chain A, Dna Recognition By The Oestrogen Receptor: From Solution To The Crystal Length = 76

Iteration: 1
 Score = 64.3 bits (155), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 25/46 (54%), Positives = 31/46 (67%)
Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIID 103
           C++C D ASG HYGV+SCEGCK FFKR+++    Y C     C ID
Sbjct: 7   CAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTID 52

>pdb|3HC6|A Chain A, Fxr With Src1 And Gsk088 Length = 232

Iteration: 1
 Score = 63.9 bits (154), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 41/150 (27%), Positives = 74/150 (49%), Gaps = 4/150 (2%)
Query: 196 LVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH 255
           LV++ K +P F TL  EDQ+ LL+    E +      RS  + +  L +    +      
Sbjct: 58  LVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFL----RSAEIFNKKLPSGHSDLLEERIR 113
Query: 256 EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYT 315
            +G+   +   +      + E+KM + E   L  I++ +PD + +K ++ VE L+E +  
Sbjct: 114 NSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLD 173
Query: 316 SLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            L++  +++  E P  FA+LL RL  LR+ 
Sbjct: 174 VLQKLCKIHQPENPQHFAELLGRLTELRTF 203

>pdb|3GD2|A Chain A, Isoxazole Ligand Bound To Farnesoid X Receptor (Fxr) Length = 229

Iteration: 1
 Score = 63.9 bits (154), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 41/150 (27%), Positives = 74/150 (49%), Gaps = 4/150 (2%)
Query: 196 LVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH 255
           LV++ K +P F TL  EDQ+ LL+    E +      RS  + +  L +    +      
Sbjct: 55  LVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFL----RSAEIFNKKLPSGHSDLLEERIR 110
Query: 256 EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYT 315
            +G+   +   +      + E+KM + E   L  I++ +PD + +K ++ VE L+E +  
Sbjct: 111 NSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLD 170
Query: 316 SLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            L++  +++  E P  FA+LL RL  LR+ 
Sbjct: 171 VLQKLCKIHQPENPQHFAELLGRLTELRTF 200

>pdb|1LAT|A Chain A, Glucocorticoid Receptor MutantDNA COMPLEX Length = 82

Iteration: 1
 Score = 63.9 bits (154), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 31/76 (40%), Positives = 39/76 (51%)
Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXXXXXXXXXXXX 117
           C +C D ASG HYGV +CEGCK FFKR V    +Y C+    CIID              
Sbjct: 7   CLVCSDEASGCHYGVLTCEGCKAFFKRAVEGQHNYLCKYEGKCIIDKIRRKNCPACRYRK 66
Query: 118 XLNMGMKREAVQEERQ 133
            L  GM  EA + +++
Sbjct: 67  CLQAGMNLEARKTKKK 82

>pdb|2B50|A Chain A, Human Nuclear Receptor-Ligand Complex 2 Length = 272

Iteration: 1
 Score = 63.5 bits (153), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 45/154 (29%), Positives = 80/154 (51%), Gaps = 6/154 (3%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           +L ++AK IP F++L L DQV LL+ G +E + A  +  SI  KDG+L+A G + + +  
Sbjct: 91  ELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLA--SIVNKDGLLVANG-SGFVTRE 147
Query: 255 HEAGVGGIFDRVLT---ELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
               +   F  ++    E   K   +++D ++L      I+   D  GL +   VE +++
Sbjct: 148 FLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQD 207
Query: 312 KVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +  +LE + + NH +    F KLL ++  LR +
Sbjct: 208 TILRALEFHLQANHPDAQQLFPKLLQKMADLRQL 241

>pdb|3P88|A Chain A, Fxr Bound To Isoquinolinecarboxylic Acid Length = 229

Iteration: 1
 Score = 63.5 bits (153), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 41/150 (27%), Positives = 74/150 (49%), Gaps = 4/150 (2%)
Query: 196 LVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH 255
           LV++ K +P F TL  EDQ+ LL+    E +      RS  + +  L +    +      
Sbjct: 55  LVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFL----RSAEIFNKKLPSGHSDLLEERIR 110
Query: 256 EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYT 315
            +G+   +   +      + E+KM + E   L  I++ +PD + +K ++ VE L+E +  
Sbjct: 111 NSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLD 170
Query: 316 SLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            L++  +++  E P  FA+LL RL  LR+ 
Sbjct: 171 VLQKLCKIHQPENPQHFAELLGRLTELRTF 200

>pdb|2Q5G|A Chain A, Ligand Binding Domain Of Ppar Delta Receptor In Complex With A Partial Agonist Length = 283

Iteration: 1
 Score = 63.5 bits (153), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 45/154 (29%), Positives = 80/154 (51%), Gaps = 6/154 (3%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           +L ++AK IP F++L L DQV LL+ G +E + A  +  SI  KDG+L+A G + + +  
Sbjct: 101 ELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLA--SIVNKDGLLVANG-SGFVTRE 157
Query: 255 HEAGVGGIFDRVL---TELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
               +   F  ++    E   K   +++D ++L      I+   D  GL +   VE +++
Sbjct: 158 FLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQD 217
Query: 312 KVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +  +LE + + NH +    F KLL ++  LR +
Sbjct: 218 TILRALEFHLQANHPDAQYLFPKLLQKMADLRQL 251

>pdb|2AWH|A Chain A, Human Nuclear Receptor-Ligand Complex 1 Length = 268

Iteration: 1
 Score = 63.5 bits (153), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 45/154 (29%), Positives = 80/154 (51%), Gaps = 6/154 (3%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           +L ++AK IP F++L L DQV LL+ G +E + A  +  SI  KDG+L+A G + + +  
Sbjct: 86  ELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLA--SIVNKDGLLVANG-SGFVTRE 142
Query: 255 HEAGVGGIFDRVL---TELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
               +   F  ++    E   K   +++D ++L      I+   D  GL +   VE +++
Sbjct: 143 FLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQD 202
Query: 312 KVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +  +LE + + NH +    F KLL ++  LR +
Sbjct: 203 TILRALEFHLQANHPDAQQLFPKLLQKMADLRQL 236

>pdb|3P89|A Chain A, Fxr Bound To A Quinolinecarboxylic Acid Length = 229

Iteration: 1
 Score = 63.5 bits (153), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 41/150 (27%), Positives = 74/150 (49%), Gaps = 4/150 (2%)
Query: 196 LVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH 255
           LV++ K +P F TL  EDQ+ LL+    E +      RS  + +  L +    +      
Sbjct: 55  LVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFL----RSAEIFNKKLPSGHSDLLEERIR 110
Query: 256 EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYT 315
            +G+   +   +      + E+KM + E   L  I++ +PD + +K ++ VE L+E +  
Sbjct: 111 NSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLD 170
Query: 316 SLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            L++  +++  E P  FA+LL RL  LR+ 
Sbjct: 171 VLQKLCKIHQPENPQHFAELLGRLTELRTF 200

>pdb|3ET2|A Chain A, Structure Of Ppardelta With 3-[5-Methoxy-1-(4-Methoxy- Benzenesulfonyl)-1h-Indol-3-Yl]-Propionic Acid Length = 287

Iteration: 1
 Score = 63.5 bits (153), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 45/154 (29%), Positives = 80/154 (51%), Gaps = 6/154 (3%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           +L ++AK IP F++L L DQV LL+ G +E + A  +  SI  KDG+L+A G + + +  
Sbjct: 105 ELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLA--SIVNKDGLLVANG-SGFVTRE 161
Query: 255 HEAGVGGIFDRVL---TELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
               +   F  ++    E   K   +++D ++L      I+   D  GL +   VE +++
Sbjct: 162 FLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQD 221
Query: 312 KVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +  +LE + + NH +    F KLL ++  LR +
Sbjct: 222 TILRALEFHLQANHPDAQYLFPKLLQKMADLRQL 255

>pdb|2J14|A Chain A, 3,4,5-Trisubstituted Isoxazoles As Novel Ppardelta Agonists: Part2 Length = 285

Iteration: 1
 Score = 63.5 bits (153), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 45/154 (29%), Positives = 80/154 (51%), Gaps = 6/154 (3%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           +L ++AK IP F++L L DQV LL+ G +E + A  +  SI  KDG+L+A G + + +  
Sbjct: 103 ELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLA--SIVNKDGLLVANG-SGFVTRE 159
Query: 255 HEAGVGGIFDRVL---TELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
               +   F  ++    E   K   +++D ++L      I+   D  GL +   VE +++
Sbjct: 160 FLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQD 219
Query: 312 KVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +  +LE + + NH +    F KLL ++  LR +
Sbjct: 220 TILRALEFHLQANHPDAQYLFPKLLQKMADLRQL 253

>pdb|1OSV|A Chain A, Structural Basis For Bile Acid Binding And Activation Of The Nuclear Receptor Fxr Length = 230

Iteration: 1
 Score = 63.5 bits (153), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 42/150 (28%), Positives = 73/150 (48%), Gaps = 4/150 (2%)
Query: 196 LVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH 255
           LV++ K +P F TL  EDQ+ LL+    E +      RS  + +  L A    +      
Sbjct: 56  LVEFTKRLPGFQTLDHEDQIALLKGSAVEAMFL----RSAEIFNKKLPAGHADLLEERIR 111
Query: 256 EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYT 315
           ++G+   +   +      + E+KM + E   L  I++ +PD + +K ++ VE L+E +  
Sbjct: 112 KSGISDEYITPMFSFYKSVGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLD 171
Query: 316 SLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            L++  ++   E P  FA LL RL  LR+ 
Sbjct: 172 VLQKLCKIYQPENPQHFACLLGRLTELRTF 201

>pdb|2GWX|A Chain A, Molecular Recognition Of Fatty Acids By Peroxisome Proliferator-Activated Receptors Length = 267

Iteration: 1
 Score = 63.5 bits (153), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 45/154 (29%), Positives = 80/154 (51%), Gaps = 6/154 (3%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           +L ++AK IP F++L L DQV LL+ G +E + A  +  SI  KDG+L+A G + + +  
Sbjct: 85  ELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLA--SIVNKDGLLVANG-SGFVTRE 141
Query: 255 HEAGVGGIFDRVL---TELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
               +   F  ++    E   K   +++D ++L      I+   D  GL +   VE +++
Sbjct: 142 FLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQD 201
Query: 312 KVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +  +LE + + NH +    F KLL ++  LR +
Sbjct: 202 TILRALEFHLQANHPDAQQLFPKLLQKMADLRQL 235

>pdb|1NUO|A Chain A, Two Rth Mutants With Impaired Hormone Binding Length = 261

Iteration: 1
 Score = 63.5 bits (153), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 41/169 (24%), Positives = 79/169 (46%), Gaps = 1/169 (0%)
Query: 177 VNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSIS 236
           V+ +  ++  K     + ++VD+AK +P F  LP EDQ++LL+    E++    + R   
Sbjct: 64  VDLEAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLHAAVRYDP 123
Query: 237 VKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD 296
             + + L   + V R      G+G + D +  +L   +    +D TE+  L+ ++L + D
Sbjct: 124 ESETLTLNGEMAVTRGQLKNGGLGVVSDAIF-DLGMSLSSFNLDDTEVALLQAVLLMSSD 182
Query: 297 VRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
             GL   + +E  ++    + E Y           + KLL+++  LR I
Sbjct: 183 RPGLACVERIEKYQDSFLLAFEHYINYRKHHVTHFWPKLLMKVTDLRMI 231

>pdb|1OT7|A Chain A, Structural Basis For 3-Deoxy-Cdca Binding And Activation Of Fxr Length = 229

Iteration: 1
 Score = 63.5 bits (153), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 42/150 (28%), Positives = 73/150 (48%), Gaps = 4/150 (2%)
Query: 196 LVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH 255
           LV++ K +P F TL  EDQ+ LL+    E +      RS  + +  L A    +      
Sbjct: 56  LVEFTKRLPGFQTLDHEDQIALLKGSAVEAMFL----RSAEIFNKKLPAGHADLLEERIR 111
Query: 256 EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYT 315
           ++G+   +   +      + E+KM + E   L  I++ +PD + +K ++ VE L+E +  
Sbjct: 112 KSGISDEYITPMFSFYKSVGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLD 171
Query: 316 SLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            L++  ++   E P  FA LL RL  LR+ 
Sbjct: 172 VLQKLCKIYQPENPQHFACLLGRLTELRTF 201

>pdb|3SP9|A Chain A, Structural Basis For Iloprost As A Dual PparalphaDELTA AGONIST Length = 281

Iteration: 1
 Score = 63.5 bits (153), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 45/154 (29%), Positives = 80/154 (51%), Gaps = 6/154 (3%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           +L ++AK IP F++L L DQV LL+ G +E + A  +  SI  KDG+L+A G + + +  
Sbjct: 99  ELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLA--SIVNKDGLLVANG-SGFVTRE 155
Query: 255 HEAGVGGIFDRVL---TELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
               +   F  ++    E   K   +++D ++L      I+   D  GL +   VE +++
Sbjct: 156 FLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQD 215
Query: 312 KVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +  +LE + + NH +    F KLL ++  LR +
Sbjct: 216 TILRALEFHLQANHPDAQYLFPKLLQKMADLRQL 249

>pdb|2XYJ|A Chain A, Novel Sulfonylthiadiazoles With An Unusual Binding Mode As Partial Dual Peroxisome Proliferator-Activated Receptor (Ppar) Gamma-Delta Agonists With High Potency And In-Vivo Efficacy Length = 288

Iteration: 1
 Score = 63.5 bits (153), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 45/154 (29%), Positives = 80/154 (51%), Gaps = 6/154 (3%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           +L ++AK IP F++L L DQV LL+ G +E + A  +  SI  KDG+L+A G + + +  
Sbjct: 106 ELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLA--SIVNKDGLLVANG-SGFVTRE 162
Query: 255 HEAGVGGIFDRVLT---ELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
               +   F  ++    E   K   +++D ++L      I+   D  GL +   VE +++
Sbjct: 163 FLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQD 222
Query: 312 KVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +  +LE + + NH +    F KLL ++  LR +
Sbjct: 223 TILRALEFHLQANHPDAQYLFPKLLQKMADLRQL 256

>pdb|2ZNP|A Chain A, Human Pprr Delta Ligand Binding Domain In Complex With A Synthetic Agonist Tipp204 Length = 276

Iteration: 1
 Score = 63.2 bits (152), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 45/154 (29%), Positives = 80/154 (51%), Gaps = 6/154 (3%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           +L ++AK IP F++L L DQV LL+ G +E + A  +  SI  KDG+L+A G + + +  
Sbjct: 94  ELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLA--SIVNKDGLLVANG-SGFVTRE 150
Query: 255 HEAGVGGIFDRVL---TELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
               +   F  ++    E   K   +++D ++L      I+   D  GL +   VE +++
Sbjct: 151 FLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQD 210
Query: 312 KVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +  +LE + + NH +    F KLL ++  LR +
Sbjct: 211 TILRALEFHLQANHPDAQYLFPKLLQKMADLRQL 244

>pdb|1Y0S|A Chain A, Crystal Structure Of Ppar Delta Complexed With Gw2331 Length = 272

Iteration: 1
 Score = 63.2 bits (152), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 45/154 (29%), Positives = 80/154 (51%), Gaps = 6/154 (3%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           +L ++AK IP F++L L DQV LL+ G +E + A  +  SI  KDG+L+A G + + +  
Sbjct: 90  ELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLA--SIVNKDGLLVANG-SGFVTRE 146
Query: 255 HEAGVGGIFDRVL---TELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
               +   F  ++    E   K   +++D ++L      I+   D  GL +   VE +++
Sbjct: 147 FLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQD 206
Query: 312 KVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +  +LE + + NH +    F KLL ++  LR +
Sbjct: 207 TILRALEFHLQANHPDAQYLFPKLLQKMADLRQL 240

>pdb|1GWX|A Chain A, Molecular Recognition Of Fatty Acids By Peroxisome Proliferator-Activated Receptors Length = 271

Iteration: 1
 Score = 63.2 bits (152), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 45/154 (29%), Positives = 80/154 (51%), Gaps = 6/154 (3%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           +L ++AK IP F++L L DQV LL+ G +E + A  +  SI  KDG+L+A G + + +  
Sbjct: 89  ELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLA--SIVNKDGLLVANG-SGFVTRE 145
Query: 255 HEAGVGGIFDRVL---TELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
               +   F  ++    E   K   +++D ++L      I+   D  GL +   VE +++
Sbjct: 146 FLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQD 205
Query: 312 KVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +  +LE + + NH +    F KLL ++  LR +
Sbjct: 206 TILRALEFHLQANHPDAQYLFPKLLQKMADLRQL 239

>pdb|3DCT|A Chain A, Fxr With Src1 And Gw4064 Length = 235

Iteration: 1
 Score = 63.2 bits (152), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 41/150 (27%), Positives = 73/150 (48%), Gaps = 4/150 (2%)
Query: 196 LVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH 255
           LV++ K +P F TL  EDQ+ LL+    E +      RS  + +  L +    +      
Sbjct: 61  LVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFL----RSAEIFNKKLPSGHSDLLEERIR 116
Query: 256 EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYT 315
            +G+   +   +      + E+KM + E   L  I++ +PD + +K ++ VE L+E +  
Sbjct: 117 NSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLD 176
Query: 316 SLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            L++  +++  E P  FA LL RL  LR+ 
Sbjct: 177 VLQKLCKIHQPENPQHFACLLGRLTELRTF 206

>pdb|1Q4X|A Chain A, Crystal Structure Of Human Thyroid Hormone Receptor Beta Lbd In Complex With Specific Agonist Gc-24 Length = 253

Iteration: 1
 Score = 63.2 bits (152), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 41/169 (24%), Positives = 79/169 (46%), Gaps = 1/169 (0%)
Query: 177 VNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSIS 236
           V+ +  ++  K     + ++VD+AK +P F  LP EDQ++LL+    E++    + R   
Sbjct: 56  VDLEAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDP 115
Query: 237 VKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD 296
             + + L   + V R      G+G + D +  +L   +    +D TE+  L+ ++L + D
Sbjct: 116 ESETLTLNGEMAVTRGQLKNGGLGVVSDAIF-DLGMSLSSFNLDDTEVALLQAVLLMSSD 174
Query: 297 VRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
             GL   + +E  ++    + E Y           + KLL+++  LR I
Sbjct: 175 RPGLACVERIEKYQDSFLLAFEHYINYRKHHVTHFWPKLLMKVTDLRMI 223

>pdb|1R6G|A Chain A, Crystal Structure Of The Thyroid Hormone Receptor Beta Ligand Binding Domain In Complex With A Beta Selective Compound Length = 259

Iteration: 1
 Score = 63.2 bits (152), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 41/169 (24%), Positives = 79/169 (46%), Gaps = 1/169 (0%)
Query: 177 VNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSIS 236
           V+ +  ++  K     + ++VD+AK +P F  LP EDQ++LL+    E++    + R   
Sbjct: 62  VDLEAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDP 121
Query: 237 VKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD 296
             + + L   + V R      G+G + D +  +L   +    +D TE+  L+ ++L + D
Sbjct: 122 ESETLTLNGEMAVTRGQLKNGGLGVVSDAIF-DLGMSLSSFNLDDTEVALLQAVLLMSSD 180
Query: 297 VRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
             GL   + +E  ++    + E Y           + KLL+++  LR I
Sbjct: 181 RPGLACVERIEKYQDSFLLAFEHYINYRKHHVTHFWPKLLMKVTDLRMI 229

>pdb|3FXV|A Chain A, Identification Of An N-Oxide Pyridine Gw4064 Analogue As A Potent Fxr Agonist Length = 233

Iteration: 1
 Score = 63.2 bits (152), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 41/150 (27%), Positives = 74/150 (49%), Gaps = 4/150 (2%)
Query: 196 LVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH 255
           LV++ K +P F TL  EDQ+ LL+    E +      RS  + +  L +    +  +   
Sbjct: 59  LVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFL----RSAEIFNKKLPSGHSDLLEARIR 114
Query: 256 EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYT 315
            +G+   +   +      + E+KM + E   L  I++ +PD + +K ++ VE L+E +  
Sbjct: 115 NSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLD 174
Query: 316 SLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            L++  +++  E P  FA LL RL  LR+ 
Sbjct: 175 VLQKLCKIHQPENPQHFACLLGRLTELRTF 204

>pdb|1BSX|A Chain A, Structure And Specificity Of Nuclear Receptor-Coactivator Interactions Length = 260

Iteration: 1
 Score = 63.2 bits (152), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 41/169 (24%), Positives = 79/169 (46%), Gaps = 1/169 (0%)
Query: 177 VNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSIS 236
           V+ +  ++  K     + ++VD+AK +P F  LP EDQ++LL+    E++    + R   
Sbjct: 63  VDLEAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDP 122
Query: 237 VKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD 296
             + + L   + V R      G+G + D +  +L   +    +D TE+  L+ ++L + D
Sbjct: 123 ESETLTLNGEMAVTRGQLKNGGLGVVSDAIF-DLGMSLSSFNLDDTEVALLQAVLLMSSD 181
Query: 297 VRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
             GL   + +E  ++    + E Y           + KLL+++  LR I
Sbjct: 182 RPGLACVERIEKYQDSFLLAFEHYINYRKHHVTHFWPKLLMKVTDLRMI 230

>pdb|1XZX|X Chain X, Thyroxine-Thyroid Hormone Receptor Interactions Length = 281

Iteration: 1
 Score = 63.2 bits (152), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 41/169 (24%), Positives = 79/169 (46%), Gaps = 1/169 (0%)
Query: 177 VNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSIS 236
           V+ +  ++  K     + ++VD+AK +P F  LP EDQ++LL+    E++    + R   
Sbjct: 84  VDLEAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDP 143
Query: 237 VKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD 296
             + + L   + V R      G+G + D +  +L   +    +D TE+  L+ ++L + D
Sbjct: 144 ESETLTLNGEMAVTRGQLKNGGLGVVSDAIF-DLGMSLSSFNLDDTEVALLQAVLLMSSD 202
Query: 297 VRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
             GL   + +E  ++    + E Y           + KLL+++  LR I
Sbjct: 203 RPGLACVERIEKYQDSFLLAFEHYINYRKHHVTHFWPKLLMKVTDLRMI 251

>pdb|3TKM|A Chain A, Crystal Structure Ppar Delta Binding Gw0742 Length = 275

Iteration: 1
 Score = 63.2 bits (152), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 45/154 (29%), Positives = 80/154 (51%), Gaps = 6/154 (3%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           +L ++AK IP F++L L DQV LL+ G +E + A  +  SI  KDG+L+A G + + +  
Sbjct: 93  ELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLA--SIVNKDGLLVANG-SGFVTRE 149
Query: 255 HEAGVGGIFDRVL---TELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
               +   F  ++    E   K   +++D ++L      I+   D  GL +   VE +++
Sbjct: 150 FLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQD 209
Query: 312 KVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +  +LE + + NH +    F KLL ++  LR +
Sbjct: 210 TILRALEFHLQANHPDAQYLFPKLLQKMADLRQL 243

>pdb|3BEJ|A Chain A, Structure Of Human Fxr In Complex With Mfa-1 And Co- Activator Peptide Length = 238

Iteration: 1
 Score = 63.2 bits (152), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 41/150 (27%), Positives = 73/150 (48%), Gaps = 4/150 (2%)
Query: 196 LVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH 255
           LV++ K +P F TL  EDQ+ LL+    E +      RS  + +  L +    +      
Sbjct: 64  LVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFL----RSAEIFNKKLPSGHSDLLEERIR 119
Query: 256 EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYT 315
            +G+   +   +      + E+KM + E   L  I++ +PD + +K ++ VE L+E +  
Sbjct: 120 NSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLD 179
Query: 316 SLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            L++  +++  E P  FA LL RL  LR+ 
Sbjct: 180 VLQKLCKIHQPENPQHFACLLGRLTELRTF 209

>pdb|3G9P|B Chain B, Gr Dna Binding Domain:sgk 16bp Complex-7 Length = 90

Iteration: 1
 Score = 63.2 bits (152), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 34/93 (36%), Positives = 46/93 (49%), Gaps = 5/93 (5%)
Query: 56  HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXXXXXXXXXX 115
           H+C +C D ASG HYGV +C  CK FFKR V    +Y C    +CIID            
Sbjct: 3   HMCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRY 62
Query: 116 XXXLNMGMKREAVQEERQRTKERDSNEVESTSG 148
              L  GM  EA     ++TK++     ++T+G
Sbjct: 63  RKCLQAGMNLEA-----RKTKKKIKGIQQATAG 90

>pdb|1NQ0|A Chain A, Tr Receptor Mutations Conferring Hormone Resistance And Reduced Corepressor Release Exhibit Decreased Stability In The Nterminal Lbd Length = 263

Iteration: 1
 Score = 63.2 bits (152), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 41/169 (24%), Positives = 79/169 (46%), Gaps = 1/169 (0%)
Query: 177 VNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSIS 236
           V+ +  ++  K     + ++VD+AK +P F  LP EDQ++LL+    E++    + R   
Sbjct: 66  VDLEAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDP 125
Query: 237 VKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD 296
             + + L   + V R      G+G + D +  +L   +    +D TE+  L+ ++L + D
Sbjct: 126 ESETLTLNGEMAVTRGQLKNGGLGVVSDAIF-DLGMSLSSFNLDDTEVALLQAVLLMSSD 184
Query: 297 VRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
             GL   + +E  ++    + E Y           + KLL+++  LR I
Sbjct: 185 RPGLACVERIEKYQDSFLLAFEHYINYRKHHVTHFWPKLLMKVTDLRMI 233

>pdb|1NAX|A Chain A, Thyroid Receptor Beta1 In Complex With A Beta-Selective Ligand Length = 252

Iteration: 1
 Score = 63.2 bits (152), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 41/169 (24%), Positives = 79/169 (46%), Gaps = 1/169 (0%)
Query: 177 VNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSIS 236
           V+ +  ++  K     + ++VD+AK +P F  LP EDQ++LL+    E++    + R   
Sbjct: 56  VDLEAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDP 115
Query: 237 VKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD 296
             + + L   + V R      G+G + D +  +L   +    +D TE+  L+ ++L + D
Sbjct: 116 ESETLTLNGEMAVTRGQLKNGGLGVVSDAIF-DLGMSLSSFNLDDTEVALLQAVLLMSSD 174
Query: 297 VRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
             GL   + +E  ++    + E Y           + KLL+++  LR I
Sbjct: 175 RPGLACVERIEKYQDSFLLAFEHYINYRKHHVTHFWPKLLMKVTDLRMI 223

>pdb|1N46|A Chain A, Crystal Structure Of Human Tr Beta Ligand-Binding Domain Complexed With A Potent Subtype-Selective Thyromimetic Length = 258

Iteration: 1
 Score = 63.2 bits (152), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 41/169 (24%), Positives = 79/169 (46%), Gaps = 1/169 (0%)
Query: 177 VNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSIS 236
           V+ +  ++  K     + ++VD+AK +P F  LP EDQ++LL+    E++    + R   
Sbjct: 61  VDLEAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDP 120
Query: 237 VKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD 296
             + + L   + V R      G+G + D +  +L   +    +D TE+  L+ ++L + D
Sbjct: 121 ESETLTLNGEMAVTRGQLKNGGLGVVSDAIF-DLGMSLSSFNLDDTEVALLQAVLLMSSD 179
Query: 297 VRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
             GL   + +E  ++    + E Y           + KLL+++  LR I
Sbjct: 180 RPGLACVERIEKYQDSFLLAFEHYINYRKHHVTHFWPKLLMKVTDLRMI 228

>pdb|1NQ1|A Chain A, Tr Receptor Mutations Conferring Hormone Resistance And Reduced Corepressor Release Exhibit Decreased Stability In The Nterminal Lbd Length = 263

Iteration: 1
 Score = 63.2 bits (152), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 41/169 (24%), Positives = 79/169 (46%), Gaps = 1/169 (0%)
Query: 177 VNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSIS 236
           V+ +  ++  K     + ++VD+AK +P F  LP EDQ++LL+    E++    + R   
Sbjct: 66  VDLEAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDP 125
Query: 237 VKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD 296
             + + L   + V R      G+G + D +  +L   +    +D TE+  L+ ++L + D
Sbjct: 126 ESETLTLNGEMAVTRGQLKNGGLGVVSDAIF-DLGMSLSSFNLDDTEVALLQAVLLMSSD 184
Query: 297 VRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
             GL   + +E  ++    + E Y           + KLL+++  LR I
Sbjct: 185 RPGLACVERIEKYQDSFLLAFEHYINYRKHHVTHFWPKLLMKVTDLRMI 233

>pdb|3L1B|A Chain A, Complex Structure Of Fxr Ligand-Binding Domain With A Tetrahydroazepinoindole Compound Length = 233

Iteration: 1
 Score = 62.8 bits (151), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 41/150 (27%), Positives = 73/150 (48%), Gaps = 4/150 (2%)
Query: 196 LVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH 255
           LV++ K +P F TL  EDQ+ LL+    E +      RS  + +  L +    +      
Sbjct: 59  LVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFL----RSAEIFNKKLPSGHSDLLEERIR 114
Query: 256 EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYT 315
            +G+   +   +      + E+KM + E   L  I++ +PD + +K ++ VE L+E +  
Sbjct: 115 NSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLD 174
Query: 316 SLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            L++  +++  E P  FA LL RL  LR+ 
Sbjct: 175 VLQKLCKIHQPENPQHFACLLGRLTELRTF 204

>pdb|1OSH|A Chain A, A Chemical, Genetic, And Structural Analysis Of The Nuclear Bile Acid Receptor Fxr Length = 232

Iteration: 1
 Score = 62.8 bits (151), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 41/150 (27%), Positives = 73/150 (48%), Gaps = 4/150 (2%)
Query: 196 LVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH 255
           LV++ K +P F TL  EDQ+ LL+    E +      RS  + +  L +    +      
Sbjct: 58  LVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFL----RSAEIFNKKLPSGHSDLLEERIR 113
Query: 256 EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYT 315
            +G+   +   +      + E+KM + E   L  I++ +PD + +K ++ VE L+E +  
Sbjct: 114 NSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLD 173
Query: 316 SLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            L++  +++  E P  FA LL RL  LR+ 
Sbjct: 174 VLQKLCKIHQPENPQHFACLLGRLTELRTF 203

>pdb|3FLI|A Chain A, Discovery Of Xl335, A Highly Potent, Selective And Orally- Active Agonist Of The Farnesoid X Receptor (Fxr) Length = 231

Iteration: 1
 Score = 62.8 bits (151), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 41/150 (27%), Positives = 73/150 (48%), Gaps = 4/150 (2%)
Query: 196 LVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH 255
           LV++ K +P F TL  EDQ+ LL+    E +      RS  + +  L +    +      
Sbjct: 57  LVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFL----RSAEIFNKKLPSGHSDLLEERIR 112
Query: 256 EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYT 315
            +G+   +   +      + E+KM + E   L  I++ +PD + +K ++ VE L+E +  
Sbjct: 113 NSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLD 172
Query: 316 SLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            L++  +++  E P  FA LL RL  LR+ 
Sbjct: 173 VLQKLCKIHQPENPQHFACLLGRLTELRTF 202

>pdb|3HC5|A Chain A, Fxr With Src1 And Gsk826 Length = 232

Iteration: 1
 Score = 62.8 bits (151), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 41/150 (27%), Positives = 73/150 (48%), Gaps = 4/150 (2%)
Query: 196 LVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH 255
           LV++ K +P F TL  EDQ+ LL+    E +      RS  + +  L +    +      
Sbjct: 58  LVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFL----RSAEIFNKKLPSGHSDLLEERIR 113
Query: 256 EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYT 315
            +G+   +   +      + E+KM + E   L  I++ +PD + +K ++ VE L+E +  
Sbjct: 114 NSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLD 173
Query: 316 SLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            L++  +++  E P  FA LL RL  LR+ 
Sbjct: 174 VLQKLCKIHQPENPQHFACLLGRLTELRTF 203

>pdb|1NQ2|A Chain A, Two Rth Mutants With Impaired Hormone Binding Length = 264

Iteration: 1
 Score = 62.8 bits (151), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 41/169 (24%), Positives = 79/169 (46%), Gaps = 1/169 (0%)
Query: 177 VNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSIS 236
           V+ +  ++  K     + ++VD+AK +P F  LP EDQ++LL+    E++    + R   
Sbjct: 67  VDLEAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRTAVRYEP 126
Query: 237 VKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD 296
             + + L   + V R      G+G + D +  +L   +    +D TE+  L+ ++L + D
Sbjct: 127 ESETLTLNGEMAVTRGQLKNGGLGVVSDAIF-DLGMSLSSFNLDDTEVALLQAVLLMSSD 185
Query: 297 VRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
             GL   + +E  ++    + E Y           + KLL+++  LR I
Sbjct: 186 RPGLACVERIEKYQDSFLLAFEHYINYRKHHVTHFWPKLLMKVTDLRMI 234

>pdb|3JZC|A Chain A, Crystal Structure Of Tr-Beta Bound To The Selective Thyromimetic Triac Length = 263

Iteration: 1
 Score = 62.4 bits (150), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 41/169 (24%), Positives = 79/169 (46%), Gaps = 1/169 (0%)
Query: 177 VNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSIS 236
           V+ +  ++  K     + ++VD+AK +P F  LP EDQ++LL+    E++    + R   
Sbjct: 66  VDLEAFSHFTKIITPAITRVVDFAKKLPMFXELPXEDQIILLKGCCMEIMSLRAAVRYDP 125
Query: 237 VKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD 296
             + + L   + V R      G+G + D +  +L   +    +D TE+  L+ ++L + D
Sbjct: 126 ESETLTLNGEMAVTRGQLKNGGLGVVSDAIF-DLGMSLSSFNLDDTEVALLQAVLLMSSD 184
Query: 297 VRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
             GL   + +E  ++    + E Y           + KLL+++  LR I
Sbjct: 185 RPGLAXVERIEKYQDSFLLAFEHYINYRKHHVTHFWPKLLMKVTDLRMI 233

>pdb|3IMY|A Chain A, Structure Of Tr-Beta Bound To Selective Thyromimetic Gc-1 Length = 261

Iteration: 1
 Score = 62.4 bits (150), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 41/169 (24%), Positives = 79/169 (46%), Gaps = 1/169 (0%)
Query: 177 VNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSIS 236
           V+ +  ++  K     + ++VD+AK +P F  LP EDQ++LL+    E++    + R   
Sbjct: 64  VDLEAFSHFTKIITPAITRVVDFAKKLPMFXELPCEDQIILLKGCCMEIMSLRAAVRYDP 123
Query: 237 VKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD 296
             + + L   + V R      G+G + D +  +L   +    +D TE+  L+ ++L + D
Sbjct: 124 ESETLTLNGEMAVTRGQLKNGGLGVVSDAIF-DLGMSLSSFNLDDTEVALLQAVLLMSSD 182
Query: 297 VRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
             GL   + +E  ++    + E Y           + KLL+++  LR I
Sbjct: 183 RPGLAXVERIEKYQDSFLLAFEHYINYRKHHVTHFWPKLLMKVTDLRMI 231

>pdb|3GWS|X Chain X, Crystal Structure Of T3-Bound Thyroid Hormone Receptor Length = 259

Iteration: 1
 Score = 62.4 bits (150), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 41/169 (24%), Positives = 79/169 (46%), Gaps = 1/169 (0%)
Query: 177 VNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSIS 236
           V+ +  ++  K     + ++VD+AK +P F  LP EDQ++LL+    E++    + R   
Sbjct: 63  VDLEAFSHFTKIITPAITRVVDFAKKLPMFXELPCEDQIILLKGCCMEIMSLRAAVRYDP 122
Query: 237 VKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD 296
             + + L   + V R      G+G + D +  +L   +    +D TE+  L+ ++L + D
Sbjct: 123 ESETLTLNGEMAVTRGQLKNGGLGVVSDAIF-DLGMSLSSFNLDDTEVALLQAVLLMSSD 181
Query: 297 VRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
             GL   + +E  ++    + E Y           + KLL+++  LR I
Sbjct: 182 RPGLAXVERIEKYQDSFLLAFEHYINYRKHHVTHFWPKLLMKVTDLRMI 230

>pdb|3RUT|A Chain A, Fxr With Src1 And Gsk359 Length = 229

Iteration: 1
 Score = 62.4 bits (150), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 41/150 (27%), Positives = 73/150 (48%), Gaps = 4/150 (2%)
Query: 196 LVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH 255
           LV++ K +P F TL  EDQ+ LL+    E +      RS  + +  L +    +      
Sbjct: 55  LVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFL----RSAEIFNKKLPSGHSDLLEERIR 110
Query: 256 EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYT 315
            +G+   +   +      + E+KM + E   L  I++ +PD + +K ++ VE L+E +  
Sbjct: 111 NSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLD 170
Query: 316 SLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            L++  +++  E P  FA LL RL  LR+ 
Sbjct: 171 VLQKLCKIHQPENPQHFACLLGRLTELRTF 200

>pdb|3D57|A Chain A, Tr Variant D355r Length = 266

Iteration: 1
 Score = 62.4 bits (150), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 41/169 (24%), Positives = 78/169 (46%), Gaps = 1/169 (0%)
Query: 177 VNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSIS 236
           V+ +  ++  K     + ++VD+AK +P F  LP EDQ++LL+    E++    + R   
Sbjct: 70  VDLEAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDP 129
Query: 237 VKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD 296
             + + L   + V R      G+G + D +   L   +    +D TE+  L+ ++L + D
Sbjct: 130 ESETLTLNGEMAVTRGQLKNGGLGVVSDAIF-RLGMSLSSFNLDDTEVALLQAVLLMSSD 188
Query: 297 VRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
             GL   + +E  ++    + E Y           + KLL+++  LR I
Sbjct: 189 RPGLACVERIEKYQDSFLLAFEHYINYRKHHVTHFWPKLLMKVTDLRMI 237

>pdb|2PIN|A Chain A, Thyroid Receptor Beta In Complex With Inhibitor Length = 253

Iteration: 1
 Score = 62.4 bits (150), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 41/169 (24%), Positives = 78/169 (46%), Gaps = 1/169 (0%)
Query: 177 VNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSIS 236
           V+ +  ++  K     + ++VD+AK +P F  LP EDQ++LL+    E++    + R   
Sbjct: 56  VDLEAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDP 115
Query: 237 VKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD 296
             + + L   + V R      G+G + D +   L   +    +D TE+  L+ ++L + D
Sbjct: 116 ESETLTLNGEMAVTRGQLKNGGLGVVSDAIF-RLGMSLSSFNLDDTEVALLQAVLLMSSD 174
Query: 297 VRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
             GL   + +E  ++    + E Y           + KLL+++  LR I
Sbjct: 175 RPGLACVERIEKYQDSFLLAFEHYINYRKHHVTHFWPKLLMKVTDLRMI 223

>pdb|1YNW|A Chain A, Crystal Structure Of Vitamin D Receptor And 9-Cis Retinoic Acid Receptor Dna-Binding Domains Bound To A Dr3 Response Element Length = 110

Iteration: 1
 Score = 61.2 bits (147), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 28/84 (33%), Positives = 46/84 (54%), Gaps = 2/84 (2%)
Query: 56  HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXXXXXXXXXX 115
            +C +CGDRA+G H+   +CEGCKGFF+R++++   + C    +C I             
Sbjct: 7   RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCAANGDCRITKDNRRACQACRL 66
Query: 116 XXXLNMGMKREAV--QEERQRTKE 137
              +++GM +E +   EE QR +E
Sbjct: 67  KRCVDIGMMKEFILTDEEVQRKRE 90

>pdb|3GZ9|A Chain A, Crystal Structure Of Peroxisome Proliferator-Activated Receptor Delta (Ppard) In Complex With A Full Agonist Length = 269

Iteration: 1
 Score = 60.8 bits (146), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 44/154 (28%), Positives = 79/154 (51%), Gaps = 6/154 (3%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           +L ++AK IP F +L L DQV LL+ G +E + A  +  S+  KDG+L+A G + + +  
Sbjct: 89  ELTEFAKSIPSFGSLFLNDQVTLLKYGVHEAIFAMLA--SLVNKDGLLVANG-SGFVTRE 145
Query: 255 HEAGVGGIFDRVLT---ELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
               +   F  ++    E   K   +++D ++L      I+   D  GL +   VE +++
Sbjct: 146 FLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQD 205
Query: 312 KVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +  +LE + + NH +    F KLL ++  LR +
Sbjct: 206 TILRALEFHLQANHPDAQYLFPKLLQKMADLRQL 239

>pdb|4HN6|A Chain A, Gr Dna Binding Domain R460d/d462r - Tslp Ngre Complex Length = 114

Iteration: 1
 Score = 60.8 bits (146), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 34/92 (36%), Positives = 44/92 (47%), Gaps = 5/92 (5%)
Query: 57  LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXXXXXXXXXXX 116
           LC +C D ASG HYGV +C  CK FFKR V    +Y C     CIID             
Sbjct: 28  LCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGDNRCIIDKIRRKNCPACRYR 87
Query: 117 XXLNMGMKREAVQEERQRTKERDSNEVESTSG 148
             L  GM  EA     ++TK++     ++T+G
Sbjct: 88  KCLQAGMNLEA-----RKTKKKIKGIQQATTG 114

>pdb|2NXX|E Chain E, Crystal Structure Of The Ligand-Binding Domains Of The T.Castaneum (Coleoptera) Heterodimer Ecrusp Bound To Ponasterone A Length = 248

Iteration: 1
 Score = 60.1 bits (144), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 46/154 (29%), Positives = 75/154 (48%), Gaps = 9/154 (5%)
Query: 196 LVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH 255
           +V++AK +P F  L  EDQ+ LL+A  +E+++   + R     D IL        R S +
Sbjct: 68  IVEFAKRLPGFDKLLREDQIALLKACSSEVMMFRMARRYDVQTDSILFVNNQPYSRDSYN 127
Query: 256 EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD---VRGLKSQQVVEMLREK 312
            AG+G   + +L      M  M++D  E   L  I++F+     + G K +++ E+  E 
Sbjct: 128 LAGMGETIEDLL-HFCRTMYSMRVDNAEYALLTAIVIFSERPALIEGWKVEKIQEIYLE- 185
Query: 313 VYTSLEEYTRVNHSEEPGR-FAKLLLRLPSLRSI 345
              +L  Y       +PG  FAKLL  L  LR++
Sbjct: 186 ---ALRAYVDNRRKPKPGTIFAKLLSVLTELRTL 216

>pdb|3G6T|A Chain A, Gr Gamma Dna-Binding Domain:fkbp5 16bp Complex-34 Length = 91

Iteration: 1
 Score = 59.7 bits (143), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 34/94 (36%), Positives = 47/94 (50%), Gaps = 6/94 (6%)
Query: 56  HLCSICGDRASGKHYGVYSCEGCKGFFKRTVR-KDLSYACREGRNCIIDXXXXXXXXXXX 114
           H+C +C D ASG HYGV +C  CK FFKR V  +  +Y C    +CIID           
Sbjct: 3   HMCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGRQHNYLCAGRNDCIIDKIRRKNCPACR 62
Query: 115 XXXXLNMGMKREAVQEERQRTKERDSNEVESTSG 148
               L  GM  EA     ++TK++     ++T+G
Sbjct: 63  YRKCLQAGMNLEA-----RKTKKKIKGIQQATAG 91

>pdb|1KB2|A Chain A, Crystal Structure Of Vdr Dna-Binding Domain Bound To Mouse Osteopontin (Spp) Response Element Length = 110

Iteration: 1
 Score = 59.3 bits (142), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 28/84 (33%), Positives = 46/84 (54%), Gaps = 2/84 (2%)
Query: 56  HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXXXXXXXXXX 115
            +C +CGDRA+G H+   +CEGCKGFF+R++++   + C    +C I             
Sbjct: 7   RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRL 66
Query: 116 XXXLNMGMKREAV--QEERQRTKE 137
              +++GM +E +   EE QR +E
Sbjct: 67  KRCVDIGMMKEFILTDEEVQRKRE 90

>pdb|1Z5X|E Chain E, Hemipteran Ecdysone Receptor Ligand-Binding Domain Complexed With Ponasterone A Length = 310

Iteration: 1
 Score = 59.3 bits (142), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 51/176 (28%), Positives = 88/176 (50%), Gaps = 7/176 (3%)
Query: 173 DQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSH 232
           +++ V E++  +I + T   +  +V+++K +P F  L  EDQ+ LL+A  +E+++   + 
Sbjct: 109 EEENVAEERFRHITEITILTVQLIVEFSKRLPGFDKLIREDQIALLKACSSEVMMFRMAR 168
Query: 233 RSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIIL 292
           R  +  D IL A      R S   AG+G   + +L      M  MK+D  E   L  I++
Sbjct: 169 RYDAETDSILFATNQPYTRESYTVAGMGDTVEDLL-RFCRHMCAMKVDNAEYALLTAIVI 227
Query: 293 FNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGR---FAKLLLRLPSLRSI 345
           F+ +   L     VE ++E    +L+ Y  V +  +P     FAKLL  L  LR++
Sbjct: 228 FS-ERPSLSEGWKVEKIQEIYIEALKAY--VENRRKPYATTIFAKLLSVLTELRTL 280

>pdb|1GDC|A Chain A, Refined Solution Structure Of The Glucocorticoid Receptor Dna-Binding Domain Length = 72

Iteration: 1
 Score = 59.3 bits (142), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 30/71 (42%), Positives = 34/71 (47%)
Query: 57  LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXXXXXXXXXXX 116
           LC +C D ASG HYGV +C  CK FFKR V    +Y C    +CIID             
Sbjct: 1   LCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYR 60
Query: 117 XXLNMGMKREA 127
             L  GM  EA
Sbjct: 61  KCLQAGMNLEA 71

>pdb|2GDA|A Chain A, Refined Solution Structure Of The Glucocorticoid Receptor Dna-Binding Domain Length = 72

Iteration: 1
 Score = 58.9 bits (141), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 30/71 (42%), Positives = 34/71 (47%)
Query: 57  LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXXXXXXXXXXX 116
           LC +C D ASG HYGV +C  CK FFKR V    +Y C    +CIID             
Sbjct: 1   LCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYR 60
Query: 117 XXLNMGMKREA 127
             L  GM  EA
Sbjct: 61  KCLQAGMNLEA 71

>pdb|1R4O|A Chain A, Crystallographic Analysis Of The Interaction Of The Glucocorticoid Receptor With Dna Length = 92

Iteration: 1
 Score = 58.9 bits (141), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 33/91 (36%), Positives = 44/91 (48%), Gaps = 5/91 (5%)
Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXXXXXXXXXXXX 117
           C +C D ASG HYGV +C  CK FFKR V    +Y C    +CIID              
Sbjct: 7   CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRK 66
Query: 118 XLNMGMKREAVQEERQRTKERDSNEVESTSG 148
            L  GM  EA     ++TK++     ++T+G
Sbjct: 67  CLQAGMNLEA-----RKTKKKIKGIQQATAG 92

>pdb|1R4R|B Chain B, Crystallographic Analysis Of The Interaction Of The Glucocorticoid Receptor With Dna Length = 92

Iteration: 1
 Score = 58.9 bits (141), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 33/91 (36%), Positives = 44/91 (48%), Gaps = 5/91 (5%)
Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXXXXXXXXXXXX 117
           C +C D ASG HYGV +C  CK FFKR V    +Y C    +CIID              
Sbjct: 7   CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRK 66
Query: 118 XLNMGMKREAVQEERQRTKERDSNEVESTSG 148
            L  GM  EA     ++TK++     ++T+G
Sbjct: 67  CLQAGMNLEA-----RKTKKKIKGIQQATAG 92

>pdb|1YJE|A Chain A, Crystal Structure Of The Rngfi-B Ligand-Binding Domain Length = 264

Iteration: 1
 Score = 58.5 bits (140), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 42/149 (28%), Positives = 73/149 (48%), Gaps = 5/149 (3%)
Query: 199 WAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG 258
           WA+ IP F  L   DQ LLL + + EL I   ++RS   +  ++   G+ ++R      G
Sbjct: 86  WAEKIPGFIELSPGDQDLLLESAFLELFILRLAYRSKPGEGKLIFCSGLVLHRLQCAR-G 144
Query: 259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLE 318
            G   D +L      +  + +D     CL  ++L   D  GL+  + VE L+ ++ + L+
Sbjct: 145 FGDWIDNILA-FSRSLHSLGVDVPAFACLSALVLIT-DRHGLQDPRRVEELQNRIASCLK 202
Query: 319 EY-TRVNHSEEPGR-FAKLLLRLPSLRSI 345
           E+   V    +P    ++LL +LP LR++
Sbjct: 203 EHMAAVAGDPQPASCLSRLLGKLPELRTL 231

>pdb|3V3E|B Chain B, Crystal Structure Of The Human Nur77 Ligand-Binding Domain Length = 257

Iteration: 1
 Score = 58.5 bits (140), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 42/149 (28%), Positives = 73/149 (48%), Gaps = 5/149 (3%)
Query: 199 WAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG 258
           WA+ IP F  L   DQ LLL + + EL I   ++RS   +  ++   G+ ++R      G
Sbjct: 71  WAEKIPGFAELSPADQDLLLESAFLELFILRLAYRSKPGEGKLIFCSGLVLHRLQCAR-G 129
Query: 259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLE 318
            G   D +L      +  + +D     CL  ++L   D  GL+  + VE L+ ++ + L+
Sbjct: 130 FGDWIDSILA-FSRSLHSLLVDVPAFACLSALVLIT-DRHGLQEPRRVEELQNRIASCLK 187
Query: 319 EYTRVNHSE-EPGR-FAKLLLRLPSLRSI 345
           E+      E +P    ++LL +LP LR++
Sbjct: 188 EHVAAVAGEPQPASCLSRLLGKLPELRTL 216

>pdb|2QW4|A Chain A, Human Nr4a1 Ligand-Binding Domain Length = 273

Iteration: 1
 Score = 58.5 bits (140), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 42/149 (28%), Positives = 73/149 (48%), Gaps = 5/149 (3%)
Query: 199 WAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG 258
           WA+ IP F  L   DQ LLL + + EL I   ++RS   +  ++   G+ ++R      G
Sbjct: 95  WAEKIPGFAELSPADQDLLLESAFLELFILRLAYRSKPGEGKLIFCSGLVLHRLQCAR-G 153
Query: 259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLE 318
            G   D +L      +  + +D     CL  ++L   D  GL+  + VE L+ ++ + L+
Sbjct: 154 FGDWIDSILA-FSRSLHSLLVDVPAFACLSALVLIT-DRHGLQEPRRVEELQNRIASCLK 211
Query: 319 EYTRVNHSE-EPGR-FAKLLLRLPSLRSI 345
           E+      E +P    ++LL +LP LR++
Sbjct: 212 EHVAAVAGEPQPASCLSRLLGKLPELRTL 240

>pdb|2C7A|A Chain A, Structure Of The Progesterone Receptor-Dna Complex Length = 78

Iteration: 1
 Score = 57.8 bits (138), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 24/49 (48%), Positives = 31/49 (63%)
Query: 55  KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIID 103
           + +C ICGD ASG HYGV +C  CK FFKR +    +Y C    +CI+D
Sbjct: 2   QKICLICGDEASGCHYGVLTCGSCKVFFKRAMEGQHNYLCAGRNDCIVD 50

>pdb|1RGD|A Chain A, Structure Refinement Of The Glucocorticoid Receptor-Dna Binding Domain From Nmr Data By Relaxation Matrix Calculations Length = 71

Iteration: 1
 Score = 57.4 bits (137), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 29/70 (41%), Positives = 33/70 (47%)
Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXXXXXXXXXXXX 117
           C +C D ASG HYGV +C  CK FFKR V    +Y C    +CIID              
Sbjct: 1   CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRK 60
Query: 118 XLNMGMKREA 127
            L  GM  EA
Sbjct: 61  CLQAGMNLEA 70

>pdb|4HN5|A Chain A, Gr Dna Binding Domain - Tslp Ngre Complex Length = 117

Iteration: 1
 Score = 57.4 bits (137), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 34/92 (36%), Positives = 45/92 (48%), Gaps = 5/92 (5%)
Query: 57  LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXXXXXXXXXXX 116
           LC +C D ASG HYGV +C  CK FFKR V    +Y C    +CIID             
Sbjct: 31  LCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYR 90
Query: 117 XXLNMGMKREAVQEERQRTKERDSNEVESTSG 148
             L  GM  EA     ++TK++     ++T+G
Sbjct: 91  KCLQAGMNLEA-----RKTKKKIKGIQQATTG 117

>pdb|1GLU|A Chain A, Crystallographic Analysis Of The Interaction Of The Glucocorticoid Receptor With Dna Length = 81

Iteration: 1
 Score = 57.0 bits (136), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 29/75 (38%), Positives = 36/75 (48%)
Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDXXXXXXXXXXXXXX 117
           C +C D ASG HYGV +C  CK FFKR V    +Y C    +CIID              
Sbjct: 7   CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRK 66
Query: 118 XLNMGMKREAVQEER 132
            L  GM  EA + ++
Sbjct: 67  CLQAGMNLEARKTKK 81

>pdb|1R20|D Chain D, Crystal Structure Of The Ligand-Binding Domains Of The Heterodimer EcrUSP BOUND TO THE SYNTHETIC AGONIST BYI06830 Length = 265

Iteration: 1
 Score = 57.0 bits (136), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 40/153 (26%), Positives = 74/153 (48%), Gaps = 5/153 (3%)
Query: 196 LVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH 255
           +V++AK +P F+ +   DQ+ LL+A  +E+++   + R  +  D +L A      R +  
Sbjct: 83  IVEFAKGLPGFSKISQSDQITLLKACSSEVMMLRVARRYDAATDSVLFANNQAYTRDNYR 142
Query: 256 EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYT 315
           +AG+  + + +L      M  M MD      L  I++F+ D  GL+   +VE ++     
Sbjct: 143 KAGMAYVIEDLL-HFCRCMYSMMMDNVHYALLTAIVIFS-DRPGLEQPSLVEEIQRYYLN 200
Query: 316 SLEEYTRVNHSEEPGR---FAKLLLRLPSLRSI 345
           +L  Y    +S  P     F K+L  L  +R++
Sbjct: 201 TLRVYILNQNSASPRSAVIFGKILGILTEIRTL 233

>pdb|3VHU|A Chain A, Mineralocorticoid Receptor Ligand-Binding Domain With Spironolactone Length = 294

Iteration: 1
 Score = 55.5 bits (132), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 35/135 (25%), Positives = 67/135 (49%), Gaps = 4/135 (2%)
Query: 179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVK 238
           E   + + +   KQ+ Q+V WAK +P F  LPLEDQ+ L++  W  LL  + S RS    
Sbjct: 73  ENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQYSWMSLLSFALSWRSYKHT 132
Query: 239 DG--ILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD 296
           +   +  AP +       H++ +  +  + + ++  +   +++   E   ++ ++L +  
Sbjct: 133 NSQFLYFAPDLVFNEEKMHQSAMYEL-CQGMHQISLQFVRLQLTFEEYTIMKVLLLLSTI 191
Query: 297 VR-GLKSQQVVEMLR 310
            + GLKSQ   E +R
Sbjct: 192 PKDGLKSQAAFEEMR 206

>pdb|3VHV|A Chain A, Mineralocorticoid Receptor Ligand-Binding Domain With Non-Steroidal Antagonist Length = 260

Iteration: 1
 Score = 55.5 bits (132), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 35/135 (25%), Positives = 67/135 (49%), Gaps = 4/135 (2%)
Query: 179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVK 238
           E   + + +   KQ+ Q+V WAK +P F  LPLEDQ+ L++  W  LL  + S RS    
Sbjct: 39  ENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQYSWMSLLSFALSWRSYKHT 98
Query: 239 DG--ILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD 296
           +   +  AP +       H++ +  +  + + ++  +   +++   E   ++ ++L +  
Sbjct: 99  NSQFLYFAPDLVFNEEKMHQSAMYEL-CQGMHQISLQFVRLQLTFEEYTIMKVLLLLSTI 157
Query: 297 VR-GLKSQQVVEMLR 310
            + GLKSQ   E +R
Sbjct: 158 PKDGLKSQAAFEEMR 172

>pdb|2AA6|A Chain A, Mineralocorticoid Receptor S810l Mutant With Bound Progesterone Length = 275

Iteration: 1
 Score = 55.5 bits (132), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 35/135 (25%), Positives = 67/135 (49%), Gaps = 4/135 (2%)
Query: 179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVK 238
           E   + + +   KQ+ Q+V WAK +P F  LPLEDQ+ L++  W  LL  + S RS    
Sbjct: 54  ENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQYSWMSLLSFALSWRSYKHT 113
Query: 239 DG--ILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD 296
           +   +  AP +       H++ +  +  + + ++  +   +++   E   ++ ++L +  
Sbjct: 114 NSQFLYFAPDLVFNEEKMHQSAMYELC-QGMHQISLQFVRLQLTFEEYTIMKVLLLLSTI 172
Query: 297 VR-GLKSQQVVEMLR 310
            + GLKSQ   E +R
Sbjct: 173 PKDGLKSQAAFEEMR 187

>pdb|1I7G|A Chain A, Crystal Structure Of The Ligand Binding Domain From Human Ppar-Alpha In Complex With The Agonist Az 242 Length = 287

Iteration: 1
 Score = 54.7 bits (130), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 42/154 (27%), Positives = 75/154 (48%), Gaps = 6/154 (3%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           +L ++AK IP F  L L DQV LL+ G  E + A  S  S+  KDG+L+A G   + +  
Sbjct: 105 ELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLS--SVMNKDGMLVAYG-NGFITRE 161
Query: 255 HEAGVGGIFDRVLT---ELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
               +   F  ++    +   K   +++D +++      I+   D  GL +   +E ++E
Sbjct: 162 FLKSLRKPFCDIMEPKFDFAMKFNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKMQE 221
Query: 312 KVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +   L  + + NH ++   F KLL ++  LR +
Sbjct: 222 GIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQL 255

>pdb|1R1K|D Chain D, Crystal Structure Of The Ligand-Binding Domains Of The Heterodimer EcrUSP BOUND TO PONASTERONE A Length = 266

Iteration: 1
 Score = 54.7 bits (130), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 40/153 (26%), Positives = 73/153 (47%), Gaps = 5/153 (3%)
Query: 196 LVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH 255
           +V++AK +P F  +   DQ+ LL+A  +E+++   + R  +  D +L A      R +  
Sbjct: 84  IVEFAKGLPGFAKISQSDQITLLKACSSEVMMLRVARRYDAATDSVLFANNQAYTRDNYR 143
Query: 256 EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYT 315
           +AG+  + + +L      M  M MD      L  I++F+ D  GL+   +VE ++     
Sbjct: 144 KAGMAYVIEDLL-HFCRCMYSMMMDNVHYALLTAIVIFS-DRPGLEQPLLVEEIQRYYLN 201
Query: 316 SLEEYTRVNHSEEPG---RFAKLLLRLPSLRSI 345
           +L  Y    +S  P     F K+L  L  +R++
Sbjct: 202 TLRVYILNQNSASPRCAVIFGKILGILTEIRTL 234

>pdb|2ZNN|A Chain A, Human Pprr Alpha Ligand Binding Domain In Complex With A Synthetic Agonist Tipp703 Length = 273

Iteration: 1
 Score = 54.7 bits (130), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 42/154 (27%), Positives = 75/154 (48%), Gaps = 6/154 (3%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           +L ++AK IP F  L L DQV LL+ G  E + A  S  S+  KDG+L+A G   + +  
Sbjct: 91  ELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLS--SVMNKDGMLVAYG-NGFITRE 147
Query: 255 HEAGVGGIFDRVL---TELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
               +   F  ++    +   K   +++D +++      I+   D  GL +   +E ++E
Sbjct: 148 FLKSLRKPFCDIMEPKFDFAMKFNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKMQE 207
Query: 312 KVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +   L  + + NH ++   F KLL ++  LR +
Sbjct: 208 GIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQL 241

>pdb|2REW|A Chain A, Crystal Structure Of Pparalpha Ligand Binding Domain With Bms-631707 Length = 277

Iteration: 1
 Score = 54.7 bits (130), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 42/154 (27%), Positives = 75/154 (48%), Gaps = 6/154 (3%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           +L ++AK IP F  L L DQV LL+ G  E + A  S  S+  KDG+L+A G   + +  
Sbjct: 95  ELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLS--SVMNKDGMLVAYG-NGFITRE 151
Query: 255 HEAGVGGIFDRVLT---ELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
               +   F  ++    +   K   +++D +++      I+   D  GL +   +E ++E
Sbjct: 152 FLKSLRKPFCDIMEPKFDFAMKFNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKMQE 211
Query: 312 KVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +   L  + + NH ++   F KLL ++  LR +
Sbjct: 212 GIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQL 245

>pdb|1R4I|A Chain A, Crystal Structure Of Androgen Receptor Dna-Binding Domain Bound To A Direct Repeat Response Element Length = 105

Iteration: 1
 Score = 54.7 bits (130), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 23/46 (50%), Positives = 25/46 (54%)
Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIID 103
           C ICGD ASG HYG  +C  CK FFKR       Y C    +C ID
Sbjct: 10  CLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTID 55

>pdb|3SP6|A Chain A, Structural Basis For Iloprost As A Dual PparalphaDELTA AGONIST Length = 285

Iteration: 1
 Score = 54.3 bits (129), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 42/154 (27%), Positives = 75/154 (48%), Gaps = 6/154 (3%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           +L ++AK IP F  L L DQV LL+ G  E + A  S  S+  KDG+L+A G   + +  
Sbjct: 103 ELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLS--SVMNKDGMLVAYG-NGFITRE 159
Query: 255 HEAGVGGIFDRVLT---ELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
               +   F  ++    +   K   +++D +++      I+   D  GL +   +E ++E
Sbjct: 160 FLKSLRKPFCDIMEPKFDFAMKFNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKMQE 219
Query: 312 KVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +   L  + + NH ++   F KLL ++  LR +
Sbjct: 220 GIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQL 253

>pdb|3ET1|A Chain A, Structure Of Pparalpha With 3-[5-Methoxy-1-(4-Methoxy- Benzenesulfonyl)-1h-Indol-3-Yl]-Propionic Acid Length = 291

Iteration: 1
 Score = 54.3 bits (129), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 42/154 (27%), Positives = 75/154 (48%), Gaps = 6/154 (3%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           +L ++AK IP F  L L DQV LL+ G  E + A  S  S+  KDG+L+A G   + +  
Sbjct: 109 ELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLS--SVMNKDGMLVAYG-NGFITRE 165
Query: 255 HEAGVGGIFDRVLT---ELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
               +   F  ++    +   K   +++D +++      I+   D  GL +   +E ++E
Sbjct: 166 FLKSLRKPFCDIMEPKFDFAMKFNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKMQE 225
Query: 312 KVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +   L  + + NH ++   F KLL ++  LR +
Sbjct: 226 GIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQL 259

>pdb|1K7L|A Chain A, The 2.5 Angstrom Resolution Crystal Structure Of The Human Pparalpha Ligand Binding Domain Bound With Gw409544 And A Co-Activator Peptide. Length = 288

Iteration: 1
 Score = 54.3 bits (129), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 42/154 (27%), Positives = 75/154 (48%), Gaps = 6/154 (3%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           +L ++AK IP F  L L DQV LL+ G  E + A  S  S+  KDG+L+A G   + +  
Sbjct: 106 ELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLS--SVMNKDGMLVAYG-NGFITRE 162
Query: 255 HEAGVGGIFDRVLT---ELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
               +   F  ++    +   K   +++D +++      I+   D  GL +   +E ++E
Sbjct: 163 FLKSLRKPFCDIMEPKFDFAMKFNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKMQE 222
Query: 312 KVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +   L  + + NH ++   F KLL ++  LR +
Sbjct: 223 GIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQL 256

>pdb|2P54|A Chain A, A Crystal Structure Of Ppar Alpha Bound With Src1 Peptide And Gw735 Length = 267

Iteration: 1
 Score = 54.3 bits (129), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 42/154 (27%), Positives = 75/154 (48%), Gaps = 6/154 (3%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           +L ++AK IP F  L L DQV LL+ G  E + A  S  S+  KDG+L+A G   + +  
Sbjct: 85  ELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLS--SVMNKDGMLVAYG-NGFITRE 141
Query: 255 HEAGVGGIFDRVL---TELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
               +   F  ++    +   K   +++D +++      I+   D  GL +   +E ++E
Sbjct: 142 FLKSLRKPFCDIMEPKFDFAMKFNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKMQE 201
Query: 312 KVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +   L  + + NH ++   F KLL ++  LR +
Sbjct: 202 GIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQL 235

>pdb|2NPA|A Chain A, The Crystal Structure Of The Human Pparaplpha Ligand Binding Domain In Complex With A A-Hydroxyimino Phenylpropanoic Acid Length = 270

Iteration: 1
 Score = 54.3 bits (129), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 42/154 (27%), Positives = 75/154 (48%), Gaps = 6/154 (3%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           +L ++AK IP F  L L DQV LL+ G  E + A  S  S+  KDG+L+A G   + +  
Sbjct: 88  ELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLS--SVMNKDGMLVAYG-NGFITRE 144
Query: 255 HEAGVGGIFDRVLT---ELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
               +   F  ++    +   K   +++D +++      I+   D  GL +   +E ++E
Sbjct: 145 FLKSLRKPFCDIMEPKFDFAMKFNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKMQE 204
Query: 312 KVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +   L  + + NH ++   F KLL ++  LR +
Sbjct: 205 GIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQL 238

>pdb|3G8I|A Chain A, Aleglitazar, A New, Potent, And Balanced Ppar AlphaGAMMA Agonist For The Treatment Of Type Ii Diabetes Length = 270

Iteration: 1
 Score = 54.3 bits (129), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 42/154 (27%), Positives = 75/154 (48%), Gaps = 6/154 (3%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           +L ++AK IP F  L L DQV LL+ G  E + A  S  S+  KDG+L+A G   + +  
Sbjct: 88  ELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLS--SVMNKDGMLVAYG-NGFITRE 144
Query: 255 HEAGVGGIFDRVLT---ELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
               +   F  ++    +   K   +++D +++      I+   D  GL +   +E ++E
Sbjct: 145 FLKSLRKPFCDIMEPKFDFAMKFNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKMQE 204
Query: 312 KVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +   L  + + NH ++   F KLL ++  LR +
Sbjct: 205 GIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQL 238

>pdb|1KKQ|A Chain A, Crystal Structure Of The Human Ppar-Alpha Ligand-Binding Domain In Complex With An Antagonist Gw6471 And A Smrt Corepressor Motif Length = 269

Iteration: 1
 Score = 54.3 bits (129), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 42/154 (27%), Positives = 75/154 (48%), Gaps = 6/154 (3%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           +L ++AK IP F  L L DQV LL+ G  E + A  S  S+  KDG+L+A G   + +  
Sbjct: 87  ELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLS--SVMNKDGMLVAYG-NGFITRE 143
Query: 255 HEAGVGGIFDRVL---TELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
               +   F  ++    +   K   +++D +++      I+   D  GL +   +E ++E
Sbjct: 144 FLKSLRKPFCDIMEPKFDFAMKFNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKMQE 203
Query: 312 KVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +   L  + + NH ++   F KLL ++  LR +
Sbjct: 204 GIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQL 237

>pdb|1N4H|A Chain A, Characterization Of Ligands For The Orphan Nuclear Receptor Rorbeta Length = 259

Iteration: 1
 Score = 53.9 bits (128), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 35/153 (22%), Positives = 78/153 (50%), Gaps = 9/153 (5%)
Query: 196 LVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL---APGVTVYRS 252
           +V++AK I  F  L   DQ+LLL++G  E+++         + + +L      G+ ++++
Sbjct: 73  VVEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPLNNTVLFEGKYGGMQMFKA 132
Query: 253 SAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
              +  V   FD         +  +++ + E+    + +L +PD   L   + V+ L+EK
Sbjct: 133 LGSDDLVNEAFD-----FAKNLCSLQLTEEEIALFSSAVLISPDRAWLLEPRKVQKLQEK 187
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +Y +L+   + NH ++    AKL+ ++P++ ++
Sbjct: 188 IYFALQHVIQKNHLDDET-LAKLIAKIPTITAV 219

>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 = 53.9 bits (128), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 41/154 (26%), Positives = 83/154 (53%), Gaps = 5/154 (3%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           +++ +AK IP F  L  EDQ+ LL++   E+++   S++S S++D +  + G   ++   
Sbjct: 117 KVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLR-SNQSFSLED-MSWSCGGPDFKYCI 174
Query: 255 HEAGVGGIFDRVLTELVS---KMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
           ++    G    +L  LV     ++++K+ + E   L  I L +PD  G++    +E L++
Sbjct: 175 NDVTKAGHTLELLEPLVKFQVGLKKLKLHEEEHVLLMAICLLSPDRPGVQDHVRIEALQD 234
Query: 312 KVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           ++   L+ Y R+ H      +AK++ +L  LRS+
Sbjct: 235 RLCDVLQAYIRIQHPGGRLLYAKMIQKLADLRSL 268

>pdb|1Y9R|A Chain A, Crystal Structure Of The Human Mineralocorticoid Receptor Ligand-Binding Domain Bound To Deoxycorticosterone And Harboring The S810l Mutation Responsible For A Severe Form Of Hypertension Length = 255

Iteration: 1
 Score = 53.9 bits (128), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 35/135 (25%), Positives = 67/135 (49%), Gaps = 4/135 (2%)
Query: 179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVK 238
           E   + + +   KQ+ Q+V WAK +P F  LPLEDQ+ L++  W  LL  + S RS    
Sbjct: 34  ENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQYSWMCLLSFALSWRSYKHT 93
Query: 239 DG--ILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD 296
           +   +  AP +       H++ +  +  + + ++  +   +++   E   ++ ++L +  
Sbjct: 94  NSQFLYFAPDLVFNEEKMHQSAMYEL-CQGMHQISLQFVRLQLTFEEYTIMKVLLLLSTI 152
Query: 297 VR-GLKSQQVVEMLR 310
            + GLKSQ   E +R
Sbjct: 153 PKDGLKSQAAFEEMR 167

>pdb|2OAX|A Chain A, Crystal Structure Of The S810l Mutant Mineralocorticoid Receptor Associated With Sc9420 Length = 256

Iteration: 1
 Score = 53.9 bits (128), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 35/135 (25%), Positives = 67/135 (49%), Gaps = 4/135 (2%)
Query: 179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVK 238
           E   + + +   KQ+ Q+V WAK +P F  LPLEDQ+ L++  W  LL  + S RS    
Sbjct: 35  ENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQYSWMCLLSFALSWRSYKHT 94
Query: 239 DG--ILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD 296
           +   +  AP +       H++ +  +  + + ++  +   +++   E   ++ ++L +  
Sbjct: 95  NSQFLYFAPDLVFNEEKMHQSAMYEL-CQGMHQISLQFVRLQLTFEEYTIMKVLLLLSTI 153
Query: 297 VR-GLKSQQVVEMLR 310
            + GLKSQ   E +R
Sbjct: 154 PKDGLKSQAAFEEMR 168

>pdb|1ILG|A Chain A, Crystal Structure Of Apo Human Pregnane X Receptor Ligand Binding Domain Length = 316

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 44/156 (28%), Positives = 77/156 (49%), Gaps = 12/156 (7%)
Query: 196 LVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH 255
           ++ +AK I +F  LP+EDQ+ LL+    EL    F +   + + G          R S  
Sbjct: 136 IISFAKVISYFRDLPIEDQISLLKGAAFELCQLRF-NTVFNAETGTW-----ECGRLSYC 189
Query: 256 EAGVGGIFDRVLTELVSK----MREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
                G F ++L E + K    ++++++ + E   ++ I LF+PD  G+   +VV+ L+E
Sbjct: 190 LEDTAGGFQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQE 249
Query: 312 KVYTSLEEYTRVNHSEEPGR--FAKLLLRLPSLRSI 345
           +   +L+ Y   N  +   R  F K++  L  LRSI
Sbjct: 250 QFAITLKSYIECNRPQPAHRFLFLKIMAMLTELRSI 285

>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 = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 41/154 (26%), Positives = 83/154 (53%), Gaps = 5/154 (3%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           +++ +AK IP F  L  EDQ+ LL++   E+++   S++S S++D +  + G   ++   
Sbjct: 115 KVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLR-SNQSFSLED-MSWSCGGPDFKYCI 172
Query: 255 HEAGVGGIFDRVLTELVS---KMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
           ++    G    +L  LV     ++++K+ + E   L  I L +PD  G++    +E L++
Sbjct: 173 NDVTKAGHTLELLEPLVKFQVGLKKLKLHEEEHVLLMAICLLSPDRPGVQDHVRIEALQD 232
Query: 312 KVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           ++   L+ Y R+ H      +AK++ +L  LRS+
Sbjct: 233 RLCDVLQAYIRIQHPGGRLLYAKMIQKLADLRSL 266

>pdb|1K4W|A Chain A, X-Ray Structure Of The Orphan Nuclear Receptor Ror Beta Ligand-Binding Domain In The Active Conformation Length = 252

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 35/153 (22%), Positives = 78/153 (50%), Gaps = 9/153 (5%)
Query: 196 LVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL---APGVTVYRS 252
           +V++AK I  F  L   DQ+LLL++G  E+++         + + +L      G+ ++++
Sbjct: 73  VVEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPLNNTVLFEGKYGGMQMFKA 132
Query: 253 SAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
              +  V   FD         +  +++ + E+    + +L +PD   L   + V+ L+EK
Sbjct: 133 LGSDDLVNEAFD-----FAKNLCSLQLTEEEIALFSSAVLISPDRAWLLEPRKVQKLQEK 187
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +Y +L+   + NH ++    AKL+ ++P++ ++
Sbjct: 188 IYFALQHVIQKNHLDDET-LAKLIAKIPTITAV 219

>pdb|1SKX|A Chain A, Structural Disorder In The Complex Of Human Pxr And The Macrolide Antibiotic Rifampicin Length = 313

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 44/156 (28%), Positives = 77/156 (49%), Gaps = 12/156 (7%)
Query: 196 LVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH 255
           ++ +AK I +F  LP+EDQ+ LL+    EL    F+    + + G          R S  
Sbjct: 136 IISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFN-TVFNAETGTW-----ECGRLSYC 189
Query: 256 EAGVGGIFDRVLTELVSK----MREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
                G F ++L E + K    ++++++ + E   ++ I LF+PD  G+   +VV+ L+E
Sbjct: 190 LEDTAGGFQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQE 249
Query: 312 KVYTSLEEYTRVNHSEEPGR--FAKLLLRLPSLRSI 345
           +   +L+ Y   N  +   R  F K++  L  LRSI
Sbjct: 250 QFAITLKSYIECNRPQPAHRFLFLKIMAMLTELRSI 285

>pdb|1NQ7|A Chain A, Characterization Of Ligands For The Orphan Nuclear Receptor Rorbeta Length = 244

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 35/153 (22%), Positives = 78/153 (50%), Gaps = 9/153 (5%)
Query: 196 LVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL---APGVTVYRS 252
           +V++AK I  F  L   DQ+LLL++G  E+++         + + +L      G+ ++++
Sbjct: 66  VVEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPLNNTVLFEGKYGGMQMFKA 125
Query: 253 SAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
              +  V   FD         +  +++ + E+    + +L +PD   L   + V+ L+EK
Sbjct: 126 LGSDDLVNEAFD-----FAKNLCSLQLTEEEIALFSSAVLISPDRAWLLEPRKVQKLQEK 180
Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +Y +L+   + NH ++    AKL+ ++P++ ++
Sbjct: 181 IYFALQHVIQKNHLDDET-LAKLIAKIPTITAV 212

>pdb|3CTB|A Chain A, Tethered Pxr-LbdSRC-1p Apoprotein Length = 344

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 44/156 (28%), Positives = 77/156 (49%), Gaps = 12/156 (7%)
Query: 196 LVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH 255
           ++ +AK I +F  LP+EDQ+ LL+    EL    F+    + + G          R S  
Sbjct: 136 IISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFN-TVFNAETGTW-----ECGRLSYC 189
Query: 256 EAGVGGIFDRVLTELVSK----MREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
                G F ++L E + K    ++++++ + E   ++ I LF+PD  G+   +VV+ L+E
Sbjct: 190 LEDTAGGFQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQE 249
Query: 312 KVYTSLEEYTRVNHSEEPGR--FAKLLLRLPSLRSI 345
           +   +L+ Y   N  +   R  F K++  L  LRSI
Sbjct: 250 QFAITLKSYIECNRPQPAHRFLFLKIMAMLTELRSI 285

>pdb|3MNO|A Chain A, Crystal Structure Of The Agonist Form Of Mouse Glucocorticoid Receptor Stabilized By (A611v, F608s) Mutations At 1.55a Length = 261

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 43/166 (25%), Positives = 84/166 (50%), Gaps = 17/166 (10%)
Query: 191 KQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGVT 248
           +Q+   V WAK IP F  L L+DQ+ LL+  W  L++ +   RS     G LL  AP + 
Sbjct: 53  RQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMSLMVFALGWRSYRQASGNLLCFAPDLI 112
Query: 249 VYRSSAHEAGVGGIFDRV--LTELVSKMREMKMDKTELGCLRTIILFNPDVR-GLKSQQV 305
           +   +     +  ++D+   +  + ++++ +++   E  C++T++L +   + GLKSQ++
Sbjct: 113 I---NEQRMTLPCMYDQCKHMLFISTELQRLQVSYEEYLCMKTLLLLSSVPKEGLKSQEL 169
Query: 306 VEMLREKVYTSLEEYTRV------NHSEEPGRFAKLLLRLPSLRSI 345
            + +R    T ++E  +       N S+   RF +L   L S+  +
Sbjct: 170 FDEIR---MTYIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHDV 212

>pdb|2O9I|A Chain A, Crystal Structure Of The Human Pregnane X Receptor Lbd In Complex With An Src-1 Coactivator Peptide And T0901317 Length = 293

Iteration: 1
 Score = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 46/160 (28%), Positives = 80/160 (50%), Gaps = 20/160 (12%)
Query: 196 LVDWAKHIPHFTTLPLEDQVLLLRAGWNEL----LIASFSHRSISVKDGILLAPGVTVYR 251
           ++ +AK I +F  LP+EDQ+ LL+    EL        F+  + + + G L         
Sbjct: 113 IISFAKVISYFRDLPIEDQISLLKGAAFELSQLRFNTVFNAETGTWECGRL--------- 163
Query: 252 SSAHEAGVGGIFDRVLTELVSK----MREMKMDKTELGCLRTIILFNPDVRGLKSQQVVE 307
           S   E   GG F ++L E + K    ++++++ + E   ++ I LF+PD  G+   +VV+
Sbjct: 164 SYCLEDTAGG-FQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVD 222
Query: 308 MLREKVYTSLEEYTRVNHSEEPGR--FAKLLLRLPSLRSI 345
            L+E+   +L+ Y   N  +   R  F K++  L  LRSI
Sbjct: 223 QLQEQFAITLKSYIECNRPQPAHRFLFLKIMAMLTELRSI 262

>pdb|3E7C|A Chain A, Glucocorticoid Receptor Lbd Bound To Gsk866 Length = 257

Iteration: 1
 Score = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 44/166 (26%), Positives = 82/166 (49%), Gaps = 17/166 (10%)
Query: 191 KQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGVT 248
           +Q+   V WAK IP F  L L+DQ+ LL+  W  L+  +   RS       LL  AP + 
Sbjct: 49  RQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMYLMAFALGWRSYRQSSANLLCFAPDLI 108
Query: 249 VYRSSAHEAGVGGIFDRV--LTELVSKMREMKMDKTELGCLRTIILFNPDVR-GLKSQQV 305
           +   +     + G++D+   +  + S++  +++   E  C++T++L +   + GLKSQ++
Sbjct: 109 I---NEQRMTLPGMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSSVPKDGLKSQEL 165
Query: 306 VEMLREKVYTSLEEYTRV------NHSEEPGRFAKLLLRLPSLRSI 345
            + +R    T ++E  +       N S+   RF +L   L S+  +
Sbjct: 166 FDEIR---MTYIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEV 208

>pdb|3CLD|A Chain A, Ligand Binding Domain Of The Glucocorticoid Receptor Complexed With Fluticazone Furoate Length = 259

Iteration: 1
 Score = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 44/166 (26%), Positives = 82/166 (49%), Gaps = 17/166 (10%)
Query: 191 KQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGVT 248
           +Q+   V WAK IP F  L L+DQ+ LL+  W  L+  +   RS       LL  AP + 
Sbjct: 51  RQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMYLMAFALGWRSYRQSSANLLCFAPDLI 110
Query: 249 VYRSSAHEAGVGGIFDRV--LTELVSKMREMKMDKTELGCLRTIILFNPDVR-GLKSQQV 305
           +   +     + G++D+   +  + S++  +++   E  C++T++L +   + GLKSQ++
Sbjct: 111 I---NEQRMTLPGMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSSVPKDGLKSQEL 167
Query: 306 VEMLREKVYTSLEEYTRV------NHSEEPGRFAKLLLRLPSLRSI 345
            + +R    T ++E  +       N S+   RF +L   L S+  +
Sbjct: 168 FDEIR---MTYIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEV 210

>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 = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 42/166 (25%), Positives = 73/166 (43%), Gaps = 3/166 (1%)
Query: 182 ATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGI 241
            T+        + Q++ + K +P F +LP+EDQ+ LL+    E+     +          
Sbjct: 56  VTHFADINTFMVLQVIKFTKDLPVFRSLPIEDQISLLKGAAVEICHIVLNTTFCLQTQNF 115
Query: 242 LLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLK 301
           L  P        A   G    F  +L      +R++++ + E   L  + LF+PD  G+ 
Sbjct: 116 LCGPLRYTIEDGA-RVGFQVEFLELLFHFHGTLRKLQLQEPEYVLLAAMALFSPDRPGVT 174
Query: 302 SQQVVEMLREKVYTSLEEYTRVNHSEEPGRF--AKLLLRLPSLRSI 345
            +  ++ L+E++  +L+ Y +        RF  AKLL  L  LRSI
Sbjct: 175 QRDEIDQLQEEMALTLQSYIKGQQRRPRDRFLYAKLLGLLAELRSI 220

>pdb|2AA2|A Chain A, Mineralocorticoid Receptor With Bound Aldosterone Length = 275

Iteration: 1
 Score = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 34/135 (25%), Positives = 66/135 (48%), Gaps = 4/135 (2%)
Query: 179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVK 238
           E   + + +   KQ+ Q+V WAK +P F  LPLEDQ+ L++  W  L   + S RS    
Sbjct: 54  ENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQYSWMSLSSFALSWRSYKHT 113
Query: 239 DG--ILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD 296
           +   +  AP +       H++ +  +  + + ++  +   +++   E   ++ ++L +  
Sbjct: 114 NSQFLYFAPDLVFNEEKMHQSAMYELC-QGMHQISLQFVRLQLTFEEYTIMKVLLLLSTI 172
Query: 297 VR-GLKSQQVVEMLR 310
            + GLKSQ   E +R
Sbjct: 173 PKDGLKSQAAFEEMR 187

>pdb|2A3I|A Chain A, Structural And Biochemical Mechanisms For The Specificity Of Hormone Binding And Coactivator Assembly By Mineralocorticoid Receptor Length = 253

Iteration: 1
 Score = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 34/135 (25%), Positives = 66/135 (48%), Gaps = 4/135 (2%)
Query: 179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVK 238
           E   + + +   KQ+ Q+V WAK +P F  LPLEDQ+ L++  W  L   + S RS    
Sbjct: 32  ENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQYSWMSLSSFALSWRSYKHT 91
Query: 239 DG--ILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD 296
           +   +  AP +       H++ +  +  + + ++  +   +++   E   ++ ++L +  
Sbjct: 92  NSQFLYFAPDLVFNEEKMHQSAMYEL-CQGMHQISLQFVRLQLTFEEYTIMKVLLLLSTI 150
Query: 297 VR-GLKSQQVVEMLR 310
            + GLKSQ   E +R
Sbjct: 151 PKDGLKSQAAFEEMR 165

>pdb|3MNP|A Chain A, Crystal Structure Of The Agonist Form Of Mouse Glucocorticoid Receptor Stabilized By (A611v, V708a, E711g) Mutations At 1.50a Length = 261

Iteration: 1
 Score = 52.4 bits (124), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 43/166 (25%), Positives = 84/166 (50%), Gaps = 17/166 (10%)
Query: 191 KQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGVT 248
           +Q+   V WAK IP F  L L+DQ+ LL+  W  L++ +   RS     G LL  AP + 
Sbjct: 53  RQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMVFALGWRSYRQASGNLLCFAPDLI 112
Query: 249 VYRSSAHEAGVGGIFDRV--LTELVSKMREMKMDKTELGCLRTIILFNPDVR-GLKSQQV 305
           +   +     +  ++D+   +  + ++++ +++   E  C++T++L +   + GLKSQ++
Sbjct: 113 I---NEQRMTLPCMYDQCKHMLFISTELQRLQVSYEEYLCMKTLLLLSSVPKEGLKSQEL 169
Query: 306 VEMLREKVYTSLEEYTRV------NHSEEPGRFAKLLLRLPSLRSI 345
            + +R    T ++E  +       N S+   RF +L   L S+  +
Sbjct: 170 FDEIR---MTYIKELGKAIAKRGGNSSQNWQRFYQLTKLLDSMHDV 212

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 45/200 (22%), Positives = 82/200 (41%), Gaps = 25/200 (12%)
Query: 171 PADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASF 230
           P  Q ++  +    +C+A    L + + + K++P F  LPL+ Q++L+R+ W  LL+   
Sbjct: 38  PGVQRLITLKDPQVVCEAASAGLLKTLRFVKYLPCFQILPLDQQLVLVRSCWAPLLMLEL 97
Query: 231 SHRSISVK---------------------DGILLAPGVTVYRSSAHEAGVGGIFD----R 265
           +   +  +                     +G   A      +     A  G +      +
Sbjct: 98  AQDHLHFEMMEIPETNTTQEMLTTRRQETEGPEPAEPQATEQPQMVSAEAGHLLPAAAVQ 157
Query: 266 VLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNH 325
            +     K   + +D  E   L+  +LFNPD+ GL+  + +E L+ +    L E+ R+  
Sbjct: 158 AIKSFFFKCWSLNIDTKEYAYLKGTVLFNPDLPGLQCVKYIEGLQWRTQQILTEHIRMMQ 217
Query: 326 SEEPGRFAKLLLRLPSLRSI 345
            E   R A+L   L  LR I
Sbjct: 218 REYQIRSAELNSALFLLRFI 237

>pdb|3MNE|A Chain A, Crystal Structure Of The Agonist Form Of Mouse Glucocorticoid Receptor Stabilized By F608s Mutation At 1.96a Length = 261

Iteration: 1
 Score = 51.6 bits (122), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 43/166 (25%), Positives = 83/166 (50%), Gaps = 17/166 (10%)
Query: 191 KQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGVT 248
           +Q+   V WAK IP F  L L+DQ+ LL+  W  L+  +   RS     G LL  AP + 
Sbjct: 53  RQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMSLMAFALGWRSYRQASGNLLCFAPDLI 112
Query: 249 VYRSSAHEAGVGGIFDRV--LTELVSKMREMKMDKTELGCLRTIILFNPDVR-GLKSQQV 305
           +   +     +  ++D+   +  + ++++ +++   E  C++T++L +   + GLKSQ++
Sbjct: 113 I---NEQRMTLPCMYDQCKHMLFISTELQRLQVSYEEYLCMKTLLLLSSVPKEGLKSQEL 169
Query: 306 VEMLREKVYTSLEEYTRV------NHSEEPGRFAKLLLRLPSLRSI 345
            + +R    T ++E  +       N S+   RF +L   L S+  +
Sbjct: 170 FDEIR---MTYIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHDV 212

>pdb|1I38|A Chain A, Crystal Structure Of The Rat Androgen Receptor Ligand Binding Domain T877a Mutant Complex With Dihydrotestosterone Length = 260

Iteration: 1
 Score = 51.6 bits (122), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 41/162 (25%), Positives = 79/162 (48%), Gaps = 7/162 (4%)
Query: 190 DKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGV 247
           ++QL  +V WAK +P F  L ++DQ+ +++  W  L++ +   RS +  +  +L  AP +
Sbjct: 50  ERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDL 109
Query: 248 TVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFN-PDVRGLKSQQVV 306
                  H++ +     R +  L  +   +++   E  C++ ++LF+   V GLK+Q+  
Sbjct: 110 VFNEYRMHKSRMYSQCVR-MRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFF 168
Query: 307 EMLREKVYTSLEEYT---RVNHSEEPGRFAKLLLRLPSLRSI 345
           + LR      L+      R N +    RF +L   L S++ I
Sbjct: 169 DELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPI 210

>pdb|1I37|A Chain A, Crystal Structure Of The Rat Androgen Receptor Ligand Binding Domain Complex With Dihydrotestosterone Length = 260

Iteration: 1
 Score = 51.6 bits (122), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 41/162 (25%), Positives = 79/162 (48%), Gaps = 7/162 (4%)
Query: 190 DKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGV 247
           ++QL  +V WAK +P F  L ++DQ+ +++  W  L++ +   RS +  +  +L  AP +
Sbjct: 50  ERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDL 109
Query: 248 TVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFN-PDVRGLKSQQVV 306
                  H++ +     R +  L  +   +++   E  C++ ++LF+   V GLK+Q+  
Sbjct: 110 VFNEYRMHKSRMYSQCVR-MRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFF 168
Query: 307 EMLREKVYTSLEEYT---RVNHSEEPGRFAKLLLRLPSLRSI 345
           + LR      L+      R N +    RF +L   L S++ I
Sbjct: 169 DELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPI 210

>pdb|3G8O|A Chain A, Progesterone Receptor With Bound Pyrrolidine 1 Length = 263

Iteration: 1
 Score = 51.6 bits (122), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 31/131 (23%), Positives = 67/131 (51%), Gaps = 4/131 (3%)
Query: 183 TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGIL 242
           T++ +  ++QL  +V W+K +P F  L ++DQ+ L++  W  L++     RS     G +
Sbjct: 46  TSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQM 105
Query: 243 L--APGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNP-DVRG 299
           L  AP + +      E+    +    + ++  +  ++++ + E  C++ ++L N   + G
Sbjct: 106 LYFAPDLILNEQRMKESSFYSL-CLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEG 164
Query: 300 LKSQQVVEMLR 310
           L+SQ   E +R
Sbjct: 165 LRSQTQFEEMR 175

>pdb|1E3K|A Chain A, Human Progesteron Receptor Ligand Binding Domain In Complex With The Ligand Metribolone (R1881) Length = 258

Iteration: 1
 Score = 51.2 bits (121), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 31/131 (23%), Positives = 67/131 (51%), Gaps = 4/131 (3%)
Query: 183 TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGIL 242
           T++ +  ++QL  +V W+K +P F  L ++DQ+ L++  W  L++     RS     G +
Sbjct: 41  TSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQM 100
Query: 243 L--APGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNP-DVRG 299
           L  AP + +      E+    +    + ++  +  ++++ + E  C++ ++L N   + G
Sbjct: 101 LYFAPDLILNEQRMKESSFYSLC-LTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEG 159
Query: 300 LKSQQVVEMLR 310
           L+SQ   E +R
Sbjct: 160 LRSQTQFEEMR 170

>pdb|1SR7|A Chain A, Progesterone Receptor Hormone Binding Domain With Bound Mometasone Furoate Length = 259

Iteration: 1
 Score = 51.2 bits (121), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 31/131 (23%), Positives = 67/131 (51%), Gaps = 4/131 (3%)
Query: 183 TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGIL 242
           T++ +  ++QL  +V W+K +P F  L ++DQ+ L++  W  L++     RS     G +
Sbjct: 42  TSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQM 101
Query: 243 L--APGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNP-DVRG 299
           L  AP + +      E+    +    + ++  +  ++++ + E  C++ ++L N   + G
Sbjct: 102 LYFAPDLILNEQRMKESSFYSLC-LTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEG 160
Query: 300 LKSQQVVEMLR 310
           L+SQ   E +R
Sbjct: 161 LRSQTQFEEMR 171

>pdb|2Q7K|A Chain A, The Androgen Receptor Prostate Cancer Mutant H874y Ligand Binding Domain Bound With Testosterone And An Ar 20-30 Peptide Length = 257

Iteration: 1
 Score = 51.2 bits (121), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 41/162 (25%), Positives = 79/162 (48%), Gaps = 7/162 (4%)
Query: 190 DKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGV 247
           ++QL  +V WAK +P F  L ++DQ+ +++  W  L++ +   RS +  +  +L  AP +
Sbjct: 47  ERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDL 106
Query: 248 TVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFN-PDVRGLKSQQVV 306
                  H++ +     R +  L  +   +++   E  C++ ++LF+   V GLK+Q+  
Sbjct: 107 VFNEYRMHKSRMYSQCVR-MRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFF 165
Query: 307 EMLREKVYTSLEEYT---RVNHSEEPGRFAKLLLRLPSLRSI 345
           + LR      L+      R N +    RF +L   L S++ I
Sbjct: 166 DELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPI 207

>pdb|1A28|A Chain A, Hormone-Bound Human Progesterone Receptor Ligand-Binding Domain Length = 256

Iteration: 1
 Score = 51.2 bits (121), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 31/131 (23%), Positives = 67/131 (51%), Gaps = 4/131 (3%)
Query: 183 TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGIL 242
           T++ +  ++QL  +V W+K +P F  L ++DQ+ L++  W  L++     RS     G +
Sbjct: 39  TSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQM 98
Query: 243 L--APGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNP-DVRG 299
           L  AP + +      E+    +    + ++  +  ++++ + E  C++ ++L N   + G
Sbjct: 99  LYFAPDLILNEQRMKESSFYSLC-LTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEG 157
Query: 300 LKSQQVVEMLR 310
           L+SQ   E +R
Sbjct: 158 LRSQTQFEEMR 168

>pdb|2AX6|A Chain A, Crystal Structure Of The Androgen Receptor Ligand Binding Domain T877a Mutant In Complex With Hydroxyflutamide Length = 256

Iteration: 1
 Score = 51.2 bits (121), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 41/162 (25%), Positives = 79/162 (48%), Gaps = 7/162 (4%)
Query: 190 DKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGV 247
           ++QL  +V WAK +P F  L ++DQ+ +++  W  L++ +   RS +  +  +L  AP +
Sbjct: 46  ERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDL 105
Query: 248 TVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFN-PDVRGLKSQQVV 306
                  H++ +     R +  L  +   +++   E  C++ ++LF+   V GLK+Q+  
Sbjct: 106 VFNEYRMHKSRMYSQCVR-MRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFF 164
Query: 307 EMLREKVYTSLEEYT---RVNHSEEPGRFAKLLLRLPSLRSI 345
           + LR      L+      R N +    RF +L   L S++ I
Sbjct: 165 DELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPI 206

>pdb|1XJ7|A Chain A, Complex Androgen Receptor Lbd And Rac3 Peptide Length = 257

Iteration: 1
 Score = 51.2 bits (121), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 41/162 (25%), Positives = 79/162 (48%), Gaps = 7/162 (4%)
Query: 190 DKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGV 247
           ++QL  +V WAK +P F  L ++DQ+ +++  W  L++ +   RS +  +  +L  AP +
Sbjct: 47  ERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDL 106
Query: 248 TVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFN-PDVRGLKSQQVV 306
                  H++ +     R +  L  +   +++   E  C++ ++LF+   V GLK+Q+  
Sbjct: 107 VFNEYRMHKSRMYSQCVR-MRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFF 165
Query: 307 EMLREKVYTSLEEYT---RVNHSEEPGRFAKLLLRLPSLRSI 345
           + LR      L+      R N +    RF +L   L S++ I
Sbjct: 166 DELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPI 207

>pdb|1T73|A Chain A, Crystal Structure Of The Androgen Receptor Ligand Binding Domain In Complex With A Fxxff Motif Length = 269

Iteration: 1
 Score = 51.2 bits (121), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 41/162 (25%), Positives = 79/162 (48%), Gaps = 7/162 (4%)
Query: 190 DKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGV 247
           ++QL  +V WAK +P F  L ++DQ+ +++  W  L++ +   RS +  +  +L  AP +
Sbjct: 59  ERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDL 118
Query: 248 TVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFN-PDVRGLKSQQVV 306
                  H++ +     R +  L  +   +++   E  C++ ++LF+   V GLK+Q+  
Sbjct: 119 VFNEYRMHKSRMYSQCVR-MRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFF 177
Query: 307 EMLREKVYTSLEEYT---RVNHSEEPGRFAKLLLRLPSLRSI 345
           + LR      L+      R N +    RF +L   L S++ I
Sbjct: 178 DELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPI 219

>pdb|3H52|A Chain A, Crystal Structure Of The Antagonist Form Of Human Glucocorticoid Receptor Length = 254

Iteration: 1
 Score = 51.2 bits (121), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 43/166 (25%), Positives = 80/166 (48%), Gaps = 17/166 (10%)
Query: 191 KQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGVT 248
           +Q+   V WAK IP F  L L+DQ+ LL+  W  L+  +   RS       LL  AP + 
Sbjct: 46  RQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMSLMAFALGWRSYRQSSANLLCFAPDLI 105
Query: 249 VYRSSAHEAGVGGIFDRV--LTELVSKMREMKMDKTELGCLRTIILFNPDVR-GLKSQQV 305
           +   +     +  ++D+   +  + S++  +++   E  C++T++L +   + GLKSQ +
Sbjct: 106 I---NEQRMTLPDMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSSVPKDGLKSQAL 162
Query: 306 VEMLREKVYTSLEEYTRV------NHSEEPGRFAKLLLRLPSLRSI 345
            + +R    T ++E  +       N S+   RF +L   L S+  +
Sbjct: 163 FDAIR---MTYIKELGKAIVKREGNSSQNSQRFYQLTKLLDSMHEV 205

>pdb|2AM9|A Chain A, Crystal Structure Of Human Androgen Receptor Ligand Binding Domain In Complex With Testosterone Length = 266

Iteration: 1
 Score = 51.2 bits (121), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 41/162 (25%), Positives = 79/162 (48%), Gaps = 7/162 (4%)
Query: 190 DKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGV 247
           ++QL  +V WAK +P F  L ++DQ+ +++  W  L++ +   RS +  +  +L  AP +
Sbjct: 56  ERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDL 115
Query: 248 TVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFN-PDVRGLKSQQVV 306
                  H++ +     R +  L  +   +++   E  C++ ++LF+   V GLK+Q+  
Sbjct: 116 VFNEYRMHKSRMYSQCVR-MRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFF 174
Query: 307 EMLREKVYTSLEEYT---RVNHSEEPGRFAKLLLRLPSLRSI 345
           + LR      L+      R N +    RF +L   L S++ I
Sbjct: 175 DELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPI 216

>pdb|1T5Z|A Chain A, Crystal Structure Of The Androgen Receptor Ligand Binding Domain (Lbd) With Dht And A Peptide Derived From Its Physiological Coactivator Ara70 Length = 251

Iteration: 1
 Score = 51.2 bits (121), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 41/162 (25%), Positives = 79/162 (48%), Gaps = 7/162 (4%)
Query: 190 DKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGV 247
           ++QL  +V WAK +P F  L ++DQ+ +++  W  L++ +   RS +  +  +L  AP +
Sbjct: 41  ERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDL 100
Query: 248 TVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFN-PDVRGLKSQQVV 306
                  H++ +     R +  L  +   +++   E  C++ ++LF+   V GLK+Q+  
Sbjct: 101 VFNEYRMHKSRMYSQCVR-MRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFF 159
Query: 307 EMLREKVYTSLEEYT---RVNHSEEPGRFAKLLLRLPSLRSI 345
           + LR      L+      R N +    RF +L   L S++ I
Sbjct: 160 DELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPI 201

>pdb|2AX9|A Chain A, Crystal Structure Of The Androgen Receptor Ligand Binding Domain In Complex With R-3 Length = 256

Iteration: 1
 Score = 51.2 bits (121), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 41/162 (25%), Positives = 79/162 (48%), Gaps = 7/162 (4%)
Query: 190 DKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGV 247
           ++QL  +V WAK +P F  L ++DQ+ +++  W  L++ +   RS +  +  +L  AP +
Sbjct: 46  ERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDL 105
Query: 248 TVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFN-PDVRGLKSQQVV 306
                  H++ +     R +  L  +   +++   E  C++ ++LF+   V GLK+Q+  
Sbjct: 106 VFNEYRMHKSRMYSQCVR-MRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFF 164
Query: 307 EMLREKVYTSLEEYT---RVNHSEEPGRFAKLLLRLPSLRSI 345
           + LR      L+      R N +    RF +L   L S++ I
Sbjct: 165 DELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPI 206

>pdb|1E3G|A Chain A, Human Androgen Receptor Ligand Binding In Complex With The Ligand Metribolone (R1881) Length = 263

Iteration: 1
 Score = 51.2 bits (121), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 41/162 (25%), Positives = 79/162 (48%), Gaps = 7/162 (4%)
Query: 190 DKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGV 247
           ++QL  +V WAK +P F  L ++DQ+ +++  W  L++ +   RS +  +  +L  AP +
Sbjct: 53  ERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDL 112
Query: 248 TVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFN-PDVRGLKSQQVV 306
                  H++ +     R +  L  +   +++   E  C++ ++LF+   V GLK+Q+  
Sbjct: 113 VFNEYRMHKSRMYSQCVR-MRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFF 171
Query: 307 EMLREKVYTSLEEYT---RVNHSEEPGRFAKLLLRLPSLRSI 345
           + LR      L+      R N +    RF +L   L S++ I
Sbjct: 172 DELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPI 213

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

Iteration: 1
 Score = 51.2 bits (121), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 45/193 (23%), Positives = 90/193 (46%), Gaps = 13/193 (6%)
Query: 165 VDMKQEPADQDIVNEQQATNICKATDKQLFQLV--------DWAKHIPHFTTLPLEDQVL 216
           VD   +P+  D  + ++ +       +Q +QL+         +A+ IP +  L  EDQ L
Sbjct: 24  VDTTPDPSCLDYSHYEEQSMSEADKVQQFYQLLTSSVDVIKQFAEKIPGYFDLLPEDQEL 83
Query: 217 LLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMRE 276
           L ++   EL +   ++R+      ++   G  ++R+    +    + D  + E    +  
Sbjct: 84  LFQSASLELFVLRLAYRARIDDTKLIFCNGTVLHRTQCLRSFGEWLND--IMEFSRSLHN 141
Query: 277 MKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGR--FAK 334
           +++D +   CL  + L   +  GL+  + VE L+ K+  SL ++   N   +  +  F++
Sbjct: 142 LEIDISAFACLCALTLIT-ERHGLREPKKVEQLQMKIIGSLRDHVTYNAEAQKKQHYFSR 200
Query: 335 LLLRLPSLRSIEV 347
           LL +LP LRS+ V
Sbjct: 201 LLGKLPELRSLSV 213

>pdb|2W8Y|A Chain A, Ru486 Bound To The Progesterone Receptor In A Destabilized Agonistic Conformation Length = 260

Iteration: 1
 Score = 51.2 bits (121), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 31/131 (23%), Positives = 67/131 (51%), Gaps = 4/131 (3%)
Query: 183 TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGIL 242
           T++ +  ++QL  +V W+K +P F  L ++DQ+ L++  W  L++     RS     G +
Sbjct: 43  TSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQM 102
Query: 243 L--APGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNP-DVRG 299
           L  AP + +      E+    +    + ++  +  ++++ + E  C++ ++L N   + G
Sbjct: 103 LYFAPDLILNEQRMKESSFYSLC-LTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEG 161
Query: 300 LKSQQVVEMLR 310
           L+SQ   E +R
Sbjct: 162 LRSQTQFEEMR 172

>pdb|2HVC|A Chain A, The Crystal Structure Of Ligand-Binding Domain (Lbd) Of Human Androgen Receptor In Complex With A Selective Modulator Lgd2226 Length = 250

Iteration: 1
 Score = 51.2 bits (121), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 41/162 (25%), Positives = 79/162 (48%), Gaps = 7/162 (4%)
Query: 190 DKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGV 247
           ++QL  +V WAK +P F  L ++DQ+ +++  W  L++ +   RS +  +  +L  AP +
Sbjct: 41  ERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDL 100
Query: 248 TVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFN-PDVRGLKSQQVV 306
                  H++ +     R +  L  +   +++   E  C++ ++LF+   V GLK+Q+  
Sbjct: 101 VFNEYRMHKSRMYSQCVR-MRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFF 159
Query: 307 EMLREKVYTSLEEYT---RVNHSEEPGRFAKLLLRLPSLRSI 345
           + LR      L+      R N +    RF +L   L S++ I
Sbjct: 160 DELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPI 201

>pdb|1SQN|A Chain A, Progesterone Receptor Ligand Binding Domain With Bound Norethindrone Length = 261

Iteration: 1
 Score = 51.2 bits (121), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 31/131 (23%), Positives = 67/131 (51%), Gaps = 4/131 (3%)
Query: 183 TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGIL 242
           T++ +  ++QL  +V W+K +P F  L ++DQ+ L++  W  L++     RS     G +
Sbjct: 44  TSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQM 103
Query: 243 L--APGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNP-DVRG 299
           L  AP + +      E+    +    + ++  +  ++++ + E  C++ ++L N   + G
Sbjct: 104 LYFAPDLILNEQRMKESSFYSL-CLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEG 162
Query: 300 LKSQQVVEMLR 310
           L+SQ   E +R
Sbjct: 163 LRSQTQFEEMR 173

>pdb|1NHZ|A Chain A, Crystal Structure Of The Antagonist Form Of Glucocorticoid Receptor Length = 280

Iteration: 1
 Score = 51.2 bits (121), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 43/166 (25%), Positives = 81/166 (48%), Gaps = 17/166 (10%)
Query: 191 KQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGVT 248
           +Q+   V WAK IP F  L L+DQ+ LL+  W  L+  +   RS       LL  AP + 
Sbjct: 72  RQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMSLMAFALGWRSYRQSSANLLCFAPDLI 131
Query: 249 VYRSSAHEAGVGGIFDRV--LTELVSKMREMKMDKTELGCLRTIILFNPDVR-GLKSQQV 305
           +   +     +  ++D+   +  + S++  +++   E  C++T++L +   + GLKSQ++
Sbjct: 132 I---NEQRMTLPDMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSSVPKDGLKSQEL 188
Query: 306 VEMLREKVYTSLEEYTRV------NHSEEPGRFAKLLLRLPSLRSI 345
            + +R    T ++E  +       N S+   RF +L   L S+  +
Sbjct: 189 FDEIR---MTYIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEV 231

>pdb|2ABI|A Chain A, Crystal Structure Of The Human Mineralocorticoid Receptor Ligand-Binding Domain Bound To Deoxycorticosterone Length = 256

Iteration: 1
 Score = 51.2 bits (121), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 34/135 (25%), Positives = 66/135 (48%), Gaps = 4/135 (2%)
Query: 179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVK 238
           E   + + +   KQ+ Q+V WAK +P F  LPLEDQ+ L++  W  L   + S RS    
Sbjct: 35  ENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQYSWMCLSSFALSWRSYKHT 94
Query: 239 DG--ILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD 296
           +   +  AP +       H++ +  +  + + ++  +   +++   E   ++ ++L +  
Sbjct: 95  NSQFLYFAPDLVFNEEKMHQSAMYEL-CQGMHQISLQFVRLQLTFEEYTIMKVLLLLSTI 153
Query: 297 VR-GLKSQQVVEMLR 310
            + GLKSQ   E +R
Sbjct: 154 PKDGLKSQAAFEEMR 168

>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 = 50.8 bits (120), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 38/157 (24%), Positives = 82/157 (52%), Gaps = 9/157 (5%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           +++ +AK IP F  L  EDQ++LL++   E+++   S+ S ++ D +    G   Y+   
Sbjct: 76  KVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLR-SNESFTMDD-MSWTCGNQDYKYRV 133
Query: 255 HEAGVGGIFDRVLTELVS---KMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
            +    G    ++  L+     ++++ + + E   L  I + +PD  G++   ++E +++
Sbjct: 134 SDVTKAGFSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQD 193
Query: 312 KVYTSLEEYTRVNHSEEPGR---FAKLLLRLPSLRSI 345
           ++  +L+ Y R  H   PG    +AK++ +L  LRS+
Sbjct: 194 RLSNTLQTYIRCRHP-PPGSHLLYAKMIQKLADLRSL 229

>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 = 50.8 bits (120), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 38/157 (24%), Positives = 82/157 (52%), Gaps = 9/157 (5%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           +++ +AK IP F  L  EDQ++LL++   E+++   S+ S ++ D +    G   Y+   
Sbjct: 76  KVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLR-SNESFTMDD-MSWTCGNQDYKYRV 133
Query: 255 HEAGVGGIFDRVLTELVS---KMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
            +    G    ++  L+     ++++ + + E   L  I + +PD  G++   ++E +++
Sbjct: 134 SDVTKAGFSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQD 193
Query: 312 KVYTSLEEYTRVNHSEEPGR---FAKLLLRLPSLRSI 345
           ++  +L+ Y R  H   PG    +AK++ +L  LRS+
Sbjct: 194 RLSNTLQTYIRCRHP-PPGSHLLYAKMIQKLADLRSL 229

>pdb|3KBA|A Chain A, Progesterone Receptor Bound To Sulfonamide Pyrrolidine Partial Agonist Length = 253

Iteration: 1
 Score = 50.8 bits (120), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 31/131 (23%), Positives = 67/131 (51%), Gaps = 4/131 (3%)
Query: 183 TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGIL 242
           T++ +  ++QL  +V W+K +P F  L ++DQ+ L++  W  L++     RS     G +
Sbjct: 36  TSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQM 95
Query: 243 L--APGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNP-DVRG 299
           L  AP + +      E+    +    + ++  +  ++++ + E  C++ ++L N   + G
Sbjct: 96  LYFAPDLILNEQRMKESSFYSL-CLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEG 154
Query: 300 LKSQQVVEMLR 310
           L+SQ   E +R
Sbjct: 155 LRSQTQFEEMR 165

>pdb|1GS4|A Chain A, Structural Basis For The Glucocorticoid Response In A Mutant Human Androgen Receptor (Arccr) Derived From An Androgen-Independent Prostate Cancer Length = 248

Iteration: 1
 Score = 50.8 bits (120), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 41/162 (25%), Positives = 79/162 (48%), Gaps = 7/162 (4%)
Query: 190 DKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGV 247
           ++QL  +V WAK +P F  L ++DQ+ +++  W  L++ +   RS +  +  +L  AP +
Sbjct: 40  ERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDL 99
Query: 248 TVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFN-PDVRGLKSQQVV 306
                  H++ +     R +  L  +   +++   E  C++ ++LF+   V GLK+Q+  
Sbjct: 100 VFNEYRMHKSRMYSQCVR-MRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFF 158
Query: 307 EMLREKVYTSLEEYT---RVNHSEEPGRFAKLLLRLPSLRSI 345
           + LR      L+      R N +    RF +L   L S++ I
Sbjct: 159 DELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPI 200

>pdb|2Z4J|A Chain A, Crystal Structure Of Ar Lbd With Shp Peptide Nr Box 2 Length = 248

Iteration: 1
 Score = 50.8 bits (120), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 41/162 (25%), Positives = 79/162 (48%), Gaps = 7/162 (4%)
Query: 190 DKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGV 247
           ++QL  +V WAK +P F  L ++DQ+ +++  W  L++ +   RS +  +  +L  AP +
Sbjct: 39  ERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDL 98
Query: 248 TVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFN-PDVRGLKSQQVV 306
                  H++ +     R +  L  +   +++   E  C++ ++LF+   V GLK+Q+  
Sbjct: 99  VFNEYRMHKSRMYSQCVR-MRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFF 157
Query: 307 EMLREKVYTSLEEYT---RVNHSEEPGRFAKLLLRLPSLRSI 345
           + LR      L+      R N +    RF +L   L S++ I
Sbjct: 158 DELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPI 199

>pdb|3RLJ|A Chain A, Crystal Structure Of The Androgen Receptor Ligand Binding Domain In Complex With Sarm S-22 Length = 247

Iteration: 1
 Score = 50.8 bits (120), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 41/162 (25%), Positives = 79/162 (48%), Gaps = 7/162 (4%)
Query: 190 DKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGV 247
           ++QL  +V WAK +P F  L ++DQ+ +++  W  L++ +   RS +  +  +L  AP +
Sbjct: 39  ERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDL 98
Query: 248 TVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFN-PDVRGLKSQQVV 306
                  H++ +     R +  L  +   +++   E  C++ ++LF+   V GLK+Q+  
Sbjct: 99  VFNEYRMHKSRMYSQCVR-MRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFF 157
Query: 307 EMLREKVYTSLEEYT---RVNHSEEPGRFAKLLLRLPSLRSI 345
           + LR      L+      R N +    RF +L   L S++ I
Sbjct: 158 DELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPI 199

>pdb|2OZ7|A Chain A, Crystal Structure Of The Human Androgen Receptor T877a Mutant Ligand- Binding Domain With Cyproterone Acetate Length = 249

Iteration: 1
 Score = 50.8 bits (120), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 41/162 (25%), Positives = 79/162 (48%), Gaps = 7/162 (4%)
Query: 190 DKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGV 247
           ++QL  +V WAK +P F  L ++DQ+ +++  W  L++ +   RS +  +  +L  AP +
Sbjct: 39  ERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDL 98
Query: 248 TVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFN-PDVRGLKSQQVV 306
                  H++ +     R +  L  +   +++   E  C++ ++LF+   V GLK+Q+  
Sbjct: 99  VFNEYRMHKSRMYSQCVR-MRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFF 157
Query: 307 EMLREKVYTSLEEYT---RVNHSEEPGRFAKLLLRLPSLRSI 345
           + LR      L+      R N +    RF +L   L S++ I
Sbjct: 158 DELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPI 199

>pdb|1XOW|A Chain A, Crystal Structure Of The Human Androgen Receptor Ligand Binding Domain Bound With An Androgen Receptor Nh2- Terminal Peptide, Ar20-30, And R1881 Length = 249

Iteration: 1
 Score = 50.8 bits (120), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 41/162 (25%), Positives = 79/162 (48%), Gaps = 7/162 (4%)
Query: 190 DKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGV 247
           ++QL  +V WAK +P F  L ++DQ+ +++  W  L++ +   RS +  +  +L  AP +
Sbjct: 39  ERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDL 98
Query: 248 TVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFN-PDVRGLKSQQVV 306
                  H++ +     R +  L  +   +++   E  C++ ++LF+   V GLK+Q+  
Sbjct: 99  VFNEYRMHKSRMYSQCVR-MRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFF 157
Query: 307 EMLREKVYTSLEEYT---RVNHSEEPGRFAKLLLRLPSLRSI 345
           + LR      L+      R N +    RF +L   L S++ I
Sbjct: 158 DELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPI 199

>pdb|3RLL|A Chain A, Crystal Structure Of The T877a Androgen Receptor Ligand Binding Domain In Complex With (S)-N-(4-Cyano-3-(Trifluoromethyl)phenyl)-3-(4- Cyanonaphthalen-1-Yloxy)-2-Hydroxy-2-Methylpropanamide Length = 247

Iteration: 1
 Score = 50.8 bits (120), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 41/162 (25%), Positives = 79/162 (48%), Gaps = 7/162 (4%)
Query: 190 DKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGV 247
           ++QL  +V WAK +P F  L ++DQ+ +++  W  L++ +   RS +  +  +L  AP +
Sbjct: 39  ERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDL 98
Query: 248 TVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFN-PDVRGLKSQQVV 306
                  H++ +     R +  L  +   +++   E  C++ ++LF+   V GLK+Q+  
Sbjct: 99  VFNEYRMHKSRMYSQCVR-MRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFF 157
Query: 307 EMLREKVYTSLEEYT---RVNHSEEPGRFAKLLLRLPSLRSI 345
           + LR      L+      R N +    RF +L   L S++ I
Sbjct: 158 DELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPI 199

>pdb|3L3X|A Chain A, Crystal Structure Of Dht-Bound Androgen Receptor In Complex With The First Motif Of Steroid Receptor Coactivator 3 Length = 250

Iteration: 1
 Score = 50.8 bits (120), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 41/162 (25%), Positives = 79/162 (48%), Gaps = 7/162 (4%)
Query: 190 DKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGV 247
           ++QL  +V WAK +P F  L ++DQ+ +++  W  L++ +   RS +  +  +L  AP +
Sbjct: 41  ERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDL 100
Query: 248 TVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFN-PDVRGLKSQQVV 306
                  H++ +     R +  L  +   +++   E  C++ ++LF+   V GLK+Q+  
Sbjct: 101 VFNEYRMHKSRMYSQCVR-MRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFF 159
Query: 307 EMLREKVYTSLEEYT---RVNHSEEPGRFAKLLLRLPSLRSI 345
           + LR      L+      R N +    RF +L   L S++ I
Sbjct: 160 DELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPI 201

>pdb|1N83|A Chain A, Crystal Structure Of The Complex Between The Orphan Nuclear Hormone Receptor Ror(Alpha)-Lbd And Cholesterol Length = 270

Iteration: 1
 Score = 50.8 bits (120), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 40/155 (25%), Positives = 76/155 (49%), Gaps = 13/155 (8%)
Query: 196 LVDWAKHIPHFTTLPLEDQVLLLRAGWNELLI-----ASFSHRSISVKDGILLAPGVTVY 250
           +V++AK I  F  L   DQ++LL+AG  E++      A  S  +    DG   +P   V+
Sbjct: 81  VVEFAKRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQNNTVYFDGKYASPD--VF 138
Query: 251 RSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLR 310
           +S   E  +  +F     E    +  M + + E+      +L + D   L+ +  +E L+
Sbjct: 139 KSLGCEDFISFVF-----EFGKSLCSMHLTEDEIALFSAFVLMSADRSWLQEKVKIEKLQ 193
Query: 311 EKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +K+  +L+   + NH E+ G   KL+ ++ +LR++
Sbjct: 194 QKIQLALQHVLQKNHRED-GILTKLICKVSTLRAL 227

>pdb|3BQD|A Chain A, Doubling The Size Of The Glucocorticoid Receptor Ligand Binding Pocket By Deacylcortivazol Length = 255

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 43/166 (25%), Positives = 81/166 (48%), Gaps = 17/166 (10%)
Query: 191 KQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGVT 248
           +Q+   V WAK IP F  L L+DQ+ LL+  W  L+  +   RS       LL  AP + 
Sbjct: 47  RQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMSLMAFALGWRSYRQSSANLLCFAPDLI 106
Query: 249 VYRSSAHEAGVGGIFDRV--LTELVSKMREMKMDKTELGCLRTIILFNPDVR-GLKSQQV 305
           +   +     +  ++D+   +  + S++  +++   E  C++T++L +   + GLKSQ++
Sbjct: 107 I---NEQRMTLPCMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSSVPKDGLKSQEL 163
Query: 306 VEMLREKVYTSLEEYTRV------NHSEEPGRFAKLLLRLPSLRSI 345
            + +R    T ++E  +       N S+   RF +L   L S+  +
Sbjct: 164 FDEIR---MTYIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEV 206

>pdb|1M2Z|A Chain A, Crystal Structure Of A Dimer Complex Of The Human Glucocorticoid Receptor Ligand-Binding Domain Bound To Dexamethasone And A Tif2 Coactivator Motif Length = 257

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 43/166 (25%), Positives = 81/166 (48%), Gaps = 17/166 (10%)
Query: 191 KQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGVT 248
           +Q+   V WAK IP F  L L+DQ+ LL+  W  L+  +   RS       LL  AP + 
Sbjct: 49  RQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMSLMAFALGWRSYRQSSANLLCFAPDLI 108
Query: 249 VYRSSAHEAGVGGIFDRV--LTELVSKMREMKMDKTELGCLRTIILFNPDVR-GLKSQQV 305
           +   +     +  ++D+   +  + S++  +++   E  C++T++L +   + GLKSQ++
Sbjct: 109 I---NEQRMTLPCMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSSVPKDGLKSQEL 165
Query: 306 VEMLREKVYTSLEEYTRV------NHSEEPGRFAKLLLRLPSLRSI 345
            + +R    T ++E  +       N S+   RF +L   L S+  +
Sbjct: 166 FDEIR---MTYIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEV 208

>pdb|3M7R|A Chain A, Crystal Structure Of Vdr H305q Mutant Length = 253

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 40/157 (25%), Positives = 82/157 (52%), Gaps = 9/157 (5%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYR--- 251
           +++ +AK IP F  L  EDQ++LL++   E+++   S+ S ++ D +    G   Y+   
Sbjct: 70  KVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLR-SNESFTMDD-MSWTCGNQDYKYRV 127
Query: 252 SSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
           S   +AG        L +    ++++ + + E   L  I + +PD  G++   ++E +++
Sbjct: 128 SDVTKAGQSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQD 187
Query: 312 KVYTSLEEYTRVNHSEEPGR---FAKLLLRLPSLRSI 345
           ++  +L+ Y R  H   PG    +AK++ +L  LRS+
Sbjct: 188 RLSNTLQTYIRCRHP-PPGSHLLYAKMIQKLADLRSL 223

>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 = 49.7 bits (117), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 38/157 (24%), Positives = 84/157 (53%), Gaps = 9/157 (5%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           +++ +AK IP F  L  +DQ++LL++   E+++   S++S ++ D +    G   Y+   
Sbjct: 84  KVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLR-SNQSFTMDD-MSWDCGSQDYKYDV 141
Query: 255 HEAGVGGIFDRVLTELVS---KMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
            +    G    ++  L+     ++++ + + E   L  I + +PD  G++  ++VE +++
Sbjct: 142 TDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAKLVEAIQD 201
Query: 312 KVYTSLEEYTRVNHSEEPGR---FAKLLLRLPSLRSI 345
           ++  +L+ Y R  H   PG    +AK++ +L  LRS+
Sbjct: 202 RLSNTLQTYIRCRHP-PPGSHQLYAKMIQKLADLRSL 237

>pdb|1DB1|A Chain A, Crystal Structure Of The Nuclear Receptor For Vitamin D Complexed To Vitamin D Length = 259

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 40/157 (25%), Positives = 82/157 (52%), Gaps = 9/157 (5%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYR--- 251
           +++ +AK IP F  L  EDQ++LL++   E+++   S+ S ++ D +    G   Y+   
Sbjct: 72  KVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLR-SNESFTM-DDMSWTCGNQDYKYRV 129
Query: 252 SSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
           S   +AG        L +    ++++ + + E   L  I + +PD  G++   ++E +++
Sbjct: 130 SDVTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQD 189
Query: 312 KVYTSLEEYTRVNHSEEPGR---FAKLLLRLPSLRSI 345
           ++  +L+ Y R  H   PG    +AK++ +L  LRS+
Sbjct: 190 RLSNTLQTYIRCRHP-PPGSHLLYAKMIQKLADLRSL 225

>pdb|4E2J|A Chain A, X-Ray Crystal Structure Of The Ancestral Glucocorticoid Receptor 2 Ligand Binding Domain In Complex With Mometasone Furoate And Tif-2 Coactivator Fragment Length = 250

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 43/166 (25%), Positives = 81/166 (48%), Gaps = 17/166 (10%)
Query: 191 KQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGVT 248
           +Q+   V WAK +P F  L L+DQ+ LL+  W  L+  S   RS    +G +L  AP + 
Sbjct: 43  RQVVSAVKWAKALPGFRNLHLDDQMTLLQYSWMSLMAFSLGWRSYKQSNGNMLCFAPDLV 102
Query: 249 VYRSSAHEAGVGGIFDRV--LTELVSKMREMKMDKTELGCLRTIILFNPDVR-GLKSQQV 305
           +   +     +  ++D+   + ++ S+   +++   E  C++ ++L +   + GLKSQ V
Sbjct: 103 I---NEERMQLPYMYDQCQQMLKISSEFVRLQVSYDEYLCMKVLLLLSTVPKDGLKSQAV 159
Query: 306 VEMLREKVYTSLEEYTRV------NHSEEPGRFAKLLLRLPSLRSI 345
            + +R    T ++E  +       N S+   RF +L   L S+  +
Sbjct: 160 FDEIR---MTYIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEM 202

>pdb|1S0Z|A Chain A, Crystal Structure Of The Vdr Lbd Complexed To Seocalcitol. Length = 263

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 40/157 (25%), Positives = 82/157 (52%), Gaps = 9/157 (5%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYR--- 251
           +++ +AK IP F  L  EDQ++LL++   E+++   S+ S ++ D +    G   Y+   
Sbjct: 76  KVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLR-SNESFTMDD-MSWTCGNQDYKYRV 133
Query: 252 SSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
           S   +AG        L +    ++++ + + E   L  I + +PD  G++   ++E +++
Sbjct: 134 SDVTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQD 193
Query: 312 KVYTSLEEYTRVNHSEEPGR---FAKLLLRLPSLRSI 345
           ++  +L+ Y R  H   PG    +AK++ +L  LRS+
Sbjct: 194 RLSNTLQTYIRCRHP-PPGSHLLYAKMIQKLADLRSL 229

>pdb|3GN8|A Chain A, X-Ray Crystal Structure Of Ancgr2 In Complex With Dexamethasone Length = 249

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 43/166 (25%), Positives = 81/166 (48%), Gaps = 17/166 (10%)
Query: 191 KQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGVT 248
           +Q+   V WAK +P F  L L+DQ+ LL+  W  L+  S   RS    +G +L  AP + 
Sbjct: 41  RQVVSAVKWAKALPGFRNLHLDDQMTLLQYSWMSLMAFSLGWRSYKQSNGNMLCFAPDLV 100
Query: 249 VYRSSAHEAGVGGIFDRV--LTELVSKMREMKMDKTELGCLRTIILFNPDVR-GLKSQQV 305
           +   +     +  ++D+   + ++ S+   +++   E  C++ ++L +   + GLKSQ V
Sbjct: 101 I---NEERMQLPYMYDQCQQMLKISSEFVRLQVSYDEYLCMKVLLLLSTVPKDGLKSQAV 157
Query: 306 VEMLREKVYTSLEEYTRV------NHSEEPGRFAKLLLRLPSLRSI 345
            + +R    T ++E  +       N S+   RF +L   L S+  +
Sbjct: 158 FDEIR---MTYIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEM 200

>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 = 49.7 bits (117), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 40/157 (25%), Positives = 82/157 (52%), Gaps = 9/157 (5%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYR--- 251
           +++ +AK IP F  L  EDQ++LL++   E+++   S+ S ++ D +    G   Y+   
Sbjct: 93  KVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLR-SNESFTMDD-MSWTCGNQDYKYRV 150
Query: 252 SSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
           S   +AG        L +    ++++ + + E   L  I + +PD  G++   ++E +++
Sbjct: 151 SDVTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQD 210
Query: 312 KVYTSLEEYTRVNHSEEPGR---FAKLLLRLPSLRSI 345
           ++  +L+ Y R  H   PG    +AK++ +L  LRS+
Sbjct: 211 RLSNTLQTYIRCRHP-PPGSHLLYAKMIQKLADLRSL 246

>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 = 49.7 bits (117), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 38/157 (24%), Positives = 84/157 (53%), Gaps = 9/157 (5%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           +++ +AK IP F  L  +DQ++LL++   E+++   S++S ++ D +    G   Y+   
Sbjct: 78  KVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLR-SNQSFTM-DDMSWDCGSQDYKYDV 135
Query: 255 HEAGVGGIFDRVLTELVS---KMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
            +    G    ++  L+     ++++ + + E   L  I + +PD  G++  ++VE +++
Sbjct: 136 TDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAKLVEAIQD 195
Query: 312 KVYTSLEEYTRVNHSEEPGR---FAKLLLRLPSLRSI 345
           ++  +L+ Y R  H   PG    +AK++ +L  LRS+
Sbjct: 196 RLSNTLQTYIRCRHP-PPGSHQLYAKMIQKLADLRSL 231

>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 = 49.7 bits (117), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 38/157 (24%), Positives = 84/157 (53%), Gaps = 9/157 (5%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           +++ +AK IP F  L  +DQ++LL++   E+++   S++S ++ D +    G   Y+   
Sbjct: 74  KVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLR-SNQSFTM-DDMSWDCGSQDYKYDV 131
Query: 255 HEAGVGGIFDRVLTELVS---KMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
            +    G    ++  L+     ++++ + + E   L  I + +PD  G++  ++VE +++
Sbjct: 132 TDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAKLVEAIQD 191
Query: 312 KVYTSLEEYTRVNHSEEPGR---FAKLLLRLPSLRSI 345
           ++  +L+ Y R  H   PG    +AK++ +L  LRS+
Sbjct: 192 RLSNTLQTYIRCRHP-PPGSHQLYAKMIQKLADLRSL 227

>pdb|3B0T|A Chain A, Human Vdr Ligand Binding Domain In Complex With Maxacalcitol Length = 254

Iteration: 1
 Score = 49.7 bits (117), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 40/157 (25%), Positives = 82/157 (52%), Gaps = 9/157 (5%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYR--- 251
           +++ +AK IP F  L  EDQ++LL++   E+++   S+ S ++ D +    G   Y+   
Sbjct: 71  KVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLR-SNESFTMDD-MSWTCGNQDYKYRV 128
Query: 252 SSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
           S   +AG        L +    ++++ + + E   L  I + +PD  G++   ++E +++
Sbjct: 129 SDVTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQD 188
Query: 312 KVYTSLEEYTRVNHSEEPGR---FAKLLLRLPSLRSI 345
           ++  +L+ Y R  H   PG    +AK++ +L  LRS+
Sbjct: 189 RLSNTLQTYIRCRHP-PPGSHLLYAKMIQKLADLRSL 224

>pdb|3AZ1|A Chain A, Crystal Structure Analysis Of Vitamin D Receptor Length = 253

Iteration: 1
 Score = 49.7 bits (117), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 40/157 (25%), Positives = 82/157 (52%), Gaps = 9/157 (5%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYR--- 251
           +++ +AK IP F  L  EDQ++LL++   E+++   S+ S ++ D +    G   Y+   
Sbjct: 70  KVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLR-SNESFTMDD-MSWTCGNQDYKYRV 127
Query: 252 SSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE 311
           S   +AG        L +    ++++ + + E   L  I + +PD  G++   ++E +++
Sbjct: 128 SDVTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQD 187
Query: 312 KVYTSLEEYTRVNHSEEPGR---FAKLLLRLPSLRSI 345
           ++  +L+ Y R  H   PG    +AK++ +L  LRS+
Sbjct: 188 RLSNTLQTYIRCRHP-PPGSHLLYAKMIQKLADLRSL 223

>pdb|4FNE|A Chain A, X-Ray Crystal Structure Of The Ancestral 3-Keto Steroid Receptor - Doc Complex Length = 254

Iteration: 1
 Score = 48.5 bits (114), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 40/174 (22%), Positives = 84/174 (48%), Gaps = 17/174 (9%)
Query: 183 TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGIL 242
           +++ +  +KQL  +V WAK +P F  L L+DQ+ L++  W  L+  +   RS    +G +
Sbjct: 37  SSLNRLAEKQLVSVVKWAKALPGFRNLHLDDQMTLIQYSWMGLMAFAMGWRSYKHTNGQM 96
Query: 243 L--APGVTVYRSSAHEAGVGGIFD--RVLTELVSKMREMKMDKTELGCLRTIILFNPDVR 298
           L  AP +        ++    ++D  + + ++  +   +++ + E  C++ ++L +   +
Sbjct: 97  LYFAPDLIFNEQRMQQS---AMYDLCQGMQQISQEFVRLQVTQEEFLCMKALLLLSTVPK 153
Query: 299 -GLKSQQVVEMLREKVYTSLEEYTRV------NHSEEPGRFAKLLLRLPSLRSI 345
            GLKSQ   + +R      ++E  R       N ++   RF +L   L S+  +
Sbjct: 154 EGLKSQASFDEMR---MNYIKELNRAIAKKENNSAQNWQRFYQLTKLLDSMHDL 204

>pdb|2Q3Y|A Chain A, Ancestral Corticiod Receptor In Complex With Doc Length = 249

Iteration: 1
 Score = 47.8 bits (112), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 40/171 (23%), Positives = 79/171 (46%), Gaps = 11/171 (6%)
Query: 183 TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGIL 242
           +++ +   KQ+  +V WAK +P F  L L+DQ+ L++  W  L+  S   RS    +G +
Sbjct: 33  SSLNRLAGKQMVSVVKWAKALPGFRNLHLDDQMTLIQYSWMSLMAFSLGWRSYKHTNGQM 92
Query: 243 L--APGVTVYRSSAHEAGVGGIFD--RVLTELVSKMREMKMDKTELGCLRTIILFNPDVR 298
           L  AP +        ++    ++D  + + ++  +   +++   E  C++ ++L +   +
Sbjct: 93  LYFAPDLIFNEERMQQS---AMYDLCQGMRQISQEFVRLQVTYEEFLCMKVLLLLSTVPK 149
Query: 299 -GLKSQQVVEMLREKVYTSLEEY---TRVNHSEEPGRFAKLLLRLPSLRSI 345
            GLKSQ   + +R      L         N S+   RF +L   L S+  +
Sbjct: 150 DGLKSQASFDEMRMNYIKELRRAIARNENNSSQNWQRFYQLTKLLDSMHDL 200

>pdb|1XNX|A Chain A, Crystal Structure Of Constitutive Androstane Receptor Length = 256

Iteration: 1
 Score = 47.8 bits (112), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 38/153 (24%), Positives = 68/153 (44%), Gaps = 3/153 (1%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           Q++ + K +P F +L +EDQ+ LL+    E+L  S +       +     P       + 
Sbjct: 79  QIIKFTKDLPLFRSLTMEDQISLLKGAAVEILHISLNTTFCLQTENFFCGPLCYKMEDAV 138
Query: 255 HEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVY 314
           H AG    F   +      ++ + + + E   +    LF+PD  G+  ++ ++ L+E++ 
Sbjct: 139 H-AGFQYEFLESILHFHKNLKGLHLQEPEYVLMAATALFSPDRPGVTQREEIDQLQEEMA 197
Query: 315 TSLEEYTRVNHSEEPGRF--AKLLLRLPSLRSI 345
             L  +     S    RF  AKL+  L  LRSI
Sbjct: 198 LILNNHIMEQQSRLQSRFLYAKLMGLLADLRSI 230

>pdb|2Q1H|A Chain A, Ancestral Corticoid Receptor In Complex With Aldosterone Length = 250

Iteration: 1
 Score = 47.8 bits (112), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 40/171 (23%), Positives = 79/171 (46%), Gaps = 11/171 (6%)
Query: 183 TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGIL 242
           +++ +   KQ+  +V WAK +P F  L L+DQ+ L++  W  L+  S   RS    +G +
Sbjct: 33  SSLNRLAGKQMVSVVKWAKALPGFRNLHLDDQMTLIQYSWMSLMAFSLGWRSYKHTNGQM 92
Query: 243 L--APGVTVYRSSAHEAGVGGIFD--RVLTELVSKMREMKMDKTELGCLRTIILFNPDVR 298
           L  AP +        ++    ++D  + + ++  +   +++   E  C++ ++L +   +
Sbjct: 93  LYFAPDLIFNEERMQQS---AMYDLCQGMRQISQEFVRLQVTYEEFLCMKVLLLLSTVPK 149
Query: 299 -GLKSQQVVEMLREKVYTSLEEYT---RVNHSEEPGRFAKLLLRLPSLRSI 345
            GLKSQ   + +R      L         N S+   RF +L   L S+  +
Sbjct: 150 DGLKSQASFDEMRMNYIKELRRAIAKKENNSSQNWQRFYQLTKLLDSMHDL 200

>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 = 47.8 bits (112), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 38/153 (24%), Positives = 68/153 (44%), Gaps = 3/153 (1%)
Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA 254
           Q++ + K +P F +L +EDQ+ LL+    E+L  S +       +     P       + 
Sbjct: 65  QIIKFTKDLPLFRSLTMEDQISLLKGAAVEILHISLNTTFCLQTENFFCGPLCYKMEDAV 124
Query: 255 HEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVY 314
           H AG    F   +      ++ + + + E   +    LF+PD  G+  ++ ++ L+E++ 
Sbjct: 125 H-AGFQYEFLESILHFHKNLKGLHLQEPEYVLMAATALFSPDRPGVTQREEIDQLQEEMA 183
Query: 315 TSLEEYTRVNHSEEPGRF--AKLLLRLPSLRSI 345
             L  +     S    RF  AKL+  L  LRSI
Sbjct: 184 LILNNHIMEQQSRLQSRFLYAKLMGLLADLRSI 216

>pdb|3RY9|A Chain A, Crystal Structure Of The Resurrected Ancestral Glucocorticoid Receptor 1 In Complex With Doc Length = 250

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 37/128 (28%), Positives = 63/128 (49%), Gaps = 14/128 (10%)
Query: 191 KQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGVT 248
           +Q+   V WAK +P F  L L+DQ+ LL+  W  L+  S   RS    +G +L  AP + 
Sbjct: 41  RQMISAVKWAKALPGFRNLHLDDQMTLLQYSWMSLMAFSLGWRSYQHTNGNMLYFAPDLI 100
Query: 249 -----VYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVR-GLKS 302
                + +SS +E   G    ++  E V     +++   E  C++ ++L +   + GLKS
Sbjct: 101 FNEERMQQSSMYELCKG--MHKISLEFV----RLQVSYEEYLCMKVLLLLSTVPKDGLKS 154
Query: 303 QQVVEMLR 310
           Q   + +R
Sbjct: 155 QAAFDEIR 162

>pdb|2AX8|A Chain A, Crystal Structure Of The Androgen Receptor Ligand Binding Domain W741l Mutant In Complex With S-1 Length = 256

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 40/162 (24%), Positives = 78/162 (48%), Gaps = 7/162 (4%)
Query: 190 DKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGV 247
           ++QL  +V WAK +P F  L ++DQ+ +++     L++ +   RS +  +  +L  AP +
Sbjct: 46  ERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSLMGLMVFAMGWRSFTNVNSRMLYFAPDL 105
Query: 248 TVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFN-PDVRGLKSQQVV 306
                  H++ +     R +  L  +   +++   E  C++ ++LF+   V GLK+Q+  
Sbjct: 106 VFNEYRMHKSRMYSQCVR-MRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFF 164
Query: 307 EMLREKVYTSLEEYT---RVNHSEEPGRFAKLLLRLPSLRSI 345
           + LR      L+      R N +    RF +L   L S++ I
Sbjct: 165 DELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPI 206

>pdb|1Z95|A Chain A, Crystal Structure Of The Androgen Receptor Ligand-Binding Domain W741l Mutant Complex With R-Bicalutamide Length = 246

Iteration: 1
 Score = 45.4 bits (106), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 40/162 (24%), Positives = 78/162 (48%), Gaps = 7/162 (4%)
Query: 190 DKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGV 247
           ++QL  +V WAK +P F  L ++DQ+ +++     L++ +   RS +  +  +L  AP +
Sbjct: 38  ERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSLMGLMVFAMGWRSFTNVNSRMLYFAPDL 97
Query: 248 TVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFN-PDVRGLKSQQVV 306
                  H++ +     R +  L  +   +++   E  C++ ++LF+   V GLK+Q+  
Sbjct: 98  VFNEYRMHKSRMYSQCVR-MRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFF 156
Query: 307 EMLREKVYTSLEEYT---RVNHSEEPGRFAKLLLRLPSLRSI 345
           + LR      L+      R N +    RF +L   L S++ I
Sbjct: 157 DELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPI 198

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	347
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	1e-135
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	1e-104
1lbd_A	282	RXR_LBD, retinoid X receptor; transcription factor	1e-100
2nxx_A	235	Ultraspiracle (USP, NR2B4); hormone receptor, APO	8e-90
2p1t_A	240	Retinoic acid receptor RXR-alpha; protein-ligand c	3e-86
3ipq_A	283	Oxysterols receptor LXR-alpha; LXR homodimer, LXR	1e-84
1pzl_A	237	Hepatocyte nuclear factor 4-alpha; transcription;	4e-83
1xdk_B	303	RAR-beta, retinoic acid receptor, beta; nuclear re	1e-82
2hc4_A	302	Vitamin D receptor; alpha helical sandwich, gene r	4e-81
1z5x_E	310	Ecdysone receptor ligand binding domain; ponastero	2e-79
1g2n_A	264	Ultraspiracle protein; antiparallel alpha-helical	5e-79
2e2r_A	244	Estrogen-related receptor gamma; ERR gamma, BPA, n	2e-78
3ltx_A	243	Estrogen receptor; constitutive, nuclear receptor,	6e-78
1ovl_A	271	Orphan nuclear receptor NURR1 (MSe 414, 496, 511);	7e-78
3k6p_A	248	Steroid hormone receptor ERR1; estrogen related re	2e-77
1ymt_A	246	Steroidogenic factor 1; SF-1, ligand-binding domai	3e-76
2iz2_A	243	FTZ-F1 alpha, nuclear hormone receptor FTZ-F1; nuc	1e-75
1hg4_A	279	Ultraspiracle; nuclear hormone receptor, transcrip	2e-75
3kmr_A	266	Retinoic acid receptor alpha; nuclear receptor tra	6e-75
3cjw_A	244	COUP transcription factor 2; COUP-TFII, nuclear re	9e-75
1osh_A	232	BIle acid receptor; nuclear receptor, ligand bindi	9e-74
2r40_D	266	Ecdysone receptor, 20-hydroxy-ecdysone receptor; n	6e-73
1fcy_A	236	RAR-gamma-1, retinoic acid receptor gamma-1; isoty	1e-72
2ocf_A	298	Estrogen receptor; estrogen receptor, LBD, monobod	1e-72
3plz_A	257	FTZ-F1 related protein; alpha helical sandwhich, f	4e-72
3u9q_A	269	Peroxisome proliferator-activated receptor gamma;	2e-70
1xvp_B	246	Orphan nuclear receptor NR1I3; CAR, RXR, citco, SR	2e-70
3p0u_A	249	Nuclear receptor subfamily 2 group C member 2; lig	4e-70
3oll_A	240	Estrogen receptor beta; steroid binding, phosphory	9e-70
3cqv_A	199	Nuclear receptor subfamily 1 group D member 2; rev	1e-69
3tx7_B	352	Nuclear receptor subfamily 5 group A member 2; LRH	1e-69
1xpc_A	248	Estrogen receptor; nuclear receptor, transcription	1e-69
3vhv_A	260	Mineralocorticoid receptor; nuclear receptor, tran	3e-68
2p54_A	267	PPAR-alpha, peroxisome proliferator-activated rece	9e-68
1nrl_A	316	Orphan nuclear receptor PXR; PXR, xenobiotic, SRC-	2e-67
1yje_A	264	Orphan nuclear receptor NR4A1; NGFI-B, NUR77, liga	3e-67
3n00_A	245	REV-ERBA-alpha; reverba ncorid1, anti-parallel B-s	3e-67
1pdu_A	244	DHR38, nuclear hormone receptor HR38; nuclear rece	8e-67
1sqn_A	261	PR, progesterone receptor; nuclear receptor, stero	9e-67
2nxx_E	248	Ecdysone receptor (ECR, NRH1); hormone receptor, A	2e-66
3ilz_A	267	Thyroid hormone receptor, alpha isoform 1 variant;	3e-66
3vhu_A	294	Mineralocorticoid receptor; nuclear receptor, tran	6e-66
1yye_A	268	ER-beta, estrogen receptor beta; ER-beta, nuclear	2e-65
1t7r_A	269	Androgen receptor; nuclear receptor, transcription	1e-63
3b0t_A	254	Vitamin D3 receptor; nuclear receptor, transcripti	1e-62
1l2j_A	271	Estrogen receptor beta; nuclear receptor, transcri	1e-62
3f5c_B	268	Nuclear receptor subfamily 0 group B member 1; tra	2e-62
3mnp_A	261	Glucocorticoid receptor; protein-ligand complex, s	7e-62
1ynw_B	99	Retinoic acid receptor RXR-alpha, retinoid X recep	9e-62
2o4j_A	292	Vitamin D3 receptor; nuclear receptor-ligand compl	7e-61
2han_A	93	Protein ultraspiracle; transcription regulation, t	3e-57
1n83_A	270	Nuclear receptor ROR-alpha; three-layered alpha he	5e-57
1nq7_A	244	Nuclear receptor ROR-beta; ligand-binding domain,	2e-56
1dsz_B	85	RXR-alpha, retinoic acid receptor RXR-alpha; RAR,	2e-56
2a66_A	113	Orphan nuclear receptor NR5A2; protein-DNA complex	3e-55
3g9m_A	90	Glucocorticoid receptor; glucocorticoid, DNA-bindi	6e-55
1lo1_A	98	Steroid hormone receptor ERR2; estrogen related re	1e-54
2ebl_A	89	COUP transcription factor 1; DNA-binding, metal-bi	1e-54
1dsz_A	86	RAR-alpha, retinoic acid receptor alpha; RAR, nucl	1e-54
1cit_A	89	NGFI-B, protein (orphan nuclear receptor NGFI-B);	2e-54
1a6y_A	94	Orphan nuclear receptor NR1D1; orphan receptor, DN	3e-54
2han_B	119	Ecdysone receptor; transcription regulation, trans	1e-53
1hcq_A	84	Protein (estrogen receptor); protein-DNA complex,	2e-53
3cbb_A	78	HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DN	3e-53
1r4i_A	105	Androgen receptor; AR, steroid receptor, protein-D	5e-52
3l0l_A	248	Nuclear receptor ROR-gamma; nuclear receptor, rorg	1e-51
1kb2_A	110	Vitamin D3 receptor; VDR, nuclear receptor, protei	1e-51
3up3_A	243	Acedaf-12; ligand binding domain, nematode, steroi	3e-51
2nll_B	103	Protein (thyroid hormone receptor); complex (trans	3e-51
3gyt_A	244	Nuclear hormone receptor of the steroid/thyroid ho	2e-46
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-08

>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 =  392 bits (1007), Expect = e-135
 Identities = 223/349 (63%), Positives = 267/349 (76%), Gaps = 6/349 (1%)

Query: 3   PDTATLLVNFNSGGANSMSSFGSNNHSSSHNNGSSNSSIISPYPPNHPLCGSKHLCSICG 62
           P T TL  +  S   +S  +  S++       G +    +  +P  +    +KH+C+ICG
Sbjct: 85  PTTPTLGFSTGSPQLSSPMNPVSSSEDIKPPLGLNGVLKVPAHPSGNMASFTKHICAICG 144

Query: 63  DRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMG 122
           DR+SGKHYGVYSCEGCKGFFKRTVRKDL+Y CR+ ++C+IDKRQRNRCQYCRYQKCL MG
Sbjct: 145 DRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMG 204

Query: 123 MKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQRVDMKQEPADQDIVNEQQA 182
           MKREAVQEERQR K+R+ NEVESTS    +MPVERILEAE  V+ K E   +  +    +
Sbjct: 205 MKREAVQEERQRGKDRNENEVESTSSANEDMPVERILEAELAVEPKTETYVEANMGLNPS 264

Query: 183 T------NICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSIS 236
           +      NIC+A DKQLF LV+WAK IPHF+ LPL+DQV+LLRAGWNELLIASFSHRSI+
Sbjct: 265 SPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIA 324

Query: 237 VKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD 296
           VKDGILLA G+ V+R+SAH AGVG IFDRVLTELVSKMR+M+MDKTELGCLR I+LFNPD
Sbjct: 325 VKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPD 384

Query: 297 VRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            +GL +   VE LREKVY SLE Y +  + E+PGRFAKLLLRLP+LRSI
Sbjct: 385 SKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSI 433

>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 =  311 bits (797), Expect = e-104
 Identities = 100/377 (26%), Positives = 161/377 (42%), Gaps = 56/377 (14%)

Query: 21  SSFGSNNHSSSHNNGSSNSSIISPYPPNHPLC-GSKHLCSICGDRASGKHYGVYSCEGCK 79
               +     +     S  + +   P   P        C +CGD+ASG HYGV++CEGCK
Sbjct: 15  MYQSAIKVEPASPPYYSEKTQLYNKPHEEPSNSLMAIECRVCGDKASGFHYGVHACEGCK 74

Query: 80  GFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRTKERD 139
           GFF+RT+R  L Y  R   NC I K+ RN+CQYCR+QKCL +GM   A++  R    E++
Sbjct: 75  GFFRRTIRLKLIY-DRCDLNCRIHKKSRNKCQYCRFQKCLAVGMSHNAIRFGRMPQAEKE 133

Query: 140 SNEVESTSGTLIEMPVERILEAEQR---------------------------------VD 166
               E +S      P    L A  +                                  D
Sbjct: 134 KLLAEISSDIDQLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYD 193

Query: 167 MKQEPADQDIVNEQQATN---------------ICKATDKQLFQLVDWAKHIPHFTTLPL 211
           M      +D +  +  T                    + + + ++ ++AK IP F  L L
Sbjct: 194 MNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDL 253

Query: 212 EDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYR---SSAHEAGVGGIFDRVLT 268
            DQV LL+ G +E++    +  S+  KDG+L++ G          +     G   +    
Sbjct: 254 NDQVTLLKYGVHEIIYTMLA--SLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKF- 310

Query: 269 ELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEE 328
           E   K   +++D ++L     +I+ + D  GL + + +E +++ +  +LE   ++NH E 
Sbjct: 311 EFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPES 370

Query: 329 PGRFAKLLLRLPSLRSI 345
              FAKLL ++  LR I
Sbjct: 371 SQLFAKLLQKMTDLRQI 387

>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 =  297 bits (761), Expect = e-100
 Identities = 156/245 (63%), Positives = 184/245 (75%), Gaps = 9/245 (3%)

Query: 107 RNRCQYCRYQKCLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQRVD 166
            +        +      KREAVQEERQR K+R+ NEVESTS    +MPVERILEAE  V+
Sbjct: 7   HHHHSSGLVPRG---SHKREAVQEERQRGKDRNENEVESTSSANEDMPVERILEAELAVE 63

Query: 167 MKQEPADQDIVNEQQAT------NICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRA 220
            K E   +  +    ++      NIC+A DKQLF LV+WAK IPHF+ LPL+DQV+LLRA
Sbjct: 64  PKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRA 123

Query: 221 GWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMD 280
           GWNELLIASFSHRSI+VKDGILLA G+ V+R+SAH AGVG IFDRVLTELVSKMR+M+MD
Sbjct: 124 GWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMD 183

Query: 281 KTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLP 340
           KTELGCLR I+LFNPD +GL +   VE LREKVY SLE Y +  + E+PGRFAKLLLRLP
Sbjct: 184 KTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLP 243

Query: 341 SLRSI 345
           +LRSI
Sbjct: 244 ALRSI 248

>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 =  268 bits (686), Expect = 8e-90
 Identities = 139/202 (68%), Positives = 163/202 (80%), Gaps = 3/202 (1%)

Query: 146 TSGTLIEMPVERILEAEQRVDMKQEPADQDIVNEQQAT--NICKATDKQLFQLVDWAKHI 203
           TS    +MP+ERI+EAE+RV+    P    +VNE   T  NIC+AT KQLFQLV WAK +
Sbjct: 2   TSNLQADMPLERIIEAEKRVECND-PLVALVVNENNTTVNNICQATHKQLFQLVQWAKLV 60

Query: 204 PHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIF 263
           PHFT+LPL DQV LLRAGWNELLIA+FSHRS+  +D I+LA G+TV +S+AH  GVG I+
Sbjct: 61  PHFTSLPLTDQVQLLRAGWNELLIAAFSHRSMQAQDAIVLATGLTVNKSTAHAVGVGNIY 120

Query: 264 DRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRV 323
           DRVL+ELV+KM+EMKMDKTELGCLR IIL+NPDVRG+KS Q VEMLREK+Y  LEEYTR 
Sbjct: 121 DRVLSELVNKMKEMKMDKTELGCLRAIILYNPDVRGIKSVQEVEMLREKIYGVLEEYTRT 180

Query: 324 NHSEEPGRFAKLLLRLPSLRSI 345
            H  EPGRFAKLLLRLP+LRSI
Sbjct: 181 THPNEPGRFAKLLLRLPALRSI 202

>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 =  259 bits (663), Expect = 3e-86
 Identities = 139/206 (67%), Positives = 159/206 (77%), Gaps = 6/206 (2%)

Query: 146 TSGTLIEMPVERILEAEQRVDMKQEP------ADQDIVNEQQATNICKATDKQLFQLVDW 199
           TS    +MPVERILEAE  V+ K E                  TNIC+A DKQLF LV+W
Sbjct: 1   TSSANEDMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEW 60

Query: 200 AKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV 259
           AK IPHF+ LPL+DQV+LLRAGWNELLIASFSHRSI+VKDGILLA G+ V+R+SAH AGV
Sbjct: 61  AKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGV 120

Query: 260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEE 319
           G IFDRVLTELVSKMR+M+MDKTELGCLR I+LFNPD +GL +   VE LREKVY SLE 
Sbjct: 121 GAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEA 180

Query: 320 YTRVNHSEEPGRFAKLLLRLPSLRSI 345
           Y +  + E+PGRFAKLLLRLP+LRSI
Sbjct: 181 YCKHKYPEQPGRFAKLLLRLPALRSI 206

>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 =  256 bits (656), Expect = 1e-84
 Identities = 52/260 (20%), Positives = 109/260 (41%), Gaps = 27/260 (10%)

Query: 105 RQRNRCQYCRYQKCLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMP------VERI 158
           + +++ Q+            ++ +QEE Q           S    L ++       +E++
Sbjct: 2   KHQHQHQHQH--------QHQQPLQEEEQAHATSLPPRASSPPQILPQLSPEQLGMIEKL 53

Query: 159 LEAEQRVDMKQEPADQDI-------------VNEQQATNICKATDKQLFQLVDWAKHIPH 205
           + A+Q+ + +       +               +Q+  +  +     + ++VD+AK +P 
Sbjct: 54  VAAQQQCNRRSFSDRLRVTPWPMAPDPHSREARQQRFAHFTELAIVSVQEIVDFAKQLPG 113

Query: 206 FTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDR 265
           F  L  EDQ+ LL+    E+++   S R     + I      +  R    +AG+   F  
Sbjct: 114 FLQLSREDQIALLKTSAIEVMLLETSRRYNPGSESITFLKDFSYNREDFAKAGLQVEFIN 173

Query: 266 VLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNH 325
            + E    M E++++  E   L  I +F+ D   ++ Q  VE L+     +L  Y  ++H
Sbjct: 174 PIFEFSRAMNELQLNDAEFALLIAISIFSADRPNVQDQLQVERLQHTYVEALHAYVSIHH 233

Query: 326 SEEPGRFAKLLLRLPSLRSI 345
             +   F ++L++L SLR++
Sbjct: 234 PHDRLMFPRMLMKLVSLRTL 253

>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 =  251 bits (642), Expect = 4e-83
 Identities = 72/206 (34%), Positives = 106/206 (51%), Gaps = 5/206 (2%)

Query: 145 STSGTLIEMPVERILEAEQRVDMKQEP-----ADQDIVNEQQATNICKATDKQLFQLVDW 199
           S+        +  +L+AE        P      D          ++C++  +QL  LV+W
Sbjct: 1   SSYELASLPSINALLQAEVLSRQITSPVSGINGDIRAKKIASIADVCESMKEQLLVLVEW 60

Query: 200 AKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV 259
           AK+IP F  LPL+DQV LLRA   E L+   + RS+  KD +LL     V R     A +
Sbjct: 61  AKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVLLLGNDYIVPRHCPELAEM 120

Query: 260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEE 319
             +  R+L ELV   +E+++D  E   L+ II F+PD +GL     ++ LR +V  SLE+
Sbjct: 121 SRVSIRILDELVLPFQELQIDDNEYAYLKAIIFFDPDAKGLSDPGKIKRLRSQVQVSLED 180

Query: 320 YTRVNHSEEPGRFAKLLLRLPSLRSI 345
           Y      +  GRF +LLL LP+L+SI
Sbjct: 181 YINDRQYDSRGRFGELLLLLPTLQSI 206

>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 =  252 bits (645), Expect = 1e-82
 Identities = 62/236 (26%), Positives = 112/236 (47%), Gaps = 14/236 (5%)

Query: 123 MKREAVQEERQRTKERDSNEVESTSGTL---IEMPVERILEAEQRVDMKQEPADQDIVNE 179
           M +E+V+ +R + K+  S +  + S  +   ++   E+I +A Q          +   N 
Sbjct: 1   MSKESVRNDRNKKKKEPSKQECTESYEMTAELDDLTEKIRKAHQETFPSLCQLGKYTTNS 60

Query: 180 ----------QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIAS 229
                            +   K + ++V++AK +P FT L + DQ+ LL+A   ++LI  
Sbjct: 61  SADHRVRLDLGLWDKFSELATKCIIKIVEFAKRLPGFTGLTIADQITLLKAACLDILILR 120

Query: 230 FSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRT 289
              R    +D +  + G+T+ R+  H AG G + D V     +++  ++MD TE G L  
Sbjct: 121 ICTRYTPEQDTMTFSDGLTLNRTQMHNAGFGPLTDLVF-TFANQLLPLEMDDTETGLLSA 179

Query: 290 IILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           I L   D + L+    V+ L+E +  +L+ Y R     +P  F K+L+++  LRSI
Sbjct: 180 ICLICGDRQDLEEPTKVDKLQEPLLEALKIYIRKRRPSKPHMFPKILMKITDLRSI 235

>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 =  248 bits (634), Expect = 4e-81
 Identities = 50/247 (20%), Positives = 102/247 (41%), Gaps = 12/247 (4%)

Query: 107 RNRCQYCRYQKCLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQRVD 166
            +   + R++  +  G    +             ++  S S       V+  L     + 
Sbjct: 26  DSYSDFVRFRPPVREGPVTRSASRAASL---HSLSDASSDSFNHSPESVDTKLNFSNLLM 82

Query: 167 MKQEPADQDIVNEQQA------TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRA 220
           M Q+    D   E Q        ++       + +++ +AK IP F  L  EDQ+ LL++
Sbjct: 83  MYQDSGSPDSSEEDQQSRLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKS 142

Query: 221 GWNELLIASFSHRSISVKDGILL--APGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMK 278
              E+++   + +S S++D       P      +   +AG        L +    ++++K
Sbjct: 143 SAIEIIMLRSN-QSFSLEDMSWSCGGPDFKYCINDVTKAGHTLELLEPLVKFQVGLKKLK 201

Query: 279 MDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLR 338
           + + E   L  I L +PD  G++    +E L++++   L+ Y R+ H      +AK++ +
Sbjct: 202 LHEEEHVLLMAICLLSPDRPGVQDHVRIEALQDRLCDVLQAYIRIQHPGGRLLYAKMIQK 261

Query: 339 LPSLRSI 345
           L  LRS+
Sbjct: 262 LADLRSL 268

>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 =  243 bits (623), Expect = 2e-79
 Identities = 62/262 (23%), Positives = 107/262 (40%), Gaps = 17/262 (6%)

Query: 94  CREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEM 153
            R+ +    DK + N    C        G+K+E   +      +  S           E 
Sbjct: 26  KRKEKKAQKDKDKPNSTTSCSPD-----GIKQEIDPQRLDTDSQLLSVNGVKPITPEQEE 80

Query: 154 PVERILEAEQRVDMKQEPADQDIVN---------EQQATNICKATDKQLFQLVDWAKHIP 204
            + R++  +   +       + IVN         E++  +I + T   +  +V+++K +P
Sbjct: 81  LIHRLVYFQNEYEHPSPEDIKRIVNAAPEEENVAEERFRHITEITILTVQLIVEFSKRLP 140

Query: 205 HFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFD 264
            F  L  EDQ+ LL+A  +E+++   + R  +  D IL A      R S   AG+G   +
Sbjct: 141 GFDKLIREDQIALLKACSSEVMMFRMARRYDAETDSILFATNQPYTRESYTVAGMGDTVE 200

Query: 265 RVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVN 324
            +L      M  MK+D  E   L  I++F+ +   L     VE ++E    +L+ Y    
Sbjct: 201 DLL-RFCRHMCAMKVDNAEYALLTAIVIFS-ERPSLSEGWKVEKIQEIYIEALKAYVENR 258

Query: 325 HS-EEPGRFAKLLLRLPSLRSI 345
                   FAKLL  L  LR++
Sbjct: 259 RKPYATTIFAKLLSVLTELRTL 280

>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 =  241 bits (617), Expect = 5e-79
 Identities = 97/221 (43%), Positives = 141/221 (63%), Gaps = 27/221 (12%)

Query: 152 EMPVERILEAEQRVDMKQE-------PADQDIVNEQQA--TNICKATDKQLFQLVDWAKH 202
           E+ +ER+LE E  V    E         D ++  + +A  +++C+  +KQ+  LV WA+ 
Sbjct: 5   ELSIERLLEMESLVADPSEEFQFLRVGPDSNVPPKFRAPVSSLCQIGNKQIAALVVWARD 64

Query: 203 IPHFTTLPLEDQVLLLRAGWNELLIASFSHRSI------------------SVKDGILLA 244
           IPHF+ L +EDQ+LL++  WNELL+ + + RS+                  S    + L 
Sbjct: 65  IPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLTEERDGVDGTGNRTTSPPQLMCLM 124

Query: 245 PGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQ 304
           PG+T++R+SA +AGVG IFDRVL+EL  KMR +++D+ E   L+ IIL NPDV+GLK++Q
Sbjct: 125 PGMTLHRNSALQAGVGQIFDRVLSELSLKMRTLRVDQAEYVALKAIILLNPDVKGLKNRQ 184

Query: 305 VVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            VE+LREK++  L+EY R + S E GRFA LLLRLP+LRSI
Sbjct: 185 EVEVLREKMFLCLDEYCRRSRSSEEGRFAALLLRLPALRSI 225

>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 =  239 bits (612), Expect = 2e-78
 Identities = 60/198 (30%), Positives = 106/198 (53%), Gaps = 5/198 (2%)

Query: 152 EMPVERILEAEQRVDMKQEPADQDIVNEQQA----TNICKATDKQLFQLVDWAKHIPHFT 207
           + P  +I+      + ++  A  D           T +C   D++L  ++ WAKHIP F+
Sbjct: 16  KKPYNKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFS 75

Query: 208 TLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVL 267
           TL L DQ+ LL++ W E+LI    +RS+S +D ++ A    +    +  AG+  + + +L
Sbjct: 76  TLSLADQMSLLQSAWMEILILGVVYRSLSFEDELVYADDYIMDEDQSKLAGLLDLNNAIL 135

Query: 268 TELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSE 327
            +LV K + MK++K E   L+ I L N D   ++  + V+ L++ ++ +L++Y    H E
Sbjct: 136 -QLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHME 194

Query: 328 EPGRFAKLLLRLPSLRSI 345
           +P R  K+L+ LP LR  
Sbjct: 195 DPRRAGKMLMTLPLLRQT 212

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

 Score =  238 bits (608), Expect = 6e-78
 Identities = 48/199 (24%), Positives = 94/199 (47%), Gaps = 6/199 (3%)

Query: 152 EMPVERILEAEQRVDMKQEPADQDIVNEQQA----TNICKATDKQLFQLVDWAKHIPHFT 207
           +     IL+A  +  +    +  +            ++ K  +++L  L++WAK++P +T
Sbjct: 4   KSQTVTILQALNKAALPVLESHHNHGQPPTKVHLLNSLVKLAERELVHLINWAKNVPGYT 63

Query: 208 TLPLEDQVLLLRAGWNELLIASFSHRSISV-KDGILLAPGVTVYRSSAHEAGVGGIFDRV 266
            L L DQV L+   W ELL+ + + RSI      +  AP + + RSS     +  IF++V
Sbjct: 64  DLSLSDQVHLIECCWMELLLLNCAFRSIEHGGKSLAFAPDLVLDRSSWSTVEMTEIFEQV 123

Query: 267 LTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHS 326
              +  +M +  + K EL  L+ ++L N +VR L S   +  +++ +  ++ +  +  H 
Sbjct: 124 A-AVSEQMMQNHLHKDELLLLQAMVLVNAEVRRLASYNQIFNMQQSLLDAIVDTAQKYHP 182

Query: 327 EEPGRFAKLLLRLPSLRSI 345
           +       +LL L  +R  
Sbjct: 183 DNVRHVPAVLLLLTHIRQA 201

>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 =  239 bits (611), Expect = 7e-78
 Identities = 49/237 (20%), Positives = 97/237 (40%), Gaps = 16/237 (6%)

Query: 122 GMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQRVDMKQEPADQDIVNEQQ 181
            ++ ++++  R R   +  +  E +  +     +  ++ A    +      D        
Sbjct: 5   VVRTDSLKGRRGRLPSKPKSPQEPSPPSPPVSLISALVRAHVDSNPAMTSLDYSRFQANP 64

Query: 182 A-----------TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASF 230
                                 +  +  WA+ IP F  LP  DQ LL  + + EL +   
Sbjct: 65  DYQMSGDDTQHIQQFYDLLTGSMEIIRGWAEKIPGFADLPKADQDLLFESAFLELFVLRL 124

Query: 231 SHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTI 290
           ++RS  V+  ++   GV ++R      G G   D ++ E  S ++ M +D +   C+  +
Sbjct: 125 AYRSNPVEGKLIFCNGVVLHRLQCVR-GFGEWIDSIV-EFSSNLQNMNIDISAFSCIAAL 182

Query: 291 ILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNH--SEEPGRFAKLLLRLPSLRSI 345
            +   +  GLK  + VE L+ K+   L+++   N+     P   +KLL +LP LR++
Sbjct: 183 AMVT-ERHGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLGKLPELRTL 238

>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 =  237 bits (606), Expect = 2e-77
 Identities = 54/202 (26%), Positives = 101/202 (50%), Gaps = 9/202 (4%)

Query: 152 EMPVERILEAEQRVDMKQEPADQDIVNEQQA----TNICKATDKQLFQLVDWAKHIPHFT 207
           + PV  ++     V+ ++  A  D             +C   D+++   + WAK IP F+
Sbjct: 16  QGPVNALVSHLLVVEPEKLYAMPDPAGPDGHLPAVATLCDLFDREIVVTISWAKSIPGFS 75

Query: 208 TLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVL 267
           +L L DQ+ +L++ W E+L+   + RS+ ++D +  A  + +    A  AG+G +   +L
Sbjct: 76  SLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQDELAFAEDLVLDEEGARAAGLGELGAALL 135

Query: 268 TELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNH-- 325
            +LV +++ +++++ E   L+ + L N D   ++  + VE LRE ++ +L EY       
Sbjct: 136 -QLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQLREALHEALLEYEAGRAGP 194

Query: 326 --SEEPGRFAKLLLRLPSLRSI 345
               E  R  +LLL LP LR  
Sbjct: 195 GGGAERRRAGRLLLTLPLLRQT 216

>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 =  233 bits (597), Expect = 3e-76
 Identities = 59/213 (27%), Positives = 104/213 (48%), Gaps = 12/213 (5%)

Query: 145 STSGTLIEMPVERILEAEQ--------RVDMKQEPADQDIVNEQQATNICKATDKQLFQL 196
           S+ G  +   + ++L+ E          V   QEPA          + +C+  D+    +
Sbjct: 2   SSGGPNVPELILQLLQLEPEEDQVRARIVGCLQEPAKSRSDQPAPFSLLCRMADQTFISI 61

Query: 197 VDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISV--KDGILLAPGVTVYRSSA 254
           VDWA+    F  L + DQ+ LL+  W+ELL+    +R +    +D ILL  G  V  S+ 
Sbjct: 62  VDWARRCMVFKELEVADQMTLLQNSWSELLVLDHIYRQVQYGKEDSILLVTGQEVELSTV 121

Query: 255 HEAGVGGIFDRV--LTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREK 312
                  +   V    ELV ++  +++D+ E  CL+ +ILF+ DV+ L +  +V+  +EK
Sbjct: 122 AVQAGSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILFSLDVKFLNNHSLVKDAQEK 181

Query: 313 VYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
              +L +YT  ++     +F +LLL L  +R++
Sbjct: 182 ANAALLDYTLSHYPHSGDKFQQLLLSLVEVRAL 214

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

 Score =  232 bits (594), Expect = 2e-75
 Identities = 93/238 (39%), Positives = 138/238 (57%), Gaps = 38/238 (15%)

Query: 146 TSGTLIEMPVERILEAEQRVDMKQEPADQDIVNEQQAT-----------NICKATDKQLF 194
           T+    +  +ERI+EAEQR + +        +     +            +C+  +KQLF
Sbjct: 2   TNSVSRDFSIERIIEAEQRAETQCGDRALTFLRVGPYSTVQPDYKGAVSALCQVVNKQLF 61

Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDG-------------- 240
           Q+V++A+ +PHF  +PL+DQV+LL+A W ELLIA+ +  SI   D               
Sbjct: 62  QMVEYARMMPHFAQVPLDDQVILLKAAWIELLIANVAWCSIVSLDDGGAGGGGGGLGHDG 121

Query: 241 -------------ILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCL 287
                        + L    + +R+SA +AGV  IFDR+L+EL  KM+ + +D+ EL CL
Sbjct: 122 SFERRSPGLQPQQLFLNQSFSYHRNSAIKAGVSAIFDRILSELSVKMKRLNLDRRELSCL 181

Query: 288 RTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           + IIL+NPD+RG+KS+  +EM REKVY  L+E+ R+ H  + GRFA+LLLRLP+LRSI
Sbjct: 182 KAIILYNPDIRGIKSRAEIEMCREKVYACLDEHCRLEHPGDDGRFAQLLLRLPALRSI 239

>3kmr_A Retinoic acid receptor alpha; nuclear receptor transcription factor ligand binding domain, binding, metal-binding, nucleus, phosphoprotein; HET: EQN; 1.80A {Homo sapiens} PDB: 3kmz_B* 3a9e_B* 4dm6_A* 1xap_A* 4dm8_A* 2lbd_A* 3lbd_A* 4lbd_A* Length = 266

 Score =  231 bits (591), Expect = 6e-75
 Identities = 59/236 (25%), Positives = 105/236 (44%), Gaps = 24/236 (10%)

Query: 120 NMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQRV---------DMKQE 170
           + G+      E    T E             +   +E++ +A Q                
Sbjct: 11  SSGLVPRGSHESYTLTPE-------------VGELIEKVRKAHQETFPALCQLGKYTTNN 57

Query: 171 PADQDIVNEQQA-TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIAS 229
            ++Q +  +        + + K + + V++AK +P FTTL + DQ+ LL+A   ++LI  
Sbjct: 58  SSEQRVSLDIDLWDKFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILR 117

Query: 230 FSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRT 289
              R    +D +  + G+T+ R+  H AG G + D V     +++  ++MD  E G L  
Sbjct: 118 ICTRYTPEQDTMTFSDGLTLNRTQMHNAGFGPLTDLVF-AFANQLLPLEMDDAETGLLSA 176

Query: 290 IILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           I L   D + L+    V+ML+E +  +L+ Y R      P  F K+L+++  LRSI
Sbjct: 177 ICLICGDRQDLEQPDRVDMLQEPLLEALKVYVRKRRPSRPHMFPKMLMKITDLRSI 232

>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 =  230 bits (587), Expect = 9e-75
 Identities = 71/202 (35%), Positives = 102/202 (50%), Gaps = 1/202 (0%)

Query: 145 STSGTLIEMPVERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIP 204
           S S + +   +  +L AE     +         N     NIC+   + LF  V+WA++IP
Sbjct: 2   SNSHSYLSGYISLLLRAEPYPTSRFGSQCMQPNNIMGIENICELAARMLFSAVEWARNIP 61

Query: 205 HFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL-APGVTVYRSSAHEAGVGGIF 263
            F  L + DQV LLR  W+EL + + +  S+ +    LL A G+     SA         
Sbjct: 62  FFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHVAPLLAAAGLHASPMSADRVVAFMDH 121

Query: 264 DRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRV 323
            R+  E V K++ + +D  E  CL+ I+LF  D  GL     VE L+EK   +LEEY R 
Sbjct: 122 IRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVESLQEKSQCALEEYVRS 181

Query: 324 NHSEEPGRFAKLLLRLPSLRSI 345
            +  +P RF KLLLRLPSLR++
Sbjct: 182 QYPNQPTRFGKLLLRLPSLRTV 203

>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 =  227 bits (580), Expect = 9e-74
 Identities = 47/198 (23%), Positives = 91/198 (45%), Gaps = 8/198 (4%)

Query: 152 EMPVERILEAEQRVDMKQEPADQDIVNEQQA----TNICKATDKQLFQLVDWAKHIPHFT 207
           +  +  I+++  +  M QE  ++ +  E  A      + +     +  LV++ K +P F 
Sbjct: 10  QTLLHFIMDSYNKQRMPQEITNKILKEEFSAEENFLILTEMATNHVQVLVEFTKKLPGFQ 69

Query: 208 TLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVL 267
           TL  EDQ+ LL+    E +      RS  + +  L +    +       +G+   +   +
Sbjct: 70  TLDHEDQIALLKGSAVEAMF----LRSAEIFNKKLPSGHSDLLEERIRNSGISDEYITPM 125

Query: 268 TELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSE 327
                 + E+KM + E   L  I++ +PD + +K ++ VE L+E +   L++  +++  E
Sbjct: 126 FSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLCKIHQPE 185

Query: 328 EPGRFAKLLLRLPSLRSI 345
            P  FA LL RL  LR+ 
Sbjct: 186 NPQHFACLLGRLTELRTF 203

>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 =  226 bits (577), Expect = 6e-73
 Identities = 49/238 (20%), Positives = 100/238 (42%), Gaps = 18/238 (7%)

Query: 122 GMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQRVDMKQE----------- 170
           G    ++   +Q  ++   N    T+    +  + R++  ++  +   E           
Sbjct: 1   GSHMASMTGGQQMGRDPLKNVPPLTANQ--KSLIARLVWYQEGYEQPSEEDLKRVTQTWQ 58

Query: 171 PADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASF 230
             + D  ++     I + T   +  +V++AK +P F  +   DQ+ LL+A  +E+++   
Sbjct: 59  SDEDDEDSDMPFRQITEMTILTVQLIVEFAKGLPGFAKISQSDQITLLKACSSEVMMLRV 118

Query: 231 SHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTI 290
           + R  +  D +L A      R +  +AG+  + + +L      M  M MD      L  I
Sbjct: 119 ARRYDAATDSVLFANNQAYTRDNYRKAGMAYVIEDLL-HFCRCMYSMMMDNVHYALLTAI 177

Query: 291 ILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPG---RFAKLLLRLPSLRSI 345
           ++F+ D  GL+   +VE ++     +L  Y    +S  P     F K+L  L  +R++
Sbjct: 178 VIFS-DRPGLEQPLLVEEIQRYYLNTLRVYILNQNSASPRCAVIFGKILGILTEIRTL 234

>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 =  224 bits (573), Expect = 1e-72
 Identities = 52/205 (25%), Positives = 95/205 (46%), Gaps = 11/205 (5%)

Query: 151 IEMPVERILEAEQRV---------DMKQEPADQDIVNEQQA-TNICKATDKQLFQLVDWA 200
           +E  + ++ +A Q                 AD  +  +        +   K + ++V++A
Sbjct: 5   LEELITKVSKAHQETFPSLCQLGKYTTNSSADHRVQLDLGLWDKFSELATKCIIKIVEFA 64

Query: 201 KHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVG 260
           K +P FT L + DQ+ LL+A   ++L+     R    +D +  + G+T+ R+  H AG G
Sbjct: 65  KRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMTFSDGLTLNRTQMHNAGFG 124

Query: 261 GIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEY 320
            + D V      ++  ++MD TE G L  I L   D   L+  + V+ L+E +  +L  Y
Sbjct: 125 PLTDLVF-AFAGQLLPLEMDDTETGLLSAICLICGDRMDLEEPEKVDKLQEPLLEALRLY 183

Query: 321 TRVNHSEEPGRFAKLLLRLPSLRSI 345
            R     +P  F ++L+++  LR I
Sbjct: 184 ARRRRPSQPYMFPRMLMKITDLRGI 208

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

 Score =  226 bits (577), Expect = 1e-72
 Identities = 56/221 (25%), Positives = 98/221 (44%), Gaps = 14/221 (6%)

Query: 137 ERDSNEVESTSGTLIEMPVERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQL 196
           +R      + S T  +  V  +L+AE  +   +    +          +    D++L  +
Sbjct: 2   KRSKKNSLALSLT-ADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHM 60

Query: 197 VDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHE 256
           ++WAK +P F  L L DQV LL   W E+L+     RS+     +L AP + + R+    
Sbjct: 61  INWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKC 120

Query: 257 -AGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDV--------RGLKSQQVVE 307
             G+  IFD +L    S+ R M +   E  CL++IIL N  V        + L+ +  + 
Sbjct: 121 VEGMVEIFDMLL-ATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIH 179

Query: 308 MLREKVYTSLEEYT---RVNHSEEPGRFAKLLLRLPSLRSI 345
            + +K+  +L        +   ++  R A+LLL L  +R +
Sbjct: 180 RVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHM 220

>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 =  223 bits (571), Expect = 4e-72
 Identities = 63/209 (30%), Positives = 107/209 (51%), Gaps = 14/209 (6%)

Query: 151 IEMPVERILEAEQRVDMKQEPADQDIVNEQQA----------TNICKATDKQLFQLVDWA 200
           I   +  +L+ E      Q      +  EQ              +CK  D+ LF +V+WA
Sbjct: 17  IPHLILELLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLFSIVEWA 76

Query: 201 KHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSI--SVKDGILLAPGVTVYRSSAHEAG 258
           +    F  L ++DQ+ LL+  W+ELLI    +R +    +  I L  G  V  S      
Sbjct: 77  RSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQA 136

Query: 259 VGGIFD--RVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTS 316
              + +      ELV+K+R ++ D+ E  CL+ ++LF+ DV+ L++ Q+VE ++E+V  +
Sbjct: 137 GATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAA 196

Query: 317 LEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           L +YT  N+ ++  +F +LLLRLP +R+I
Sbjct: 197 LLDYTMCNYPQQTEKFGQLLLRLPEIRAI 225

>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 =  220 bits (561), Expect = 2e-70
 Identities = 49/234 (20%), Positives = 102/234 (43%), Gaps = 8/234 (3%)

Query: 116 QKCLNMGMKREAVQEERQRTKERDSNEVESTSGTLI-EMPVERILEAEQRV-DMKQEPAD 173
           +   +  +K       + + +   + +    S  +I +M    + E + +   +      
Sbjct: 9   KHLYDSYIKSF--PLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQ 66

Query: 174 QDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHR 233
              V  +        + + + ++ ++AK IP F  L L DQV LL+ G +E++    +  
Sbjct: 67  SKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA-- 124

Query: 234 SISVKDGILLAPGVTVYRSSAHEAGVGGIFD--RVLTELVSKMREMKMDKTELGCLRTII 291
           S+  KDG+L++ G         ++      D      E   K   +++D ++L     +I
Sbjct: 125 SLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVI 184

Query: 292 LFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           + + D  GL + + +E +++ +  +LE   ++NH E    FAKLL ++  LR I
Sbjct: 185 ILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQI 238

>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 =  219 bits (559), Expect = 2e-70
 Identities = 39/189 (20%), Positives = 79/189 (41%), Gaps = 3/189 (1%)

Query: 159 LEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLL 218
                 + +  +P           T+        + Q++ + K +P F +LP+EDQ+ LL
Sbjct: 33  FRPPAHLFIHHQPLPTLAPVLPLVTHFADINTFMVLQVIKFTKDLPVFRSLPIEDQISLL 92

Query: 219 RAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMK 278
           +    E+     +  +  ++    L   +          G    F  +L      +R+++
Sbjct: 93  KGAAVEICHIVLN-TTFCLQTQNFLCGPLRYTIEDGARVGFQVEFLELLFHFHGTLRKLQ 151

Query: 279 MDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNH--SEEPGRFAKLL 336
           + + E   L  + LF+PD  G+  +  ++ L+E++  +L+ Y +       +   +AKLL
Sbjct: 152 LQEPEYVLLAAMALFSPDRPGVTQRDEIDQLQEEMALTLQSYIKGQQRRPRDRFLYAKLL 211

Query: 337 LRLPSLRSI 345
             L  LRSI
Sbjct: 212 GLLAELRSI 220

>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 =  218 bits (557), Expect = 4e-70
 Identities = 55/200 (27%), Positives = 95/200 (47%), Gaps = 8/200 (4%)

Query: 153 MPVERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLE 212
           + VE  L ++  V  K       +        IC++  + LF  + WA+ IP F  L  +
Sbjct: 8   IEVEGPLLSDTHVTFKL-TMPSPMPEYLNVHYICESASRLLFLSMHWARSIPAFQALGQD 66

Query: 213 DQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG-----VGGIFDRV- 266
               L+RA WNEL     +  +  +    +LA  V   ++S  E       +  + + + 
Sbjct: 67  CNTSLVRACWNELFTLGLAQCAQVMSLSTILAAIVNHLQNSIQEDKLSGDRIKQVMEHIW 126

Query: 267 -LTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNH 325
            L E  + M ++ +D  E   L+ I+LF+PD  GL S   +E  +E     L++Y +  +
Sbjct: 127 KLQEFCNSMAKLDIDGYEYAYLKAIVLFSPDHPGLTSTSQIEKFQEAAQMELQDYVQATY 186

Query: 326 SEEPGRFAKLLLRLPSLRSI 345
           SE+  R A++L+RLP+LR +
Sbjct: 187 SEDTYRLARILVRLPALRLM 206

>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 =  216 bits (553), Expect = 9e-70
 Identities = 57/205 (27%), Positives = 89/205 (43%), Gaps = 13/205 (6%)

Query: 152 EMPVERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPL 211
           E  V  +LEAE    +   P+           ++ K  DK+L  ++ WAK IP F  L L
Sbjct: 6   EQLVLTLLEAEPPHVLISRPSAPF-TEASMMMSLTKLADKELVHMISWAKKIPGFVELSL 64

Query: 212 EDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHE-AGVGGIFDRVLTEL 270
            DQV LL + W E+L+     RSI     ++ AP + + R       G+  IFD +L   
Sbjct: 65  FDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKCVEGILEIFDMLL-AT 123

Query: 271 VSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYT--------- 321
            S+ RE+K+   E  C++ +IL N  +  L +         K+   L   T         
Sbjct: 124 TSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAK 183

Query: 322 -RVNHSEEPGRFAKLLLRLPSLRSI 345
             ++  ++  R A LL+ L  +R  
Sbjct: 184 SGISSQQQSMRLANLLMLLSHVRHA 208

>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 =  215 bits (550), Expect = 1e-69
 Identities = 46/175 (26%), Positives = 79/175 (45%), Gaps = 1/175 (0%)

Query: 171 PADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASF 230
             D      +       +    + ++V++AK IP F  L   DQV LL+AG  E+L+  F
Sbjct: 11  YVDPHKSGHEIWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRF 70

Query: 231 SHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTI 290
           +    + +  +    G        H  G G + + +  E   K+  +++   E+     +
Sbjct: 71  ASLFDAKERTVTFLSGKKYSVDDLHSMGAGDLLNSMF-EFSEKLNALQLSDEEMSLFTAV 129

Query: 291 ILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +L + D  G+++   VE L+E +  +L      NH  E   F KLLL+LP LRS+
Sbjct: 130 VLVSADRSGIENVNSVEALQETLIRALRTLIMKNHPNEASIFTKLLLKLPDLRSL 184

>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 =  220 bits (562), Expect = 1e-69
 Identities = 68/253 (26%), Positives = 118/253 (46%), Gaps = 18/253 (7%)

Query: 111 QYCRYQKCLNMGMKREAVQEERQRTKERDSNEV----ESTSGTLIEMPVERILEAEQRVD 166
            Y  Y    +  +K E         +           +++S   I   +  +L+ E    
Sbjct: 68  GYQTYGHFPSRAIKSEYPDPYTSSPESIMGYSYMDSYQTSSPASIPHLILELLKCEPDEP 127

Query: 167 MKQEPADQDIVNEQQA----------TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVL 216
             Q      +  EQ              +CK  D+ LF +V+WA+    F  L ++DQ+ 
Sbjct: 128 QVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMK 187

Query: 217 LLRAGWNELLIASFSHRSI--SVKDGILLAPGVTVYRSSAHEAGVGGIFD--RVLTELVS 272
           LL+  W+ELLI    +R +    +  I L  G  V  S         + +      ELV+
Sbjct: 188 LLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQAGATLNNLMSHAQELVA 247

Query: 273 KMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRF 332
           K+R ++ D+ E  CL+ ++LF+ DV+ L++ Q+VE ++E+V  +L +YT  N+ ++  +F
Sbjct: 248 KLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKF 307

Query: 333 AKLLLRLPSLRSI 345
            +LLLRLP +R+I
Sbjct: 308 GQLLLRLPEIRAI 320

>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 =  216 bits (553), Expect = 1e-69
 Identities = 53/206 (25%), Positives = 93/206 (45%), Gaps = 13/206 (6%)

Query: 152 EMPVERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPL 211
           +  V  +L+AE  +   +    +          +    D++L  +++WAK +P F  L L
Sbjct: 7   DQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTL 66

Query: 212 EDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHE-AGVGGIFDRVLTEL 270
            DQV LL   W E+L+     RS+     +L AP + + R+      G+  IFD +L   
Sbjct: 67  HDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLL-AT 125

Query: 271 VSKMREMKMDKTELGCLRTIILFNPDV--------RGLKSQQVVEMLREKVYTSLEEYT- 321
            S+ R M +   E  CL++IIL N  V        + L+ +  +  + +K+  +L     
Sbjct: 126 SSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMA 185

Query: 322 --RVNHSEEPGRFAKLLLRLPSLRSI 345
              +   ++  R A+LLL L  +R +
Sbjct: 186 KAGLTLQQQHQRLAQLLLILSHIRHM 211

>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 =  214 bits (545), Expect = 3e-68
 Identities = 48/215 (22%), Positives = 92/215 (42%), Gaps = 17/215 (7%)

Query: 142 EVESTSGTLIEMPVERILEAEQRV-----DMKQEPADQDIVNEQQATNICKATDKQLFQL 196
            + + S  L   PV  +   E  +     D  +    ++++     + + +   KQ+ Q+
Sbjct: 2   SLSTISRALTPSPVMVLENIEPEIVYAGYDSSKPDTAENLL-----STLNRLAGKQMIQV 56

Query: 197 VDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGVTVYRSSA 254
           V WAK +P F  LPLEDQ+ L++  W  LL  + S RS    +   L  AP +       
Sbjct: 57  VKWAKVLPGFKNLPLEDQITLIQYSWMSLLSFALSWRSYKHTNSQFLYFAPDLVFNEEKM 116

Query: 255 HEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVR-GLKSQQVVEMLREKV 313
           H++ +  +    + ++  +   +++   E   ++ ++L +   + GLKSQ   E +R   
Sbjct: 117 HQSAMYELCQG-MHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKDGLKSQAAFEEMRTNY 175

Query: 314 YTSLEEYT---RVNHSEEPGRFAKLLLRLPSLRSI 345
              L +       N  +   RF +L   L S+  +
Sbjct: 176 IKELRKMVTKCPNNSGQSWQRFYQLTKLLDSMHDL 210

>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 =  212 bits (542), Expect = 9e-68
 Identities = 54/250 (21%), Positives = 102/250 (40%), Gaps = 22/250 (8%)

Query: 103 DKRQRNRCQYCRYQKCLNMGMKREAVQEERQRTKERDSNEVESTSGT---LIEMPVERIL 159
           D +   +  Y             EA  +     K +    +   +      +   +E + 
Sbjct: 1   DLKSLAKRIY-------------EAYLKNFNMNKVKARVILSGKASNNPPFVIHDMETLC 47

Query: 160 EAEQRVDMKQEP-ADQDIVNEQQATNIC-KATDKQLFQLVDWAKHIPHFTTLPLEDQVLL 217
            AE+ +  K      Q+   E +  + C   + + + +L ++AK IP F  L L DQV L
Sbjct: 48  MAEKTLVAKLVANGIQNKEAEVRIFHCCQCTSVETVTELTEFAKAIPGFANLDLNDQVTL 107

Query: 218 LRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRV--LTELVSKMR 275
           L+ G  E + A  S  S+  KDG+L+A G         ++      D +    +   K  
Sbjct: 108 LKYGVYEAIFAMLS--SVMNKDGMLVAYGNGFITREFLKSLRKPFCDIMEPKFDFAMKFN 165

Query: 276 EMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKL 335
            +++D +++      I+   D  GL +   +E ++E +   L  + + NH ++   F KL
Sbjct: 166 ALELDDSDISLFVAAIICCGDRPGLLNVGHIEKMQEGIVHVLRLHLQSNHPDDIFLFPKL 225

Query: 336 LLRLPSLRSI 345
           L ++  LR +
Sbjct: 226 LQKMADLRQL 235

>1nrl_A Orphan nuclear receptor PXR; PXR, xenobiotic, SRC-1, ligand binding domain, transcription; HET: SRL; 2.00A {Homo sapiens} SCOP: a.123.1.1 PDB: 1ilh_A* 1ilg_A* 1m13_A* 2qnv_A* 3r8d_A* 3ctb_A 3ctc_A 3hvl_A* 1skx_A* 2o9i_A* Length = 316

 Score =  213 bits (545), Expect = 2e-67
 Identities = 50/243 (20%), Positives = 92/243 (37%), Gaps = 19/243 (7%)

Query: 107 RNRCQYCRYQKCLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQRVD 166
                 C   + L    + EA +  + R               L  + V   L  E    
Sbjct: 58  GVLSSGCELPESLQAPSREEAAKWSQVRKD-------------LCSLKVSLQLRGEDGSV 104

Query: 167 MKQEPADQDIVNEQQA--TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNE 224
              +P       E  +   ++   +      ++ +AK I +F  LP+EDQ+ LL+    E
Sbjct: 105 WNYKPPADSGGKEIFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFE 164

Query: 225 LLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTEL 284
           L    F+       +      G   Y       G   +    + +    ++++++ + E 
Sbjct: 165 LCQLRFNTVF--NAETGTWECGRLSYCLEDTAGGFQQLLLEPMLKFHYMLKKLQLHEEEY 222

Query: 285 GCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGR--FAKLLLRLPSL 342
             ++ I LF+PD  G+   +VV+ L+E+   +L+ Y   N  +   R  F K++  L  L
Sbjct: 223 VLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLKIMAMLTEL 282

Query: 343 RSI 345
           RSI
Sbjct: 283 RSI 285

>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 =  211 bits (539), Expect = 3e-67
 Identities = 45/237 (18%), Positives = 85/237 (35%), Gaps = 19/237 (8%)

Query: 122 GMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQRVDMKQEPADQDIVNEQQ 181
           G                  + ++    +   + +  ++ A           D     E  
Sbjct: 1   GSSHH--HHHHSSGLVPRGSHMQPPDASPTNL-LTSLIRAHLDSGPNTAKLDYSKFQELV 57

Query: 182 A-----------TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASF 230
                                 L  +  WA+ IP F  L   DQ LLL + + EL I   
Sbjct: 58  LPRFGKEDAGDVQQFYDLLSGSLDVIRKWAEKIPGFIELSPGDQDLLLESAFLELFILRL 117

Query: 231 SHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTI 290
           ++RS   +  ++   G+ ++R      G G   D +L      +  + +D     CL  +
Sbjct: 118 AYRSKPGEGKLIFCSGLVLHRLQCAR-GFGDWIDNIL-AFSRSLHSLGVDVPAFACLSAL 175

Query: 291 ILFNPDVRGLKSQQVVEMLREKVYTSLEEY--TRVNHSEEPGRFAKLLLRLPSLRSI 345
           +L   D  GL+  + VE L+ ++ + L+E+        +     ++LL +LP LR++
Sbjct: 176 VLIT-DRHGLQDPRRVEELQNRIASCLKEHMAAVAGDPQPASCLSRLLGKLPELRTL 231

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

 Score =  210 bits (537), Expect = 3e-67
 Identities = 48/200 (24%), Positives = 83/200 (41%), Gaps = 3/200 (1%)

Query: 146 TSGTLIEMPVERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPH 205
               L   P      A                 ++   +   +    + ++V++AKHIP 
Sbjct: 33  AHDKLGSSP--GNFNANHASGSPYPHGRSGRTVQEIWEDFSMSFTPAVREVVEFAKHIPG 90

Query: 206 FTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDR 265
           F  L   DQV LL+AG  E+L+  F+         ++     T         G+G +   
Sbjct: 91  FRDLSQHDQVTLLKAGTFEVLMVRFASLFNVKDQTVMFLSRTTYSLQELGAMGMGDLLSA 150

Query: 266 VLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNH 325
           +  +   K+  + + + ELG    ++L + D  G+++   VE L+E +  +L      N 
Sbjct: 151 MF-DFSEKLNSLALTEEELGLFTAVVLVSADRSGMENSASVEQLQETLLRALRALVLKNR 209

Query: 326 SEEPGRFAKLLLRLPSLRSI 345
             E  RF KLLL+LP LR++
Sbjct: 210 PLETSRFTKLLLKLPDLRTL 229

>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 =  209 bits (534), Expect = 8e-67
 Identities = 40/199 (20%), Positives = 83/199 (41%), Gaps = 11/199 (5%)

Query: 155 VERILEAEQRVDMKQEPADQDIVNEQQAT------NICKATDKQLFQLVDWAKHIPHFTT 208
           +  ++ +           D     EQ  +         +     +  +  +A+ IP +  
Sbjct: 16  ITALVRSHVDTTPDPSCLDYSHYEEQSMSEADKVQQFYQLLTSSVDVIKQFAEKIPGYFD 75

Query: 209 LPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLT 268
           L  EDQ LL ++   EL +   ++R+      ++   G  ++R+       G   + ++ 
Sbjct: 76  LLPEDQELLFQSASLELFVLRLAYRARIDDTKLIFCNGTVLHRTQCLR-SFGEWLNDIM- 133

Query: 269 ELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEE 328
           E    +  +++D +   CL  + L   +  GL+  + VE L+ K+  SL ++   N   +
Sbjct: 134 EFSRSLHNLEIDISAFACLCALTLIT-ERHGLREPKKVEQLQMKIIGSLRDHVTYNAEAQ 192

Query: 329 P--GRFAKLLLRLPSLRSI 345
                F++LL +LP LRS+
Sbjct: 193 KKQHYFSRLLGKLPELRSL 211

>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 =  210 bits (535), Expect = 9e-67
 Identities = 40/211 (18%), Positives = 88/211 (41%), Gaps = 11/211 (5%)

Query: 145 STSGTLIEMPVERILEAEQRVDMKQEPADQDIVNEQQA----TNICKATDKQLFQLVDWA 200
           + S       +  ++     ++     A  D      +    T++ +  ++QL  +V W+
Sbjct: 2   TFSPGQDIQLIPPLINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWS 61

Query: 201 KHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGVTVYRSSAHEAG 258
           K +P F  L ++DQ+ L++  W  L++     RS     G +L  AP + +      E+ 
Sbjct: 62  KSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESS 121

Query: 259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNP-DVRGLKSQQVVEMLREKVYTSL 317
              +   +  ++  +  ++++ + E  C++ ++L N   + GL+SQ   E +R      L
Sbjct: 122 FYSLCLTMW-QIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIREL 180

Query: 318 EEYTRVNH---SEEPGRFAKLLLRLPSLRSI 345
            +   +          RF +L   L +L  +
Sbjct: 181 IKAIGLRQKGVVSSSQRFYQLTKLLDNLHDL 211

>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 =  208 bits (532), Expect = 2e-66
 Identities = 57/218 (26%), Positives = 96/218 (44%), Gaps = 16/218 (7%)

Query: 129 QEERQRTKERDSNEVESTSGTLIEMPVERILEAEQRVDMKQEPADQDIVNEQQATNICKA 188
           QEE         NE E  S   ++  + + ++ E + D++               +I + 
Sbjct: 14  QEELIHRLVYFQNEYEHPSEEDVKRIINQPMDGEDQCDVR-------------FRHITEI 60

Query: 189 TDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVT 248
           T   +  +V++AK +P F  L  EDQ+ LL+A  +E+++   + R     D IL      
Sbjct: 61  TILTVQLIVEFAKRLPGFDKLLREDQIALLKACSSEVMMFRMARRYDVQTDSILFVNNQP 120

Query: 249 VYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEM 308
             R S + AG+G   + +L      M  M++D  E   L  I++F+ +   L     VE 
Sbjct: 121 YSRDSYNLAGMGETIEDLL-HFCRTMYSMRVDNAEYALLTAIVIFS-ERPALIEGWKVEK 178

Query: 309 LREKVYTSLEEYTRVNHSEEPGR-FAKLLLRLPSLRSI 345
           ++E    +L  Y       +PG  FAKLL  L  LR++
Sbjct: 179 IQEIYLEALRAYVDNRRKPKPGTIFAKLLSVLTELRTL 216

>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 =  208 bits (532), Expect = 3e-66
 Identities = 57/235 (24%), Positives = 98/235 (41%), Gaps = 12/235 (5%)

Query: 122 GMKREAVQEERQRTKERDSNE-------VESTSGTLIEMPVERILEAEQRVDMKQEPA-- 172
           G   E +    Q+  E    E        E+   T  +    +        D+ Q P   
Sbjct: 1   GSHMEEMIRSLQQRPEPTPEEWDLIHIATEAHRSTNAQGSHWKQRRKFLPDDIGQSPIVS 60

Query: 173 --DQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASF 230
             D D V+ +  +   K     + ++VD+AK +P F+ LP EDQ++LL+    E++    
Sbjct: 61  MPDGDKVDLEAFSEFTKIITPAITRVVDFAKKLPMFSELPXEDQIILLKGCCMEIMSLRA 120

Query: 231 SHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTI 290
           + R     D + L+  + V R      G+G + D +  EL   +    +D TE+  L+ +
Sbjct: 121 AVRYDPESDTLTLSGEMAVKREQLKNGGLGVVSDAIF-ELGKSLSAFNLDDTEVALLQAV 179

Query: 291 ILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +L + D  GL     +E  +E    + E Y        P  + KLL+++  LR I
Sbjct: 180 LLMSTDRSGLLXVDKIEKSQEAYLLAFEHYVNHRKHNIPHFWPKLLMKVTDLRMI 234

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

 Score =  209 bits (533), Expect = 6e-66
 Identities = 48/212 (22%), Positives = 90/212 (42%), Gaps = 7/212 (3%)

Query: 140 SNEVESTSGTLIEMPVERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDW 199
             ++ + S  L   PV  +   E  +      + +    E   + + +   KQ+ Q+V W
Sbjct: 34  VPQLSTISRALTPSPVMVLENIEPEIVYAGYDSSKPDTAENLLSTLNRLAGKQMIQVVKW 93

Query: 200 AKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGVTVYRSSAHEA 257
           AK +P F  LPLEDQ+ L++  W  LL  + S RS    +   L  AP +       H++
Sbjct: 94  AKVLPGFKNLPLEDQITLIQYSWMSLLSFALSWRSYKHTNSQFLYFAPDLVFNEEKMHQS 153

Query: 258 GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVR-GLKSQQVVEMLREKVYTS 316
            +  +    + ++  +   +++   E   ++ ++L +   + GLKSQ   E +R      
Sbjct: 154 AMYELCQG-MHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKDGLKSQAAFEEMRTNYIKE 212

Query: 317 LEEYT---RVNHSEEPGRFAKLLLRLPSLRSI 345
           L +       N  +   RF +L   L S+  +
Sbjct: 213 LRKMVTKCPNNSGQSWQRFYQLTKLLDSMHDL 244

>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 =  206 bits (526), Expect = 2e-65
 Identities = 57/205 (27%), Positives = 89/205 (43%), Gaps = 13/205 (6%)

Query: 152 EMPVERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPL 211
           E  V  +LEAE    +   P+           ++ K  DK+L  ++ WAK IP F  L L
Sbjct: 4   EQLVLTLLEAEPPHVLISRPSAPF-TEASMMMSLTKLADKELVHMISWAKKIPGFVELSL 62

Query: 212 EDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHE-AGVGGIFDRVLTEL 270
            DQV LL + W E+L+     RSI     ++ AP + + R       G+  IFD +L   
Sbjct: 63  FDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKCVEGILEIFDMLL-AT 121

Query: 271 VSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYT--------- 321
            S+ RE+K+   E  C++ +IL N  +  L +         K+   L   T         
Sbjct: 122 TSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAK 181

Query: 322 -RVNHSEEPGRFAKLLLRLPSLRSI 345
             ++  ++  R A LL+ L  +R  
Sbjct: 182 SGISSQQQSMRLANLLMLLSHVRHA 206

>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 =  202 bits (515), Expect = 1e-63
 Identities = 48/209 (22%), Positives = 93/209 (44%), Gaps = 8/209 (3%)

Query: 144 ESTSGTLIEMPVERILEA-EQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKH 202
               G   +     +LEA E  V       +Q        +++ +  ++QL  +V WAK 
Sbjct: 12  SHIEGYECQPIFLNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKA 71

Query: 203 IPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGVTVYRSSAHEAGVG 260
           +P F  L ++DQ+ +++  W  L++ +   RS +  +  +L  AP +       H++ + 
Sbjct: 72  LPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHKSRMY 131

Query: 261 GIFDRVLTELVSKMREMKMDKTELGCLRTIILFN-PDVRGLKSQQVVEMLREKVYTSLEE 319
               R+   L  +   +++   E  C++ ++LF+   V GLK+Q+  + LR      L+ 
Sbjct: 132 SQCVRMR-HLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFFDELRMNYIKELDR 190

Query: 320 YT---RVNHSEEPGRFAKLLLRLPSLRSI 345
                R N +    RF +L   L S++ I
Sbjct: 191 IIACKRKNPTSCSRRFYQLTKLLDSVQPI 219

>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 =  199 bits (507), Expect = 1e-62
 Identities = 37/190 (19%), Positives = 81/190 (42%), Gaps = 3/190 (1%)

Query: 159 LEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLL 218
                RV+        ++       ++       + +++ +AK IP F  L  EDQ++LL
Sbjct: 35  FRPPVRVNDGGGSVTLELSQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLL 94

Query: 219 RAGWNELLIASFSHRSISVKDGILLAPGVTVYR-SSAHEAGVGGIFDRVLTELVSKMREM 277
           ++   E+++   +                  YR S   +AG        L +    ++++
Sbjct: 95  KSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVSDVTKAGHSLELIEPLIKFQVGLKKL 154

Query: 278 KMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGR--FAKL 335
            + + E   L  I + +PD  G++   ++E +++++  +L+ Y R  H        +AK+
Sbjct: 155 NLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLLYAKM 214

Query: 336 LLRLPSLRSI 345
           + +L  LRS+
Sbjct: 215 IQKLADLRSL 224

>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 =  199 bits (508), Expect = 1e-62
 Identities = 59/236 (25%), Positives = 91/236 (38%), Gaps = 13/236 (5%)

Query: 121 MGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQRVDMKQEPADQDIVNEQ 180
           MG                             E  V  +LEAE    +   P+        
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMRELLLDALSPEQLVLTLLEAEPPHVLISRPSAPF-TEAS 59

Query: 181 QATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDG 240
              ++ K  DK+L  ++ WAK IP F  L L DQV LL + W E+L+     RSI     
Sbjct: 60  MMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGK 119

Query: 241 ILLAPGVTVYRSSAHE-AGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRG 299
           ++ AP + + R       G+  IFD +L    S+ RE+K+   E  C++ +IL N  +  
Sbjct: 120 LIFAPDLVLDRDEGKCVEGILEIFDMLL-ATTSRFRELKLQHKEYLCVKAMILLNSSMYP 178

Query: 300 LKSQQVVEMLREKVYTSLEEYT----------RVNHSEEPGRFAKLLLRLPSLRSI 345
           L +         K+   L   T           ++  ++  R A LL+ L  +R  
Sbjct: 179 LVTATQDADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHA 234

>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 =  199 bits (506), Expect = 2e-62
 Identities = 50/244 (20%), Positives = 92/244 (37%), Gaps = 35/244 (14%)

Query: 129 QEERQRTKERDS--NEVESTSGTLIEMPVERILEAEQRVDMKQEPADQDIVNEQQATNIC 186
           +E+ Q+           + T  T  E P     +A         P  Q ++  +    +C
Sbjct: 2   EEQPQQISVASGTPVSADQTPATPQEQPRAPWWDAS--------PGVQRLITLKDPQVVC 53

Query: 187 KATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPG 246
           +A    L + + + K++P F  LPL+ Q++L+R+ W  LL+   +   +  +   +    
Sbjct: 54  EAASAGLLKTLRFVKYLPCFQILPLDQQLVLVRSCWAPLLMLELAQDHLHFEMMEIPETN 113

Query: 247 V---------------------TVYRSSAHEAGVGGIFD----RVLTELVSKMREMKMDK 281
                                    +     A  G +      + +     K   + +D 
Sbjct: 114 TTQEMLTTRRQETEGPEPAEPQATEQPQMVSAEAGHLLPAAAVQAIKSFFFKCWSLNIDT 173

Query: 282 TELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPS 341
            E   L+  +LFNPD+ GL+  + +E L+ +    L E+ R+   E   R A+L   L  
Sbjct: 174 KEYAYLKGTVLFNPDLPGLQCVKYIEGLQWRTQQILTEHIRMMQREYQIRSAELNSALFL 233

Query: 342 LRSI 345
           LR I
Sbjct: 234 LRFI 237

>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 =  197 bits (503), Expect = 7e-62
 Identities = 51/217 (23%), Positives = 92/217 (42%), Gaps = 17/217 (7%)

Query: 140 SNEVESTSGTLIEMPVERILEAEQRV-----DMKQEPADQDIVNEQQATNICKATDKQLF 194
           S+ V +    L    V  +   E  V     D     +   I+     T +     +Q+ 
Sbjct: 2   SHMVPAALPQLTPTLVSLLEVIEPEVLYAGYDSSVPDSAWRIM-----TTLNMLGGRQVI 56

Query: 195 QLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL--APGVTVYRS 252
             V WAK IP F  L L+DQ+ LL+  W  L++ +   RS     G LL  AP + +   
Sbjct: 57  AAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMVFALGWRSYRQASGNLLCFAPDLIINEQ 116

Query: 253 SAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVR-GLKSQQVVEMLRE 311
                 +      +L  + ++++ +++   E  C++T++L +   + GLKSQ++ + +R 
Sbjct: 117 RMTLPCMYDQCKHML-FISTELQRLQVSYEEYLCMKTLLLLSSVPKEGLKSQELFDEIRM 175

Query: 312 KVYTSLEEY---TRVNHSEEPGRFAKLLLRLPSLRSI 345
                L +       N S+   RF +L   L S+  +
Sbjct: 176 TYIKELGKAIAKRGGNSSQNWQRFYQLTKLLDSMHDV 212

>1ynw_B Retinoic acid receptor RXR-alpha, retinoid X receptor; VDR, nuclear receptor, protein-DNA complex, transcripti complex; 3.00A {Homo sapiens} SCOP: g.39.1.2 Length = 99

 Score =  191 bits (487), Expect = 9e-62
 Identities = 78/96 (81%), Positives = 89/96 (92%)

Query: 54  SKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYC 113
           +KH+C+ICGDR+SGKHYGVYSCEGCKGFFKRTVRKDL+Y CR+ ++C+IDKRQRNRCQYC
Sbjct: 2   TKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYC 61

Query: 114 RYQKCLNMGMKREAVQEERQRTKERDSNEVESTSGT 149
           RYQKCL MGMKREAVQEERQR K+R+ NEVESTS  
Sbjct: 62  RYQKCLAMGMKREAVQEERQRGKDRNENEVESTSSA 97

>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 =  196 bits (499), Expect = 7e-61
 Identities = 38/193 (19%), Positives = 85/193 (44%), Gaps = 5/193 (2%)

Query: 157 RILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVL 216
           R      R+D        D+       ++       + +++ +AK IP F  L  +DQ++
Sbjct: 36  RDFRPPVRMDGSTGSVTLDLSPLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIV 95

Query: 217 LLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRS--SAHEAGVGGIFDRVLTELVSKM 274
           LL++   E+++   + +S ++ D                  +AG        L +    +
Sbjct: 96  LLKSSAIEVIMLRSN-QSFTMDDMSWDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGL 154

Query: 275 REMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEE--PGRF 332
           +++ + + E   L  I + +PD  G++  ++VE +++++  +L+ Y R  H        +
Sbjct: 155 KKLNLHEEEHVLLMAICIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLY 214

Query: 333 AKLLLRLPSLRSI 345
           AK++ +L  LRS+
Sbjct: 215 AKMIQKLADLRSL 227

>2han_A Protein ultraspiracle; transcription regulation, transcription factor, DNA-binding, nuclear protein, nuclear receptor, zinc finger; 1.95A {Drosophila melanogaster} SCOP: g.39.1.2 Length = 93

 Score =  179 bits (457), Expect = 3e-57
 Identities = 81/89 (91%), Positives = 82/89 (92%)

Query: 48  NHPLCGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQR 107
           NHPL GSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDL+YACRE RNCIIDKRQR
Sbjct: 3   NHPLSGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYACRENRNCIIDKRQR 62

Query: 108 NRCQYCRYQKCLNMGMKREAVQEERQRTK 136
           NRCQYCRYQKCL  GMKREAVQEERQ   
Sbjct: 63  NRCQYCRYQKCLTCGMKREAVQEERQGIH 91

>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 =  185 bits (471), Expect = 5e-57
 Identities = 39/195 (20%), Positives = 83/195 (42%), Gaps = 4/195 (2%)

Query: 152 EMPVERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQ-LVDWAKHIPHFTTLP 210
           +   E + +   +  +++E  +      +    +C     +  Q +V++AK I  F  L 
Sbjct: 36  QYLREELQQITWQTFLQEEIENYQNKQREVMWQLCAIKITEAIQYVVEFAKRIDGFMELC 95

Query: 211 LEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTEL 270
             DQ++LL+AG  E++      R+   ++  +   G           G       V  E 
Sbjct: 96  QNDQIVLLKAGSLEVVFIRMC-RAFDSQNNTVYFDGKYASPDVFKSLGCEDFISFVF-EF 153

Query: 271 VSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPG 330
              +  M + + E+      +L + D   L+ +  +E L++K+  +L+   + NH  E G
Sbjct: 154 GKSLCSMHLTEDEIALFSAFVLMSADRSWLQEKVKIEKLQQKIQLALQHVLQKNHR-EDG 212

Query: 331 RFAKLLLRLPSLRSI 345
              KL+ ++ +LR++
Sbjct: 213 ILTKLICKVSTLRAL 227

>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 =  183 bits (465), Expect = 2e-56
 Identities = 36/191 (18%), Positives = 83/191 (43%), Gaps = 4/191 (2%)

Query: 156 ERILEAEQRVDMKQEPADQDIVNEQQATNIC-KATDKQLFQLVDWAKHIPHFTTLPLEDQ 214
           E + +   +    +E       + +     C       +  +V++AK I  F  L   DQ
Sbjct: 25  EELHQLAWQTHTYEEIKAYQSKSREALWQQCAIQITHAIQYVVEFAKRITGFMELCQNDQ 84

Query: 215 VLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKM 274
           +LLL++G  E+++        +  +  +L  G           G   + +    +    +
Sbjct: 85  ILLLKSGCLEVVLVRMCRAF-NPLNNTVLFEGKYGGMQMFKALGSDDLVNEAF-DFAKNL 142

Query: 275 REMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAK 334
             +++ + E+    + +L +PD   L   + V+ L+EK+Y +L+   + NH ++    AK
Sbjct: 143 CSLQLTEEEIALFSSAVLISPDRAWLLEPRKVQKLQEKIYFALQHVIQKNHLDDE-TLAK 201

Query: 335 LLLRLPSLRSI 345
           L+ ++P++ ++
Sbjct: 202 LIAKIPTITAV 212

>1dsz_B RXR-alpha, retinoic acid receptor RXR-alpha; RAR, nuclear receptor, protein-DNA, transcription/DNA complex; HET: DNA; 1.70A {Homo sapiens} SCOP: g.39.1.2 PDB: 1by4_A* 1rxr_A 1r0n_A 1r0o_A 2nll_A* Length = 85

 Score =  177 bits (450), Expect = 2e-56
 Identities = 69/82 (84%), Positives = 78/82 (95%)

Query: 53  GSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQY 112
            +KH+C+ICGDR+SGKHYGVYSCEGCKGFFKRTVRKDL+Y CR+ ++C+IDKRQRNRCQY
Sbjct: 3   FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQY 62

Query: 113 CRYQKCLNMGMKREAVQEERQR 134
           CRYQKCL MGMKREAVQEERQR
Sbjct: 63  CRYQKCLAMGMKREAVQEERQR 84

>2a66_A Orphan nuclear receptor NR5A2; protein-DNA complex, zinc finger, DNA- binding domain, transcription factor, FTZ-F1, C-terminal extension; 2.20A {Homo sapiens} PDB: 2ff0_A Length = 113

 Score =  175 bits (445), Expect = 3e-55
 Identities = 48/86 (55%), Positives = 61/86 (70%)

Query: 53  GSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQY 112
             + LC +CGD+ SG HYG+ +CE CKGFFKRTV+ +  Y C E +NC IDK QR RC Y
Sbjct: 7   DLEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQNCQIDKTQRKRCPY 66

Query: 113 CRYQKCLNMGMKREAVQEERQRTKER 138
           CR+QKCL++GMK EAV+ +R R    
Sbjct: 67  CRFQKCLSVGMKLEAVRADRMRGGRN 92

>3g9m_A Glucocorticoid receptor; glucocorticoid, DNA-binding, allostery, lever ARM, transcription, hormone; HET: DNA; 1.61A {Rattus norvegicus} PDB: 3g6p_A* 3g6q_B* 3g6r_B* 3g6u_A* 3g8u_A* 3g8x_A* 3g97_B* 3g99_A* 3g9i_A* 3g9j_A* 3fyl_A* 3g9o_B* 3g9p_B* 3g6t_A* 1r4o_A 1r4r_A 1glu_A* 1gdc_A 2gda_A 1rgd_A ... Length = 90

 Score =  173 bits (441), Expect = 6e-55
 Identities = 38/86 (44%), Positives = 51/86 (59%)

Query: 55  KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCR 114
            H+C +C D ASG HYGV +C  CK FFKR V    +Y C    +CIIDK +R  C  CR
Sbjct: 2   SHMCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACR 61

Query: 115 YQKCLNMGMKREAVQEERQRTKERDS 140
           Y+KCL  GM  EA + +++    + +
Sbjct: 62  YRKCLQAGMNLEARKTKKKIKGIQQA 87

>1lo1_A Steroid hormone receptor ERR2; estrogen related receptor 2, DNA binding domain, HERR2, hormone nuclear receptor; NMR {Homo sapiens} SCOP: g.39.1.2 Length = 98

 Score =  173 bits (440), Expect = 1e-54
 Identities = 43/95 (45%), Positives = 61/95 (64%), Gaps = 1/95 (1%)

Query: 54  SKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYC 113
            K LC +CGD ASG HYGV SCE CK FFKRT++ ++ Y+C     C I KR+R  CQ C
Sbjct: 3   PKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQAC 62

Query: 114 RYQKCLNMGMKREAVQEERQRT-KERDSNEVESTS 147
           R+ K L +GM +E V+ +R R  +++    ++S +
Sbjct: 63  RFMKALKVGMLKEGVRLDRVRGGRQKYKRRLDSEN 97

>2ebl_A COUP transcription factor 1; DNA-binding, metal-binding, nuclear protein, receptor, transcription regulation, zinc, EAR3, erbal3 tfcoup1; NMR {Homo sapiens} Length = 89

 Score =  172 bits (439), Expect = 1e-54
 Identities = 48/81 (59%), Positives = 62/81 (76%)

Query: 53  GSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQY 112
            S   C +CGD++SGKHYG ++CEGCK FFKR+VR++L+Y CR  RNC ID+  RN+CQY
Sbjct: 5   SSGIECVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRANRNCPIDQHHRNQCQY 64

Query: 113 CRYQKCLNMGMKREAVQEERQ 133
           CR +KCL +GM+REAVQ    
Sbjct: 65  CRLKKCLKVGMRREAVQRGSG 85

>1dsz_A RAR-alpha, retinoic acid receptor alpha; RAR, nuclear receptor, protein-DNA, transcription/DNA complex; HET: DNA; 1.70A {Homo sapiens} SCOP: g.39.1.2 PDB: 1hra_A Length = 86

 Score =  172 bits (439), Expect = 1e-54
 Identities = 43/83 (51%), Positives = 62/83 (74%)

Query: 55  KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCR 114
              C +C D++SG HYGV +CEGCKGFF+R+++K++ Y C   +NCII+K  RNRCQYCR
Sbjct: 4   YKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCR 63

Query: 115 YQKCLNMGMKREAVQEERQRTKE 137
            QKC  +GM +E+V+ +R + K+
Sbjct: 64  LQKCFEVGMSKESVRNDRNKKKK 86

>1cit_A NGFI-B, protein (orphan nuclear receptor NGFI-B); early immediate response gene product, transcription factor, monomeric protein-DNA complex; HET: DNA; 2.70A {Rattus norvegicus} SCOP: g.39.1.2 Length = 89

 Score =  172 bits (438), Expect = 2e-54
 Identities = 44/81 (54%), Positives = 61/81 (75%)

Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQK 117
           C++CGD AS +HYGV +CEGCKGFFKRTV+K   Y C   ++C +DKR+RNRCQ+CR+QK
Sbjct: 3   CAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQK 62

Query: 118 CLNMGMKREAVQEERQRTKER 138
           CL +GM +E V+ +  + +  
Sbjct: 63  CLAVGMVKEVVRTDSLKGRRG 83

>1a6y_A Orphan nuclear receptor NR1D1; orphan receptor, DNA-binding, reverb, REV- ERB, transcription regulation, transcription/DNA complex; HET: DNA 5IU; 2.30A {Homo sapiens} SCOP: g.39.1.2 PDB: 1ga5_A* 1hlz_A Length = 94

 Score =  172 bits (437), Expect = 3e-54
 Identities = 45/91 (49%), Positives = 64/91 (70%), Gaps = 1/91 (1%)

Query: 50  PLCGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYA-CREGRNCIIDKRQRN 108
            L G   LC +CGD ASG HYGV +CEGCKGFF+R++++++ Y  C +  NC I +  RN
Sbjct: 2   KLNGMVLLCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRN 61

Query: 109 RCQYCRYQKCLNMGMKREAVQEERQRTKERD 139
           RCQ CR++KCL++GM R+AV+  R   +E+ 
Sbjct: 62  RCQQCRFKKCLSVGMSRDAVRFGRIPKREKQ 92

>2han_B Ecdysone receptor; transcription regulation, transcription factor, DNA-binding, nuclear protein, nuclear receptor, zinc finger; 1.95A {Drosophila melanogaster} SCOP: g.39.1.2 PDB: 1r0o_B 1r0n_B Length = 119

 Score =  171 bits (435), Expect = 1e-53
 Identities = 44/104 (42%), Positives = 59/104 (56%)

Query: 53  GSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQY 112
             + LC +CGDRASG HY   +CEGCKGFF+R+V K   Y C+ GR C +D   R +CQ 
Sbjct: 6   VQEELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQE 65

Query: 113 CRYQKCLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVE 156
           CR +KCL +GM+ E V  E Q   +R   + +     +   P  
Sbjct: 66  CRLKKCLAVGMRPECVVPENQCAMKRREKKAQKEKDKMTTSPSS 109

>1hcq_A Protein (estrogen receptor); protein-DNA complex, complexed with drug, transcription/DNA complex; HET: DNA; 2.40A {Homo sapiens} SCOP: g.39.1.2 PDB: 1hcp_A 4aa6_A Length = 84

 Score =  169 bits (430), Expect = 2e-53
 Identities = 36/81 (44%), Positives = 51/81 (62%)

Query: 54  SKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYC 113
               C++C D ASG HYGV+SCEGCK FFKR+++    Y C     C IDK +R  CQ C
Sbjct: 3   ETRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQAC 62

Query: 114 RYQKCLNMGMKREAVQEERQR 134
           R +KC  +GM +  ++++R+ 
Sbjct: 63  RLRKCYEVGMMKGGIRKDRRG 83

>3cbb_A HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DNA binding domain, nuclear; zinc finger; 2.00A {Homo sapiens} Length = 78

 Score =  169 bits (429), Expect = 3e-53
 Identities = 49/76 (64%), Positives = 63/76 (82%)

Query: 57  LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQ 116
           LC+ICGDRA+GKHYG  SC+GCKGFF+R+VRK+  Y+CR  R C++DK +RN+C+YCR +
Sbjct: 2   LCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLK 61

Query: 117 KCLNMGMKREAVQEER 132
           KC   GMK+EAVQ ER
Sbjct: 62  KCFRAGMKKEAVQNER 77

>1r4i_A Androgen receptor; AR, steroid receptor, protein-DNA complex, transcription/DNA complex; 3.10A {Rattus norvegicus} SCOP: g.39.1.2 Length = 105

 Score =  166 bits (423), Expect = 5e-52
 Identities = 35/95 (36%), Positives = 47/95 (49%)

Query: 55  KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCR 114
           +  C ICGD ASG HYG  +C  CK FFKR       Y C    +C IDK +R  C  CR
Sbjct: 7   QKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCR 66

Query: 115 YQKCLNMGMKREAVQEERQRTKERDSNEVESTSGT 149
            +KC   GM   A + ++    +       S++G+
Sbjct: 67  LRKCYEAGMTLGARKLKKLGNLKLQEEGENSSAGS 101

>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 =  170 bits (433), Expect = 1e-51
 Identities = 31/195 (15%), Positives = 73/195 (37%), Gaps = 6/195 (3%)

Query: 152 EMPVERILEAEQRVDMKQEPADQDIVNEQQA-TNICKATDKQLFQLVDWAKHIPHFTTLP 210
           ++ +E +L     +  ++E       +  +          + +  +V++AK +  F  L 
Sbjct: 27  QLRLEDLLRQRSNIFSREEVTGYQRKSMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELC 86

Query: 211 LEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTEL 270
             DQ++LL+AG  E+++     R+ +  +  +   G           G   +   +  + 
Sbjct: 87  QNDQIVLLKAGAMEVVLVRMC-RAYNADNRTVFFEGKYGGMELFRALGCSELISSIF-DF 144

Query: 271 VSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPG 330
              +  +   + E+     ++L N    GL+ ++ VE L+  +  +   +    H     
Sbjct: 145 SHSLSALHFSEDEIALYTALVLINAHRPGLQEKRKVEQLQYNLELAFHHHLCKTH---RQ 201

Query: 331 RFAKLLLRLPSLRSI 345
                L     LRS+
Sbjct: 202 SILAKLPPKGKLRSL 216

>1kb2_A Vitamin D3 receptor; VDR, nuclear receptor, protein-DNA complex, transcription/DNA complex; 2.70A {Homo sapiens} SCOP: g.39.1.2 PDB: 1kb4_A 1kb6_A 1ynw_A Length = 110

 Score =  165 bits (420), Expect = 1e-51
 Identities = 32/106 (30%), Positives = 59/106 (55%)

Query: 53  GSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQY 112
               +C +CGDRA+G H+   +CEGCKGFF+R++++   + C    +C I K  R  CQ 
Sbjct: 4   NVPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQA 63

Query: 113 CRYQKCLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERI 158
           CR ++C+++GM +E +  + +  ++R+          L +    ++
Sbjct: 64  CRLKRCVDIGMMKEFILTDEEVQRKREMILKRKEEEALKDSLRPKL 109

>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 =  169 bits (430), Expect = 3e-51
 Identities = 37/206 (17%), Positives = 76/206 (36%), Gaps = 12/206 (5%)

Query: 152 EMPVERILEAEQRVDMKQE---PADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTT 208
              ++ I EA + ++   E    A   + NE+   +I    D  + + V  AK +P F  
Sbjct: 10  LQALDLIQEAFKGMNDPMEQGRQATSFLKNEKSPADIMNIMDVTMRRFVKMAKRLPAFND 69

Query: 209 LPLEDQVLLLRAGWNELLIASFSHRSISVKDGIL---LAPGVTVYRSSAHEAGVGGIFDR 265
           L  + +  LL+ G  E+L      R  S         L     V  +   +       ++
Sbjct: 70  LSQDGKFALLKGGMIEMLTVRGVRRFDSSSGSWTTPTLGESSEVSINMFDQLNADVRSEQ 129

Query: 266 V--LTELVSKMRE-MKMDKTELGCLRTIILFNPD--VRGLKSQQVVEMLREKVYTSLEEY 320
                +      E ++ +   +  +  I+LF+P   +   + ++++    E+    L  Y
Sbjct: 130 KMRFLQFFKIFHEDIRSNDLVISMIMLIVLFSPRDSITDPEDRRIIARHHEQFSALLNRY 189

Query: 321 TRVNHSEEPGR-FAKLLLRLPSLRSI 345
               + ++  +   +L   L  LR I
Sbjct: 190 LESLYGDDAHQLNEQLPTALRMLREI 215

>2nll_B Protein (thyroid hormone receptor); complex (transcription regulation/DNA), DNA-binding, nuclear protein, zinc- finger, multigene family; HET: DNA 5IU; 1.90A {Homo sapiens} SCOP: g.39.1.2 PDB: 3m9e_A* Length = 103

 Score =  164 bits (418), Expect = 3e-51
 Identities = 43/99 (43%), Positives = 65/99 (65%), Gaps = 2/99 (2%)

Query: 57  LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDL--SYACREGRNCIIDKRQRNRCQYCR 114
           LC +CGD+A+G HY   +CEGCKGFF+RT++K+L  SY+C+    C+IDK  RN+CQ CR
Sbjct: 3   LCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQECR 62

Query: 115 YQKCLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEM 153
           ++KC+ +GM  + V ++ +R  +R   E         E+
Sbjct: 63  FKKCIYVGMATDLVLDDSKRLAKRKLIEENREKRRREEL 101

>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 =  157 bits (397), Expect = 2e-46
 Identities = 37/206 (17%), Positives = 74/206 (35%), Gaps = 12/206 (5%)

Query: 152 EMPVERILEAEQRVDMKQEPADQDIVNEQQA---TNICKATDKQLFQLVDWAKHIPHFTT 208
              ++ I ++ Q ++   +   Q     ++    T+I    D  + +LV  AK +  F  
Sbjct: 10  LKELDSIRDSFQCMNEPLDNDQQASTLAKKEHNPTDILNVMDITMRRLVKMAKRLGAFNE 69

Query: 209 LPLEDQVLLLRAGWNELLIASFSHR----SISVKDGILLAPGVTVYRSSAHEAGVGGIFD 264
           +    +  LL+ G  E+L               +  +     ++          +     
Sbjct: 70  ISEAGKFSLLKGGMIEMLTIRGVTVFNADKGVWQTPVDGHSQISFNMFDKLRPDIKDTQK 129

Query: 265 RVLTELVSKMRE-MKMDKTELGCLRTIILFNPDVRGLKSQQ---VVEMLREKVYTSLEEY 320
           +      + +   ++ +   +  +  ++LF+    GL SQQ    VE L     + L  Y
Sbjct: 130 KGFLHFFNLLHSDVRKNDLAIDIIVLMVLFDSKREGLVSQQDKETVEKLHRNYESLLHRY 189

Query: 321 TRVNHSEE-PGRFAKLLLRLPSLRSI 345
               H EE   RFA +   L +LR +
Sbjct: 190 LYSIHKEEAEQRFASIPKALVALRKV 215

>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 = 53.3 bits (127), Expect = 6e-08
 Identities = 47/309 (15%), Positives = 97/309 (31%), Gaps = 88/309 (28%)

Query: 76  EGCKGFFKRTVRKD-------LSYACRE-GRNCIIDKRQRNRCQ--------Y--CRYQK 117
           E  + F +  +R +       +    R+      +   QR+R          Y   R Q 
Sbjct: 77  EMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQP 136

Query: 118 CLNMGMKREAVQEERQRTKERDSNEVESTSGTLIE-MP----------VERILEAEQR-- 164
            L +   R+A+ E R                 LI+ +           V    + + +  
Sbjct: 137 YLKL---RQALLELR------------PAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMD 181

Query: 165 -----VDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPH------------FT 207
                +++K   + + ++   Q   +    D       D + +I                
Sbjct: 182 FKIFWLNLKNCNSPETVLEMLQ--KLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLK 239

Query: 208 TLPLEDQVLLLRAGWNELLIASFSH--------RSISVKDGILLAPGVTVYRSSAHEAGV 259
           + P E+ +L+L    N     +F+         R   V D   L+   T + S  H +  
Sbjct: 240 SKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTD--FLSAATTTHISLDHHS-- 295

Query: 260 GGIFDRVLTELVSKMREMKMDKTELGCL-RTIILFNPDVRGLKSQQVVEMLREKVYTSLE 318
             +    +  L+ K  + +        L R ++  NP    +    + E +R+ + T  +
Sbjct: 296 MTLTPDEVKSLLLKYLDCRPQD-----LPREVLTTNPRRLSI----IAESIRDGLAT-WD 345

Query: 319 EYTRVNHSE 327
            +  VN  +
Sbjct: 346 NWKHVNCDK 354

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	347
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	100.0
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	100.0
1lbd_A	282	RXR_LBD, retinoid X receptor; transcription factor	100.0
2han_A	93	Protein ultraspiracle; transcription regulation, t	100.0
1ynw_B	99	Retinoic acid receptor RXR-alpha, retinoid X recep	100.0
2ebl_A	89	COUP transcription factor 1; DNA-binding, metal-bi	100.0
1dsz_B	85	RXR-alpha, retinoic acid receptor RXR-alpha; RAR,	100.0
3cbb_A	78	HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DN	100.0
1dsz_A	86	RAR-alpha, retinoic acid receptor alpha; RAR, nucl	100.0
1hcq_A	84	Protein (estrogen receptor); protein-DNA complex,	100.0
2nxx_A	235	Ultraspiracle (USP, NR2B4); hormone receptor, APO	100.0
1xdk_B	303	RAR-beta, retinoic acid receptor, beta; nuclear re	100.0
2p1t_A	240	Retinoic acid receptor RXR-alpha; protein-ligand c	100.0
1a6y_A	94	Orphan nuclear receptor NR1D1; orphan receptor, DN	100.0
1cit_A	89	NGFI-B, protein (orphan nuclear receptor NGFI-B);	100.0
4hn5_A	117	Glucocorticoid receptor; glucocorticoid receptor,	100.0
1lo1_A	98	Steroid hormone receptor ERR2; estrogen related re	100.0
3g9m_A	90	Glucocorticoid receptor; glucocorticoid, DNA-bindi	100.0
1kb2_A	110	Vitamin D3 receptor; VDR, nuclear receptor, protei	100.0
2nll_B	103	Protein (thyroid hormone receptor); complex (trans	100.0
1g2n_A	264	Ultraspiracle protein; antiparallel alpha-helical	100.0
2e2r_A	244	Estrogen-related receptor gamma; ERR gamma, BPA, n	100.0
2a66_A	113	Orphan nuclear receptor NR5A2; protein-DNA complex	100.0
3k6p_A	248	Steroid hormone receptor ERR1; estrogen related re	100.0
3ltx_A	243	Estrogen receptor; constitutive, nuclear receptor,	100.0
2han_B	119	Ecdysone receptor; transcription regulation, trans	100.0
1r4i_A	105	Androgen receptor; AR, steroid receptor, protein-D	100.0
1hg4_A	279	Ultraspiracle; nuclear hormone receptor, transcrip	100.0
3cqv_A	199	Nuclear receptor subfamily 1 group D member 2; rev	100.0
1fcy_A	236	RAR-gamma-1, retinoic acid receptor gamma-1; isoty	100.0
1ovl_A	271	Orphan nuclear receptor NURR1 (MSe 414, 496, 511);	99.98
3n00_A	245	REV-ERBA-alpha; reverba ncorid1, anti-parallel B-s	99.97
3kmr_A	266	Retinoic acid receptor alpha; nuclear receptor tra	99.97
2iz2_A	243	FTZ-F1 alpha, nuclear hormone receptor FTZ-F1; nuc	99.97
1pzl_A	237	Hepatocyte nuclear factor 4-alpha; transcription;	99.97
3mnp_A	261	Glucocorticoid receptor; protein-ligand complex, s	99.97
3ilz_A	267	Thyroid hormone receptor, alpha isoform 1 variant;	99.97
3ipq_A	283	Oxysterols receptor LXR-alpha; LXR homodimer, LXR	99.97
1nq7_A	244	Nuclear receptor ROR-beta; ligand-binding domain,	99.97
3b0t_A	254	Vitamin D3 receptor; nuclear receptor, transcripti	99.97
2r40_D	266	Ecdysone receptor, 20-hydroxy-ecdysone receptor; n	99.97
3vhv_A	260	Mineralocorticoid receptor; nuclear receptor, tran	99.97
3plz_A	257	FTZ-F1 related protein; alpha helical sandwhich, f	99.97
1ymt_A	246	Steroidogenic factor 1; SF-1, ligand-binding domai	99.97
1yye_A	268	ER-beta, estrogen receptor beta; ER-beta, nuclear	99.97
3oll_A	240	Estrogen receptor beta; steroid binding, phosphory	99.97
1l2j_A	271	Estrogen receptor beta; nuclear receptor, transcri	99.97
2ocf_A	298	Estrogen receptor; estrogen receptor, LBD, monobod	99.97
3vhu_A	294	Mineralocorticoid receptor; nuclear receptor, tran	99.97
2o4j_A	292	Vitamin D3 receptor; nuclear receptor-ligand compl	99.97
2nxx_E	248	Ecdysone receptor (ECR, NRH1); hormone receptor, A	99.97
1pdu_A	244	DHR38, nuclear hormone receptor HR38; nuclear rece	99.97
1n83_A	270	Nuclear receptor ROR-alpha; three-layered alpha he	99.97
1xpc_A	248	Estrogen receptor; nuclear receptor, transcription	99.97
1xvp_B	246	Orphan nuclear receptor NR1I3; CAR, RXR, citco, SR	99.97
2hc4_A	302	Vitamin D receptor; alpha helical sandwich, gene r	99.97
3p0u_A	249	Nuclear receptor subfamily 2 group C member 2; lig	99.97
1sqn_A	261	PR, progesterone receptor; nuclear receptor, stero	99.97
1t7r_A	269	Androgen receptor; nuclear receptor, transcription	99.97
3vi8_A	273	Peroxisome proliferator-activated receptor alpha;	99.97
1z5x_E	310	Ecdysone receptor ligand binding domain; ponastero	99.97
1osh_A	232	BIle acid receptor; nuclear receptor, ligand bindi	99.97
3v3e_B	257	Nuclear receptor subfamily 4 group A member 1; orp	99.97
3cjw_A	244	COUP transcription factor 2; COUP-TFII, nuclear re	99.97
3tx7_B	352	Nuclear receptor subfamily 5 group A member 2; LRH	99.96
1nrl_A	316	Orphan nuclear receptor PXR; PXR, xenobiotic, SRC-	99.96
3f5c_B	268	Nuclear receptor subfamily 0 group B member 1; tra	99.96
3l0l_A	248	Nuclear receptor ROR-gamma; nuclear receptor, rorg	99.96
3u9q_A	269	Peroxisome proliferator-activated receptor gamma;	99.96
3up3_A	243	Acedaf-12; ligand binding domain, nematode, steroi	99.96
3gyt_A	244	Nuclear hormone receptor of the steroid/thyroid ho	99.94
2lze_A	87	A primordial catalytic fold generated by in vitro	99.86
2lze_A	87	A primordial catalytic fold generated by in vitro	93.89

>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=4.9e-69  Score=512.82  Aligned_cols=294  Identities=73%  Similarity=1.194  Sum_probs=251.4

Q ss_pred             CCCCcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHH
Q psy3092          53 GSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEER  132 (347)
Q Consensus        53 ~~~~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r  132 (347)
                      .....|.||||+|+|+||||.+|+|||+||||+|+++..|.|+++++|.+++..|++||+|||+||+++||++++||.+|
T Consensus       135 ~~~~~C~VCg~~a~g~hygv~sC~~Ck~FFrR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r  214 (467)
T 3dzy_A          135 FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER  214 (467)
T ss_dssp             --CEECTTTSSEECSEETTEECCHHHHHHHHHHHHTTCCCCCSSSSCCCCCSSSSSSCHHHHHHHHHHTTCCGGGCCCCS
T ss_pred             CCCCcceeCCCCCCCCcCCCcchhhhhHhccccccCCCceeCCCCCCCCCCcccccccccchhhhhhhccccchhhhccc
Confidence            34567999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             hhhhccccccccCCCCCCCCCcHHHHHHHHHhccCCCCCCcc------ccchhHHHhhhhHHHHHHHHHHHHHHhhCCCC
Q psy3092         133 QRTKERDSNEVESTSGTLIEMPVERILEAEQRVDMKQEPADQ------DIVNEQQATNICKATDKQLFQLVDWAKHIPHF  206 (347)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~l~~~~~w~k~~p~F  206 (347)
                      ++.+.+.....+.+.....+.++++++++...+.........      ..........++++.+.+++.+++|+|+||+|
T Consensus       215 ~~~k~r~~~~~~~~~~~~~~~~~~~ll~a~~~~e~~~~~~~~~~~~~~~~~~~~~~~~l~e~a~~~L~~vVeWAK~iP~F  294 (467)
T 3dzy_A          215 QRGKDRNENEVESTSSANEDMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHF  294 (467)
T ss_dssp             CCCCCCSCSSCTTSTTCSCSSCHHHHHHHHHC----------------------CCTTHHHHHHHHHHHHHHHHHHSTTS
T ss_pred             cccccccccccccccccCCCCchhhhhhhhhhhcccchhhhhhcccCCCCcccchHHHHHHHHHHHHHHHHHHHHhCcch
Confidence            876554333333333344566788888776544332211110      01112234567888999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCchhhHHhhHHHHHHHHHhcCCCHhHHHH
Q psy3092         207 TTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGC  286 (347)
Q Consensus       207 ~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~~~~~~~~~~~l~~~l~~L~l~~~E~~l  286 (347)
                      ++|+.+||+.|||++|.+++++.++++++..++.+++++|..++++.....++..++++++.+++.+|++|++|++||++
T Consensus       295 ~~L~~~DQi~LLK~~w~elliL~~a~rs~~~~~~~ll~~g~~i~~~~~~~~~~~~~~~~il~~lv~~l~~L~ld~~E~~l  374 (467)
T 3dzy_A          295 SELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGC  374 (467)
T ss_dssp             TTSCHHHHHHHHHHHHHHHHHHHHHHHTSSSTTBCCCSSSCCCBTHHHHTTTCHHHHHHHHHHTHHHHHHHTCCHHHHHH
T ss_pred             hcCCHHHHHHHHHhHHHHHHHHHHHHHhccCCCceEecCCceechhhhhhhcchHHHHHHHHHHHHHHHHhcCCHHHHHH
Confidence            99999999999999999999999999999888999999999998888777777888899998999999999999999999


Q ss_pred             HHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhhhhhhccC
Q psy3092         287 LRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIE  346 (347)
Q Consensus       287 L~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll~~lr~i~  346 (347)
                      |+||+||+||+++|++.+.|+++|++++.+|++|++.++++++.||++||++||+||+|+
T Consensus       375 LkAIvLfnpd~~gL~~~~~Ve~lQe~~~~aL~~Y~~~~~p~~p~Rf~kLLl~Lp~LRsi~  434 (467)
T 3dzy_A          375 LRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIG  434 (467)
T ss_dssp             HHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTHHHHHHHHH
T ss_pred             HHHHHHhCcCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999885

>3dzy_D Peroxisome proliferator-activated receptor gamma; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_D* 3e00_D* 2env_A

Probab=100.00  E-value=1.3e-60  Score=450.13  Aligned_cols=287  Identities=33%  Similarity=0.612  Sum_probs=213.0

Q ss_pred             CCcCcccCCCCCCcccccccchhhHHHHHhhhcCCCccc-ccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHh
Q psy3092          55 KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYA-CREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQ  133 (347)
Q Consensus        55 ~~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~-C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~  133 (347)
                      ...|.||||+|+|+||||.+|+|||+||||++.++..|. |  +++|.+++..|+.||+|||+||+++||++++||.+|+
T Consensus        50 ~~~C~vC~~~~~g~hygv~~C~~C~~FFrR~~~~~~~~~~c--~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~vq~~R~  127 (419)
T 3dzy_D           50 AIECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLIYDRC--DLNCRIHKKSRNKCQYCRFQKCLAVGMSHNAIRFGRM  127 (419)
T ss_dssp             CCCCSSSCSCCCSBCSSSBCCHHHHHHHHHHHTTTCCCCCC--CSCCCCCTTGGGTCHHHHHHHHHHTTCCGGGCCCSCC
T ss_pred             CCcCeECCCcCCCCccCcccchhhhHHHccchhcccccccc--cCCCCcccccCccchhhhHHHHhhcccchhheecccc
Confidence            456999999999999999999999999999999998885 6  4689999999999999999999999999999999998


Q ss_pred             hhhccccccccCCCCC-CCCCc---HHH----HHHHHHhc------------cCC---CCCCc----------------c
Q psy3092         134 RTKERDSNEVESTSGT-LIEMP---VER----ILEAEQRV------------DMK---QEPAD----------------Q  174 (347)
Q Consensus       134 ~~~~~~~~~~~~~~~~-~~~~~---~~~----l~~~~~~~------------~~~---~~~~~----------------~  174 (347)
                      +.+.+.....+..... .....   +..    +.++....            ...   ..+..                .
T Consensus       128 ~~~~k~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~a~~~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~l~~ae~~~~~~  207 (419)
T 3dzy_D          128 PQAEKEKLLAEISSDIDQLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFK  207 (419)
T ss_dssp             TTTTGGGSTTTTTSTTTTSCSTTHHHHHHHHHHHHHHHTTCSSCHHHHHHHHHCCSSSCCCEEECSHHHHHCCC------
T ss_pred             cccccccccccccccccCCCCchhhHHHHHHHHHHhhhccCCccchhccccccCCCCCCCCcccccchhhhhcccccccc
Confidence            7544322111111000 00111   111    11111100            000   00000                0


Q ss_pred             cc------chhH--HHhhhhHH-HHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecC
Q psy3092         175 DI------VNEQ--QATNICKA-TDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAP  245 (347)
Q Consensus       175 ~~------~~~~--~~~~~~~~-~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~  245 (347)
                      ..      ..+.  .....+.. ....+..+|+|||++|+|.+|+.+||+.|||++|.+++++.++...  ..++.++.+
T Consensus       208 ~~~~~~~~~~e~~~~~~~~~~~~~~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w~Ell~L~~a~~~--~~~~~~~~~  285 (419)
T 3dzy_D          208 HITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLM--NKDGVLISE  285 (419)
T ss_dssp             ----------CHHHHHHHHHHHHHHHHHHHHHHHHTTSTTTTTSCHHHHHHHHHHHHHHHHHHHHGGGB--CSSEEEEGG
T ss_pred             cCCCcccccchhhhHHHHHHHHHHHHHHHHHHHHhccCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHh--cCCCceeec
Confidence            00      0000  01111222 2345777999999999999999999999999999999999988443  446677776


Q ss_pred             Cccc-cccchhh--cCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q psy3092         246 GVTV-YRSSAHE--AGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTR  322 (347)
Q Consensus       246 g~~i-~~~~~~~--~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~  322 (347)
                      |..+ .++....  .+++++++.+ .+++.+|++|+||++||+||+||+||+||++||++...|+++|+++..+|++|+.
T Consensus       286 ~~~~~~~~~~~~~~~~~~~l~~~i-~~f~~~l~~L~ld~~E~alLkAivLf~pD~~gL~~~~~Ve~lQe~~~~aL~~yi~  364 (419)
T 3dzy_D          286 GQGFMTREFLKSLRKPFGDFMEPK-FEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLK  364 (419)
T ss_dssp             GTEEEEHHHHHSSSGGGSGGGHHH-HHHHHHHHHTCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcccccHHHHHhhhhhHHHHHHHH-HHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            6543 3332221  2355666654 4899999999999999999999999999999999999999999999999999999


Q ss_pred             hcCCCCchHHHHHHhhhhhhhccC
Q psy3092         323 VNHSEEPGRFAKLLLRLPSLRSIE  346 (347)
Q Consensus       323 ~~~~~~~~Rf~~LL~ll~~lr~i~  346 (347)
                      .++++.+.||++||++||+||+|+
T Consensus       365 ~~~p~~~~rf~kLLl~Lp~LR~i~  388 (419)
T 3dzy_D          365 LNHPESSQLFAKLLQKMTDLRQIV  388 (419)
T ss_dssp             HHCTTCTTHHHHHHHHHHHHHHHH
T ss_pred             HhCCChhhHHHHHHHHHHHHHHHH
Confidence            999999999999999999999985

>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=3.8e-41  Score=303.05  Aligned_cols=231  Identities=68%  Similarity=0.999  Sum_probs=174.0

Q ss_pred             HHHHhcCcchhHHHHHHhhhhccccccccCCCCCCCCCcHHHHHHHHHhccCCCCCC------ccccchhHHHhhhhHHH
Q psy3092         116 QKCLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQRVDMKQEPA------DQDIVNEQQATNICKAT  189 (347)
Q Consensus       116 ~KCl~vGM~~~~vq~~r~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~  189 (347)
                      -||++|||++++||.+|++.+.+.....+.+.....+.+++++++++...+......      .........+..+++++
T Consensus        13 ~kCl~vGMkkeaVq~~R~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~a   92 (282)
T 1lbd_A           13 GLVPRGSHKREAVQEERQRGKDRNENEVESTSSANEDMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAA   92 (282)
T ss_dssp             --------------------------------CCTTTSCHHHHHHHHHTTCCCHHHHHHHTTCCCSSCTTCHHHHHHHHH
T ss_pred             CCcCccCCcHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHhcCCccccccccccccCCCccccHHHHHHHHH
Confidence            489999999999999999877654433444444455678999998887655422110      11122334678999999


Q ss_pred             HHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCchhhHHhhHHH
Q psy3092         190 DKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTE  269 (347)
Q Consensus       190 ~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~~~~~~~~~~~  269 (347)
                      ..+++.+++|||.||+|..|+.+||+.|||++|.+++++..+++++...+.+++++|..++++.....++..++++++.+
T Consensus        93 ~~~l~~~vewaK~ip~F~~L~~~DQ~~LLk~~~~el~il~~a~rs~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~  172 (282)
T 1lbd_A           93 DKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTE  172 (282)
T ss_dssp             HHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHGGGGSSSEEECTTSCEEEHHHHHHTTTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcChhcCCHHHHHHHHHHHHHHHHHHHHHHhcccCCCceEecCCcccccchhhhcccHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999889999999998887776666777888888889


Q ss_pred             HHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhhhhhhccC
Q psy3092         270 LVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIE  346 (347)
Q Consensus       270 l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll~~lr~i~  346 (347)
                      ++.+|++|++|++||++|+||+||||+++|+++...|+++|++++.+|.+|+..++++++.||++||++||.||+++
T Consensus       173 ~~~~l~~L~ld~~E~~lLkaivL~~pd~~gLs~~~~v~~lq~~~~~~L~~y~~~~~~~~~~Rf~~LL~~L~~Lr~~~  249 (282)
T 1lbd_A          173 LVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIG  249 (282)
T ss_dssp             HHHHTTTTCCCHHHHHHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHSCCSTTTHHHHHTTHHHHHHHH
T ss_pred             HHHHHHhhcCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999988899999999999999999999999999999999999999875

>2han_A Protein ultraspiracle; transcription regulation, transcription factor, DNA-binding, nuclear protein, nuclear receptor, zinc finger; 1.95A {Drosophila melanogaster} SCOP: g.39.1.2

Probab=100.00  E-value=3.2e-38  Score=230.73  Aligned_cols=84  Identities=92%  Similarity=1.595  Sum_probs=75.7

Q ss_pred             CCCCcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHH
Q psy3092          53 GSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEER  132 (347)
Q Consensus        53 ~~~~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r  132 (347)
                      .+...|.||||+|+|+||||.+|+|||+||||+|.++..|.|+.+++|.|++..|+.||+|||+||+++||++++||.+|
T Consensus         8 ~~~~~C~VCgd~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R   87 (93)
T 2han_A            8 GSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYACRENRNCIIDKRQRNRCQYCRYQKCLTCGMKREAVQEER   87 (93)
T ss_dssp             --CCBCTTTCSBCCEEETTEEECHHHHHHHHHHHHHTCCCCCSSCSCCCCSTTTGGGCHHHHHHHHHHHTCCGGGSCCCC
T ss_pred             CCCCCCcEeCCCCcCeecCcchhHHHHHHHHhhhccccCcCcCCCCcCCcCCCCCccCccccHHHHhHhCCCHHHhhhcc
Confidence            34467999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             hhhh
Q psy3092         133 QRTK  136 (347)
Q Consensus       133 ~~~~  136 (347)
                      ++.+
T Consensus        88 ~~~~   91 (93)
T 2han_A           88 QGIH   91 (93)
T ss_dssp             ----
T ss_pred             Cccc
Confidence            8654

>1ynw_B Retinoic acid receptor RXR-alpha, retinoid X receptor; VDR, nuclear receptor, protein-DNA complex, transcripti complex; 3.00A {Homo sapiens} SCOP: g.39.1.2

Probab=100.00  E-value=1.3e-37  Score=229.89  Aligned_cols=91  Identities=84%  Similarity=1.538  Sum_probs=71.9

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhh
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRT  135 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~  135 (347)
                      ..|.||||+|+|+||||++|+|||+||||+|.++..|.|+.+++|.|++..|+.||+|||+||+++||++++||.+|++.
T Consensus         4 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~~   83 (99)
T 1ynw_B            4 HICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRG   83 (99)
T ss_dssp             -CBTTTBSCCCBCCTTSCBCSHHHHHHHHHHHTTCCCCCSSSSCCCCCSTTSSSCHHHHHHHHHHTTCCSTTCC------
T ss_pred             CCCceeCCCCcceeeCccchHHHHHHHHhhhccccccccCCCCcccccccCCccCccccHHHHhHcCCCHHHhhhccccc
Confidence            46999999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             hccccccccCC
Q psy3092         136 KERDSNEVEST  146 (347)
Q Consensus       136 ~~~~~~~~~~~  146 (347)
                      +.+++.+.+++
T Consensus        84 ~~~~~~~~~~~   94 (99)
T 1ynw_B           84 KDRNENEVEST   94 (99)
T ss_dssp             -----------
T ss_pred             cccCcccccCC
Confidence            77655444443

>2ebl_A COUP transcription factor 1; DNA-binding, metal-binding, nuclear protein, receptor, transcription regulation, zinc, EAR3, erbal3 tfcoup1; NMR {Homo sapiens}

Probab=100.00  E-value=7.8e-37  Score=221.20  Aligned_cols=79  Identities=59%  Similarity=1.283  Sum_probs=76.0

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhh
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQR  134 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~  134 (347)
                      ..|.||||+|+|+||||++|+|||+||||+|.++..|.|+.+++|.|++..|+.||+|||+||+++||++++||.+|++
T Consensus         8 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~   86 (89)
T 2ebl_A            8 IECVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRANRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQRGSGP   86 (89)
T ss_dssp             CBCTTTCSBCCSEETTEECCHHHHHHHHHHHTTTCCCCCSSCSCCCCCSSSSSCCSHHHHHHHHHHTCCHHHHSCSCCC
T ss_pred             CCCcEeCCCCcceEeCchhhHHhhhhhheeeeeccceecccCccCCcCccCccccccchHHHhhhccCCHHHcccCCCC
Confidence            4599999999999999999999999999999999999999999999999999999999999999999999999998775

>1dsz_B RXR-alpha, retinoic acid receptor RXR-alpha; RAR, nuclear receptor, protein-DNA, transcription/DNA complex; HET: DNA; 1.70A {Homo sapiens} SCOP: g.39.1.2 PDB: 1by4_A* 1rxr_A 1r0n_A 1r0o_A 2nll_A*

Probab=100.00  E-value=2.8e-37  Score=221.79  Aligned_cols=79  Identities=86%  Similarity=1.641  Sum_probs=76.1

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhh
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQR  134 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~  134 (347)
                      ..|.||||+|+|+||||.+|+|||+||||++.++..|.|+.+++|.|++..|+.||+|||+||+++||++++||.+|++
T Consensus         6 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~   84 (85)
T 1dsz_B            6 HICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQR   84 (85)
T ss_dssp             EECTTTCCEESSEETTEECCHHHHHHHHHHHHHTCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCCCCC
T ss_pred             CCCCEeCCCCCceeeCccchHHHHHHHHHhhccccceeecccccccccccccccCcchhHHHHhHcCCCHHHhhcccCC
Confidence            5699999999999999999999999999999999999999999999999999999999999999999999999998774

>3cbb_A HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DNA binding domain, nuclear; zinc finger; 2.00A {Homo sapiens}

Probab=100.00  E-value=5.5e-37  Score=216.86  Aligned_cols=77  Identities=64%  Similarity=1.363  Sum_probs=73.2

Q ss_pred             cCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHh
Q psy3092          57 LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQ  133 (347)
Q Consensus        57 ~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~  133 (347)
                      .|.||||+|+|+||||.+|+|||+||||++.++..|.|+.+++|.|++..|+.||+|||+||+++||++++||.+||
T Consensus         2 ~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~Rd   78 (78)
T 3cbb_A            2 LCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNERD   78 (78)
T ss_dssp             BCTTTSSBCCSEETTEECCHHHHHHHHHHHHTTCCCCCSSCSCCCCSTTTTTTCHHHHHHHHHHHTCCGGGCCCC--
T ss_pred             CCeEeCCCCCceEeCCcchhhhceeeeEEEecccCcccccccccCcCccccccChhhhhHHHhHcCCCHHHccccCC
Confidence            49999999999999999999999999999999999999999999999999999999999999999999999998875

>1dsz_A RAR-alpha, retinoic acid receptor alpha; RAR, nuclear receptor, protein-DNA, transcription/DNA complex; HET: DNA; 1.70A {Homo sapiens} SCOP: g.39.1.2 PDB: 1hra_A

Probab=100.00  E-value=1.3e-36  Score=219.09  Aligned_cols=81  Identities=53%  Similarity=1.227  Sum_probs=73.6

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhh
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRT  135 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~  135 (347)
                      ..|.||||+|+|+||||.||+|||+||||++.++..|.|..+++|.|++..|+.||+|||+||+++||++++||.+|++.
T Consensus         5 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~~   84 (86)
T 1dsz_A            5 KPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNKK   84 (86)
T ss_dssp             -CCTTTCSCCCSEETTEECCHHHHHHHHHHHHTTCCCCCSSCSCCCCSTTTGGGCHHHHHHHHHHTTCCGGGSCCC----
T ss_pred             CCCcEECCCccceeeCchhHHHHHHHHHHHhhcccceeeccCCccccCccccccchhhhHHHHHHhCCCHHHhhhccccc
Confidence            46999999999999999999999999999999999999999999999999999999999999999999999999998865


Q ss_pred             h
Q psy3092         136 K  136 (347)
Q Consensus       136 ~  136 (347)
                      +
T Consensus        85 k   85 (86)
T 1dsz_A           85 K   85 (86)
T ss_dssp             -
T ss_pred             c
Confidence            4

>1hcq_A Protein (estrogen receptor); protein-DNA complex, complexed with drug, transcription/DNA complex; HET: DNA; 2.40A {Homo sapiens} SCOP: g.39.1.2 PDB: 1hcp_A 4aa6_A

Probab=100.00  E-value=3.1e-36  Score=215.87  Aligned_cols=78  Identities=46%  Similarity=1.080  Sum_probs=68.5

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHh
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQ  133 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~  133 (347)
                      ..|.||||+|+|+||||.||+|||+||||+|.++..|.|+.+++|.|++..|+.||+|||+||+++||++++||.+|.
T Consensus         5 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~   82 (84)
T 1hcq_A            5 RYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRKDRR   82 (84)
T ss_dssp             CBCTTTCSBCCEEETTEEECHHHHHHHHHHHSSCCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHHTCCC--------
T ss_pred             CcCcEECCCCCCeeeCccchHHhhhhhhhccccccccccccCccCCcCCcCcccChhhhhHHHhHcCCCHHHhcccCC
Confidence            569999999999999999999999999999999999999999999999999999999999999999999999999874

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

Probab=100.00  E-value=1.1e-33  Score=247.63  Aligned_cols=196  Identities=68%  Similarity=1.088  Sum_probs=173.2

Q ss_pred             CCCCcHHHHHHHHHhccCCCCCCcc--ccchhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHH
Q psy3092         150 LIEMPVERILEAEQRVDMKQEPADQ--DIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLI  227 (347)
Q Consensus       150 ~~~~~~~~l~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~  227 (347)
                      ..+.+++++++++...+.. .....  ...+...+..++++....++.+++|||++|+|..|+.+||+.|||++|.++++
T Consensus         6 ~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~l~~~vewaK~ip~F~~L~~~DQ~~LLk~~~~el~~   84 (235)
T 2nxx_A            6 QADMPLERIIEAEKRVECN-DPLVALVVNENNTTVNNICQATHKQLFQLVQWAKLVPHFTSLPLTDQVQLLRAGWNELLI   84 (235)
T ss_dssp             --CCCHHHHHHHHHHTCCC-CCCCBCCCSCSSSHHHHHHHHHHHHHHHHHHHHHHSTTSTTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHhcCCC-ccccccccCccccHHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHhHHHHHH
Confidence            3467788999988776654 22111  11233567899999999999999999999999999999999999999999999


Q ss_pred             HHhhcccccCCCceEecCCccccccchhhcCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHH
Q psy3092         228 ASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVE  307 (347)
Q Consensus       228 l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~  307 (347)
                      +..+|+++...+.+++++|..++++.....++..++++++.+++.+|++|++|++||++|+||+|||||++|+++...++
T Consensus        85 L~~a~rs~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~~lLkaivL~~pd~~gL~~~~~v~  164 (235)
T 2nxx_A           85 AAFSHRSMQAQDAIVLATGLTVNKSTAHAVGVGNIYDRVLSELVNKMKEMKMDKTELGCLRAIILYNPDVRGIKSVQEVE  164 (235)
T ss_dssp             HHHHHTTSSSSSSEECSSSCEECSSSCSSSSCSSSHHHHHHHTHHHHHHHTCCHHHHHHHHHHHHCCTTSTTCSCHHHHH
T ss_pred             HHHHHhcccCCCceEecCCcccccchhhhhchHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCCCHHHHH
Confidence            99999999888999999999998877666667778888888999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhcCCCCchHHHHHHhhhhhhhccC
Q psy3092         308 MLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIE  346 (347)
Q Consensus       308 ~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll~~lr~i~  346 (347)
                      ++|+++..+|.+|+..++++++.||++||++||.||+++
T Consensus       165 ~~q~~~~~aL~~y~~~~~~~~~~Rf~~LL~~L~~Lr~~~  203 (235)
T 2nxx_A          165 MLREKIYGVLEEYTRTTHPNEPGRFAKLLLRLPALRSIG  203 (235)
T ss_dssp             HHHHHHHHHHHHHHHHHCTTCTTHHHHHHTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCCChhhHHHHHHHHhHHHHHHH
Confidence            999999999999999999999999999999999999875

>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=1.8e-33  Score=254.89  Aligned_cols=223  Identities=27%  Similarity=0.422  Sum_probs=163.7

Q ss_pred             cchhHHHHHHhhhhcccccccc-CCCCCC--CCCcHHHHHHHHHhccCCCCC---Ccc-------ccchhHHHhhhhHHH
Q psy3092         123 MKREAVQEERQRTKERDSNEVE-STSGTL--IEMPVERILEAEQRVDMKQEP---ADQ-------DIVNEQQATNICKAT  189 (347)
Q Consensus       123 M~~~~vq~~r~~~~~~~~~~~~-~~~~~~--~~~~~~~l~~~~~~~~~~~~~---~~~-------~~~~~~~~~~~~~~~  189 (347)
                      |++++||.+|.+.++++..... ......  .+..++.++++..........   ...       .......+..++++.
T Consensus         1 M~rEaVr~~R~~~~~~~~~~~~~~~~~~~~~~~~li~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (303)
T 1xdk_B            1 MSKESVRNDRNKKKKEPSKQECTESYEMTAELDDLTEKIRKAHQETFPSLCQLGKYTTNSSADHRVRLDLGLWDKFSELA   80 (303)
T ss_dssp             -----------------------------CCTHHHHHHHHHHHHHHSCCSSSSCCBCCCTTCSSCCSCCHHHHHHHHHHH
T ss_pred             CCHHHHhhccccccccccccCCCCCCCCCHHHHHHHHHHHHHHHHhCccHhhhcccCCCCCccccccchHHHHHHHHHHH
Confidence            8899999999875543211110 000000  112245566665443221110   000       001123578899999


Q ss_pred             HHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCchhhHHhhHHH
Q psy3092         190 DKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTE  269 (347)
Q Consensus       190 ~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~~~~~~~~~~~  269 (347)
                      ...++.+|+|||.+|+|..|+.+||+.|||++|.+++++..++++....+.+++++|..+.++.....++.++++.++ +
T Consensus        81 ~~~l~~~VewaK~iP~F~~L~~~DQi~LLk~~~~el~lL~~a~~s~~~~~~l~~~~g~~~~~~~~~~~g~~~~~~~i~-~  159 (303)
T 1xdk_B           81 TKCIIKIVEFAKRLPGFTGLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMHNAGFGPLTDLVF-T  159 (303)
T ss_dssp             HHHHHHHHHHHHTSTTTSSSCHHHHHHHHHHHHHHHHHHHHHTTEETTTTEEECTTCBEEEHHHHHHTTTGGGHHHHH-H
T ss_pred             HHHHHHHHHHHHcCcccccCCHHHHHHHHHhhHHHHHHHHHHHHhcccCCeEEecCCceecHHHHhhcCcHHHHHHHH-H
Confidence            999999999999999999999999999999999999999999999888888999999988877776667777777765 7


Q ss_pred             HHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhhhhhhccC
Q psy3092         270 LVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIE  346 (347)
Q Consensus       270 l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll~~lr~i~  346 (347)
                      ++.+|++|++|++||+||+||+||+||++||++...|+++|+++..+|.+|+..++++++.||++||++||.||+|+
T Consensus       160 ~~~~l~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL~~L~~Lr~l~  236 (303)
T 1xdk_B          160 FANQLLPLEMDDTETGLLSAICLICGDRQDLEEPTKVDKLQEPLLEALKIYIRKRRPSKPHMFPKILMKITDLRSIS  236 (303)
T ss_dssp             HHHHHGGGCCCHHHHHHHHHHHHSCSCSSSCSSHHHHHHHTHHHHHHHHHHHHHHCTTCTTHHHHHHTHHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999875

>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=1.4e-33  Score=248.00  Aligned_cols=196  Identities=70%  Similarity=1.078  Sum_probs=168.2

Q ss_pred             CCCcHHHHHHHHHhccCCCCCCcc------ccchhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHH
Q psy3092         151 IEMPVERILEAEQRVDMKQEPADQ------DIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNE  224 (347)
Q Consensus       151 ~~~~~~~l~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~  224 (347)
                      .+.+++++++++...+........      ...+...++.++++++.+++.+++|+|++|+|+.|+.+||+.|||++|.+
T Consensus         6 ~~~~~~~~l~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~vewak~ip~F~~L~~~DQ~~LLk~~w~e   85 (240)
T 2p1t_A            6 EDMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNE   85 (240)
T ss_dssp             -CCCHHHHHHHHHHHC-------------------CHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHhcCCccccccccccccCCCCcccHHHHHHHHHHHHHHHHHHHHHhCcChhcCCHHHHHHHHHHHHHH
Confidence            456788888888766654322111      11233457889999999999999999999999999999999999999999


Q ss_pred             HHHHHhhcccccCCCceEecCCccccccchhhcCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHH
Q psy3092         225 LLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQ  304 (347)
Q Consensus       225 ~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~  304 (347)
                      ++++..+++++..++++++++|..++++.....++..++++++.+++.+|++|++|++||++|+||+||||+++|+++..
T Consensus        86 ~~il~~a~rs~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~~~Lkai~l~~pd~~gl~~~~  165 (240)
T 2p1t_A           86 LLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPA  165 (240)
T ss_dssp             HHHHHHHHHTTTSSSEEECTTSCEEEHHHHHTTTCHHHHHHHHHHTHHHHHHTTCCHHHHHHHHHHHHSCTTCTTCSCHH
T ss_pred             HHHHHHHHhhccCCCceEecCCcccccchhhhhchHHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHhcCCCCCCCCHH
Confidence            99999999998888999999998888776666677778888888999999999999999999999999999999999988


Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhhhhhhccC
Q psy3092         305 VVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIE  346 (347)
Q Consensus       305 ~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll~~lr~i~  346 (347)
                      .++++|+++..+|++|+..++++++.||++||++||.||+++
T Consensus       166 ~ve~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~~Lr~~~  207 (240)
T 2p1t_A          166 EVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIG  207 (240)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHHHH
Confidence            899999999999999999999999999999999999999875

>1a6y_A Orphan nuclear receptor NR1D1; orphan receptor, DNA-binding, reverb, REV- ERB, transcription regulation, transcription/DNA complex; HET: DNA 5IU; 2.30A {Homo sapiens} SCOP: g.39.1.2 PDB: 1ga5_A* 1hlz_A

Probab=100.00  E-value=4.8e-36  Score=219.63  Aligned_cols=83  Identities=52%  Similarity=1.119  Sum_probs=74.5

Q ss_pred             CCcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcc-cccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHh
Q psy3092          55 KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSY-ACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQ  133 (347)
Q Consensus        55 ~~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~-~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~  133 (347)
                      ...|.||||+|+|+||||.+|+|||+||||+|.++..| .|..+++|.|++..|+.||+|||+||+++||++++||.+|+
T Consensus         7 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~   86 (94)
T 1a6y_A            7 VLLCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGRI   86 (94)
T ss_dssp             -CBCTTTSSBCCEEETTEEECHHHHHHHHHHHSSCCCCCCCSSTTCCCCCTTTTTSCHHHHHHHHTTTTCCSTTCCCCC-
T ss_pred             CCcCcEeCCCCcceEeCccchhhhhhehheeeecccceEEccCCCCCccCccccccccchhHHHhhHccCCHHHhccCcC
Confidence            35699999999999999999999999999999999999 59999999999999999999999999999999999999887


Q ss_pred             hhhc
Q psy3092         134 RTKE  137 (347)
Q Consensus       134 ~~~~  137 (347)
                      +...
T Consensus        87 ~~~~   90 (94)
T 1a6y_A           87 PKRE   90 (94)
T ss_dssp             ----
T ss_pred             cCch
Confidence            6543

>1cit_A NGFI-B, protein (orphan nuclear receptor NGFI-B); early immediate response gene product, transcription factor, monomeric protein-DNA complex; HET: DNA; 2.70A {Rattus norvegicus} SCOP: g.39.1.2

Probab=100.00  E-value=1.8e-35  Score=214.28  Aligned_cols=78  Identities=56%  Similarity=1.226  Sum_probs=74.6

Q ss_pred             cCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhh
Q psy3092          57 LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQR  134 (347)
Q Consensus        57 ~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~  134 (347)
                      .|.||||+|+|+||||.||+|||+||||+|.++..|.|..+++|.|++..|+.||+|||+||+++||++++||.++..
T Consensus         2 ~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~~~~   79 (89)
T 1cit_A            2 RCAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTDSLK   79 (89)
T ss_dssp             CCSSSCCCCCEEETTEEECHHHHHHHHHHHHHTCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHTTCCGGGSCCGGGT
T ss_pred             CCeEeCCCCcceEeCccchhhhhhhceeeEEecceeeeccCCccccCCCCcccChhhhhHHHhHcCCCHHHeeccccc
Confidence            499999999999999999999999999999999999999999999999999999999999999999999999987654

>4hn5_A Glucocorticoid receptor; glucocorticoid receptor, steroid receptors, NGRE, repre transcription; HET: DNA; 1.90A {Homo sapiens} PDB: 4hn6_A*

Probab=100.00  E-value=2.4e-35  Score=223.59  Aligned_cols=81  Identities=47%  Similarity=0.971  Sum_probs=70.5

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhh
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRT  135 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~  135 (347)
                      ..|.||||+|+|+||||.+|+|||+||||++.++..|.|+.+++|.+++..|+.||+|||+||+++||++++||.+|+..
T Consensus        30 ~~C~VCgd~a~G~HyGv~sC~aCk~FFRRsv~~~~~y~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~avq~kR~~k  109 (117)
T 4hn5_A           30 KLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEARKTKKKIK  109 (117)
T ss_dssp             CBCTTTCSBCCEEETTEEECHHHHHHHHHHHSSCCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHHTCCTTC--------
T ss_pred             CcCCcCCCcCcccccCCcccchhhhhhhcceecCCceecCCCCccccCcccccCCcccchHHHhHcCCCHHHhccccccc
Confidence            56999999999999999999999999999999999999999999999999999999999999999999999999988654


Q ss_pred             h
Q psy3092         136 K  136 (347)
Q Consensus       136 ~  136 (347)
                      .
T Consensus       110 ~  110 (117)
T 4hn5_A          110 G  110 (117)
T ss_dssp             -
T ss_pred             c
Confidence            3

>1lo1_A Steroid hormone receptor ERR2; estrogen related receptor 2, DNA binding domain, HERR2, hormone nuclear receptor; NMR {Homo sapiens} SCOP: g.39.1.2

Probab=100.00  E-value=5.9e-36  Score=220.61  Aligned_cols=81  Identities=51%  Similarity=1.027  Sum_probs=77.3

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhh
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRT  135 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~  135 (347)
                      ..|.||||+|+|+||||++|+|||+||||+|.++..|.|+.+++|.|++..|+.||+|||+||+++||++++||.+|++.
T Consensus         5 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~~   84 (98)
T 1lo1_A            5 RLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKALKVGMLKEGVRLDRVRG   84 (98)
T ss_dssp             CEETTTTEECSEESSSSEECHHHHHHHHHHHHTTCCCCCSSCSCCCCCHHHHHHCHHHHHHHHHHHTCCGGGSCSSCCTT
T ss_pred             CCCcEeCCCCcCeeeCccchhhhhhhheeeecccCccccCccccccccccccccccchhHHHHhHcCCCHHHeecccccC
Confidence            56999999999999999999999999999999999999999999999999999999999999999999999999988764


Q ss_pred             h
Q psy3092         136 K  136 (347)
Q Consensus       136 ~  136 (347)
                      .
T Consensus        85 ~   85 (98)
T 1lo1_A           85 G   85 (98)
T ss_dssp             C
T ss_pred             c
Confidence            4

>3g9m_A Glucocorticoid receptor; glucocorticoid, DNA-binding, allostery, lever ARM, transcription, hormone; HET: DNA; 1.61A {Rattus norvegicus} SCOP: g.39.1.2 PDB: 3g6p_A* 3g6q_B* 3g6r_B* 3g6u_A* 3g8u_A* 3g8x_A* 3g97_B* 3g99_A* 3g9i_A* 3g9j_A* 3fyl_A* 3g9o_B* 3g9p_B* 3g6t_A* 1r4o_A 1r4r_A 1glu_A* 1gdc_A 2gda_A 1rgd_A ...

Probab=100.00  E-value=5.6e-35  Score=213.24  Aligned_cols=83  Identities=46%  Similarity=0.959  Sum_probs=75.0

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhh
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRT  135 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~  135 (347)
                      .+|.||||+|+|+||||.+|+|||+||||++.++..|.|..+++|.+++..|+.|++|||+||+++||++++||.+|+..
T Consensus         3 ~~C~VCg~~a~g~hyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~avq~~r~~~   82 (90)
T 3g9m_A            3 HMCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEARKTKKKIK   82 (90)
T ss_dssp             CBCTTTCSBCCEEETTEEECHHHHHHHHHHHHSCCCCCCSSSSCCCCCTTGGGTCHHHHHHHHHHHTCCTTHHHHHC---
T ss_pred             CcCccCCCcCcccccCCccchhHhHHhhhhhhcCCceeCCCCCccccCcccccCCcchhhHHHHHcCCCHHHhccccccc
Confidence            46999999999999999999999999999999999999999999999999999999999999999999999999998765


Q ss_pred             hcc
Q psy3092         136 KER  138 (347)
Q Consensus       136 ~~~  138 (347)
                      ..+
T Consensus        83 ~~~   85 (90)
T 3g9m_A           83 GIQ   85 (90)
T ss_dssp             ---
T ss_pred             ccc
Confidence            443

>1kb2_A Vitamin D3 receptor; VDR, nuclear receptor, protein-DNA complex, transcription/DNA complex; 2.70A {Homo sapiens} SCOP: g.39.1.2 PDB: 1kb4_A 1kb6_A 1ynw_A

Probab=100.00  E-value=4.3e-35  Score=220.66  Aligned_cols=79  Identities=38%  Similarity=1.014  Sum_probs=74.1

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhh
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQR  134 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~  134 (347)
                      ..|.||||+|+|+||||.+|+|||+||||++.++..|.|+.+++|.|++..|+.||+|||+||+++||++++||.+|+.
T Consensus         7 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~   85 (110)
T 1kb2_A            7 RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDEEV   85 (110)
T ss_dssp             CBCTTTCSBCCSEETTEECCHHHHHHHHHHHHTTCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCHHHH
T ss_pred             CCCcEeCCCCCceEeCchhHhhhhhhheeeeecccceeeCCCCCccCCcccceecccccHhhhhhcCCcHHhcccHHHH
Confidence            5699999999999999999999999999999999999999999999999999999999999999999999976665543

>2nll_B Protein (thyroid hormone receptor); complex (transcription regulation/DNA), DNA-binding, nuclear protein, zinc- finger, multigene family; HET: DNA 5IU; 1.90A {Homo sapiens} SCOP: g.39.1.2 PDB: 3m9e_A*

Probab=100.00  E-value=6.4e-35  Score=217.38  Aligned_cols=82  Identities=49%  Similarity=1.133  Sum_probs=76.7

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCC--cccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHh
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDL--SYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQ  133 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~--~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~  133 (347)
                      ..|.||||+|+|+||||+||+|||+||||++..+.  .|.|..+++|.|++..|+.|++|||+||+++||++++||.+++
T Consensus         2 ~~C~VCgd~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~~~   81 (103)
T 2nll_B            2 ELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQECRFKKCIYVGMATDLVLDDSK   81 (103)
T ss_dssp             CBCTTTCSBCCSEETTEECCHHHHHHHHHHHHTTCGGGCCCSSCTTCCCSTTTTTSCHHHHHHHHHHTTCCGGGSCCHHH
T ss_pred             CCCeEeCCcCcCeecCcccHHHhhhhheecccccccchhhhhccCCcCcCccCccccchhhhHhhhHhCCCHHHhhhhhh
Confidence            46999999999999999999999999999999875  8999999999999999999999999999999999999999887


Q ss_pred             hhhc
Q psy3092         134 RTKE  137 (347)
Q Consensus       134 ~~~~  137 (347)
                      +..+
T Consensus        82 ~~~k   85 (103)
T 2nll_B           82 RLAK   85 (103)
T ss_dssp             HHHH
T ss_pred             hHHh
Confidence            6543

>1g2n_A Ultraspiracle protein; antiparallel alpha-helical sandwich, structural proteomics in europe, spine, structural genomics, gene regulation; HET: EPH; 1.65A {Heliothis virescens} SCOP: a.123.1.1 PDB: 2r40_A* 1r20_A* 1r1k_A* 3ixp_A*

Probab=100.00  E-value=1.1e-32  Score=245.47  Aligned_cols=196  Identities=49%  Similarity=0.829  Sum_probs=169.5

Q ss_pred             CCCcHHHHHHHHHhccCCCCCCc-----cccc-h---hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHH
Q psy3092         151 IEMPVERILEAEQRVDMKQEPAD-----QDIV-N---EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAG  221 (347)
Q Consensus       151 ~~~~~~~l~~~~~~~~~~~~~~~-----~~~~-~---~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~  221 (347)
                      .+.+++++++++...++......     .... .   ...+..++++....++.+++|||++|+|..|+.+||+.|||++
T Consensus         4 ~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~   83 (264)
T 1g2n_A            4 QELSIERLLEMESLVADPSEEFQFLRVGPDSNVPPKFRAPVSSLCQIGNKQIAALVVWARDIPHFSQLEMEDQILLIKGS   83 (264)
T ss_dssp             CCCCHHHHHHHHHCCCCCCCCCCSBCCCTTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHhcCCCCccccccccCCCcccchhhhhHHHHHHHHHHHHHHHHHHHHHcCCChhcCCHHHHHHHHHHh
Confidence            45678888888877665222111     0011 1   2578899999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhcccccC----CCc--------------eEecCCccccccchhhcCchhhHHhhHHHHHHHHHhcCCCHhH
Q psy3092         222 WNELLIASFSHRSISV----KDG--------------ILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTE  283 (347)
Q Consensus       222 ~~~~~~l~~a~~s~~~----~~~--------------~~~~~g~~i~~~~~~~~~~~~~~~~~~~~l~~~l~~L~l~~~E  283 (347)
                      |.+++++..+++++..    .+.              +++++|..++++.....++.+++++.+.+++.+|++|++|++|
T Consensus        84 w~el~lL~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~ld~~E  163 (264)
T 1g2n_A           84 WNELLLFAIAWRSMEFLTEERDGVDGTGNRTTSPPQLMCLMPGMTLHRNSALQAGVGQIFDRVLSELSLKMRTLRVDQAE  163 (264)
T ss_dssp             HHHHHHHHHHHHHGGGSCCC----------CCCCCCEEEEETTEEEEHHHHHHHTCHHHHHHHHHHTHHHHHHTTCCHHH
T ss_pred             hHHHHHHHHHHHccccccccccccccccccccccccceeecCCcccCchhhhhccHHHHHHHHHHHHHHHHHHhCCCHHH
Confidence            9999999999999877    666              8899999888877766777788878888999999999999999


Q ss_pred             HHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhhhhhhccC
Q psy3092         284 LGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIE  346 (347)
Q Consensus       284 ~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll~~lr~i~  346 (347)
                      |++|+||+|||||++||++...|+++|+++..+|++|+..++++++.||++||++||.||+++
T Consensus       164 ~~lLkAivL~npd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~Rf~~LL~~L~~Lr~l~  226 (264)
T 1g2n_A          164 YVALKAIILLNPDVKGLKNRQEVEVLREKMFLCLDEYCRRSRSSEEGRFAALLLRLPALRSIS  226 (264)
T ss_dssp             HHHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHSTTCTTHHHHHHTHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCHhhHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999875

>2e2r_A Estrogen-related receptor gamma; ERR gamma, BPA, nuclear receptor, transcription; HET: 2OH; 1.60A {Homo sapiens} SCOP: a.123.1.1 PDB: 2zas_A* 2zbs_A 2zkc_A* 2p7g_A* 1vjb_A* 1tfc_A 2p7a_A* 2p7z_A* 2gpu_A* 1kv6_A 2gp7_A 2gpp_A* 2gpo_A* 2gpv_A* 1s9q_A* 1s9p_A* 2ewp_A*

Probab=100.00  E-value=1.6e-32  Score=241.48  Aligned_cols=195  Identities=30%  Similarity=0.507  Sum_probs=166.6

Q ss_pred             CCCcHHHHHHHHHhccCCCCCC----ccccchhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHH
Q psy3092         151 IEMPVERILEAEQRVDMKQEPA----DQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELL  226 (347)
Q Consensus       151 ~~~~~~~l~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~  226 (347)
                      .+.++++++......++.....    .........+..++++....++.+++|||++|+|..|+.+||+.|||++|.+++
T Consensus        15 ~~~~~~~~~~~l~~~ep~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~   94 (244)
T 2e2r_A           15 AKKPYNKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEIL   94 (244)
T ss_dssp             --CCCCHHHHHHHHTCCCCCCCCCCTTSCCCHHHHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHhhCCCcccCCCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHhHHHHH
Confidence            4566677777776655432110    111123356889999999999999999999999999999999999999999999


Q ss_pred             HHHhhcccccCCCceEecCCccccccchhhcCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHH
Q psy3092         227 IASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVV  306 (347)
Q Consensus       227 ~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i  306 (347)
                      ++..+++++..++.+++++|..+.++.....++.++++.+. +++.+|++|++|++||++|+||+|||||++|+++...|
T Consensus        95 ~L~~a~rs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-~~~~~l~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~v  173 (244)
T 2e2r_A           95 ILGVVYRSLSFEDELVYADDYIMDEDQSKLAGLLDLNNAIL-QLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVEAV  173 (244)
T ss_dssp             HHHHHHHTTTSSSCEEEETTEEECHHHHHHTTCHHHHHHHH-HHHHHHHHHTCCHHHHHHHHHHHHHTCCCTTCSCHHHH
T ss_pred             HHHHHHHhcccCCeEEecCCEeecHHHhhhccHHHHHHHHH-HHHHHHHHHcCCHHHHHHHHHHHHhccCCCCCcCHHHH
Confidence            99999999998899999999877766555566677776654 89999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhhhhhhccC
Q psy3092         307 EMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIE  346 (347)
Q Consensus       307 ~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll~~lr~i~  346 (347)
                      +++|+++..+|++|+..++++++.||++||++||.||+++
T Consensus       174 ~~lq~~~~~aL~~y~~~~~~~~~~Rf~~LL~~L~~Lr~~~  213 (244)
T 2e2r_A          174 QKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTS  213 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999875

>2a66_A Orphan nuclear receptor NR5A2; protein-DNA complex, zinc finger, DNA- binding domain, transcription factor, FTZ-F1, C-terminal extension; 2.20A {Homo sapiens} PDB: 2ff0_A

Probab=100.00  E-value=3.9e-35  Score=221.39  Aligned_cols=80  Identities=60%  Similarity=1.249  Sum_probs=76.6

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhh
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRT  135 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~  135 (347)
                      ..|.||||+|+|+||||.+|+|||+||||+|..+..|.|+.+++|.|++..|+.||+|||+||+++||++++||.+|++.
T Consensus        10 ~~C~VCgd~a~G~HyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~R~~Cr~CR~~KCl~vGM~~~~vq~~R~~~   89 (113)
T 2a66_A           10 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMRG   89 (113)
T ss_dssp             CBCTTTCCBEEEEETTEEEEHHHHHHHHHHHHTTCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCTTCCCS
T ss_pred             CCCcEeCCCCcceeeCcccHHHHHHHHhhhhhccccccccccccCCcCCCccccccchhHHHHhHhCCCHHHhccccccC
Confidence            46999999999999999999999999999999999999999999999999999999999999999999999999988753

>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=2.6e-32  Score=240.60  Aligned_cols=194  Identities=27%  Similarity=0.462  Sum_probs=163.1

Q ss_pred             CCcHHHHHHHHHhccCCCCCC----ccccchhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHH
Q psy3092         152 EMPVERILEAEQRVDMKQEPA----DQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLI  227 (347)
Q Consensus       152 ~~~~~~l~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~  227 (347)
                      ++++++++.+....++.....    ..+......+..++++..+.++.+++|||++|+|..|+.+||+.|||++|.++++
T Consensus        16 ~~~~~~~~~~l~~~ep~~~~~~~~~~~~~~~~~~~~~l~e~a~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~l   95 (248)
T 3k6p_A           16 QGPVNALVSHLLVVEPEKLYAMPDPAGPDGHLPAVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLV   95 (248)
T ss_dssp             TSCTHHHHHHHHHHSCCCCCCCC-------CCCHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHhcCCcccccCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHhcCcccccCCHHHHHHHHHHHHHHHHH
Confidence            445677777777666532111    1112233568899999999999999999999999999999999999999999999


Q ss_pred             HHhhcccccCCCceEecCCccccccchhhcCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHH
Q psy3092         228 ASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVE  307 (347)
Q Consensus       228 l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~  307 (347)
                      +..+++++..++.+++++|..+.++.....++.++++. +.+++.+|++|++|++||++|+||+|||||++|+++...|+
T Consensus        96 L~~a~~s~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~-l~~~~~~l~~L~ld~~E~~lLkAivL~npd~~gL~~~~~ve  174 (248)
T 3k6p_A           96 LGVAQRSLPLQDELAFAEDLVLDEEGARAAGLGELGAA-LLQLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVE  174 (248)
T ss_dssp             HHHHHHHTTSSSCEEEETTEEECHHHHHHTTTTTHHHH-HHHHHHHHHTTTCCHHHHHHHHHHHHHTCCCTTCSCHHHHH
T ss_pred             HHHHHHccCCCCeEEeCCCcccChhhhhhccHHHHHHH-HHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCHHHHH
Confidence            99999999888999999999888766555555555544 56899999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhcCC----CCchHHHHHHhhhhhhhccC
Q psy3092         308 MLREKVYTSLEEYTRVNHS----EEPGRFAKLLLRLPSLRSIE  346 (347)
Q Consensus       308 ~~r~~~~~~L~~y~~~~~~----~~~~Rf~~LL~ll~~lr~i~  346 (347)
                      ++|+++..+|.+|+..+++    +++.||++||++||.||+++
T Consensus       175 ~lq~~~~~aL~~y~~~~~~~~~~~~~~Rf~~LL~~Lp~Lr~l~  217 (248)
T 3k6p_A          175 QLREALHEALLEYEAGRAGPGGGAERRRAGRLLLTLPLLRQTA  217 (248)
T ss_dssp             HHHHHHHHHHHHHHHTC----CCCCCH-HHHHHTTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCCCCccchHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999998    89999999999999999885

>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=2.5e-32  Score=240.09  Aligned_cols=168  Identities=27%  Similarity=0.467  Sum_probs=154.4

Q ss_pred             hhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCc-eEecCCccccccchhh
Q psy3092         178 NEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDG-ILLAPGVTVYRSSAHE  256 (347)
Q Consensus       178 ~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~-~~~~~g~~i~~~~~~~  256 (347)
                      ....+..++++....++.+++|||++|+|..|+.+||+.|||++|.+++++..+++++..++. +++++|..+.++....
T Consensus        34 ~~~~~~~~~~~a~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~~~l~~~~g~~~~~~~~~~  113 (243)
T 3ltx_A           34 KVHLLNSLVKLAERELVHLINWAKNVPGYTDLSLSDQVHLIECCWMELLLLNCAFRSIEHGGKSLAFAPDLVLDRSSWST  113 (243)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTTTTSEEEEETTEEEEHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHcCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCCeEEecCCcccchhhhcc
Confidence            446688999999999999999999999999999999999999999999999999998877654 7889998888776665


Q ss_pred             cCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHH
Q psy3092         257 AGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLL  336 (347)
Q Consensus       257 ~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL  336 (347)
                      .++.++++.+. +++.+|++|++|++||++|+||+|||||++|+++...|+++|+++..+|.+|+..++++++.||++||
T Consensus       114 ~~~~~~~~~i~-~~~~~l~~L~ld~~E~~lLkaivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL  192 (243)
T 3ltx_A          114 VEMTEIFEQVA-AVSEQMMQNHLHKDELLLLQAMVLVNAEVRRLASYNQIFNMQQSLLDAIVDTAQKYHPDNVRHVPAVL  192 (243)
T ss_dssp             TTCHHHHHHHH-HHHHHHHHTTCCHHHHHHHHHHHHHTSCCSCCTTHHHHHHHHHHHHHHHHHHHHHHSTTCSSHHHHHH
T ss_pred             cCHHHHHHHHH-HHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHH
Confidence            66777777655 89999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhhccC
Q psy3092         337 LRLPSLRSIE  346 (347)
Q Consensus       337 ~ll~~lr~i~  346 (347)
                      ++||.||+++
T Consensus       193 ~~Lp~Lr~l~  202 (243)
T 3ltx_A          193 LLLTHIRQAG  202 (243)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999999875

>2han_B Ecdysone receptor; transcription regulation, transcription factor, DNA-binding, nuclear protein, nuclear receptor, zinc finger; 1.95A {Drosophila melanogaster} SCOP: g.39.1.2 PDB: 1r0o_B 1r0n_B

Probab=100.00  E-value=2e-34  Score=220.43  Aligned_cols=80  Identities=53%  Similarity=1.088  Sum_probs=76.4

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhh
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRT  135 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~  135 (347)
                      ..|.||||+|+|+||||++|+|||+||||+|.++..|.|+.+++|.|++..|+.||+|||+||+++||++++||.+++..
T Consensus         9 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~   88 (119)
T 2han_B            9 ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECRLKKCLAVGMRPECVVPENQCA   88 (119)
T ss_dssp             CBCTTTCSBCCEEETTEEECHHHHHHHHHHHHTTCCCCCSSCSCCCCSTTGGGTCHHHHHHHHHHTTCCGGGSSCSSHHH
T ss_pred             CcCeEeCCcCCcceECchhHHhhHHhhhhheEeccccccccccccccCccccccchhhHHHHHHHhCCCHHHccchhhhh
Confidence            56999999999999999999999999999999999999999999999999999999999999999999999999877653

>1r4i_A Androgen receptor; AR, steroid receptor, protein-DNA complex, transcription/DNA complex; 3.10A {Rattus norvegicus} SCOP: g.39.1.2

Probab=100.00  E-value=2.4e-34  Score=214.49  Aligned_cols=79  Identities=42%  Similarity=0.880  Sum_probs=70.3

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhh
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQR  134 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~  134 (347)
                      ..|.||||+|+|+||||.+|+|||+||||+|..+..|.|+.+++|.|++..|+.||+|||+||+++||++++++..+..
T Consensus         8 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~~k~~k~~   86 (105)
T 1r4i_A            8 KTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLGARKLKKLG   86 (105)
T ss_dssp             CBCSSSCSBEEEEETTEEEEHHHHHHHHHHHTSCCCCCCSSSSCCCCCTTTTTTCHHHHHHHHHHHTCCSCC-------
T ss_pred             CCCcEeCCCCCceEeCCcchhhhhhhhceeEEecCceeeccCCccccCccccccchhchHHHHHhhhcccchhhhcccc
Confidence            4699999999999999999999999999999999999999999999999999999999999999999999998876643

>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=3.7e-32  Score=244.07  Aligned_cols=196  Identities=47%  Similarity=0.793  Sum_probs=155.2

Q ss_pred             CCCcHHHHHHHHHhccCCCCCC-----------ccccchhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHH
Q psy3092         151 IEMPVERILEAEQRVDMKQEPA-----------DQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLR  219 (347)
Q Consensus       151 ~~~~~~~l~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk  219 (347)
                      .+.+++++++++...+......           .........+..+++++...++.+++|||++|+|..|+.+||+.|||
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk   86 (279)
T 1hg4_A            7 RDFSIERIIEAEQRAETQCGDRALTFLRVGPYSTVQPDYKGAVSALCQVVNKQLFQMVEYARMMPHFAQVPLDDQVILLK   86 (279)
T ss_dssp             --CCHHHHHHHHHHHHHHSTTCCCCCBCCCTTCCSCGGGHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHH
T ss_pred             CCcCHHHHHHHHHhcccccccccccccccCCCcCCCchhhhhHHHHHHHHHHHHHHHHHHHhcCCChhhCCHHHHHHHHH
Confidence            4667888888776544321110           00112234688999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcccccCCCc--------eEecCCcccc-------------------ccchhhcCchhhHHhhHHHHHH
Q psy3092         220 AGWNELLIASFSHRSISVKDG--------ILLAPGVTVY-------------------RSSAHEAGVGGIFDRVLTELVS  272 (347)
Q Consensus       220 ~~~~~~~~l~~a~~s~~~~~~--------~~~~~g~~i~-------------------~~~~~~~~~~~~~~~~~~~l~~  272 (347)
                      ++|.+++++..||+++...+.        +++++|.++.                   ++.....++..++++++.+++.
T Consensus        87 ~~~~el~~L~~a~rs~~~~~~~~~~~~~~~~~~dGs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  166 (279)
T 1hg4_A           87 AAWIELLIANVAWCSIVSLDDGGAGGGGGGLGHDGSFERRSPGLQPQQLFLNQSFSYHRNSAIKAGVSAIFDRILSELSV  166 (279)
T ss_dssp             HHHHHHHHHHHHHHTTTTC-------------------------CCCEEESSSSCEEEHHHHHHHTCHHHHHHHHHHTHH
T ss_pred             HHHHHHHHHHHHHHhhhccCcccccccccccccCccccccccccccceeeecCCcccchhhHhhcchHHHHHHHHHHHHH
Confidence            999999999999998876554        4555554322                   2222334667778888889999


Q ss_pred             HHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhhhhhhccC
Q psy3092         273 KMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIE  346 (347)
Q Consensus       273 ~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll~~lr~i~  346 (347)
                      +|++|++|++||++|+||+|||||++|+++...|+++|+++..+|++|+..++++++.||++||++||.||+++
T Consensus       167 ~~~~L~ld~~E~~lLkAivL~npd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL~~L~~Lr~~~  240 (279)
T 1hg4_A          167 KMKRLNLDRRELSCLKAIILYNPDIRGIKSRAEIEMCREKVYACLDEHCRLEHPGDDGRFAQLLLRLPALRSIS  240 (279)
T ss_dssp             HHHHHTCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHH
T ss_pred             HHHHhcCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999875

>3cqv_A Nuclear receptor subfamily 1 group D member 2; reverb beta, heme, NR1D2, DNA-binding, metal-binding, nucleus, repressor, transcription; HET: HEM; 1.90A {Homo sapiens} PDB: 2v7c_A 2v0v_A

Probab=100.00  E-value=5.1e-32  Score=231.06  Aligned_cols=168  Identities=27%  Similarity=0.450  Sum_probs=153.4

Q ss_pred             hhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhc
Q psy3092         178 NEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEA  257 (347)
Q Consensus       178 ~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~  257 (347)
                      ....+..+++.....+..+++|||++|+|.+|+.+||+.|+|++|.+++++..++++....+.+.+++|..+.++.....
T Consensus        18 ~~~~~~~~~~~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~e~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~~   97 (199)
T 3cqv_A           18 GHEIWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLFDAKERTVTFLSGKKYSVDDLHSM   97 (199)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTSGGGGGSCHHHHHHHHHHHHHHHHHHHTGGGEETTTTEEECTTSCEEEHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcCCChhhCCHHHHHHHHHHhHHHHHHHHHHHHhCCCCCeEEecCCCeecHHHHHhc
Confidence            34567888888999999999999999999999999999999999999999999987766677788999998887776666


Q ss_pred             CchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHh
Q psy3092         258 GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLL  337 (347)
Q Consensus       258 ~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~  337 (347)
                      ++.++++.+ .+++.+|++|++|++||++|+||+|||||++|+++...|+++|+++..+|.+|+..++++++.||++||+
T Consensus        98 ~~~~~~~~i-~~~~~~~~~L~ld~~E~~lLkaivL~~pd~~gL~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LL~  176 (199)
T 3cqv_A           98 GAGDLLNSM-FEFSEKLNALQLSDEEMSLFTAVVLVSADRSGIENVNSVEALQETLIRALRTLIMKNHPNEASIFTKLLL  176 (199)
T ss_dssp             TCCHHHHHH-HHHHHHHHTTCCCHHHHHHHHHHHHHTSCCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTHHHHHHHH
T ss_pred             CcHHHHHHH-HHHHHHHHHhCCCHHHHHHHHHHHHhcCCCCCCcCHHHHHHHHHHHHHHHHHHHHHHCCChhhHHHHHHH
Confidence            677777665 5899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhccC
Q psy3092         338 RLPSLRSIE  346 (347)
Q Consensus       338 ll~~lr~i~  346 (347)
                      +||+||+|+
T Consensus       177 ~L~~Lr~l~  185 (199)
T 3cqv_A          177 KLPDLRSLN  185 (199)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999999886

>1fcy_A RAR-gamma-1, retinoic acid receptor gamma-1; isotype selectivity, retinoid ligand complexes, drug design, antiparallel alpha-helical sandwich fold; HET: 564 LMU; 1.30A {Homo sapiens} SCOP: a.123.1.1 PDB: 1fcz_A* 1fcx_A* 1fd0_A* 1exa_A* 1exx_A* 1dkf_B*

Probab=100.00  E-value=5.8e-32  Score=236.87  Aligned_cols=166  Identities=28%  Similarity=0.497  Sum_probs=155.4

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV  259 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~  259 (347)
                      ..+..++++....++.+|+|||++|+|.+|+.+||+.|||++|.+++++..++++....+.+++++|..+.++.....++
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            45788999999999999999999999999999999999999999999999999998888889999999888777666677


Q ss_pred             hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhh
Q psy3092         260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRL  339 (347)
Q Consensus       260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll  339 (347)
                      .++++++. +++.+|++|++|++||++|+||+||+||++|+++...|+++|+++..+|++|+..++++++.||++||++|
T Consensus       124 ~~~~~~i~-~~~~~l~~L~ld~~E~~lLkaivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL~~L  202 (236)
T 1fcy_A          124 GPLTDLVF-AFAGQLLPLEMDDTETGLLSAICLICGDRMDLEEPEKVDKLQEPLLEALRLYARRRRPSQPYMFPRMLMKI  202 (236)
T ss_dssp             GGGHHHHH-HHHHHHGGGCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHH
T ss_pred             HHHHHHHH-HHHHHHHHHcCCHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCchhHHHHHHHHh
Confidence            77777766 69999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhccC
Q psy3092         340 PSLRSIE  346 (347)
Q Consensus       340 ~~lr~i~  346 (347)
                      |.||+|+
T Consensus       203 ~~Lr~l~  209 (236)
T 1fcy_A          203 TDLRGIS  209 (236)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9999886

>1ovl_A Orphan nuclear receptor NURR1 (MSe 414, 496, 511); NUUR1, LBD, transcription; 2.20A {Homo sapiens} SCOP: a.123.1.1

Probab=99.98  E-value=2.7e-31  Score=237.40  Aligned_cols=221  Identities=23%  Similarity=0.378  Sum_probs=158.4

Q ss_pred             cchhHHHHHHhhhhccccc-----cccCCCCCCCCCcHHHHHHHHHhccCCC--CCCcc---------ccchhHHHhhhh
Q psy3092         123 MKREAVQEERQRTKERDSN-----EVESTSGTLIEMPVERILEAEQRVDMKQ--EPADQ---------DIVNEQQATNIC  186 (347)
Q Consensus       123 M~~~~vq~~r~~~~~~~~~-----~~~~~~~~~~~~~~~~l~~~~~~~~~~~--~~~~~---------~~~~~~~~~~~~  186 (347)
                      |.+|+||.+|.+.++++..     ............-+..++.+........  .....         .......+..++
T Consensus         1 M~kE~Vr~dr~~~~r~~~~~~~~~~~~~~~~~~~~~li~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (271)
T 1ovl_A            1 MVKEVVRTDSLKGRRGRLPSKPKSPQEPSPPSPPVSLISALVRAHVDSNPAMTSLDYSRFQANPDYQMSGDDTQHIQQFY   80 (271)
T ss_dssp             -----------------------------------CHHHHHHHHHHHTSCCTTSCBCTTCCCC--------CHHHHHHHH
T ss_pred             CCccccccCccccCCCCCCCCCCCcccCCCCCCHHHHHHHHHHHHHHhCCCcchhhhhccCCCCCcccCcchHHHHHHHH
Confidence            8899999988765432211     0000101111223566777776544322  10000         011224577889


Q ss_pred             HHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCchhhHHhh
Q psy3092         187 KATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRV  266 (347)
Q Consensus       187 ~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~~~~~~~~  266 (347)
                      ++....+..+++|||++|+|..|+.+||+.|||++|.+++++..+++++..++.+++++|..++++.. ..++.++++.+
T Consensus        81 ~~~~~~l~~~v~waK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~~l~~~~g~~~~~~~~-~~~~~~~~~~l  159 (271)
T 1ovl_A           81 DLLTGSMEIIRGWAEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIFCNGVVLHRLQC-VRGFGEWIDSI  159 (271)
T ss_dssp             HHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHSBTTTTEEECTTSBEEEHHHH-TTTTTTHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCCcccCChHHHHHHHHHhHHHHHHHHHHHHhcCCCCeEEeeCCeeecHHHH-HhhHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999998888889999988776543 34566677665


Q ss_pred             HHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhc--CCCCchHHHHHHhhhhhhhc
Q psy3092         267 LTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVN--HSEEPGRFAKLLLRLPSLRS  344 (347)
Q Consensus       267 ~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~--~~~~~~Rf~~LL~ll~~lr~  344 (347)
                      . +++.+|++|++|++||+||+||+|||| .+|+++...|+++|+++..+|.+|+..+  +++++.||++||++||.||+
T Consensus       160 ~-~~~~~l~~L~ld~~E~~lLkAivL~~~-~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~~Rf~~LL~~L~~Lr~  237 (271)
T 1ovl_A          160 V-EFSSNLQNMNIDISAFSCIAALAMVTE-RHGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLGKLPELRT  237 (271)
T ss_dssp             H-HHHHHHHTTCCCHHHHHHHHHHHHSSC-CTTCSCHHHHHHHHHHHHHHHHHHHHGGGTTTTSTTHHHHHHHHHHHHHH
T ss_pred             H-HHHHHHHHhcCCHHHHHHHHHHHHhCC-CCCCCcHHHHHHHHHHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHH
Confidence            5 899999999999999999999999996 8999999999999999999999999876  45889999999999999998


Q ss_pred             cC
Q psy3092         345 IE  346 (347)
Q Consensus       345 i~  346 (347)
                      |+
T Consensus       238 l~  239 (271)
T 1ovl_A          238 LC  239 (271)
T ss_dssp             HH
T ss_pred             HH
Confidence            75

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

Probab=99.97  E-value=2.1e-31  Score=233.88  Aligned_cols=166  Identities=27%  Similarity=0.468  Sum_probs=139.7

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV  259 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~  259 (347)
                      ..+..+++.....+..+++|||.+|+|..|+.+||+.|||++|.+++++.+++++....+.+.+++|..+..+.....++
T Consensus        65 ~~~~~~~~~~~~~l~~~VewAK~lP~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~l~~~~g~~~~~~~~~~~~~  144 (245)
T 3n00_A           65 EIWEDFSMSFTPAVREVVEFAKHIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFNVKDQTVMFLSRTTYSLQELGAMGM  144 (245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTCCSCC--------------CCGGGTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEecCCCeecHHHHhhccH
Confidence            45778888888999999999999999999999999999999999999999998755556778889999888777666667


Q ss_pred             hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhh
Q psy3092         260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRL  339 (347)
Q Consensus       260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll  339 (347)
                      .++++.+. +++.+|++|++|++||++|+||+|||||++|+++...|+++|+++..+|.+|+..++++++.||++||++|
T Consensus       145 ~~~~~~i~-~~~~~l~~L~ld~~E~~lLkAIvL~npd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~RF~~LLl~L  223 (245)
T 3n00_A          145 GDLLSAMF-DFSEKLNSLALTEEELGLFTAVVLVSADRSGMENSASVEQLQETLLRALRALVLKNRPLETSRFTKLLLKL  223 (245)
T ss_dssp             HHHHHHHH-HHHHHHHHTCCCHHHHHHHHHHHHHTSCCTTCSSHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTHH
T ss_pred             HHHHHHHH-HHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHh
Confidence            77776655 89999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhccC
Q psy3092         340 PSLRSIE  346 (347)
Q Consensus       340 ~~lr~i~  346 (347)
                      |+||+|+
T Consensus       224 p~LR~l~  230 (245)
T 3n00_A          224 PDLRTLN  230 (245)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9999986

>3kmr_A Retinoic acid receptor alpha; nuclear receptor transcription factor ligand binding domain, binding, metal-binding, nucleus, phosphoprotein; HET: EQN; 1.80A {Homo sapiens} PDB: 3kmz_B* 3a9e_B* 4dm6_A* 1xap_A* 4dm8_A* 2lbd_A* 3lbd_A* 4lbd_A*

Probab=99.97  E-value=3.5e-31  Score=235.42  Aligned_cols=166  Identities=31%  Similarity=0.528  Sum_probs=154.3

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV  259 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~  259 (347)
                      ..+..+++.....++.+++|||++|+|..|+.+||+.|||++|.+++++..++++....+.+++++|..+.++.....++
T Consensus        68 ~~~~~~~e~~~~~l~~~VewaK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~~s~~~~~~l~~~~g~~~~~~~~~~~g~  147 (266)
T 3kmr_A           68 DLWDKFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMHNAGF  147 (266)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETTTTEEECTTSBEEEHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCcChhhCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCeEEecCCcccchHHHhhcch
Confidence            34788999999999999999999999999999999999999999999999999998888889999999888777666667


Q ss_pred             hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhh
Q psy3092         260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRL  339 (347)
Q Consensus       260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll  339 (347)
                      +.+.+.+. +++.+|++|++|++||++|+||+|||||++|+++...|+++|+++..+|.+|+..++++++.||++||++|
T Consensus       148 ~~~~~~i~-~~~~~l~~L~ld~~E~~lLkAIvL~~pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL~~L  226 (266)
T 3kmr_A          148 GPLTDLVF-AFANQLLPLEMDDAETGLLSAICLICGDRQDLEQPDRVDMLQEPLLEALKVYVRKRRPSRPHMFPKMLMKI  226 (266)
T ss_dssp             GGGHHHHH-HHHHHHGGGCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHH
T ss_pred             HHHHHHHH-HHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHh
Confidence            77766655 89999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhccC
Q psy3092         340 PSLRSIE  346 (347)
Q Consensus       340 ~~lr~i~  346 (347)
                      |.||+|+
T Consensus       227 p~Lr~i~  233 (266)
T 3kmr_A          227 TDLRSIS  233 (266)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9999885

>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=99.97  E-value=4.7e-31  Score=231.52  Aligned_cols=168  Identities=39%  Similarity=0.635  Sum_probs=154.3

Q ss_pred             hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcC
Q psy3092         179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG  258 (347)
Q Consensus       179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~  258 (347)
                      ..++.++++++..+++.+++|+|+||+|+.|+.+||+.|||++|.+++++..++++...++.+++++|..++.+.....+
T Consensus        40 ~~~~~~~~~~~~~~l~~~v~wak~~p~F~~L~~~DQ~~LLk~~~~~~~~L~~a~~s~~~~~~~~~~~g~~~~~~~~~~~~  119 (237)
T 1pzl_A           40 IASIADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVLLLGNDYIVPRHCPELAE  119 (237)
T ss_dssp             BCCHHHHHHHHHHHHHHHHHHHTTCHHHHTSCHHHHHHHHHHSHHHHHHHHHHHHHTTSSSEEECTTSCEEESSCGGGGG
T ss_pred             cCCHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCceeecCCcccCccchhhhh
Confidence            35678999999999999999999999999999999999999999999999999999888888889999888766554445


Q ss_pred             chhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhh
Q psy3092         259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLR  338 (347)
Q Consensus       259 ~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~l  338 (347)
                      +..++++++.+++.+|++|++|++||++|+||+||+|+.+|+++...++++|+++..+|++||..++++++.||++||++
T Consensus       120 ~~~~~~~~~~~l~~~l~~L~ld~~E~~~L~ai~l~~~~~~~l~~~~~ve~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~  199 (237)
T 1pzl_A          120 MSRVSIRILDELVLPFQELQIDDNEYAYLKAIIFFDPDAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLL  199 (237)
T ss_dssp             GHHHHHHHHHHTHHHHHHHTCCHHHHHHHHHHHHCCTTCTTCSCHHHHHHHHHHHHHHHHHHHHSSSSCCTTHHHHHHTH
T ss_pred             hHHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHHHHHhcCCChhhHHHHHHHH
Confidence            56677788889999999999999999999999999999999999999999999999999999999888899999999999


Q ss_pred             hhhhhccC
Q psy3092         339 LPSLRSIE  346 (347)
Q Consensus       339 l~~lr~i~  346 (347)
                      +|.||+++
T Consensus       200 l~~lr~~~  207 (237)
T 1pzl_A          200 LPTLQSIT  207 (237)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99999874

>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=99.97  E-value=5.2e-31  Score=233.65  Aligned_cols=191  Identities=21%  Similarity=0.290  Sum_probs=159.7

Q ss_pred             HHHHHHHHHhccCCCCCCccccchhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhccc
Q psy3092         155 VERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRS  234 (347)
Q Consensus       155 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s  234 (347)
                      +..++.++...................+..++++..++++.+++|||++|+|.+|+.+||+.|||++|.+++++..+|++
T Consensus        17 ~~~l~~~ep~~~~~~~~~~~~~~~~~~~~~l~~~a~~~l~~~VewaK~iP~F~~L~~~DQ~~LLk~~~~el~iL~~a~rs   96 (261)
T 3mnp_A           17 VSLLEVIEPEVLYAGYDSSVPDSAWRIMTTLNMLGGRQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMVFALGWRS   96 (261)
T ss_dssp             HHHHHHHSCCCCCCCCCTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCccccccCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHhCcChhcCCHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            45555555443322222222233446688999999999999999999999999999999999999999999999999998


Q ss_pred             ccCCC--ceEecCCccccccchhhcCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcC-CCCCCCCHHHHHHHHH
Q psy3092         235 ISVKD--GILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNP-DVRGLKSQQVVEMLRE  311 (347)
Q Consensus       235 ~~~~~--~~~~~~g~~i~~~~~~~~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p-~~~~l~~~~~i~~~r~  311 (347)
                      +..++  .+++++|..+.++.....++.++++.+ .+++.+|++|++|++||++|+||+|||| +++|+++...|+++|+
T Consensus        97 ~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~l-~~~~~~l~~L~ld~~E~~lLkAIvL~np~d~~gL~~~~~ve~lq~  175 (261)
T 3mnp_A           97 YRQASGNLLCFAPDLIINEQRMTLPCMYDQCKHM-LFISTELQRLQVSYEEYLCMKTLLLLSSVPKEGLKSQELFDEIRM  175 (261)
T ss_dssp             HHHHTTSSEEEETTEEECHHHHTSTTTHHHHHHH-HHHHHHHHHHTCCHHHHHHHHHHHHTSEEETTCCTTHHHHHHHHH
T ss_pred             ccCCCCCEEEecCCcccchhhhhhhhHHHHHHHH-HHHHHHHHHhCCCHHHHHHHHHHHHcCCCCcCCCccHHHHHHHHH
Confidence            77654  468899988887666555666666554 4899999999999999999999999999 9999999999999999


Q ss_pred             HHHHHHHHHHHhcCCC---CchHHHHHHhhhhhhhccC
Q psy3092         312 KVYTSLEEYTRVNHSE---EPGRFAKLLLRLPSLRSIE  346 (347)
Q Consensus       312 ~~~~~L~~y~~~~~~~---~~~Rf~~LL~ll~~lr~i~  346 (347)
                      ++..+|.+|+..++++   ++.||++||++||.||+++
T Consensus       176 ~~~~aL~~y~~~~~~~~~~~~~Rf~~LL~lL~~Lr~l~  213 (261)
T 3mnp_A          176 TYIKELGKAIAKRGGNSSQNWQRFYQLTKLLDSMHDVV  213 (261)
T ss_dssp             HHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhCCCCchhhhHHHHHHHHHHHHHHHH
Confidence            9999999999998884   5899999999999999875

>3ilz_A Thyroid hormone receptor, alpha isoform 1 variant; nuclear receptor, signaling protein; HET: B72; 1.85A {Homo sapiens} SCOP: a.123.1.1 PDB: 3jzb_A* 3hzf_A* 2h79_A* 2h77_A* 1nav_A* 3uvv_A* 1xzx_X* 1y0x_X* 1nq1_A* 3jzc_A* 1nuo_A* 3imy_A* 1nq0_A* 1bsx_A* 1r6g_A* 1nq2_A* 3gws_X* 1n46_A* 2h6w_X* 2j4a_A* ...

Probab=99.97  E-value=7e-31  Score=233.84  Aligned_cols=167  Identities=26%  Similarity=0.438  Sum_probs=155.4

Q ss_pred             hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcC
Q psy3092         179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG  258 (347)
Q Consensus       179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~  258 (347)
                      ...+..+++.....+..+|+|||++|+|..|+.+||+.|||++|.+++++..|+++....+.+++++|..+.++.....+
T Consensus        69 ~~~~~~~~~~~~~~l~~~VewaK~lP~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~l~~~~g~~~~~~~~~~~~  148 (267)
T 3ilz_A           69 LEAFSEFTKIITPAITRVVDFAKKLPMFSELPXEDQIILLKGCCMEIMSLRAAVRYDPESDTLTLSGEMAVKREQLKNGG  148 (267)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTSHHHHTSCHHHHHHHHHHHHHHHHHHHHHTTCBTTTTBEEETTTEEECHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCcchhhCCHhHHHHHHHHHHHHHHHHHHHHHhcCCCCEEEecCCeeecHHHHhccC
Confidence            35688999999999999999999999999999999999999999999999999999888888999999988887776667


Q ss_pred             chhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhh
Q psy3092         259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLR  338 (347)
Q Consensus       259 ~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~l  338 (347)
                      ++.+.+.+. +++.+|++|++|++||++|+||+|||||++||++...|+++|+++..+|++|+..++++++.||++||++
T Consensus       149 ~~~~~~~i~-~~~~~l~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~Rf~~LL~~  227 (267)
T 3ilz_A          149 LGVVSDAIF-ELGKSLSAFNLDDTEVALLQAVLLMSTDRSGLLXVDKIEKSQEAYLLAFEHYVNHRKHNIPHFWPKLLMK  227 (267)
T ss_dssp             TTHHHHHHH-HHHHHHGGGCCCHHHHHHHHHHHHSCCCSSSCSCHHHHHHHHHHHHHHHHHHHHHHTCSSTTHHHHHHHH
T ss_pred             HHHHHHHHH-HHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCchHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHH
Confidence            777766654 8999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhccC
Q psy3092         339 LPSLRSIE  346 (347)
Q Consensus       339 l~~lr~i~  346 (347)
                      ||+||+|+
T Consensus       228 Lp~Lr~l~  235 (267)
T 3ilz_A          228 VTDLRMIG  235 (267)
T ss_dssp             HHHHHHHH
T ss_pred             hHHHHHHH
Confidence            99999885

>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=99.97  E-value=9.7e-31  Score=234.86  Aligned_cols=168  Identities=25%  Similarity=0.394  Sum_probs=152.8

Q ss_pred             hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcC
Q psy3092         179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG  258 (347)
Q Consensus       179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~  258 (347)
                      ...+..++++....+..+|+|||.+|+|..|+.+||+.|||++|.+++++..|+++....+.+.+++|..+.++.....+
T Consensus        87 ~~~~~~l~e~~~~~l~~~VewaK~lP~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~~~~~g~~~~~~~~~~~g  166 (283)
T 3ipq_A           87 QQRFAHFTELAIVSVQEIVDFAKQLPGFLQLSREDQIALLKTSAIEVMLLETSRRYNPGSESITFLKDFSYNREDFAKAG  166 (283)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETTTTEEEETTTEEECHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCcChhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEeCCCceecHHHHHHcC
Confidence            34578899999999999999999999999999999999999999999999999888777788899999988877766566


Q ss_pred             chhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhh
Q psy3092         259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLR  338 (347)
Q Consensus       259 ~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~l  338 (347)
                      +...+...+.+++.+|++|++|++||+||+||+|||||++||++...|+++|+++..+|.+|+..++++++.||++||++
T Consensus       167 ~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkAIvL~npd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL~~  246 (283)
T 3ipq_A          167 LQVEFINPIFEFSRAMNELQLNDAEFALLIAISIFSADRPNVQDQLQVERLQHTYVEALHAYVSIHHPHDRLMFPRMLMK  246 (283)
T ss_dssp             CCHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHSTTCTTHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCCCcHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHH
Confidence            65333344559999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhccC
Q psy3092         339 LPSLRSIE  346 (347)
Q Consensus       339 l~~lr~i~  346 (347)
                      ||+||+|+
T Consensus       247 Lp~Lr~l~  254 (283)
T 3ipq_A          247 LVSLRTLS  254 (283)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99999885

>1nq7_A Nuclear receptor ROR-beta; ligand-binding domain, retinoids, retinoic acid, synthetic ligand, antagonist, transcription; HET: ARL; 1.50A {Rattus norvegicus} SCOP: a.123.1.1 PDB: 1k4w_A* 1n4h_A*

Probab=99.97  E-value=1.1e-30  Score=229.63  Aligned_cols=165  Identities=21%  Similarity=0.375  Sum_probs=150.3

Q ss_pred             hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcC
Q psy3092         179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG  258 (347)
Q Consensus       179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~  258 (347)
                      ...+..+++.....++.+++|||++|+|.+|+.+||+.|||++|.+++++..++++....+.+.+ +|..+.++.....+
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            34577888889999999999999999999999999999999999999999999998777777888 88877776666566


Q ss_pred             chhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhh
Q psy3092         259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLR  338 (347)
Q Consensus       259 ~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~l  338 (347)
                      +.++++.+. +++.+|++|++|++||++|+||+|||||++|+++...|+++|+++..+|++|+..++++++ ||++||++
T Consensus       128 ~~~~~~~i~-~~~~~l~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~-Rf~~LL~~  205 (244)
T 1nq7_A          128 SDDLVNEAF-DFAKNLCSLQLTEEEIALFSSAVLISPDRAWLLEPRKVQKLQEKIYFALQHVIQKNHLDDE-TLAKLIAK  205 (244)
T ss_dssp             CHHHHHHHH-HHHHHHHTTCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCSCTT-HHHHHHHT
T ss_pred             hHHHHHHHH-HHHHHHHHhCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcc-HHHHHHHH
Confidence            777777655 8999999999999999999999999999999999999999999999999999999999888 99999999


Q ss_pred             hhhhhccC
Q psy3092         339 LPSLRSIE  346 (347)
Q Consensus       339 l~~lr~i~  346 (347)
                      ||.||+|+
T Consensus       206 L~~Lr~l~  213 (244)
T 1nq7_A          206 IPTITAVC  213 (244)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99999875

>3b0t_A Vitamin D3 receptor; nuclear receptor, transcription, gene regulation; HET: MCZ; 1.30A {Homo sapiens} PDB: 3a40_X* 1s0z_A* 1s19_A* 2ham_A* 2har_A* 2has_A* 1txi_A* 2hb8_A* 2hb7_A* 3a3z_X* 3a78_A* 3auq_A* 3aur_A* 3ax8_A* 3cs4_A* 3cs6_A* 1ie9_A* 1db1_A* 1ie8_A* 3kpz_A* ...

Probab=99.97  E-value=1.5e-30  Score=230.37  Aligned_cols=165  Identities=20%  Similarity=0.353  Sum_probs=146.8

Q ss_pred             HHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecC-CccccccchhhcCc
Q psy3092         181 QATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAP-GVTVYRSSAHEAGV  259 (347)
Q Consensus       181 ~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~-g~~i~~~~~~~~~~  259 (347)
                      .+..++++....++.+|+|||++|+|.+|+.+||+.|||++|.+++++..++++....+.+.+++ |..+.++.....++
T Consensus        57 ~~~~~~~~~~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  136 (254)
T 3b0t_A           57 MLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVSDVTKAGH  136 (254)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHGGGTEETTTTEEECSSGGGEECHHHHHTTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCCcccCCHHHHHHHHHHhhHHHHHHHHHHHhccCCCeEEecCCCeeeeHHHHHHcCC
Confidence            47888999999999999999999999999999999999999999999999998766666677775 55555555544566


Q ss_pred             h-hhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCC--CCchHHHHHH
Q psy3092         260 G-GIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHS--EEPGRFAKLL  336 (347)
Q Consensus       260 ~-~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~--~~~~Rf~~LL  336 (347)
                      . .+.+. +.+++.+|++|++|++||+||+||+|||||++|+++...|+++|+++..+|++|+..+++  +++.||++||
T Consensus       137 ~~~~~~~-l~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~~Rf~~LL  215 (254)
T 3b0t_A          137 SLELIEP-LIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLLYAKMI  215 (254)
T ss_dssp             CHHHHHH-HHHHHHHHHTTCCCHHHHHHHHHHHHSCSCSTTCSCHHHHHHHHHHHHHHHHHHHHHHCCTTTTTTHHHHHH
T ss_pred             cHHHHHH-HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCccCCcCHHHHHHHHHHHHHHHHHHHHHhCCCCCchhHHHHHH
Confidence            5 45554 558999999999999999999999999999999999999999999999999999999998  8999999999


Q ss_pred             hhhhhhhccC
Q psy3092         337 LRLPSLRSIE  346 (347)
Q Consensus       337 ~ll~~lr~i~  346 (347)
                      ++||.||+|+
T Consensus       216 ~~L~~Lr~l~  225 (254)
T 3b0t_A          216 QKLADLRSLN  225 (254)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHhHHHHHHH
Confidence            9999999885

>2r40_D Ecdysone receptor, 20-hydroxy-ecdysone receptor; nuclear receptor ligand-binding domain, anti-parallel alpha- sandwich, ecdysone receptor, ECR, gene regulation; HET: FLC 20E EPH; 2.40A {Heliothis virescens} SCOP: a.123.1.1 PDB: 1r1k_D* 3ixp_D* 1r20_D*

Probab=99.97  E-value=1.3e-30  Score=231.99  Aligned_cols=165  Identities=24%  Similarity=0.357  Sum_probs=152.7

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV  259 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~  259 (347)
                      ..+..++++....++.+|+|||++|+|..|+.+||+.|||++|.+++++..++++....+.+++++|..+.++.....++
T Consensus        68 ~~~~~l~~~~~~~l~~~VewaK~lp~F~~L~~~DQi~LLk~~~~el~~L~~a~~~~~~~~~l~~~~g~~~~~~~~~~~g~  147 (266)
T 2r40_D           68 MPFRQITEMTILTVQLIVEFAKGLPGFAKISQSDQITLLKACSSEVMMLRVARRYDAATDSVLFANNQAYTRDNYRKAGM  147 (266)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEETTTTEEECTTSCEECHHHHHHTTC
T ss_pred             ccHHHHHHHHHHHHHHHHHHHhcCcccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEecCCceecHHHHhhcCH
Confidence            45889999999999999999999999999999999999999999999999999987778889999999888776666677


Q ss_pred             hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcC---CCCchHHHHHH
Q psy3092         260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNH---SEEPGRFAKLL  336 (347)
Q Consensus       260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~---~~~~~Rf~~LL  336 (347)
                      .++++.+ .+++.+|++|++|++||+||+||+||| |++|+++...|+++|+++..+|++|+..++   ++++.||++||
T Consensus       148 ~~~~~~l-~~~~~~l~~L~ld~~E~~lLkAivL~n-d~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~~~Rf~~LL  225 (266)
T 2r40_D          148 AYVIEDL-LHFCRCMYSMMMDNVHYALLTAIVIFS-DRPGLEQPLLVEEIQRYYLNTLRVYILNQNSASPRCAVIFGKIL  225 (266)
T ss_dssp             HHHHHHH-HHHHHHHHTTTCCHHHHHHHHHHHHTS-CCTTCSCHHHHHHHHHHHHHHHHHHHHHHTTTCTTHHHHHHHHH
T ss_pred             HHHHHHH-HHHHHHHhcccCCHHHHHHHhhheeec-CCCCCcCHHHHHHHHHHHHHHHHHHHHHhCCCCCchhhHHHHHH
Confidence            7777665 489999999999999999999999999 999999999999999999999999999888   78899999999


Q ss_pred             hhhhhhhccC
Q psy3092         337 LRLPSLRSIE  346 (347)
Q Consensus       337 ~ll~~lr~i~  346 (347)
                      ++||.||+|+
T Consensus       226 ~~L~~Lr~l~  235 (266)
T 2r40_D          226 GILTEIRTLG  235 (266)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999999875

>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=99.97  E-value=9.7e-31  Score=231.90  Aligned_cols=169  Identities=24%  Similarity=0.410  Sum_probs=148.2

Q ss_pred             chhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCC--CceEecCCccccccch
Q psy3092         177 VNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVK--DGILLAPGVTVYRSSA  254 (347)
Q Consensus       177 ~~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~--~~~~~~~g~~i~~~~~  254 (347)
                      .....+..++++....++.+++|||++|+|.+|+.+||+.|||++|.+++++..+|+++..+  +.+++++|..+.++..
T Consensus        37 ~~~~~~~~l~e~a~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~rs~~~~~~~~l~~~~g~~~~~~~~  116 (260)
T 3vhv_A           37 TAENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQYSWMSLLSFALSWRSYKHTNSQFLYFAPDLVFNEEKM  116 (260)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHhChHHhcCCHHHHHHHHHHhHHHHHHHHHHHHhhccCCCCeEEecCCccccHHHh
Confidence            44567889999999999999999999999999999999999999999999999999987654  4678899988877666


Q ss_pred             hhcCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcC-CCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCC---ch
Q psy3092         255 HEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNP-DVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEE---PG  330 (347)
Q Consensus       255 ~~~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p-~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~---~~  330 (347)
                      ...++.++.+. +.+++.+|++|++|++||++|+||+|||| |++||++...|+++|+++..+|.+|+..++++.   +.
T Consensus       117 ~~~~~~~~~~~-l~~~~~~l~~L~ld~~E~~lLkAIvLfnp~d~~gL~~~~~ve~lqe~~~~aL~~y~~~~~~~~~~~~~  195 (260)
T 3vhv_A          117 HQSAMYELCQG-MHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKDGLKSQAAFEEMRTNYIKELRKMVTKCPNNSGQSWQ  195 (260)
T ss_dssp             HHTTCHHHHHH-HHHHHHHHHHHTCCHHHHHHHHHHHHTSEEETTCCTTHHHHHHHHHHHHHHHHHHHHC-----CCHHH
T ss_pred             hcccHHHHHHH-HHHHHHHHHHcCCCHHHHHHHHHHHHcCCcCCCCCcCHHHHHHHHHHHHHHHHHHHHhcCCCCCcHhh
Confidence            65666665554 46899999999999999999999999999 999999999999999999999999999888754   79


Q ss_pred             HHHHHHhhhhhhhccC
Q psy3092         331 RFAKLLLRLPSLRSIE  346 (347)
Q Consensus       331 Rf~~LL~ll~~lr~i~  346 (347)
                      ||++||++||+||+|+
T Consensus       196 RF~~LL~~Lp~Lr~l~  211 (260)
T 3vhv_A          196 RFYQLTKLLDSMHDLV  211 (260)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            9999999999999875

>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=99.97  E-value=9.8e-31  Score=231.49  Aligned_cols=166  Identities=36%  Similarity=0.634  Sum_probs=148.9

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccC--CCceEecCCccccccchh-h
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISV--KDGILLAPGVTVYRSSAH-E  256 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~--~~~~~~~~g~~i~~~~~~-~  256 (347)
                      ..+..++++..+.++.+++|||++|+|..|+.+||+.|||++|.+++++..+|+++..  .+.+++++|..+..+... .
T Consensus        56 ~~~~~l~~~a~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~lL~~a~rs~~~~~~~~l~~~~g~~~~~~~~~~~  135 (257)
T 3plz_A           56 STFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQ  135 (257)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCBTTEEECTTSCEEEHHHHHTT
T ss_pred             chHHHHHHHHHHHHHHHHHHHHcCcChhcCCHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCeEEecCCCccChHHHhhh
Confidence            4578899999999999999999999999999999999999999999999999998754  477888999888766543 2


Q ss_pred             cCc--hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHH
Q psy3092         257 AGV--GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAK  334 (347)
Q Consensus       257 ~~~--~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~  334 (347)
                      .+.  .++.+. +.+++.+|++|++|++||++|+||+|||||++|+++...|+++|+++..+|.+|+..++++++.||++
T Consensus       136 ~g~~~~~~~~~-l~~~~~~l~~L~ld~~E~~lLkAivL~npd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~Rf~~  214 (257)
T 3plz_A          136 AGATLNNLMSH-AQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQ  214 (257)
T ss_dssp             SCHHHHHHHHH-HHHHHHHHHHTTCCHHHHHHHHHHHHSCTTCCSCTTHHHHHHHHHHHHHHHHHHHHHHCTTSTTHHHH
T ss_pred             cCCcHHHHHHH-HHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCchhHHHH
Confidence            232  344444 56899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhhhhhhccC
Q psy3092         335 LLLRLPSLRSIE  346 (347)
Q Consensus       335 LL~ll~~lr~i~  346 (347)
                      ||++||+||+++
T Consensus       215 LL~~Lp~Lr~l~  226 (257)
T 3plz_A          215 LLLRLPEIRAIS  226 (257)
T ss_dssp             HHTHHHHHHHHH
T ss_pred             HHHHhHHHHHHH
Confidence            999999999875

>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=99.97  E-value=1.2e-30  Score=229.91  Aligned_cols=166  Identities=31%  Similarity=0.557  Sum_probs=148.3

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccC--CCceEecCCccccccchh-h
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISV--KDGILLAPGVTVYRSSAH-E  256 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~--~~~~~~~~g~~i~~~~~~-~  256 (347)
                      ..+..++++....++.+++|||++|+|.+|+.+||+.|||++|.+++++..+++++..  .+.+++++|..+..+... .
T Consensus        45 ~~~~~l~~~a~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~rs~~~~~~~~~~~~~g~~~~~~~~~~~  124 (246)
T 1ymt_A           45 APFSLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNSWSELLVLDHIYRQVQYGKEDSILLVTGQEVELSTVAVQ  124 (246)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCTTEEECTTSCEEEHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHhChhHHhCCHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCeeEecCCCccchhhhhhh
Confidence            4578899999999999999999999999999999999999999999999999998865  577888999888765443 2


Q ss_pred             cCc--hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHH
Q psy3092         257 AGV--GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAK  334 (347)
Q Consensus       257 ~~~--~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~  334 (347)
                      .+.  .++++. +.+++.+|++|++|++||++|+||+|||||++|+++...++++|+++..+|.+|+..++++++.||++
T Consensus       125 ~~~~~~~~~~~-~~~~~~~~~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~Rf~~  203 (246)
T 1ymt_A          125 AGSLLHSLVLR-AQELVLQLHALQLDRQEFVCLKFLILFSLDVKFLNNHSLVKDAQEKANAALLDYTLSHYPHSGDKFQQ  203 (246)
T ss_dssp             CCHHHHHHHHH-HHHHHHHHHHTTCCHHHHHHHHHHHHTCSCGGGSSCHHHHHHHHHHHHHHHHHHHHHHCTTSTTHHHH
T ss_pred             cchhHHHHHHH-HHHHHHHHHHHCCCHHHHHHHHHHHhcCCcccccccHHHHHHHHHHHHHHHHHHHHhcCCchhhHHHH
Confidence            222  234444 56899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhhhhhhccC
Q psy3092         335 LLLRLPSLRSIE  346 (347)
Q Consensus       335 LL~ll~~lr~i~  346 (347)
                      ||++||.||+++
T Consensus       204 LL~~L~~Lr~~~  215 (246)
T 1ymt_A          204 LLLSLVEVRALS  215 (246)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHhHHHHHHH
Confidence            999999999875

>1yye_A ER-beta, estrogen receptor beta; ER-beta, nuclear receptor, transcription factor, agonist; HET: 196; 2.03A {Homo sapiens} SCOP: a.123.1.1 PDB: 1yy4_A*

Probab=99.97  E-value=1.7e-30  Score=231.29  Aligned_cols=166  Identities=30%  Similarity=0.499  Sum_probs=144.3

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchh-hcC
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH-EAG  258 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~-~~~  258 (347)
                      ..+..++++....++.+|+|||++|+|..|+.+||+.|||++|.+++++..+++++...+.+++++|..++++... ..+
T Consensus        31 ~~~~~l~e~a~~~l~~~VewAK~lp~F~~L~~~DQi~LLk~~w~el~lL~~a~rs~~~~~~l~~~~g~~~~~~~~~~~~~  110 (268)
T 1yye_A           31 SMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKCVEG  110 (268)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTSTTEEEEETTEEEEGGGGGGSTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCceEecCCcccChhhHhhhcc
Confidence            4478899999999999999999999999999999999999999999999999999988888899999887765433 245


Q ss_pred             chhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCC-------HHHHHHHHHHHHHHHHHHHHhcC---CCC
Q psy3092         259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKS-------QQVVEMLREKVYTSLEEYTRVNH---SEE  328 (347)
Q Consensus       259 ~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~-------~~~i~~~r~~~~~~L~~y~~~~~---~~~  328 (347)
                      +.++++.+. +++.+|++|++|++||+||+||+|||||++|+++       ++.++++|+++..+|.+|+..++   +++
T Consensus       111 ~~~~~~~l~-~~~~~l~~L~ld~~E~~lLkAIvLfnpd~~gLs~~~~~~~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~~  189 (268)
T 1yye_A          111 ILEIFDMLL-ATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAKSGISSQQQ  189 (268)
T ss_dssp             HHHHHHHHH-HHHHHHHHHTCCHHHHHHHHHHHHHTCCC----------CCHHHHHHHHHHHHHHHHHHHHHTCCCHHHH
T ss_pred             HHHHHHHHH-HHHHHHHHhCCCHHHHHHHHHHHHcCCCCCCcccchhhHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcch
Confidence            556666654 8999999999999999999999999999999864       67899999999999999998764   468


Q ss_pred             chHHHHHHhhhhhhhccC
Q psy3092         329 PGRFAKLLLRLPSLRSIE  346 (347)
Q Consensus       329 ~~Rf~~LL~ll~~lr~i~  346 (347)
                      +.||++||++||.||+|+
T Consensus       190 ~~Rf~~LLl~Lp~Lr~i~  207 (268)
T 1yye_A          190 SMRLANLLMLLSHVRHAS  207 (268)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHH
Confidence            899999999999999875

>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=99.97  E-value=2.6e-30  Score=227.04  Aligned_cols=168  Identities=30%  Similarity=0.495  Sum_probs=148.7

Q ss_pred             hhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchh-h
Q psy3092         178 NEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH-E  256 (347)
Q Consensus       178 ~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~-~  256 (347)
                      ....+..++++..+.++.+++|||++|+|..|+.+||+.|+|++|.+++++..+++++..++.+++++|..+.++... .
T Consensus        31 ~~~~~~~~~~~a~~~l~~~vewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~~l~~~~g~~~~~~~~~~~  110 (240)
T 3oll_A           31 EASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKCV  110 (240)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTSTTEEEEETBEEEEGGGGGGS
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHccCCCCeeEecCCcccchhhHHHH
Confidence            345678999999999999999999999999999999999999999999999999999988888999999888776543 2


Q ss_pred             cCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCC-------HHHHHHHHHHHHHHHHHHHHhcC---C
Q psy3092         257 AGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKS-------QQVVEMLREKVYTSLEEYTRVNH---S  326 (347)
Q Consensus       257 ~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~-------~~~i~~~r~~~~~~L~~y~~~~~---~  326 (347)
                      .++.++++.+. +++.+|++|++|++||++|+||+|||||++|+++       ++.++++|+++..+|.+|+..++   +
T Consensus       111 ~~~~~~~~~l~-~~~~~l~~L~ld~~E~~lLkAivL~~pd~~gLs~~~~~~~~~~~v~~~q~~~~~aL~~y~~~~~~~~~  189 (240)
T 3oll_A          111 EGILEIFDMLL-ATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAKSGISSQ  189 (240)
T ss_dssp             TTHHHHHHHHH-HHHHHHHHTTCCHHHHHHHHHHHHHCSCCCCCCCCC--CHHHHHHHHHHHHHHHHHHHHHHTTCCCHH
T ss_pred             hhHHHHHHHHH-HHHHHHHHhCCCHHHHHHHHHHHHcCCCCCCcccccchhhHHHHHHHHHHHHHHHHHHHHhccCCCCc
Confidence            45566666554 8999999999999999999999999999999864       56788999999999999998763   4


Q ss_pred             CCchHHHHHHhhhhhhhccC
Q psy3092         327 EEPGRFAKLLLRLPSLRSIE  346 (347)
Q Consensus       327 ~~~~Rf~~LL~ll~~lr~i~  346 (347)
                      +++.||++||++||+||+++
T Consensus       190 ~~~~Rf~~LL~~Lp~Lr~l~  209 (240)
T 3oll_A          190 QQSMRLANLLMLLSHVRHAS  209 (240)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH
T ss_pred             chhhHHHHHHHHhHHHHHHH
Confidence            67999999999999999875

>1l2j_A Estrogen receptor beta; nuclear receptor, transcription factor, antagonist transcription receptor; HET: ETC; 2.95A {Homo sapiens} SCOP: a.123.1.1

Probab=99.97  E-value=1.6e-30  Score=231.96  Aligned_cols=167  Identities=30%  Similarity=0.499  Sum_probs=143.7

Q ss_pred             hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchh-hc
Q psy3092         179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH-EA  257 (347)
Q Consensus       179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~-~~  257 (347)
                      ...+..++++....++.+|+|||++|+|.+|+.+||+.|||++|.+++++..+|+++...+.+++++|..+.++... ..
T Consensus        58 ~~~~~~l~~~a~~~l~~~VewAK~lP~F~~L~~~DQi~LLk~~w~el~iL~~a~rs~~~~~~l~~~~g~~~~~~~~~~~~  137 (271)
T 1l2j_A           58 ASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKCVE  137 (271)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHTTHHHHHHHHHHHHTSSSTTEECSSSSCCEETGGGGGST
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHhCcccccCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCeeeecCCccccchhhhhhc
Confidence            34578899999999999999999999999999999999999999999999999999988888889999877765433 24


Q ss_pred             CchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCC-------HHHHHHHHHHHHHHHHHHHHhc---CCC
Q psy3092         258 GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKS-------QQVVEMLREKVYTSLEEYTRVN---HSE  327 (347)
Q Consensus       258 ~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~-------~~~i~~~r~~~~~~L~~y~~~~---~~~  327 (347)
                      ++.++++.+. +++.+|++|++|++||+||+||+|||||++|+++       ++.++++|++|..+|.+||..+   +++
T Consensus       138 g~~~~~~~l~-~~~~~l~~L~ld~~E~~lLkAIvLfnpd~~gLs~~~~~~~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~  216 (271)
T 1l2j_A          138 GILEIFDMLL-ATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAKSGISSQQ  216 (271)
T ss_dssp             THHHHHHHHH-HHHHHHHHTTCCHHHHHHHHHHHHHHC----CCCCGGGHHHHHHHHHHHHHHHHHHHHHHHTTCCCHHH
T ss_pred             cHHHHHHHHH-HHHHHHHHhCCCHHHHHHHHHHHHcCCCcCCCccchhhHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcc
Confidence            5566676654 8999999999999999999999999999999876       3578899999999999999876   346


Q ss_pred             CchHHHHHHhhhhhhhccC
Q psy3092         328 EPGRFAKLLLRLPSLRSIE  346 (347)
Q Consensus       328 ~~~Rf~~LL~ll~~lr~i~  346 (347)
                      ++.||++||++||.||+++
T Consensus       217 ~~~Rf~~LLl~Lp~Lr~i~  235 (271)
T 1l2j_A          217 QSMRLANLLMLLSHVRHAS  235 (271)
T ss_dssp             HHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHH
Confidence            8899999999999999875

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

Probab=99.97  E-value=1.3e-30  Score=234.99  Aligned_cols=166  Identities=30%  Similarity=0.540  Sum_probs=144.8

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccch-hhcC
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA-HEAG  258 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~-~~~~  258 (347)
                      ..+..++++..+.++.+|+|||++|+|.+|+.+||+.|||++|.+++++..+|+++...+.+++++|..++++.. ...+
T Consensus        44 ~~~~~l~e~a~~~L~~~VewAK~lP~F~~L~~~DQi~LLk~~w~el~lL~~a~rs~~~~~~l~~~~g~~~~~~~~~~~~g  123 (298)
T 2ocf_A           44 SMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEG  123 (298)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTSTTEEEEETTEEEEHHHHTTSTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCcchhcCCHHHHHHHHHHhhHHHHHHHHHHHhcccCCceeecCCceechhhhhhhhh
Confidence            457889999999999999999999999999999999999999999999999999998888899999988776543 2345


Q ss_pred             chhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCC--------CCCCCHHHHHHHHHHHHHHHHHHHHhcC---CC
Q psy3092         259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDV--------RGLKSQQVVEMLREKVYTSLEEYTRVNH---SE  327 (347)
Q Consensus       259 ~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~--------~~l~~~~~i~~~r~~~~~~L~~y~~~~~---~~  327 (347)
                      +.++++.+. +++.+|++|++|++||+||+||+|||||+        +||++...|+++|+++..+|.+|+..++   ++
T Consensus       124 ~~~~~~~l~-~~~~~l~~L~ld~~Ey~lLkAIvLfnpd~~~LS~~~~~gL~~~~~ve~lqe~~~~aL~~y~~~~~~~~~~  202 (298)
T 2ocf_A          124 MVEIFDMLL-ATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQ  202 (298)
T ss_dssp             HHHHHHHHH-HHHHHHHHTTCCHHHHHHHHHHHHHHCSCCC-----------CHHHHHHHHHHHHHHHHHHHHTTCCHHH
T ss_pred             HHHHHHHHH-HHHHhHhhhCcCHHHHHHHHHHHHcCCCccccccccccccccHHHHHHHHHHHHHHHHHHHHhcCCCCCc
Confidence            566676655 79999999999999999999999999999        6777788999999999999999998764   46


Q ss_pred             CchHHHHHHhhhhhhhccC
Q psy3092         328 EPGRFAKLLLRLPSLRSIE  346 (347)
Q Consensus       328 ~~~Rf~~LL~ll~~lr~i~  346 (347)
                      ++.||++||++||.||+|+
T Consensus       203 ~~~RF~~LLl~Lp~Lr~i~  221 (298)
T 2ocf_A          203 QHQRLAQLLLILSHIRHMS  221 (298)
T ss_dssp             HHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            7899999999999999875

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

Probab=99.97  E-value=3.2e-30  Score=231.75  Aligned_cols=169  Identities=24%  Similarity=0.410  Sum_probs=146.4

Q ss_pred             chhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCC--CceEecCCccccccch
Q psy3092         177 VNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVK--DGILLAPGVTVYRSSA  254 (347)
Q Consensus       177 ~~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~--~~~~~~~g~~i~~~~~  254 (347)
                      .....+..++++....++.+++|||.+|+|.+|+.+||+.|||++|.+++++..+|+++..+  +.+++++|..+.++..
T Consensus        71 ~~~~~~~~l~e~a~~~l~~~VewAK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~rS~~~~~~~~l~~~~g~~~~~~~~  150 (294)
T 3vhu_A           71 TAENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQYSWMSLLSFALSWRSYKHTNSQFLYFAPDLVFNEEKM  150 (294)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHTCTTTTSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECHHHH
T ss_pred             ChHHHHHHHHHHHHHHHHHHHHHHHhCcchhhCCHHHHHHHHHHhHHHHHHHHHHHHhhhcCCCCeEEeCCCccccHHHh
Confidence            34466889999999999999999999999999999999999999999999999999987654  4678899988877666


Q ss_pred             hhcCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcC-CCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCC---ch
Q psy3092         255 HEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNP-DVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEE---PG  330 (347)
Q Consensus       255 ~~~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p-~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~---~~  330 (347)
                      ...++.++.+. +.+++.+|++|++|++||++|+||+|||| +++||++...|+++|+++..+|.+|+..++++.   +.
T Consensus       151 ~~~~~~~~~~~-l~~~~~~l~~L~ld~~EyalLkAIvLfnp~d~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~~~~~~~~~  229 (294)
T 3vhu_A          151 HQSAMYELCQG-MHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKDGLKSQAAFEEMRTNYIKELRKMVTKCPNNSGQSWQ  229 (294)
T ss_dssp             HHTTCHHHHHH-HHHHHHHHHHHTCCHHHHHHHHHHHHTSEEETTCCTTHHHHHHHHHHHHHHHHHHHC------CHHHH
T ss_pred             hcccHHHHHHH-HHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCcHHHHHHHHHHHHHHHHHHHHhcCCCCccHhH
Confidence            55566655544 56899999999999999999999999999 999999999999999999999999998877654   79


Q ss_pred             HHHHHHhhhhhhhccC
Q psy3092         331 RFAKLLLRLPSLRSIE  346 (347)
Q Consensus       331 Rf~~LL~ll~~lr~i~  346 (347)
                      ||++||++||+||+|+
T Consensus       230 RF~~LL~lLp~Lr~l~  245 (294)
T 3vhu_A          230 RFYQLTKLLDSMHDLV  245 (294)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            9999999999999875

>2o4j_A Vitamin D3 receptor; nuclear receptor-ligand complex, hormone/growth factor receptor complex; HET: VD4; 1.74A {Rattus norvegicus} SCOP: a.123.1.1 PDB: 1rk3_A* 1rjk_A* 1rkh_A* 1rkg_A* 2o4r_A*

Probab=99.97  E-value=4.3e-30  Score=231.41  Aligned_cols=166  Identities=19%  Similarity=0.353  Sum_probs=147.9

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecC-CccccccchhhcC
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAP-GVTVYRSSAHEAG  258 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~-g~~i~~~~~~~~~  258 (347)
                      ..+..+++.....++.+|+|||++|+|.+|+.+||+.|||++|.+++++..++++....+.+.+++ |..+.++.....+
T Consensus        59 ~~~~~l~~~~~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~g  138 (292)
T 2o4j_A           59 SMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMSWDCGSQDYKYDVTDVSKAG  138 (292)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHGGGTEETTTTEEECSSGGGEECHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCcchhhccHHHHHHHHHHhHHHHHHHHHHHHhcCCCCeEEecCCCeEEcHHHHHhcC
Confidence            347888999999999999999999999999999999999999999999999998766566667773 7666666655556


Q ss_pred             ch-hhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCC--CCchHHHHH
Q psy3092         259 VG-GIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHS--EEPGRFAKL  335 (347)
Q Consensus       259 ~~-~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~--~~~~Rf~~L  335 (347)
                      +. .+++. +.+++.+|++|++|++||+||+||+|||||++||++...|+++|+++..+|.+|+..+++  +++.||++|
T Consensus       139 ~~~~~~~~-l~~~~~~l~~L~ld~~E~~lLkAIvLfnpd~~gL~~~~~Ve~lq~~~~~aL~~y~~~~~p~~~~~~Rf~~L  217 (292)
T 2o4j_A          139 HTLELIEP-LIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKM  217 (292)
T ss_dssp             CCHHHHHH-HHHHHHHHHHTCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHSCTTTTTTHHHHH
T ss_pred             CcHHHHHH-HHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCCchhhHHHHH
Confidence            66 55555 458999999999999999999999999999999999999999999999999999999988  889999999


Q ss_pred             HhhhhhhhccC
Q psy3092         336 LLRLPSLRSIE  346 (347)
Q Consensus       336 L~ll~~lr~i~  346 (347)
                      |++||.||+|+
T Consensus       218 L~~L~~Lr~l~  228 (292)
T 2o4j_A          218 IQKLADLRSLN  228 (292)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999999875

>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=99.97  E-value=5.4e-30  Score=225.84  Aligned_cols=166  Identities=28%  Similarity=0.392  Sum_probs=151.1

Q ss_pred             hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcC
Q psy3092         179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG  258 (347)
Q Consensus       179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~  258 (347)
                      ...+..++++....+..+++|||++|+|..|+.+||+.|||++|.+++++..++++....+.+++++|..+.++.....+
T Consensus        51 ~~~~~~l~~~~~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~~~~~~~~~~~~~g~~~~~~~~~~~~  130 (248)
T 2nxx_E           51 DVRFRHITEITILTVQLIVEFAKRLPGFDKLLREDQIALLKACSSEVMMFRMARRYDVQTDSILFVNNQPYSRDSYNLAG  130 (248)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEETTTTEEECTTSCEECHHHHHHTT
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHcCCchhhCCHHHHHHHHHHhHHHHHHHHHHHHhcCCCCeEEecCCceecHHHHHhcc
Confidence            34578888999999999999999999999999999999999999999999999998877788899999888776666666


Q ss_pred             chhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCC-CCchHHHHHHh
Q psy3092         259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHS-EEPGRFAKLLL  337 (347)
Q Consensus       259 ~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~-~~~~Rf~~LL~  337 (347)
                      +.++++.+. +++.+|++|++|++||++|+||+||+ +++|+++...|+++|+++..+|++|+..+++ +++.||++||+
T Consensus       131 ~~~~~~~i~-~~~~~l~~L~ld~~E~~lLkAivL~~-d~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~Rf~~LL~  208 (248)
T 2nxx_E          131 MGETIEDLL-HFCRTMYSMRVDNAEYALLTAIVIFS-ERPALIEGWKVEKIQEIYLEALRAYVDNRRKPKPGTIFAKLLS  208 (248)
T ss_dssp             CHHHHHHHH-HHHHHHHHTTCCHHHHHHHHHHHHTC-CCSSCTTHHHHHHHHHHHHHHHHHHHHHSCCSSHHHHHHHHHH
T ss_pred             hHHHHHHHH-HHHHHHHHhcCCHHHHHHHHHHHHcC-CCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCchhhHHHHHHH
Confidence            767776655 89999999999999999999999997 8999999999999999999999999998884 68999999999


Q ss_pred             hhhhhhccC
Q psy3092         338 RLPSLRSIE  346 (347)
Q Consensus       338 ll~~lr~i~  346 (347)
                      +||.||+|+
T Consensus       209 ~L~~Lr~l~  217 (248)
T 2nxx_E          209 VLTELRTLG  217 (248)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999999875

>1pdu_A DHR38, nuclear hormone receptor HR38; nuclear receptor, ligand-binding domain, hormone/growth factor receptor complex; 2.30A {Drosophila melanogaster} SCOP: a.123.1.1

Probab=99.97  E-value=2.7e-30  Score=226.81  Aligned_cols=166  Identities=22%  Similarity=0.404  Sum_probs=150.0

Q ss_pred             hhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhc
Q psy3092         178 NEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEA  257 (347)
Q Consensus       178 ~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~  257 (347)
                      ....+..++++....+..+++|||++|+|.+|+.+||+.|||++|.+++++..++++....+.+++++|..+.++.... 
T Consensus        45 ~~~~~~~~~~~~~~~l~~~VewAK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~rs~~~~~~l~~~~g~~~~~~~~~~-  123 (244)
T 1pdu_A           45 EADKVQQFYQLLTSSVDVIKQFAEKIPGYFDLLPEDQELLFQSASLELFVLRLAYRARIDDTKLIFCNGTVLHRTQCLR-  123 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHCCSSCSEEECTTSBEEEHHHHHH-
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCceEeeCCeeecHHHHHh-
Confidence            4466888999999999999999999999999999999999999999999999999998777888999998887765432 


Q ss_pred             CchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCC--CCchHHHHH
Q psy3092         258 GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHS--EEPGRFAKL  335 (347)
Q Consensus       258 ~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~--~~~~Rf~~L  335 (347)
                      ++.++++.+ .+++.+|++|++|++||+||+||+||| +++||++...|+++|+++..+|.+|+..+++  +++.||++|
T Consensus       124 ~~~~~~~~l-~~~~~~l~~L~ld~~E~~lLkAIvLfn-d~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~~~Rf~~L  201 (244)
T 1pdu_A          124 SFGEWLNDI-MEFSRSLHNLEIDISAFACLCALTLIT-ERHGLREPKKVEQLQMKIIGSLRDHVTYNAEAQKKQHYFSRL  201 (244)
T ss_dssp             HHTTHHHHH-HHHHHHHHHHCCCHHHHHHHHHHHHSS-CCTTCSCHHHHHHHHHHHHHHHHHHHHHCHHHHTSTTHHHHH
T ss_pred             HHHHHHHHH-HHHHHHHHHHcCCHHHHHHHHHHHHhC-CCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCcchhhHHHHH
Confidence            455666665 489999999999999999999999998 8999999999999999999999999988776  689999999


Q ss_pred             HhhhhhhhccC
Q psy3092         336 LLRLPSLRSIE  346 (347)
Q Consensus       336 L~ll~~lr~i~  346 (347)
                      |++||+||+|+
T Consensus       202 L~~L~~Lr~l~  212 (244)
T 1pdu_A          202 LGKLPELRSLS  212 (244)
T ss_dssp             HTHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999999886

>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=99.97  E-value=1.2e-29  Score=226.00  Aligned_cols=164  Identities=21%  Similarity=0.313  Sum_probs=144.7

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV  259 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~  259 (347)
                      ..+..+++.....++.+|+|||++|+|..|+.+||+.|||++|.+++++..|+++....+.+.+ +|..+..+.....++
T Consensus        65 ~~~~~~~~~~~~~l~~~VewaK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~~~~~~~~~~l~-~g~~~~~~~~~~~~~  143 (270)
T 1n83_A           65 VMWQLCAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQNNTVYF-DGKYASPDVFKSLGC  143 (270)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHSTTTTTSCHHHHHHHHHHHHHHHHHHHGGGGEETTTTEEEE-TTEEECGGGGGGGSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCChhhcCHHHHHHHHHHhHHHHHHHHHHHHhcCCCCeEEe-CCccccHHHHHhcCH
Confidence            4577788889999999999999999999999999999999999999999999997665565555 676655554444566


Q ss_pred             hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhh
Q psy3092         260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRL  339 (347)
Q Consensus       260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll  339 (347)
                      ..+.+.+. +++.+|++|++|++||+||+||+|||||++|+++...|+++|+++..+|.+|+..+++ ++.||++||++|
T Consensus       144 ~~~~~~i~-~~~~~l~~L~ld~~E~~lLkAivLfnpd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~-~~~Rf~~LL~~L  221 (270)
T 1n83_A          144 EDFISFVF-EFGKSLCSMHLTEDEIALFSAFVLMSADRSWLQEKVKIEKLQQKIQLALQHVLQKNHR-EDGILTKLICKV  221 (270)
T ss_dssp             HHHHHHHH-HHHHHHHTTCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCT-TSCHHHHHHHHH
T ss_pred             HHHHHHHH-HHHHHHHHHCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCC-chhHHHHHHHHH
Confidence            66666655 8999999999999999999999999999999999999999999999999999998887 579999999999


Q ss_pred             hhhhccC
Q psy3092         340 PSLRSIE  346 (347)
Q Consensus       340 ~~lr~i~  346 (347)
                      |.||+|+
T Consensus       222 ~~Lr~l~  228 (270)
T 1n83_A          222 STLRALC  228 (270)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9999885

>1xpc_A Estrogen receptor; nuclear receptor, transcription factor, ER-alpha, antagonist hormone-growth factor receptor complex; HET: AIT; 1.60A {Homo sapiens} SCOP: a.123.1.1 PDB: 1sj0_A* 1xp1_A* 1xp9_A* 1xp6_A* 1yim_A* 1yin_A* 3ert_A* 1r5k_A* 3erd_A* 1l2i_A* 2iok_A* 1a52_A* 2ouz_A* 1ere_A* 1err_A* 2qxs_A* 3q95_A* 3q97_A* 2b1z_A* 1zky_A* ...

Probab=99.97  E-value=9.5e-31  Score=230.84  Aligned_cols=166  Identities=29%  Similarity=0.517  Sum_probs=146.2

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccch-hhcC
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSA-HEAG  258 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~-~~~~  258 (347)
                      ..+..+++...+.++.+++|||++|+|.+|+.+||+.|||++|.+++++..+++++..++.+++++|..++++.. ...+
T Consensus        35 ~~~~~l~~~a~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~~l~~~~g~~~~~~~~~~~~~  114 (248)
T 1xpc_A           35 SMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEG  114 (248)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTSTTEEEEETTEEEEHHHHTTSTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCccccCCHHHHHHHHHHHhHHHHHHHHHHHhccccCceeecCCceeCccchhhhcc
Confidence            457889999999999999999999999999999999999999999999999999998888899999987766543 2245


Q ss_pred             chhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCC--------CHHHHHHHHHHHHHHHHHHHHhcC---CC
Q psy3092         259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLK--------SQQVVEMLREKVYTSLEEYTRVNH---SE  327 (347)
Q Consensus       259 ~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~--------~~~~i~~~r~~~~~~L~~y~~~~~---~~  327 (347)
                      +.++++.+. +++.+|++|++|++||++|+||+|||||+.+++        +...|+++|+++..+|.+|+..++   ++
T Consensus       115 ~~~~~~~l~-~~~~~l~~L~ld~~E~~lLkAivL~~pd~~~ls~~~~~gl~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~  193 (248)
T 1xpc_A          115 MVEIFDMLL-ATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQ  193 (248)
T ss_dssp             HHHHHHHHH-HHHHHHHHHTCCHHHHHHHHHHHHHHTTTTCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCHHH
T ss_pred             HHHHHHHHH-HHHHHHHHhCCCHHHHHHHHHHHHcCCcccccccccccccccHHHHHHHHHHHHHHHHHHHHccCCCCcc
Confidence            556666655 699999999999999999999999999996553        467899999999999999998764   36


Q ss_pred             CchHHHHHHhhhhhhhccC
Q psy3092         328 EPGRFAKLLLRLPSLRSIE  346 (347)
Q Consensus       328 ~~~Rf~~LL~ll~~lr~i~  346 (347)
                      ++.||++||++||.||+++
T Consensus       194 ~~~Rf~~LL~~L~~Lr~~~  212 (248)
T 1xpc_A          194 QHQRLAQLLLILSHIRHMS  212 (248)
T ss_dssp             HHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHHHH
Confidence            8899999999999999875

>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=99.97  E-value=4.7e-30  Score=226.16  Aligned_cols=167  Identities=23%  Similarity=0.360  Sum_probs=144.8

Q ss_pred             hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcC
Q psy3092         179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG  258 (347)
Q Consensus       179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~  258 (347)
                      ...+..++++....++.+|+|||++|+|..|+.+||+.|||++|.+++++..++++....+. ++.++..+..+.....+
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            34688999999999999999999999999999999999999999999999999988766554 45555555554444456


Q ss_pred             chhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhc--CCCCchHHHHHH
Q psy3092         259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVN--HSEEPGRFAKLL  336 (347)
Q Consensus       259 ~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~--~~~~~~Rf~~LL  336 (347)
                      +...+.+.+.+++.+|++|++|++||+||+||+|||||++|+++...|+++|+++..+|.+|+..+  +++++.||++||
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            663333445689999999999999999999999999999999999999999999999999999854  568899999999


Q ss_pred             hhhhhhhccC
Q psy3092         337 LRLPSLRSIE  346 (347)
Q Consensus       337 ~ll~~lr~i~  346 (347)
                      ++||.||+|+
T Consensus       212 ~~L~~Lr~i~  221 (246)
T 1xvp_B          212 GLLAELRSIN  221 (246)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999999886

>2hc4_A Vitamin D receptor; alpha helical sandwich, gene regulation; HET: VDX; 2.20A {Danio rerio} PDB: 2hbh_A* 2hcd_A* 3dr1_A* 3o1d_A* 3o1e_A*

Probab=99.97  E-value=1.5e-29  Score=228.74  Aligned_cols=165  Identities=22%  Similarity=0.379  Sum_probs=141.9

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCce-EecC-Cccccccchhhc
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGI-LLAP-GVTVYRSSAHEA  257 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~-~~~~-g~~i~~~~~~~~  257 (347)
                      ..+..++++....++.+|+|||++|+|..|+.+||+.|||++|.+++++..++++ ...+.. .+++ +..+.++.....
T Consensus       102 ~~~~~l~e~~~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w~el~lL~~a~~~-~~~~~~~l~~~~~~~~~~~~~~~~  180 (302)
T 2hc4_A          102 SMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLRSNQSF-SLEDMSWSCGGPDFKYCINDVTKA  180 (302)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHTTSTTTTTSCHHHHHHHHHHHHHHHHHHHGGGTE-ETTTTEEECSSSTTEECHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHh-ccCCCeEEecCCCeeecHHHHHHc
Confidence            3468899999999999999999999999999999999999999999999999654 444444 4443 344444444444


Q ss_pred             Cc-hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHH
Q psy3092         258 GV-GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLL  336 (347)
Q Consensus       258 ~~-~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL  336 (347)
                      ++ ..+++ .+.+++.+|++|++|++||+||+||+|||||++||++...|+++|++|..+|++|+..++++++.||++||
T Consensus       181 g~~~~~~~-~l~~~~~~l~~L~ld~~E~alLkAIvLfnpd~~gL~~~~~Ve~lqe~~~~aL~~y~~~~~p~~~~RF~~LL  259 (302)
T 2hc4_A          181 GHTLELLE-PLVKFQVGLKKLKLHEEEHVLLMAICLLSPDRPGVQDHVRIEALQDRLCDVLQAYIRIQHPGGRLLYAKMI  259 (302)
T ss_dssp             TCCHHHHH-HHHHHHHHHHTTCCCHHHHHHHHHHHHTCSCSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHH
T ss_pred             cCcHHHHH-HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHHHHHHHHHHHHHCCChhHHHHHHH
Confidence            55 34444 45589999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhhccC
Q psy3092         337 LRLPSLRSIE  346 (347)
Q Consensus       337 ~ll~~lr~i~  346 (347)
                      ++||.||+|+
T Consensus       260 l~L~~Lr~l~  269 (302)
T 2hc4_A          260 QKLADLRSLN  269 (302)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999999875

>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=99.97  E-value=5.5e-30  Score=225.86  Aligned_cols=167  Identities=28%  Similarity=0.512  Sum_probs=139.4

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCce-EecCCcccc----ccch
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGI-LLAPGVTVY----RSSA  254 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~-~~~~g~~i~----~~~~  254 (347)
                      .+++.++++..+.++.+|+|||++|+|.+|+.+||+.|||++|.+++++..|+++...+... ..++|....    .+..
T Consensus        34 ~~~~~~~e~a~~~L~~~VewaK~iP~F~~L~~~DQ~~LLk~~w~el~~L~~a~~s~~~~~~~~l~~~~~~~~~~~~~~~~  113 (249)
T 3p0u_A           34 LNVHYICESASRLLFLSMHWARSIPAFQALGQDCNTSLVRACWNELFTLGLAQCAQVMSLSTILAAIVNHLQNSIQEDKL  113 (249)
T ss_dssp             SCSSCHHHHHHHHHHHHHHHHHTCTTTGGGCHHHHHHHHHTTHHHHHHHHHHHTTTSCCCCCCCCC-CC---CC------
T ss_pred             cCHHHHHHHHHHHHHHHHHHHHcCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHcccCCcchhhcccccccccccccccc
Confidence            35788999999999999999999999999999999999999999999999999987765443 334443321    1222


Q ss_pred             hhcCchhhHHhh--HHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHH
Q psy3092         255 HEAGVGGIFDRV--LTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRF  332 (347)
Q Consensus       255 ~~~~~~~~~~~~--~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf  332 (347)
                      .......+.+.+  +.+++.+|++|++|++||++|+||+|||||++|+++...|+++|+++..+|.+|+..++++++.||
T Consensus       114 ~~~~~~~~~~~i~~l~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~Rf  193 (249)
T 3p0u_A          114 SGDRIKQVMEHIWKLQEFCNSMAKLDIDGYEYAYLKAIVLFSPDHPGLTSTSQIEKFQEAAQMELQDYVQATYSEDTYRL  193 (249)
T ss_dssp             ---CCCCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHTCSCSTTCCCSHHHHHHHHHHHHHHHHHHHHHTTTCSTHH
T ss_pred             hhhhhhhHHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCChHHHH
Confidence            222333344433  568999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhhhhhhccC
Q psy3092         333 AKLLLRLPSLRSIE  346 (347)
Q Consensus       333 ~~LL~ll~~lr~i~  346 (347)
                      ++||++||.||+|+
T Consensus       194 ~~LL~~L~~Lr~i~  207 (249)
T 3p0u_A          194 ARILVRLPALRLMS  207 (249)
T ss_dssp             HHHHTTHHHHHTSC
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999999986

>1sqn_A PR, progesterone receptor; nuclear receptor, steroid receptor, norethindrone, birth control, hormone/growth factor receptior complex; HET: NDR; 1.45A {Homo sapiens} SCOP: a.123.1.1 PDB: 3g8o_A* 3g8n_A* 3d90_A* 1e3k_A* 1sr7_A* 1zuc_B* 3zr7_A* 2w8y_A* 3zra_A* 3zrb_A* 4a2j_A* 4apu_A* 1a28_A* 2ovh_A* 2ovm_A* 3hq5_A* 3kba_A*

Probab=99.97  E-value=2.9e-30  Score=229.05  Aligned_cols=167  Identities=21%  Similarity=0.413  Sum_probs=145.9

Q ss_pred             hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCC--ceEecCCccccccchhh
Q psy3092         179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKD--GILLAPGVTVYRSSAHE  256 (347)
Q Consensus       179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~--~~~~~~g~~i~~~~~~~  256 (347)
                      ...+..++++....++.+++|||++|+|.+|+.+||+.|||++|.+++++..+++++..++  .+++++|..++++....
T Consensus        40 ~~~~~~l~e~a~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~~~~l~~~~~~~~~~~~~~~  119 (261)
T 1sqn_A           40 SSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKE  119 (261)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECGGGCCS
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHhCccHhhCCHHHHHHHHHhhHHHHHHHHHHHHhhhcCCCCeEEeCCCcccchHhhhh
Confidence            3457889999999999999999999999999999999999999999999999999877654  36788888777655433


Q ss_pred             cCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcC-CCCCCCCHHHHHHHHHHHHHHHHHHHHhc---CCCCchHH
Q psy3092         257 AGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNP-DVRGLKSQQVVEMLREKVYTSLEEYTRVN---HSEEPGRF  332 (347)
Q Consensus       257 ~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p-~~~~l~~~~~i~~~r~~~~~~L~~y~~~~---~~~~~~Rf  332 (347)
                      .++.++.+. +.+++.+|++|++|++||++|+||+|||| +++|+++...|+++|+++..+|.+|+..+   +++++.||
T Consensus       120 ~~~~~~~~~-i~~~~~~l~~L~ld~~E~~lLkAIvLfnp~~~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~~~~Rf  198 (261)
T 1sqn_A          120 SSFYSLCLT-MWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSSSQRF  198 (261)
T ss_dssp             HHHHHHHHH-HHHHHHHHHHHTCCHHHHHHHHHHHHTSEECTTCCTTHHHHHHHHHHHHHHHHHHHHTTC-CHHHHHHHH
T ss_pred             hhHHHHHHH-HHHHHHHHHHHCCCHHHHHHHHHHHHcCCCcccccccHHHHHHHHHHHHHHHHHHHHhhCCCCCchHHHH
Confidence            334444443 55899999999999999999999999999 89999999999999999999999999864   34688999


Q ss_pred             HHHHhhhhhhhccC
Q psy3092         333 AKLLLRLPSLRSIE  346 (347)
Q Consensus       333 ~~LL~ll~~lr~i~  346 (347)
                      ++||++||.||+++
T Consensus       199 ~~LL~~L~~Lr~~~  212 (261)
T 1sqn_A          199 YQLTKLLDNLHDLV  212 (261)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHhHHHHHHH
Confidence            99999999999874

>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=99.97  E-value=4.7e-30  Score=228.75  Aligned_cols=167  Identities=23%  Similarity=0.430  Sum_probs=148.0

Q ss_pred             hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCC--ceEecCCccccccchhh
Q psy3092         179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKD--GILLAPGVTVYRSSAHE  256 (347)
Q Consensus       179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~--~~~~~~g~~i~~~~~~~  256 (347)
                      ...+..+++..++.++.+++|||++|+|.+|+.+||+.|||++|.+++++..+|+++..++  .+++++|..++++....
T Consensus        48 ~~~~~~l~e~a~~~l~~~VewAK~ip~F~~L~~~DQv~LLk~~w~el~iL~~a~rs~~~~~~~~l~~~~g~~~~~~~~~~  127 (269)
T 1t7r_A           48 AALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHK  127 (269)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhCccHhhCCHHHHHHHHHHhHHHHHHHHHHHHhcccCCCCeEEeCCCceecHHhhhh
Confidence            4567889999999999999999999999999999999999999999999999999887644  46778898887766555


Q ss_pred             cCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcC-CCCCCCCHHHHHHHHHHHHHHHHHHHHhcC---CCCchHH
Q psy3092         257 AGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNP-DVRGLKSQQVVEMLREKVYTSLEEYTRVNH---SEEPGRF  332 (347)
Q Consensus       257 ~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p-~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~---~~~~~Rf  332 (347)
                      .++.++++. +.+++.+|++|++|++||+||+||+|||| +++||++...|+++|+++..+|.+|+..++   ++++.||
T Consensus       128 ~~~~~~~~~-i~~~~~~l~~L~ld~~E~~lLkAIvLfnp~~~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~~~~Rf  206 (269)
T 1t7r_A          128 SRMYSQCVR-MRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFFDELRMNYIKELDRIIACKRKNPTSCSRRF  206 (269)
T ss_dssp             TTCHHHHHH-HHHHHHHHHHTTCCHHHHHHHHHHHHTSEEETTCCTTHHHHHHHHHHHHHHHHHHHHTTCCSHHHHHHHH
T ss_pred             hhHHHHHHH-HHHHHHHHHHhCCCHHHHHHHHHHHHcCCCccCCCccHHHHHHHHHHHHHHHHHHHHHhCCCCCcHHHHH
Confidence            555555544 56999999999999999999999999999 899999999999999999999999998765   3568999


Q ss_pred             HHHHhhhhhhhccC
Q psy3092         333 AKLLLRLPSLRSIE  346 (347)
Q Consensus       333 ~~LL~ll~~lr~i~  346 (347)
                      ++||++||.||+++
T Consensus       207 ~~LL~~L~~Lr~l~  220 (269)
T 1t7r_A          207 YQLTKLLDSVQPIA  220 (269)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999999875

>3vi8_A Peroxisome proliferator-activated receptor alpha; nuclear receptor, protein-ligand complex, PPAR, transcriptio; HET: 13M; 1.75A {Homo sapiens} PDB: 2znn_A* 3et1_A* 3kdu_A* 3kdt_A* 2rew_A* 1i7g_A* 3g8i_A* 1kkq_A* 1k7l_A* 3sp6_A* 2npa_A* 2p54_A* 3fei_A* 3tkm_A* 2znq_A* 2znp_A* 3sp9_A* 3gwx_A* 3dy6_A* 1gwx_A* ...

Probab=99.97  E-value=1.3e-29  Score=225.75  Aligned_cols=189  Identities=23%  Similarity=0.279  Sum_probs=146.7

Q ss_pred             HHHHHHHHHhccCCCCCCcc--ccchhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhc
Q psy3092         155 VERILEAEQRVDMKQEPADQ--DIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSH  232 (347)
Q Consensus       155 ~~~l~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~  232 (347)
                      .+.+..++..+.....+...  ......-+..+....+..+..+|+|||++|+|.+|+.+||+.|||++|.+++++.+++
T Consensus        49 ~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~iVewAK~iPgF~~L~~~DQi~LLk~~w~ElllL~~a~  128 (273)
T 3vi8_A           49 METLCMAEKTLVAKLVANGIQNKEAEVRIFHCCQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSS  128 (273)
T ss_dssp             HHHHHHHHHHHSGGGGSCC--CCCHHHHHHHHHHHHHHHHHHHHHHHGGGSTTTTTSCHHHHHHHHHHHHHHHHHHHHGG
T ss_pred             hHHHHhhhhhhhhccCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHccCcCcccCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            45666666554432222111  1111234667777888899999999999999999999999999999999999999998


Q ss_pred             ccccCCCceEecCCccccccchh---hcCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHH
Q psy3092         233 RSISVKDGILLAPGVTVYRSSAH---EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEML  309 (347)
Q Consensus       233 ~s~~~~~~~~~~~g~~i~~~~~~---~~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~  309 (347)
                      ++...  +..+..|.........   ..++..+++. +.+++.+|++|++|++||+||+||+||+||++||++...|+++
T Consensus       129 ~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-l~~~~~~~~~L~ld~~E~alLkAivLf~pd~~gL~~~~~Ve~l  205 (273)
T 3vi8_A          129 VMNKD--GMLVAYGNGFITREFLKSLRKPFCDIMEP-KFDFAMKFNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKM  205 (273)
T ss_dssp             GEETT--EEEETTTTEEEEHHHHHHSCTTTHHHHHH-HHHHHHHHHTTCCCHHHHHHHHHHHHSCTTCTTCSCHHHHHHH
T ss_pred             HhcCC--CCeeeeCCCccchHHHHHhhhhHHHHHHH-HHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCcccHHHHHHH
Confidence            76443  3333333322222211   1233344444 5589999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhcCCCCchHHHHHHhhhhhhhccC
Q psy3092         310 REKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIE  346 (347)
Q Consensus       310 r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll~~lr~i~  346 (347)
                      |+++..+|.+|+..++++.+.||++||++||.||+|+
T Consensus       206 qe~~~~aL~~yi~~~~p~~~~rF~kLL~~Lp~LR~l~  242 (273)
T 3vi8_A          206 QEGIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQLV  242 (273)
T ss_dssp             HHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCChhhHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999986

>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=99.97  E-value=1.2e-29  Score=229.75  Aligned_cols=166  Identities=29%  Similarity=0.409  Sum_probs=151.4

Q ss_pred             hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcC
Q psy3092         179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG  258 (347)
Q Consensus       179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~  258 (347)
                      ...+..++++....++.+|+|||.+|+|..|+.+||+.|||++|.+++++..|+++....+.+++++|..+.++.....+
T Consensus       115 ~~~~~~l~el~~~~l~~~VewAK~lP~F~~L~~~DQi~LLk~~w~el~lL~~a~rs~~~~~~l~~~~g~~~~~~~~~~~g  194 (310)
T 1z5x_E          115 EERFRHITEITILTVQLIVEFSKRLPGFDKLIREDQIALLKACSSEVMMFRMARRYDAETDSILFATNQPYTRESYTVAG  194 (310)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEETTTTEEECTTSCEECHHHHHHTT
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHcCcchhhCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCeEEeCCCccccHHHHHhcc
Confidence            35578889999999999999999999999999999999999999999999999999887888999999888776655566


Q ss_pred             chhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcC-CCCchHHHHHHh
Q psy3092         259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNH-SEEPGRFAKLLL  337 (347)
Q Consensus       259 ~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~-~~~~~Rf~~LL~  337 (347)
                      +..+++.+. +++.+|++|++|++||+||+||+||+ |++||++...|+++|++|..+|.+|+..++ ++++.||++||+
T Consensus       195 ~~~~~~~i~-~~~~~l~~L~ld~~E~alLkAIvLf~-d~~gL~~~~~Ve~lqe~~~~aL~~y~~~~~~~~~~~RF~kLLl  272 (310)
T 1z5x_E          195 MGDTVEDLL-RFCRHMCAMKVDNAEYALLTAIVIFS-ERPSLSEGWKVEKIQEIYIEALKAYVENRRKPYATTIFAKLLS  272 (310)
T ss_dssp             THHHHHHHH-HHHHHHHHHTCCHHHHHHHHHHHHTC-CCTTCTTHHHHHHHHHHHHHHHHHHHHTTTCTTHHHHHHHHHH
T ss_pred             hhHHHHHHH-HHHHHHHHHcCCHHHHHHHHHHHHcC-CCCCCccHHHHHHHHHHHHHHHHHHHHHHCCCcHHHHHHHHHH
Confidence            777776655 79999999999999999999999997 999999999999999999999999999887 578999999999


Q ss_pred             hhhhhhccC
Q psy3092         338 RLPSLRSIE  346 (347)
Q Consensus       338 ll~~lr~i~  346 (347)
                      +||+||+|+
T Consensus       273 ~Lp~LR~l~  281 (310)
T 1z5x_E          273 VLTELRTLG  281 (310)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999999875

>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=99.97  E-value=5.2e-30  Score=224.00  Aligned_cols=164  Identities=24%  Similarity=0.379  Sum_probs=139.2

Q ss_pred             hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcC
Q psy3092         179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG  258 (347)
Q Consensus       179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~  258 (347)
                      ...+..++++....++.+++|||++|+|..|+.+||+.|||++|.+++++..|+++....    ..+|..+.++.....+
T Consensus        41 ~~~~~~~~~~~~~~l~~~vewaK~lp~F~~L~~~DQ~~LLk~~~~e~~~l~~a~~~~~~~----~~~~~~~~~~~~~~~~  116 (232)
T 1osh_A           41 EENFLILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKL----PSGHSDLLEERIRNSG  116 (232)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHTS----CHHHHHHHHHHHHTSS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCchhhCCHHHHHHHHHHhHHHHHHHHHHHHhCCcc----CCCCceecHHHHHHcC
Confidence            345788999999999999999999999999999999999999999999999998753321    1233444444333344


Q ss_pred             chhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhh
Q psy3092         259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLR  338 (347)
Q Consensus       259 ~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~l  338 (347)
                      +...+.+.+.+++.+|++|++|++||++|+||+|||||++|+++...|+++|+++..+|++|+..++++++.||++||++
T Consensus       117 ~~~~~~~~i~~~~~~l~~L~ld~~E~~lLkaivL~~pd~~gL~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LL~~  196 (232)
T 1osh_A          117 ISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLCKIHQPENPQHFACLLGR  196 (232)
T ss_dssp             CCTTTHHHHHHHHHHHHTTCCCHHHHHHHHHHHHTCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCCChHHHHHHHHHHHHHHHHHHHHHCCCchhHHHHHHHH
Confidence            44323334557999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhccC
Q psy3092         339 LPSLRSIE  346 (347)
Q Consensus       339 l~~lr~i~  346 (347)
                      ||+||+|+
T Consensus       197 L~~Lr~l~  204 (232)
T 1osh_A          197 LTELRTFN  204 (232)
T ss_dssp             HHHHHTHH
T ss_pred             HHHHHHHH
Confidence            99999875

>3v3e_B Nuclear receptor subfamily 4 group A member 1; orphan nuclear receptor, transcription; 2.06A {Homo sapiens} PDB: 3v3q_A* 2qw4_A 1yje_A

Probab=99.97  E-value=8.8e-30  Score=224.97  Aligned_cols=165  Identities=25%  Similarity=0.457  Sum_probs=148.4

Q ss_pred             hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcC
Q psy3092         179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG  258 (347)
Q Consensus       179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~  258 (347)
                      ...+..+++.....+..+|+|||++|+|.+|+.+||+.|||++|.+++++++++++....+.+++.+|..+.+.... .+
T Consensus        51 ~~~~~~~~~l~~~~i~~iV~wAK~iP~F~~L~~~DQi~LLk~~w~ElllL~~a~~~~~~~~~l~~~~~~~~~~~~~~-~~  129 (257)
T 3v3e_B           51 AGDVQQFYDLLSGSLEVIRKWAEKIPGFAELSPADQDLLLESAFLELFILRLAYRSKPGEGKLIFCSGLVLHRLQCA-RG  129 (257)
T ss_dssp             HHHHHHHHHHHHHTHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHSBGGGTEEECTTSBEEEHHHHH-HH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhccCCCCeeEeCCCccccHHHHH-hh
Confidence            34577888999999999999999999999999999999999999999999999999888899999999888776553 35


Q ss_pred             chhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHh--cCCCCchHHHHHH
Q psy3092         259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRV--NHSEEPGRFAKLL  336 (347)
Q Consensus       259 ~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~--~~~~~~~Rf~~LL  336 (347)
                      ++++++.+. +++.+|++|++|++||+||+||+||+ |++||++...|+++|+++..+|.+|+..  ++++.+.||++||
T Consensus       130 ~~~~~~~l~-~~~~~l~~L~ld~~E~a~LkAivLfs-d~~gL~~~~~Ve~lqe~~~~aL~~yi~~~~~~p~~~~rf~kLL  207 (257)
T 3v3e_B          130 FGDWIDSIL-AFSRSLHSLLVDVPAFACLSALVLIT-DRHGLQEPRRVEELQNRIASCLKEHVAAVAGEPQPASCLSRLL  207 (257)
T ss_dssp             HTTHHHHHH-HHHHHHHHTTCCHHHHHHHHHHHHSS-CCTTCSSHHHHHHHHHHHHHHHHHHHHHHHCSCC-CHHHHHHH
T ss_pred             hHHHHHHHH-HHHHHHHhcCCCHHHHHHHHHHHHhC-CCCCCCCHHHHHHHHHHHHHHHHHHHHHhcCCCcHhhHHHHHH
Confidence            566666655 89999999999999999999999998 8999999999999999999999999964  4678899999999


Q ss_pred             hhhhhhhccC
Q psy3092         337 LRLPSLRSIE  346 (347)
Q Consensus       337 ~ll~~lr~i~  346 (347)
                      ++||.||+|+
T Consensus       208 ~~Lp~LR~l~  217 (257)
T 3v3e_B          208 GKLPELRTLC  217 (257)
T ss_dssp             THHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999999986

>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=99.97  E-value=1.7e-29  Score=222.37  Aligned_cols=165  Identities=39%  Similarity=0.667  Sum_probs=135.8

Q ss_pred             HHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCce-EecCCccccccch-hhcC
Q psy3092         181 QATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGI-LLAPGVTVYRSSA-HEAG  258 (347)
Q Consensus       181 ~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~-~~~~g~~i~~~~~-~~~~  258 (347)
                      .++.++++....++.+++|||++|+|.+|+.+||+.|||++|.+++++..+++++..+... .+++|........ ....
T Consensus        38 ~~~~l~e~a~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~~~~l~~~g~~~~~~~~~~~~~  117 (244)
T 3cjw_A           38 GIENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHVAPLLAAAGLHASPMSADRVVA  117 (244)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHHSSSGGGSCHHHHHHHHHHHHHHHHHHHHHHHTCCCSCCC-----------------CC
T ss_pred             cHHHHHHHHHHHHHHHHhHHHhCCChhcCCHHHHHHHHHHHHHHHHHHHHHHHhccccccccccccccccCccchhhhHH
Confidence            4678899999999999999999999999999999999999999999999999998766543 4445543221110 0111


Q ss_pred             chhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhh
Q psy3092         259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLR  338 (347)
Q Consensus       259 ~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~l  338 (347)
                      +.+.. +.+.+++.+|++|++|++||++|+||+|||||++|+++...|+++|+++..+|.+|+..++++++.||++||++
T Consensus       118 ~~~~~-~~~~~~~~~~~~L~ld~~E~~lLkaivL~~pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~Rf~~LLl~  196 (244)
T 3cjw_A          118 FMDHI-RIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLR  196 (244)
T ss_dssp             CSHHH-HHHHHHHHHHHHTTCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTT
T ss_pred             HHHHH-HHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHH
Confidence            22222 34568999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhccC
Q psy3092         339 LPSLRSIE  346 (347)
Q Consensus       339 l~~lr~i~  346 (347)
                      ||+||+++
T Consensus       197 L~~Lr~l~  204 (244)
T 3cjw_A          197 LPSLRTVS  204 (244)
T ss_dssp             HHHHHHSC
T ss_pred             hHHHHhhh
Confidence            99999986

>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=99.96  E-value=4.3e-30  Score=235.82  Aligned_cols=166  Identities=36%  Similarity=0.634  Sum_probs=132.8

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccC--CCceEecCCccccccchh-h
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISV--KDGILLAPGVTVYRSSAH-E  256 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~--~~~~~~~~g~~i~~~~~~-~  256 (347)
                      ..+..++++..+.++.+|+|||+||+|.+|+.+||+.|||++|.+++++..+|+++..  .+.+++++|..+..+... .
T Consensus       151 ~~~~~l~e~a~~~L~~~VewAK~iP~F~~L~~~DQi~LLk~~w~ElllL~~a~rs~~~~~~~~ll~~~G~~i~~~~~~~~  230 (352)
T 3tx7_B          151 STFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQ  230 (352)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHTCCC----------CHHHHHHHHHHHHHHHHHHHHHHTCCSSCCBCTTCCBCCHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcChhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEecCCCcccHHHHHHh
Confidence            4678899999999999999999999999999999999999999999999999998765  367888999888776543 2


Q ss_pred             cCc--hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHH
Q psy3092         257 AGV--GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAK  334 (347)
Q Consensus       257 ~~~--~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~  334 (347)
                      .+.  .++++. +.+++.+|++|++|++||+||+||+|||||++||++...|+++|+++..+|.+|+..++++++.||++
T Consensus       231 ~g~~~~~l~~~-l~~l~~~l~~L~ld~~EyalLkAIvLfnpd~~gLs~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~RF~k  309 (352)
T 3tx7_B          231 AGATLNNLMSH-AQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQ  309 (352)
T ss_dssp             SCHHHHHHHHH-HHHHHHHHHHTTCCHHHHHHHHHHHHSCSCC------CHHHHHHHHHHHHHHHHHHHHCTTCTTHHHH
T ss_pred             ccccHHHHHHH-HHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHHHHhCCCccHHHHH
Confidence            232  344444 56899999999999999999999999999999999988999999999999999999999999999999


Q ss_pred             HHhhhhhhhccC
Q psy3092         335 LLLRLPSLRSIE  346 (347)
Q Consensus       335 LL~ll~~lr~i~  346 (347)
                      ||++|+.||+|+
T Consensus       310 LLllLp~LR~ls  321 (352)
T 3tx7_B          310 LLLRLPEIRAIS  321 (352)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            999999999875

>1nrl_A Orphan nuclear receptor PXR; PXR, xenobiotic, SRC-1, ligand binding domain, transcription; HET: SRL; 2.00A {Homo sapiens} SCOP: a.123.1.1 PDB: 1ilh_A* 1ilg_A* 1m13_A* 2qnv_A* 3r8d_A* 3ctb_A 3ctc_A 3hvl_A* 1skx_A* 2o9i_A*

Probab=99.96  E-value=9e-30  Score=230.73  Aligned_cols=164  Identities=22%  Similarity=0.339  Sum_probs=144.6

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV  259 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~  259 (347)
                      ..+..+++.....++.+|+|||.+|+|..|+.+||+.|||++|.+++++..++++....+.+++. |..+.++.. ..++
T Consensus       120 ~~~~~l~e~~~~~L~~~VewAK~lP~F~~L~~~DQi~LLk~~w~el~lL~~a~~~~~~~~~~l~~-~~~~~~~~~-~~g~  197 (316)
T 1nrl_A          120 SLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECG-RLSYCLEDT-AGGF  197 (316)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHHHCHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTEETTTTEEEET-TEEEEECCC-SSCH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCcchhhcCHHHHHHHHHHHHHHHHHHHHHHHhhcCCCeEEEC-CEeecHHHH-hccc
Confidence            35788999999999999999999999999999999999999999999999999887666666654 455555554 4455


Q ss_pred             h-hhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCC--CCchHHHHHH
Q psy3092         260 G-GIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHS--EEPGRFAKLL  336 (347)
Q Consensus       260 ~-~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~--~~~~Rf~~LL  336 (347)
                      . .+++. +.+++.+|++|++|++||+||+||+|||||++||++...|+++|++|..+|.+|+..+++  +++.||++||
T Consensus       198 ~~~~~~~-i~~~~~~l~~L~ld~~E~alLkAIvLfnpd~~gL~~~~~Ve~lqe~~~~aL~~y~~~~~p~~~~~~RF~kLL  276 (316)
T 1nrl_A          198 QQLLLEP-MLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLKIM  276 (316)
T ss_dssp             HHHTTSH-HHHHHHHHHHTCCCHHHHHHHHHHHHTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCCSGGGTTHHHHHH
T ss_pred             cHHHHHH-HHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCCchhHHHHHHH
Confidence            4 34444 448999999999999999999999999999999999999999999999999999999998  7899999999


Q ss_pred             hhhhhhhccC
Q psy3092         337 LRLPSLRSIE  346 (347)
Q Consensus       337 ~ll~~lr~i~  346 (347)
                      ++||.||+|+
T Consensus       277 l~Lp~LR~l~  286 (316)
T 1nrl_A          277 AMLTELRSIN  286 (316)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999999885

>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=99.96  E-value=2.1e-29  Score=223.82  Aligned_cols=168  Identities=24%  Similarity=0.362  Sum_probs=137.6

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEe----cCCccccccc--
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL----APGVTVYRSS--  253 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~----~~g~~i~~~~--  253 (347)
                      ...+.+++++...++.+|+|||++|+|..|+.+||+.|||++|.+++++..|++++..++....    .++.......  
T Consensus        47 ~~~~~l~e~a~~~L~~~V~wAK~iP~F~~L~~~DQv~LLk~~w~ElllL~~A~rs~~~~~~~~~~~~~~~~il~~~~~~~  126 (268)
T 3f5c_B           47 KDPQVVCEAASAGLLKTLRFVKYLPCFQILPLDQQLVLVRSCWAPLLMLELAQDHLHFEMMEIPETNTTQEMLTTRRQET  126 (268)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHTCHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTTCCCCCCCC-----------------
T ss_pred             CCHHHHHHHHHHHHHHHHHHHccCCCcccCCHHHHHHHHHHHhHHHHHHHHHHHhccccccccchhhhhhhhhccccccc
Confidence            3567899999999999999999999999999999999999999999999999999876544321    1111111111  


Q ss_pred             -------------------hhhcCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHH
Q psy3092         254 -------------------AHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVY  314 (347)
Q Consensus       254 -------------------~~~~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~  314 (347)
                                         ....+....+.+.+.+++.+|++|++|++||++|+||+|||||++|+++...|+++|+++.
T Consensus       127 ~~~~~~~p~~~~~~~~~~~~~~~~~~~~~i~~l~~~~~~l~~L~ld~~E~~lLkAivL~npd~~gL~~~~~ve~lq~~~~  206 (268)
T 3f5c_B          127 EGPEPAEPQATEQPQMVSAEAGHLLPAAAVQAIKSFFFKCWSLNIDTKEYAYLKGTVLFNPDLPGLQCVKYIEGLQWRTQ  206 (268)
T ss_dssp             ----------------------CCCCSSHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHH
T ss_pred             ccccccccccccccccccchhccccHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHH
Confidence                               0111111122345668999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhcCCCCchHHHHHHhhhhhhhccCC
Q psy3092         315 TSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIEV  347 (347)
Q Consensus       315 ~~L~~y~~~~~~~~~~Rf~~LL~ll~~lr~i~~  347 (347)
                      .+|.+|+..++++.+.||++||++||.||+|+.
T Consensus       207 ~aL~~y~~~~~p~~~~Rf~~LL~~Lp~LR~i~~  239 (268)
T 3f5c_B          207 QILTEHIRMMQREYQIRSAELNSALFLLRFINS  239 (268)
T ss_dssp             HHHHHHHHHHSSCSSHHHHHHHHHHHHHTTSCS
T ss_pred             HHHHHHHHHHCCChHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999874

>3l0l_A Nuclear receptor ROR-gamma; nuclear receptor, rorgamma, alternative splicing, DNA-bindin binding, nucleus, receptor, zinc-finger, acetylation, activator; HET: HC3; 1.74A {Homo sapiens} SCOP: a.123.1.0 PDB: 3b0w_A* 3kyt_A* 3l0j_A*

Probab=99.96  E-value=6.4e-29  Score=218.80  Aligned_cols=163  Identities=18%  Similarity=0.267  Sum_probs=144.1

Q ss_pred             hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcC
Q psy3092         179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG  258 (347)
Q Consensus       179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~  258 (347)
                      ...+..+++..+..+..+|+|||++|+|.+|+.+||+.|||++|.+++++..++++....+.+.+ +|..+..+.....+
T Consensus        55 ~~~~~~~~~~~~~~l~~~VewaK~iP~F~~L~~~DQi~LLk~~~~el~lL~~a~~~~~~~~~~~~-~g~~~~~~~~~~~~  133 (248)
T 3l0l_A           55 WEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNRTVFF-EGKYGGMELFRALG  133 (248)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHGGGGEETTTTEEEE-TTEEECGGGGGGGS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcCCCCEEEe-CCCcccHHHHhhcc
Confidence            34578888999999999999999999999999999999999999999999999887665565555 67666555444456


Q ss_pred             chhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhh
Q psy3092         259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLR  338 (347)
Q Consensus       259 ~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~l  338 (347)
                      ..++++.+. +++.+|++|++|++||+||+||+|||||++||++...|+++|+++..+|.+|+..+++  +.||++||++
T Consensus       134 ~~~~~~~l~-~~~~~l~~L~ld~~E~~lLkAivLfnpd~~gL~~~~~ve~lqe~~~~aL~~y~~~~~~--~~rf~~LLl~  210 (248)
T 3l0l_A          134 CSELISSIF-DFSHSLSALHFSEDEIALYTALVLINAHRPGLQEKRKVEQLQYNLELAFHHHLCKTHR--QSILAKLPPK  210 (248)
T ss_dssp             CHHHHHHHH-HHHHHHHTTCCCHHHHHHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHTTC--GGGGGGSCCT
T ss_pred             HHHHHHHHH-HHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCCccHHHHHHHHHHHHHHHHHHHHhhCh--HHHHHHhhcc
Confidence            677777766 8999999999999999999999999999999999999999999999999999998874  6799999999


Q ss_pred             hhhhhccC
Q psy3092         339 LPSLRSIE  346 (347)
Q Consensus       339 l~~lr~i~  346 (347)
                       |+||+|+
T Consensus       211 -p~LR~i~  217 (248)
T 3l0l_A          211 -GKLRSLC  217 (248)
T ss_dssp             -THHHHHH
T ss_pred             -HHHHHHH
Confidence             9999986

>3u9q_A Peroxisome proliferator-activated receptor gamma; nuclear receptor, adipogenesis, RXRA, nucleus, transcription; HET: DKA; 1.52A {Homo sapiens} SCOP: a.123.1.1 PDB: 1i7i_A* 3ty0_A* 1zeo_A* 2p4y_A* 3et3_A* 3et0_A* 2hwq_A* 2ath_A* 2f4b_A* 2g0g_A* 2g0h_A* 2gtk_A* 2fvj_A* 2hwr_A* 2prg_A* 2q8s_A* 3fej_A* 3g9e_A* 3gbk_A* 3ia6_A* ...

Probab=99.96  E-value=2e-28  Score=217.74  Aligned_cols=162  Identities=27%  Similarity=0.470  Sum_probs=138.7

Q ss_pred             HhhhhHHHHHH-HHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCcc-ccccchhh--c
Q psy3092         182 ATNICKATDKQ-LFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVT-VYRSSAHE--A  257 (347)
Q Consensus       182 ~~~~~~~~~~~-l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~-i~~~~~~~--~  257 (347)
                      ....|...... +..+|+|||++|+|.+|+.+||+.|||++|.+++++..+++.  ..++.++++|.. +.++....  .
T Consensus        74 ~~~~c~~~~~~~v~~~VewAK~iP~F~~L~~~DQi~LLk~~~~el~lL~~a~~~--~~~~~~~~~g~~~~~~~~~~~~~~  151 (269)
T 3u9q_A           74 IFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLM--NKDGVLISEGQGFMTREFLKSLRK  151 (269)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTE--ETTEEEETTTTEEEEHHHHHHSCT
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCCChhhcCHHHHHHHHHHhhHHHHHHHHHHhc--CCCCeEEeCCCccccHHHHHHhhh
Confidence            34556555555 668999999999999999999999999999999999999664  346788888765 34433322  3


Q ss_pred             CchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHh
Q psy3092         258 GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLL  337 (347)
Q Consensus       258 ~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~  337 (347)
                      ++.++.+.+ .+++.+|++|++|++||+||+||+|||||++|+++...|+++|+++..+|++|+..++++++.||++||+
T Consensus       152 ~~~~~~~~l-~~~~~~l~~L~ld~~E~alLkAIvLfnpd~~gL~~~~~Ve~lqe~~~~aL~~y~~~~~p~~~~Rf~kLL~  230 (269)
T 3u9q_A          152 PFGDFMEPK-FEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQ  230 (269)
T ss_dssp             TGGGSSHHH-HHHHHHHHTTCCCHHHHHHHHHHHHTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTSTTHHHHHHH
T ss_pred             hHHHHHHHH-HHHHHHHHhhcCCHHHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHH
Confidence            455556554 5899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhccC
Q psy3092         338 RLPSLRSIE  346 (347)
Q Consensus       338 ll~~lr~i~  346 (347)
                      +||+||+|+
T Consensus       231 ~Lp~LR~i~  239 (269)
T 3u9q_A          231 KMTDLRQIV  239 (269)
T ss_dssp             HHHHHHHHH
T ss_pred             HhHHHHHHH
Confidence            999999985

>3up3_A Acedaf-12; ligand binding domain, nematode, steroid binding protein- transcription complex; HET: XCA; 1.25A {Ancylostoma ceylanicum} PDB: 3up0_A*

Probab=99.96  E-value=4.8e-29  Score=218.43  Aligned_cols=163  Identities=20%  Similarity=0.257  Sum_probs=138.2

Q ss_pred             hhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceE---ecCCccccccchhh--c
Q psy3092         183 TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGIL---LAPGVTVYRSSAHE--A  257 (347)
Q Consensus       183 ~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~---~~~g~~i~~~~~~~--~  257 (347)
                      ..+++..+..++.+|+|||++|+|.+|+.+||+.|||++|.++++++.++++....+.+.   +.+|..+.++....  .
T Consensus        44 ~~l~~l~~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w~Ell~L~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  123 (243)
T 3up3_A           44 ADIMNIMDVTMRRFVKMAKRLPAFNDLSQDGKFALLKGGMIEMLTVRGVRRFDSSSGSWTTPTLGESSEVSINMFDQLNA  123 (243)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHEETTTTEECCTTSCTTCCEEGGGGGGSCT
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcccCCeeeecccCCCccccHHHHhhhcc
Confidence            468899999999999999999999999999999999999999999999999877777653   34555554443322  3


Q ss_pred             CchhhHHhhHHHHHHHHHh-cCCCHhHHHHHHHHHhhcCCCCCCCCH---HHHHHHHHHHHHHHHHHHHhcC-CCCchHH
Q psy3092         258 GVGGIFDRVLTELVSKMRE-MKMDKTELGCLRTIILFNPDVRGLKSQ---QVVEMLREKVYTSLEEYTRVNH-SEEPGRF  332 (347)
Q Consensus       258 ~~~~~~~~~~~~l~~~l~~-L~l~~~E~~lL~ai~l~~p~~~~l~~~---~~i~~~r~~~~~~L~~y~~~~~-~~~~~Rf  332 (347)
                      ++.+...+.+.+++.+|++ |++|++||+||+||+||+|+ +|+++.   ..|+++|+++..+|.+|+..++ ++++.||
T Consensus       124 g~~~~~~~~l~~~~~~~~~~L~ld~~E~alLkAivLfsp~-~gL~~~~~~~~Ve~lQe~~~~aL~~y~~~~~~p~~~~rf  202 (243)
T 3up3_A          124 DVRSEQKMRFLQFFKIFHEDIRSNDLVISMIMLIVLFSPR-DSITDPEDRRIIARHHEQFSALLNRYLESLYGDDAHQLN  202 (243)
T ss_dssp             TTHHHHHHHHHHHHHTSCHHHHTCHHHHHHHHHHHHSCCC-TTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHGGGHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhcCCC-CCCCCcchHHHHHHHHHHHHHHHHHHHHHhcCCChhHHH
Confidence            4444223445689999997 99999999999999999998 999865   7999999999999999998665 6889999


Q ss_pred             HHHHhhhhhhhccC
Q psy3092         333 AKLLLRLPSLRSIE  346 (347)
Q Consensus       333 ~~LL~ll~~lr~i~  346 (347)
                      ++||++||+||+|+
T Consensus       203 ~kLL~~Lp~LR~i~  216 (243)
T 3up3_A          203 EQLPTALRMLREIS  216 (243)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999999986

>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=99.94  E-value=3.1e-26  Score=199.82  Aligned_cols=161  Identities=21%  Similarity=0.234  Sum_probs=126.2

Q ss_pred             hhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccc--cchhh--cC
Q psy3092         183 TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYR--SSAHE--AG  258 (347)
Q Consensus       183 ~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~--~~~~~--~~  258 (347)
                      ..+++..+..+..+|+|||++|+|.+|+.+||+.|||++|.++++++.++++....+.+.+++|.....  .....  .+
T Consensus        44 ~~i~~l~~~~l~~iVefAK~iPgF~~L~~~DQi~LLK~~~~ElliLr~a~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~  123 (244)
T 3gyt_A           44 TDILNVMDITMRRLVKMAKRLGAFNEISEAGKFSLLKGGMIEMLTIRGVTVFNADKGVWQTPVDGHSQISFNMFDKLRPD  123 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTCGGGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETTTTEECCTTSTTCCEEGGGGGGSCTT
T ss_pred             HHHHHHHHHHHHHHHHHHccCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcccCCeEeecCCcccchhHHHHHHhhhc
Confidence            467788889999999999999999999999999999999999999999998766666666665532111  10000  11


Q ss_pred             ch----hhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCC---CHHHHHHHHHHHHHHHHHHHHhcC-CCCch
Q psy3092         259 VG----GIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLK---SQQVVEMLREKVYTSLEEYTRVNH-SEEPG  330 (347)
Q Consensus       259 ~~----~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~---~~~~i~~~r~~~~~~L~~y~~~~~-~~~~~  330 (347)
                      ..    .-+.+.+.++...   ++.++.||+||+||+||+||++|++   +...|+++|+++..+|++|+..++ ++.+.
T Consensus       124 ~~~~~~~~~~~~~~~f~~~---l~~~~~E~alLkAivLfspDr~gL~~~~d~~~Ve~lQe~~~~aL~~y~~~~~~p~~~~  200 (244)
T 3gyt_A          124 IKDTQKKGFLHFFNLLHSD---VRKNDLAIDIIVLMVLFDSKREGLVSQQDKETVEKLHRNYESLLHRYLYSIHKEEAEQ  200 (244)
T ss_dssp             THHHHHHHHHHHHHHSCHH---HHTCHHHHHHHHHHHHSCTTSTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHCSSSHHH
T ss_pred             chhhHHHHHHHHHHHHHHH---HHHhHHHHHHHHHHHHHhccCCCCCccccHHHHHHHHHHHHHHHHHHHHHhCCCCchh
Confidence            11    0011122233333   4446779999999999999999999   688999999999999999998887 68899


Q ss_pred             HHHHHHhhhhhhhccC
Q psy3092         331 RFAKLLLRLPSLRSIE  346 (347)
Q Consensus       331 Rf~~LL~ll~~lr~i~  346 (347)
                      ||++||++||+||+|+
T Consensus       201 rf~kLL~~Lp~LR~i~  216 (244)
T 3gyt_A          201 RFASIPKALVALRKVA  216 (244)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            9999999999999986

>2lze_A A primordial catalytic fold generated by in vitro evolution; ligase, de novo protein; NMR {Synthetic construct}

Probab=99.86  E-value=1.9e-23  Score=149.32  Aligned_cols=63  Identities=33%  Similarity=0.590  Sum_probs=55.5

Q ss_pred             CCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhH
Q psy3092          63 DRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREA  127 (347)
Q Consensus        63 ~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~  127 (347)
                      .++.|.||+++ |.+||+||||+ +++..|.|+.+++|.|++..|+.||+|||+|||+|||+...
T Consensus        12 ~p~~g~h~c~v-Cgd~asfFRRt-~~~~~y~C~~~~~C~i~~~~R~~C~~CR~qKCl~VgM~~~~   74 (87)
T 2lze_A           12 EPRGGKHICAI-CGNNAEDYKHT-DMDLTYTDRDYKNCESYHKCSDLCQYCRYQKDLAIHHQHHH   74 (87)
T ss_dssp             CCSCCSSSCSS-SSSSSSSCTTT-TTSCTTTSCCCCCCCCSSCCSSSCSGGGTSCCHHHHCSSCC
T ss_pred             CCCCCCEEccC-CCCccceECcc-cCCCeeEcCCCCccccCCCccCcCCcccChhhccCcCEecc
Confidence            35667788876 78899999998 56788999999999999999999999999999999998653

>2lze_A A primordial catalytic fold generated by in vitro evolution; ligase, de novo protein; NMR {Synthetic construct}

Probab=93.89  E-value=0.049  Score=38.51  Aligned_cols=18  Identities=44%  Similarity=1.021  Sum_probs=15.1

Q ss_pred             CCCCcCcccCCCCCCccc
Q psy3092          53 GSKHLCSICGDRASGKHY   70 (347)
Q Consensus        53 ~~~~~C~VCg~~a~g~Hy   70 (347)
                      ...+.|.||||.|++|+-
T Consensus        15 ~g~h~c~vCgd~asfFRR   32 (87)
T 2lze_A           15 GGKHICAICGNNAEDYKH   32 (87)
T ss_dssp             CCSSSCSSSSSSSSSCTT
T ss_pred             CCCEEccCCCCccceECc
Confidence            456789999999999865

---

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	347
d2p1ta1	230	a.123.1.1 (A:229-458) Retinoid-X receptor alpha (R	1e-64
d1pzla_	233	a.123.1.1 (A:) Hepatocyte nuclear factor 4-alpha {	3e-59
d1hg4a_	265	a.123.1.1 (A:) Ultraspiracle protein, usp {Drosoph	6e-57
d1g2na_	256	a.123.1.1 (A:) Ultraspiracle protein, usp {Helioth	2e-56
d1n46a_	251	a.123.1.1 (A:) Thyroid hormone receptor beta (TR-b	2e-55
d1pq9a_	239	a.123.1.1 (A:) Oxysterols receptor LXR-beta {Human	5e-54
d1fcya_	236	a.123.1.1 (A:) Retinoic acid receptor gamma (RAR-g	2e-53
d1pk5a_	242	a.123.1.1 (A:) Orphan nuclear receptor NR5a2 (LRH-	1e-51
d1osha_	231	a.123.1.1 (A:) Bile acid receptor FXR {Human (Homo	1e-51
d2p54a1	267	a.123.1.1 (A:202-468) Peroxisome proliferator acti	8e-51
d1xpca_	245	a.123.1.1 (A:) Estrogen receptor alpha {Human (Hom	7e-50
d2e2ra1	223	a.123.1.1 (A:234-456) Orphan nuclear receptor ERR3	2e-49
d2b50b1	265	a.123.1.1 (B:211-475) Peroxisome proliferator-acti	9e-49
d2j7ya1	236	a.123.1.1 (A:217-452) Estrogen receptor beta {Rat	2e-48
d3d24a1	227	a.123.1.1 (A:194-420) Steroid hormone receptor ERR	1e-47
d1xvpb_	246	a.123.1.1 (B:) Orphan nuclear receptor NR1I3 (CAR)	2e-47
d2fvja1	271	a.123.1.1 (A:207-477) Peroxisome proliferator acti	8e-47
d2r40d1	243	a.123.1.1 (D:287-529) Ecdysone receptor {Noctuid m	1e-46
d1ovla_	236	a.123.1.1 (A:) Orphan nuclear receptor NURR1 {Huma	6e-46
d1nrla_	292	a.123.1.1 (A:) Pregnane x receptor, PXR {Human (Ho	2e-45
d1pdua_	230	a.123.1.1 (A:) Nuclear hormone receptor HR38 {Frui	4e-44
d1ie9a_	255	a.123.1.1 (A:) Vitamin D nuclear receptor {Human (	1e-43
d1t7ra_	250	a.123.1.1 (A:) Androgen receptor {Chimpanzee (Pan	2e-43
d1sqna_	251	a.123.1.1 (A:) Progesterone receptor {Human (Homo	3e-43
d1xnxa_	232	a.123.1.1 (A:) Orphan nuclear receptor NR1I3 (CAR)	4e-43
d2qw4a1	233	a.123.1.1 (A:32-264) Orphan nuclear receptor NR4A1	7e-43
d1nhza_	247	a.123.1.1 (A:) Glucocorticoid receptor {Human (Hom	1e-40
d1n83a_	251	a.123.1.1 (A:) Orphan nuclear receptor ROR-alpha {	7e-40
d1dszb_	84	g.39.1.2 (B:) Retinoid X receptor (RXR-alpha) DNA-	2e-39
d1nq7a_	244	a.123.1.1 (A:) Orphan nuclear receptor ROR-beta {R	1e-38
d2hanb1	83	g.39.1.2 (B:5-87) Ecdysone receptor DNA-binding do	5e-36
d1kb2a_	89	g.39.1.2 (A:) Vitamin D3 receptor, VDR, DNA-bindin	3e-35
d1lo1a_	90	g.39.1.2 (A:) Steroid hormone receptor Err2 DNA-bi	2e-34
d1cita_	89	g.39.1.2 (A:) Orphan nuclear receptor NGFI-B DNA-b	3e-33
d1a6ya_	78	g.39.1.2 (A:) Orphan nuclear receptor reverb DNA-b	4e-33
d1dsza_	75	g.39.1.2 (A:) Retinoic acid receptor DNA-binding d	1e-32
d1r4ia_	74	g.39.1.2 (A:) Androgen receptor {Rat (Rattus norve	3e-30
d1hcqa_	74	g.39.1.2 (A:) Estrogen receptor DNA-binding domain	1e-29
d1lata_	71	g.39.1.2 (A:) Glucocorticoid receptor DNA-binding	5e-28
d2nllb_	103	g.39.1.2 (B:) Thyroid hormone receptor (TR-beta) D	8e-27

>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 =  202 bits (515), Expect = 1e-64
 Identities = 137/200 (68%), Positives = 157/200 (78%), Gaps = 6/200 (3%)

Query: 152 EMPVERILEAEQRVDMKQEP------ADQDIVNEQQATNICKATDKQLFQLVDWAKHIPH 205
           +MPVERILEAE  V+ K E                  TNIC+A DKQLF LV+WAK IPH
Sbjct: 1   DMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPH 60

Query: 206 FTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDR 265
           F+ LPL+DQV+LLRAGWNELLIASFSHRSI+VKDGILLA G+ V+R+SAH AGVG IFDR
Sbjct: 61  FSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDR 120

Query: 266 VLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNH 325
           VLTELVSKMR+M+MDKTELGCLR I+LFNPD +GL +   VE LREKVY SLE Y +  +
Sbjct: 121 VLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKY 180

Query: 326 SEEPGRFAKLLLRLPSLRSI 345
            E+PGRFAKLLLRLP+LRSI
Sbjct: 181 PEQPGRFAKLLLRLPALRSI 200

>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 =  188 bits (479), Expect = 3e-59
 Identities = 75/202 (37%), Positives = 113/202 (55%), Gaps = 6/202 (2%)

Query: 150 LIEMP-VERILEAEQRVDMKQEPA---DQDIVNEQQAT--NICKATDKQLFQLVDWAKHI 203
           L  +P +  +L+AE        P    + DI  ++ A+  ++C++  +QL  LV+WAK+I
Sbjct: 1   LASLPSINALLQAEVLSRQITSPVSGINGDIRAKKIASIADVCESMKEQLLVLVEWAKYI 60

Query: 204 PHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIF 263
           P F  LPL+DQV LLRA   E L+   + RS+  KD +LL     V R     A +  + 
Sbjct: 61  PAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVLLLGNDYIVPRHCPELAEMSRVS 120

Query: 264 DRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRV 323
            R+L ELV   +E+++D  E   L+ II F+PD +GL     ++ LR +V  SLE+Y   
Sbjct: 121 IRILDELVLPFQELQIDDNEYAYLKAIIFFDPDAKGLSDPGKIKRLRSQVQVSLEDYIND 180

Query: 324 NHSEEPGRFAKLLLRLPSLRSI 345
              +  GRF +LLL LP+L+SI
Sbjct: 181 RQYDSRGRFGELLLLLPTLQSI 202

>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 =  183 bits (466), Expect = 6e-57
 Identities = 92/229 (40%), Positives = 137/229 (59%), Gaps = 38/229 (16%)

Query: 155 VERILEAEQRVDMKQEP---------ADQDIVNEQQA--TNICKATDKQLFQLVDWAKHI 203
           +ERI+EAEQR + +                +  + +   + +C+  +KQLFQ+V++A+ +
Sbjct: 3   IERIIEAEQRAETQCGDRALTFLRVGPYSTVQPDYKGAVSALCQVVNKQLFQMVEYARMM 62

Query: 204 PHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDG----------------------- 240
           PHF  +PL+DQV+LL+A W ELLIA+ +  SI   D                        
Sbjct: 63  PHFAQVPLDDQVILLKAAWIELLIANVAWCSIVSLDDGGAGGGGGGLGHDGSFERRSPGL 122

Query: 241 ----ILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD 296
               + L    + +R+SA +AGV  IFDR+L+EL  KM+ + +D+ EL CL+ IIL+NPD
Sbjct: 123 QPQQLFLNQSFSYHRNSAIKAGVSAIFDRILSELSVKMKRLNLDRRELSCLKAIILYNPD 182

Query: 297 VRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +RG+KS+  +EM REKVY  L+E+ R+ H  + GRFA+LLLRLP+LRSI
Sbjct: 183 IRGIKSRAEIEMCREKVYACLDEHCRLEHPGDDGRFAQLLLRLPALRSI 231

>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 =  182 bits (463), Expect = 2e-56
 Identities = 95/221 (42%), Positives = 140/221 (63%), Gaps = 27/221 (12%)

Query: 152 EMPVERILEAEQRV-------DMKQEPADQDIVNEQQA--TNICKATDKQLFQLVDWAKH 202
           E+ +ER+LE E  V          +   D ++  + +A  +++C+  +KQ+  LV WA+ 
Sbjct: 5   ELSIERLLEMESLVADPSEEFQFLRVGPDSNVPPKFRAPVSSLCQIGNKQIAALVVWARD 64

Query: 203 IPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVK------------------DGILLA 244
           IPHF+ L +EDQ+LL++  WNELL+ + + RS+                       + L 
Sbjct: 65  IPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLTEERDGVDGTGNRTTSPPQLMCLM 124

Query: 245 PGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQ 304
           PG+T++R+SA +AGVG IFDRVL+EL  KMR +++D+ E   L+ IIL NPDV+GLK++Q
Sbjct: 125 PGMTLHRNSALQAGVGQIFDRVLSELSLKMRTLRVDQAEYVALKAIILLNPDVKGLKNRQ 184

Query: 305 VVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            VE+LREK++  L+EY R + S E GRFA LLLRLP+LRSI
Sbjct: 185 EVEVLREKMFLCLDEYCRRSRSSEEGRFAALLLRLPALRSI 225

>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 =  179 bits (455), Expect = 2e-55
 Identities = 48/222 (21%), Positives = 92/222 (41%), Gaps = 1/222 (0%)

Query: 124 KREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQRVDMKQEPADQDIVNEQQAT 183
           K E   EE +  K      V + +         + L  +          +   V+ +  +
Sbjct: 1   KPEPTDEEWELIKTVTEAHVATNAQGSHWKQKRKFLPEDIGQAPIVNAPEGGKVDLEAFS 60

Query: 184 NICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL 243
           +  K     + ++VD+AK +P F  LP EDQ++LL+    E++    + R     + + L
Sbjct: 61  HFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTL 120

Query: 244 APGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ 303
              + V R      G+G + D +  +L   +    +D TE+  L+ ++L + D  GL   
Sbjct: 121 NGEMAVTRGQLKNGGLGVVSDAIF-DLGMSLSSFNLDDTEVALLQAVLLMSSDRPGLACV 179

Query: 304 QVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           + +E  ++    + E Y           + KLL+++  LR I
Sbjct: 180 ERIEKYQDSFLLAFEHYINYRKHHVTHFWPKLLMKVTDLRMI 221

>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 =  175 bits (445), Expect = 5e-54
 Identities = 50/207 (24%), Positives = 96/207 (46%), Gaps = 13/207 (6%)

Query: 152 EMPVERILEAEQRV------DMKQ---EPADQD----IVNEQQATNICKATDKQLFQLVD 198
           E+ +++++ A+ +       D  +    P   D       +Q+  +  +     + ++VD
Sbjct: 6   ELMIQQLVAAQLQCNKRSFSDQPKVTPWPLGADPQSRDARQQRFAHFTELAIISVQEIVD 65

Query: 199 WAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG 258
           +AK +P F  L  EDQ+ LL+A   E+++   + R     + I      T  +   H AG
Sbjct: 66  FAKQVPGFLQLGREDQIALLKASTIEIMLLETARRYNHETECITFLKDFTYSKDDFHRAG 125

Query: 259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLE 318
           +   F   + E    MR + +D  E   L  I +F+ D   ++    VE L++    +L 
Sbjct: 126 LQVEFINPIFEFSRAMRRLGLDDAEYALLIAINIFSADRPNVQEPGRVEALQQPYVEALL 185

Query: 319 EYTRVNHSEEPGRFAKLLLRLPSLRSI 345
            YTR+   ++  RF ++L++L SLR++
Sbjct: 186 SYTRIKRPQDQLRFPRMLMKLVSLRTL 212

>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 =  174 bits (441), Expect = 2e-53
 Identities = 49/201 (24%), Positives = 93/201 (46%), Gaps = 11/201 (5%)

Query: 155 VERILEAEQ----------RVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIP 204
           + ++ +A Q          +         +  ++        +   K + ++V++AK +P
Sbjct: 9   ITKVSKAHQETFPSLCQLGKYTTNSSADHRVQLDLGLWDKFSELATKCIIKIVEFAKRLP 68

Query: 205 HFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFD 264
            FT L + DQ+ LL+A   ++L+     R    +D +  + G+T+ R+  H AG G + D
Sbjct: 69  GFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMTFSDGLTLNRTQMHNAGFGPLTD 128

Query: 265 RVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVN 324
            V      ++  ++MD TE G L  I L   D   L+  + V+ L+E +  +L  Y R  
Sbjct: 129 LVF-AFAGQLLPLEMDDTETGLLSAICLICGDRMDLEEPEKVDKLQEPLLEALRLYARRR 187

Query: 325 HSEEPGRFAKLLLRLPSLRSI 345
              +P  F ++L+++  LR I
Sbjct: 188 RPSQPYMFPRMLMKITDLRGI 208

>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 =  169 bits (430), Expect = 1e-51
 Identities = 60/197 (30%), Positives = 107/197 (54%), Gaps = 5/197 (2%)

Query: 154 PVERILEAEQR-VDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLE 212
           P E  ++A+      +++              +CK  D+ LF +V+WA+    F  L ++
Sbjct: 15  PDEPQVQAKIMAYLQQEQSNRNRQEKLSAFGLLCKMADQTLFSIVEWARSSIFFRELKVD 74

Query: 213 DQVLLLRAGWNELLIASFSHRSIS--VKDGILLAPGVTVYRSSAHEAGVGGIFD--RVLT 268
           DQ+ LL+  W+ELLI    +R ++   +  I L  G  V  S+          +   +  
Sbjct: 75  DQMKLLQNCWSELLILDHIYRQVAHGKEGTIFLVTGEHVDYSTIISHTEVAFNNLLSLAQ 134

Query: 269 ELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEE 328
           ELV ++R ++ D+ E  CL+ ++LF+ DV+ L++ Q+VE ++E+V  +L +YT  N+ ++
Sbjct: 135 ELVVRLRSLQFDQREFVCLKFLVLFSSDVKNLENLQLVEGVQEQVNAALLDYTVCNYPQQ 194

Query: 329 PGRFAKLLLRLPSLRSI 345
             +F +LLLRLP LR+I
Sbjct: 195 TEKFGQLLLRLPELRAI 211

>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 =  169 bits (429), Expect = 1e-51
 Identities = 47/195 (24%), Positives = 90/195 (46%), Gaps = 8/195 (4%)

Query: 155 VERILEAEQRVDMKQEPADQDIVNEQQA----TNICKATDKQLFQLVDWAKHIPHFTTLP 210
           +  I+++  +  M QE  ++ +  E  A      + +     +  LV++ K +P F TL 
Sbjct: 13  LHFIMDSYNKQRMPQEITNKILKEEFSAEENFLILTEMATNHVQVLVEFTKKLPGFQTLD 72

Query: 211 LEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTEL 270
            EDQ+ LL+    E +      RS  + +  L +    +       +G+   +   +   
Sbjct: 73  HEDQIALLKGSAVEAMF----LRSAEIFNKKLPSGHSDLLEERIRNSGISDEYITPMFSF 128

Query: 271 VSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPG 330
              + E+KM + E   L  I++ +PD + +K ++ VE L+E +   L++  +++  E P 
Sbjct: 129 YKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLCKIHQPENPQ 188

Query: 331 RFAKLLLRLPSLRSI 345
            FA LL RL  LR+ 
Sbjct: 189 HFACLLGRLTELRTF 203

>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 =  168 bits (426), Expect = 8e-51
 Identities = 44/216 (20%), Positives = 83/216 (38%), Gaps = 5/216 (2%)

Query: 135 TKERDSNEVESTSGTLIEMP---VERILEAEQRVDMKQ-EPADQDIVNEQQATNICKAT- 189
            K +    +   +          +E +  AE+ +  K      Q+   E +  + C+ T 
Sbjct: 20  NKVKARVILSGKASNNPPFVIHDMETLCMAEKTLVAKLVANGIQNKEAEVRIFHCCQCTS 79

Query: 190 DKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTV 249
            + + +L ++AK IP F  L L DQV LL+ G  E + A  S         +    G   
Sbjct: 80  VETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGMLVAYGNGFIT 139

Query: 250 YRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEML 309
                              +   K   +++D +++      I+   D  GL +   +E +
Sbjct: 140 REFLKSLRKPFCDIMEPKFDFAMKFNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKM 199

Query: 310 REKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           +E +   L  + + NH ++   F KLL ++  LR +
Sbjct: 200 QEGIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQL 235

>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 =  165 bits (418), Expect = 7e-50
 Identities = 49/205 (23%), Positives = 87/205 (42%), Gaps = 11/205 (5%)

Query: 152 EMPVERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPL 211
           +  V  +L+AE  +   +    +          +    D++L  +++WAK +P F  L L
Sbjct: 7   DQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTL 66

Query: 212 EDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELV 271
            DQV LL   W E+L+     RS+     +L AP + + R+             +L    
Sbjct: 67  HDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATS 126

Query: 272 SKMREMKMDKTELGCLRTIILFNPDVR--------GLKSQQVVEMLREKVYTSLEEYTR- 322
           S+ R M +   E  CL++IIL N  V          L+ +  +  + +K+  +L      
Sbjct: 127 SRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAK 186

Query: 323 --VNHSEEPGRFAKLLLRLPSLRSI 345
             +   ++  R A+LLL L  +R +
Sbjct: 187 AGLTLQQQHQRLAQLLLILSHIRHM 211

>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 =  162 bits (412), Expect = 2e-49
 Identities = 60/191 (31%), Positives = 103/191 (53%), Gaps = 1/191 (0%)

Query: 155 VERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQ 214
           V  +L AE               + +  T +C   D++L  ++ WAKHIP F+TL L DQ
Sbjct: 5   VSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQ 64

Query: 215 VLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKM 274
           + LL++ W E+LI    +RS+S +D ++ A    +    +  AG+  + + +L +LV K 
Sbjct: 65  MSLLQSAWMEILILGVVYRSLSFEDELVYADDYIMDEDQSKLAGLLDLNNAIL-QLVKKY 123

Query: 275 REMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAK 334
           + MK++K E   L+ I L N D   ++  + V+ L++ ++ +L++Y    H E+P R  K
Sbjct: 124 KSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGK 183

Query: 335 LLLRLPSLRSI 345
           +L+ LP LR  
Sbjct: 184 MLMTLPLLRQT 194

>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 =  162 bits (412), Expect = 9e-49
 Identities = 54/219 (24%), Positives = 97/219 (44%), Gaps = 10/219 (4%)

Query: 135 TKERDSNEVESTSGT---LIEMPVERILEAEQRVDMKQEPADQDIVNE---QQATNICKA 188
           TK++  + +   +      +   +E + +AE+ +  KQ         E            
Sbjct: 19  TKKKARSILTGKASHTAPFVIHDIETLWQAEKGLVWKQLVNGLPPYKEISVHVFYRCQCT 78

Query: 189 TDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVT 248
           T + + +L ++AK IP F++L L DQV LL+ G +E + A  +  SI  KDG+L+A G  
Sbjct: 79  TVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLA--SIVNKDGLLVANGSG 136

Query: 249 VYRSSAHEAGVGGIFD--RVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVV 306
                   +      D      E   K   +++D ++L      I+   D  GL +   V
Sbjct: 137 FVTREFLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRV 196

Query: 307 EMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           E +++ +  +LE + + NH +    F KLL ++  LR +
Sbjct: 197 EAIQDTILRALEFHLQANHPDAQQLFPKLLQKMADLRQL 235

>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 =  161 bits (407), Expect = 2e-48
 Identities = 55/204 (26%), Positives = 85/204 (41%), Gaps = 11/204 (5%)

Query: 152 EMPVERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPL 211
           E  V  +LEAE    +   P+           ++ K  DK+L  ++ WAK IP F  L L
Sbjct: 5   EQLVLTLLEAEPPNVLVSRPSMPFT-EASMMMSLTKLADKELVHMIGWAKKIPGFVELSL 63

Query: 212 EDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELV 271
            DQV LL + W E+L+     RSI     ++ AP + + R              +L    
Sbjct: 64  LDQVRLLESCWMEVLMVGLMWRSIDHPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLATT 123

Query: 272 SKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYT---------- 321
           S+ RE+K+   E  C++ +IL N  +  L S         K+   L   T          
Sbjct: 124 SRFRELKLQHKEYLCVKAMILLNSSMYPLASANQEAESSRKLTHLLNAVTDALVWVIAKS 183

Query: 322 RVNHSEEPGRFAKLLLRLPSLRSI 345
            ++  ++  R A LL+ L  +R I
Sbjct: 184 GISSQQQSVRLANLLMLLSHVRHI 207

>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 =  158 bits (401), Expect = 1e-47
 Identities = 52/195 (26%), Positives = 94/195 (48%), Gaps = 5/195 (2%)

Query: 155 VERILEAEQRVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQ 214
           V  +L  E               +      +C   D+++   + WAK IP F++L L DQ
Sbjct: 5   VSHLLVVEPEKLYAMPDPAGPDGHLPAVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQ 64

Query: 215 VLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKM 274
           + +L++ W E+L+   + RS+ ++D +  A  + +    A  AG+G +    L +LV ++
Sbjct: 65  MSVLQSVWMEVLVLGVAQRSLPLQDELAFAEDLVLDEEGARAAGLGELGAA-LLQLVRRL 123

Query: 275 REMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNH----SEEPG 330
           + +++++ E   L+ + L N D   ++  + VE LRE ++ +L EY           E  
Sbjct: 124 QALRLEREEYVLLKALALANSDSVHIEDAEAVEQLREALHEALLEYEAGRAGPGGGAERR 183

Query: 331 RFAKLLLRLPSLRSI 345
           R  +LLL LP LR  
Sbjct: 184 RAGRLLLTLPLLRQT 198

>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 =  159 bits (402), Expect = 2e-47
 Identities = 38/165 (23%), Positives = 74/165 (44%), Gaps = 3/165 (1%)

Query: 183 TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGIL 242
           T+        + Q++ + K +P F +LP+EDQ+ LL+    E+     +     ++    
Sbjct: 57  THFADINTFMVLQVIKFTKDLPVFRSLPIEDQISLLKGAAVEICHIVLNTTF-CLQTQNF 115

Query: 243 LAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKS 302
           L   +          G    F  +L      +R++++ + E   L  + LF+PD  G+  
Sbjct: 116 LCGPLRYTIEDGARVGFQVEFLELLFHFHGTLRKLQLQEPEYVLLAAMALFSPDRPGVTQ 175

Query: 303 QQVVEMLREKVYTSLEEYTRVNHS--EEPGRFAKLLLRLPSLRSI 345
           +  ++ L+E++  +L+ Y +       +   +AKLL  L  LRSI
Sbjct: 176 RDEIDQLQEEMALTLQSYIKGQQRRPRDRFLYAKLLGLLAELRSI 220

>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 =  157 bits (399), Expect = 8e-47
 Identities = 45/194 (23%), Positives = 82/194 (42%), Gaps = 3/194 (1%)

Query: 155 VERILEAEQRVDMKQEP--ADQDIVNEQQATNICKATDKQLFQ-LVDWAKHIPHFTTLPL 211
           +  ++  E ++  K      +Q      +    C+    +  Q + ++AK IP F  L L
Sbjct: 46  MNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDL 105

Query: 212 EDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELV 271
            DQV LL+ G +E++    +         I    G              G F     E  
Sbjct: 106 NDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFA 165

Query: 272 SKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGR 331
            K   +++D ++L     +I+ + D  GL + + +E +++ +  +LE   ++NH E    
Sbjct: 166 VKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQL 225

Query: 332 FAKLLLRLPSLRSI 345
           FAKLL ++  LR I
Sbjct: 226 FAKLLQKMTDLRQI 239

>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 =  156 bits (396), Expect = 1e-46
 Identities = 47/208 (22%), Positives = 92/208 (44%), Gaps = 16/208 (7%)

Query: 152 EMPVERILEAEQRV------DMKQ--EPADQDIVNEQQAT---NICKATDKQLFQLVDWA 200
           +  + R++  ++        D+K+  +    D  +E        I + T   +  +V++A
Sbjct: 9   KSLIARLVWYQEGYEQPSEEDLKRVTQTWQSDEDDEDSDMPFRQITEMTILTVQLIVEFA 68

Query: 201 KHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVG 260
           K +P F  +   DQ+ LL+A  +E+++   + R  +  D +L A      R +  +AG+ 
Sbjct: 69  KGLPGFAKISQSDQITLLKACSSEVMMLRVARRYDAATDSVLFANNQAYTRDNYRKAGMA 128

Query: 261 GIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEY 320
            + + +L      M  M MD      L  I++F+ D  GL+   +VE ++     +L  Y
Sbjct: 129 YVIEDLL-HFCRCMYSMMMDNVHYALLTAIVIFS-DRPGLEQPLLVEEIQRYYLNTLRVY 186

Query: 321 TRVNHSEEPG---RFAKLLLRLPSLRSI 345
               +S  P     F K+L  L  +R++
Sbjct: 187 ILNQNSASPRCAVIFGKILGILTEIRTL 214

>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 =  154 bits (390), Expect = 6e-46
 Identities = 45/179 (25%), Positives = 79/179 (44%), Gaps = 5/179 (2%)

Query: 169 QEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIA 228
                    + Q            +  +  WA+ IP F  LP  DQ LL  + + EL + 
Sbjct: 28  NPDYQMSGDDTQHIQQFYDLLTGSMEIIRGWAEKIPGFADLPKADQDLLFESAFLELFVL 87

Query: 229 SFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLR 288
             ++RS  V+  ++   GV ++R      G G   D ++ E  S ++ M +D +   C+ 
Sbjct: 88  RLAYRSNPVEGKLIFCNGVVLHRLQCVR-GFGEWIDSIV-EFSSNLQNMNIDISAFSCIA 145

Query: 289 TIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHS--EEPGRFAKLLLRLPSLRSI 345
            + +      GLK  + VE L+ K+   L+++   N+     P   +KLL +LP LR++
Sbjct: 146 ALAMVTER-HGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLGKLPELRTL 203

>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 =  154 bits (391), Expect = 2e-45
 Identities = 45/239 (18%), Positives = 94/239 (39%), Gaps = 5/239 (2%)

Query: 110 CQYCRYQKCLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEMPVERILEAEQRVDMKQ 169
             +  ++    +    E  +  +  ++E  +   +            ++   +  V   +
Sbjct: 26  SHFKNFRLPGVLSSGCELPESLQAPSREEAAKWSQVRKDLCSLKVSLQLRGEDGSVWNYK 85

Query: 170 EPADQDIVNEQQA-TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIA 228
            PAD           ++   +      ++ +AK I +F  LP+EDQ+ LL+    EL   
Sbjct: 86  PPADSGGKEIFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQL 145

Query: 229 SFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLR 288
            F+       +      G   Y       G   +    + +    ++++++ + E   ++
Sbjct: 146 RFNTVF--NAETGTWECGRLSYCLEDTAGGFQQLLLEPMLKFHYMLKKLQLHEEEYVLMQ 203

Query: 289 TIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGR--FAKLLLRLPSLRSI 345
            I LF+PD  G+   +VV+ L+E+   +L+ Y   N  +   R  F K++  L  LRSI
Sbjct: 204 AISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLKIMAMLTELRSI 262

>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 =  149 bits (377), Expect = 4e-44
 Identities = 40/179 (22%), Positives = 80/179 (44%), Gaps = 8/179 (4%)

Query: 169 QEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIA 228
           +E +  +    QQ   +       +  +  +A+ IP +  L  EDQ LL ++   EL + 
Sbjct: 28  EEQSMSEADKVQQFYQL---LTSSVDVIKQFAEKIPGYFDLLPEDQELLFQSASLELFVL 84

Query: 229 SFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLR 288
             ++R+      ++   G  ++R+       G   + ++ E    +  +++D +   CL 
Sbjct: 85  RLAYRARIDDTKLIFCNGTVLHRTQCLR-SFGEWLNDIM-EFSRSLHNLEIDISAFACLC 142

Query: 289 TIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPG--RFAKLLLRLPSLRSI 345
            + L      GL+  + VE L+ K+  SL ++   N   +     F++LL +LP LRS+
Sbjct: 143 ALTLITER-HGLREPKKVEQLQMKIIGSLRDHVTYNAEAQKKQHYFSRLLGKLPELRSL 200

>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 =  149 bits (377), Expect = 1e-43
 Identities = 37/185 (20%), Positives = 81/185 (43%), Gaps = 3/185 (1%)

Query: 164 RVDMKQEPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWN 223
           RV+        ++       ++       + +++ +AK IP F  L  EDQ++LL++   
Sbjct: 41  RVNDGGGSVTLELSQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAI 100

Query: 224 ELLIASFSHRSISVKDGILLAPGVTVYRSS-AHEAGVGGIFDRVLTELVSKMREMKMDKT 282
           E+++   +                  YR S   +AG        L +    ++++ + + 
Sbjct: 101 EVIMLRSNESFTMDDMSWTCGNQDYKYRVSDVTKAGHSLELIEPLIKFQVGLKKLNLHEE 160

Query: 283 ELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEE--PGRFAKLLLRLP 340
           E   L  I + +PD  G++   ++E +++++  +L+ Y R  H        +AK++ +L 
Sbjct: 161 EHVLLMAICIVSPDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLLYAKMIQKLA 220

Query: 341 SLRSI 345
            LRS+
Sbjct: 221 DLRSL 225

>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 =  148 bits (375), Expect = 2e-43
 Identities = 39/169 (23%), Positives = 80/169 (47%), Gaps = 7/169 (4%)

Query: 183 TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGIL 242
           +++ +  ++QL  +V WAK +P F  L ++DQ+ +++  W  L++ +   RS +  +  +
Sbjct: 34  SSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRM 93

Query: 243 L--APGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD-VRG 299
           L  AP +       H++ +     R+   L  +   +++   E  C++ ++LF+   V G
Sbjct: 94  LYFAPDLVFNEYRMHKSRMYSQCVRMR-HLSQEFGWLQITPQEFLCMKALLLFSIIPVDG 152

Query: 300 LKSQQVVEMLREKVYTSLEEYTRVNHSEE---PGRFAKLLLRLPSLRSI 345
           LK+Q+  + LR      L+               RF +L   L S++ I
Sbjct: 153 LKNQKFFDELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPI 201

>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 =  147 bits (373), Expect = 3e-43
 Identities = 37/169 (21%), Positives = 76/169 (44%), Gaps = 7/169 (4%)

Query: 183 TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGIL 242
           T++ +  ++QL  +V W+K +P F  L ++DQ+ L++  W  L++     RS     G +
Sbjct: 35  TSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQM 94

Query: 243 L--APGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVR-G 299
           L  AP + +      E+    +   +   +  +  ++++ + E  C++ ++L N     G
Sbjct: 95  LYFAPDLILNEQRMKESSFYSLCLTMWQ-IPQEFVKLQVSQEEFLCMKVLLLLNTIPLEG 153

Query: 300 LKSQQVVEMLREKVYTSLEEYTRVNHSEEP---GRFAKLLLRLPSLRSI 345
           L+SQ   E +R      L +   +          RF +L   L +L  +
Sbjct: 154 LRSQTQFEEMRSSYIRELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDL 202

>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 =  147 bits (371), Expect = 4e-43
 Identities = 44/210 (20%), Positives = 80/210 (38%), Gaps = 20/210 (9%)

Query: 155 VERILEAEQRV------DMKQ--EPADQDIVNEQQAT---------NICKATDKQLFQLV 197
           V+ +L A  R          Q   PA   + +              +        + Q++
Sbjct: 11  VQILLGAHTRHVGPLFDQFVQFKPPAYLFMHHRPFQPRGPVLPLLTHFADINTFMVQQII 70

Query: 198 DWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEA 257
            + K +P F +L +EDQ+ LL+    E+L  S +       +     P        A  A
Sbjct: 71  KFTKDLPLFRSLTMEDQISLLKGAAVEILHISLNTTFCLQTENFFCGPL-CYKMEDAVHA 129

Query: 258 GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSL 317
           G    F   +      ++ + + + E   +    LF+PD  G+  ++ ++ L+E++   L
Sbjct: 130 GFQYEFLESILHFHKNLKGLHLQEPEYVLMAATALFSPDRPGVTQREEIDQLQEEMALIL 189

Query: 318 EEYTRVNHSEEPGR--FAKLLLRLPSLRSI 345
             +     S    R  +AKL+  L  LRSI
Sbjct: 190 NNHIMEQQSRLQSRFLYAKLMGLLADLRSI 219

>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 =  146 bits (369), Expect = 7e-43
 Identities = 41/192 (21%), Positives = 78/192 (40%), Gaps = 9/192 (4%)

Query: 160 EAEQRVDMKQ----EPADQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQV 215
            +  ++D  +            +              L  +  WA+ IP F  L   DQ 
Sbjct: 15  PSTAKLDYSKFQELVLPHFGKEDAGDVQQFYDLLSGSLEVIRKWAEKIPGFAELSPADQD 74

Query: 216 LLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMR 275
           LLL + + EL I   ++RS   +  ++   G+ ++R      G G   D +L      + 
Sbjct: 75  LLLESAFLELFILRLAYRSKPGEGKLIFCSGLVLHRLQCA-RGFGDWIDSIL-AFSRSLH 132

Query: 276 EMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRV--NHSEEPGRFA 333
            + +D     CL  ++L      GL+  + VE L+ ++ + L+E+        +     +
Sbjct: 133 SLLVDVPAFACLSALVLITDR-HGLQEPRRVEELQNRIASCLKEHVAAVAGEPQPASCLS 191

Query: 334 KLLLRLPSLRSI 345
           +LL +LP LR++
Sbjct: 192 RLLGKLPELRTL 203

>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 =  141 bits (355), Expect = 1e-40
 Identities = 41/169 (24%), Positives = 73/169 (43%), Gaps = 7/169 (4%)

Query: 183 TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGIL 242
           T +     +Q+   V WAK IP F  L L+DQ+ LL+  W  L+  +   RS       L
Sbjct: 32  TTLNMLGGRQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMSLMAFALGWRSYRQSSANL 91

Query: 243 L--APGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVR-G 299
           L  AP + +         +      +L  + S++  +++   E  C++T++L +   + G
Sbjct: 92  LCFAPDLIINEQRMTLPDMYDQCKHML-YVSSELHRLQVSYEEYLCMKTLLLLSSVPKDG 150

Query: 300 LKSQQVVEMLREKVYTSLEEYTRVNHSEEPG---RFAKLLLRLPSLRSI 345
           LKSQ++ + +R      L +              RF +L   L S+  +
Sbjct: 151 LKSQELFDEIRMTYIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEV 199

>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 =  139 bits (350), Expect = 7e-40
 Identities = 38/191 (19%), Positives = 78/191 (40%), Gaps = 10/191 (5%)

Query: 162 EQRVDMKQEPADQDIVNEQQATN-------ICKATDKQLFQLVDWAKHIPHFTTLPLEDQ 214
           E+   +  +   Q+ +   Q                + +  +V++AK I  F  L   DQ
Sbjct: 33  EELQQITWQTFLQEEIENYQNKQREVMWQLCAIKITEAIQYVVEFAKRIDGFMELCQNDQ 92

Query: 215 VLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKM 274
           ++LL+AG  E++      R+   ++  +   G           G       V  E    +
Sbjct: 93  IVLLKAGSLEVVFIRMC-RAFDSQNNTVYFDGKYASPDVFKSLGCEDFISFVF-EFGKSL 150

Query: 275 REMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAK 334
             M + + E+      +L + D   L+ +  +E L++K+  +L+   + NH  E G   K
Sbjct: 151 CSMHLTEDEIALFSAFVLMSADRSWLQEKVKIEKLQQKIQLALQHVLQKNHR-EDGILTK 209

Query: 335 LLLRLPSLRSI 345
           L+ ++ +LR++
Sbjct: 210 LICKVSTLRAL 220

>d1dszb_ g.39.1.2 (B:) Retinoid X receptor (RXR-alpha) DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Retinoid X receptor (RXR-alpha) DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  132 bits (333), Expect = 2e-39
 Identities = 69/81 (85%), Positives = 78/81 (96%)

Query: 54  SKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYC 113
           +KH+C+ICGDR+SGKHYGVYSCEGCKGFFKRTVRKDL+Y CR+ ++C+IDKRQRNRCQYC
Sbjct: 4   TKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYC 63

Query: 114 RYQKCLNMGMKREAVQEERQR 134
           RYQKCL MGMKREAVQEERQR
Sbjct: 64  RYQKCLAMGMKREAVQEERQR 84

>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 =  135 bits (341), Expect = 1e-38
 Identities = 38/215 (17%), Positives = 90/215 (41%), Gaps = 21/215 (9%)

Query: 149 TLIEMP--VERILEA---------EQRVDMKQEPADQDIVNEQQATN-------ICKATD 190
           T+ E+    + I+++         E+   +  +    + +   Q+ +             
Sbjct: 1   TMSEIDRIAQNIIKSHLETCQYTMEELHQLAWQTHTYEEIKAYQSKSREALWQQCAIQIT 60

Query: 191 KQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVY 250
             +  +V++AK I  F  L   DQ+LLL++G  E+++           +  +L  G    
Sbjct: 61  HAIQYVVEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNP-LNNTVLFEGKYGG 119

Query: 251 RSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLR 310
                  G   + +    +    +  +++ + E+    + +L +PD   L   + V+ L+
Sbjct: 120 MQMFKALGSDDLVNEAF-DFAKNLCSLQLTEEEIALFSSAVLISPDRAWLLEPRKVQKLQ 178

Query: 311 EKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSI 345
           EK+Y +L+   + NH  +    AKL+ ++P++ ++
Sbjct: 179 EKIYFALQHVIQKNHL-DDETLAKLIAKIPTITAV 212

>d2hanb1 g.39.1.2 (B:5-87) Ecdysone receptor DNA-binding domain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 83

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Ecdysone receptor DNA-binding domain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score =  123 bits (310), Expect = 5e-36
 Identities = 43/82 (52%), Positives = 54/82 (65%)

Query: 57  LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQ 116
           LC +CGDRASG HY   +CEGCKGFF+R+V K   Y C+ GR C +D   R +CQ CR +
Sbjct: 2   LCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECRLK 61

Query: 117 KCLNMGMKREAVQEERQRTKER 138
           KCL +GM+ E V  E Q   +R
Sbjct: 62  KCLAVGMRPECVVPENQCAMKR 83

>d1kb2a_ g.39.1.2 (A:) Vitamin D3 receptor, VDR, DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Vitamin D3 receptor, VDR, DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  121 bits (305), Expect = 3e-35
 Identities = 31/83 (37%), Positives = 55/83 (66%)

Query: 57  LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQ 116
           +C +CGDRA+G H+   +CEGCKGFF+R++++   + C    +C I K  R  CQ CR +
Sbjct: 2   ICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLK 61

Query: 117 KCLNMGMKREAVQEERQRTKERD 139
           +C+++GM +E +  + +  ++R+
Sbjct: 62  RCVDIGMMKEFILTDEEVQRKRE 84

>d1lo1a_ g.39.1.2 (A:) Steroid hormone receptor Err2 DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Steroid hormone receptor Err2 DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  119 bits (300), Expect = 2e-34
 Identities = 42/84 (50%), Positives = 55/84 (65%)

Query: 55  KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCR 114
           K LC +CGD ASG HYGV SCE CK FFKRT++ ++ Y+C     C I KR+R  CQ CR
Sbjct: 4   KRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACR 63

Query: 115 YQKCLNMGMKREAVQEERQRTKER 138
           + K L +GM +E V+ +R R   +
Sbjct: 64  FMKALKVGMLKEGVRLDRVRGGRQ 87

>d1cita_ g.39.1.2 (A:) Orphan nuclear receptor NGFI-B DNA-binding domain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 89

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Orphan nuclear receptor NGFI-B DNA-binding domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score =  116 bits (292), Expect = 3e-33
 Identities = 44/81 (54%), Positives = 61/81 (75%)

Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQK 117
           C++CGD AS +HYGV +CEGCKGFFKRTV+K   Y C   ++C +DKR+RNRCQ+CR+QK
Sbjct: 3   CAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQK 62

Query: 118 CLNMGMKREAVQEERQRTKER 138
           CL +GM +E V+ +  + +  
Sbjct: 63  CLAVGMVKEVVRTDSLKGRRG 83

>d1a6ya_ g.39.1.2 (A:) Orphan nuclear receptor reverb DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Length = 78

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Orphan nuclear receptor reverb DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  115 bits (290), Expect = 4e-33
 Identities = 42/77 (54%), Positives = 59/77 (76%), Gaps = 1/77 (1%)

Query: 57  LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSY-ACREGRNCIIDKRQRNRCQYCRY 115
           LC +CGD ASG HYGV +CEGCKGFF+R++++++ Y  C +  NC I +  RNRCQ CR+
Sbjct: 2   LCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRF 61

Query: 116 QKCLNMGMKREAVQEER 132
           +KCL++GM R+AV+  R
Sbjct: 62  KKCLSVGMSRDAVRFGR 78

>d1dsza_ g.39.1.2 (A:) Retinoic acid receptor DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Retinoic acid receptor DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  114 bits (286), Expect = 1e-32
 Identities = 41/74 (55%), Positives = 58/74 (78%)

Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQK 117
           C +C D++SG HYGV +CEGCKGFF+R+++K++ Y C   +NCII+K  RNRCQYCR QK
Sbjct: 2   CFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQK 61

Query: 118 CLNMGMKREAVQEE 131
           C  +GM +E+V+ +
Sbjct: 62  CFEVGMSKESVRND 75

>d1r4ia_ g.39.1.2 (A:) Androgen receptor {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 74

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Androgen receptor
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score =  108 bits (270), Expect = 3e-30
 Identities = 33/73 (45%), Positives = 38/73 (52%)

Query: 55  KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCR 114
           +  C ICGD ASG HYG  +C  CK FFKR       Y C    +C IDK +R  C  CR
Sbjct: 2   QKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCR 61

Query: 115 YQKCLNMGMKREA 127
            +KC   GM   A
Sbjct: 62  LRKCYEAGMTLGA 74

>d1hcqa_ g.39.1.2 (A:) Estrogen receptor DNA-binding domain {Human and chicken (Homo sapiens) and (Gallus gallus) [TaxId: 9606]} Length = 74

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Estrogen receptor DNA-binding domain
species: Human and chicken (Homo sapiens) and (Gallus gallus) [TaxId: 9606]

 Score =  106 bits (265), Expect = 1e-29
 Identities = 35/71 (49%), Positives = 45/71 (63%)

Query: 55  KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCR 114
              C++C D ASG HYGV+SCEGCK FFKR+++    Y C     C IDK +R  CQ CR
Sbjct: 4   TRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACR 63

Query: 115 YQKCLNMGMKR 125
            +KC  +GM +
Sbjct: 64  LRKCYEVGMMK 74

>d1lata_ g.39.1.2 (A:) Glucocorticoid receptor DNA-binding domain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 71

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Glucocorticoid receptor DNA-binding domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score =  102 bits (255), Expect = 5e-28
 Identities = 38/69 (55%), Positives = 44/69 (63%)

Query: 58  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQK 117
           C +C D ASG HYGV +CEGCK FFKR V    +Y C+    CIIDK +R  C  CRY+K
Sbjct: 3   CLVCSDEASGCHYGVLTCEGCKAFFKRAVEGQHNYLCKYEGKCIIDKIRRKNCPACRYRK 62

Query: 118 CLNMGMKRE 126
           CL  GM  E
Sbjct: 63  CLQAGMNLE 71

>d2nllb_ g.39.1.2 (B:) Thyroid hormone receptor (TR-beta) DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Thyroid hormone receptor (TR-beta) DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 99.9 bits (248), Expect = 8e-27
 Identities = 41/99 (41%), Positives = 63/99 (63%), Gaps = 2/99 (2%)

Query: 57  LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYA--CREGRNCIIDKRQRNRCQYCR 114
           LC +CGD+A+G HY   +CEGCKGFF+RT++K+L  +  C+    C+IDK  RN+CQ CR
Sbjct: 3   LCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQECR 62

Query: 115 YQKCLNMGMKREAVQEERQRTKERDSNEVESTSGTLIEM 153
           ++KC+ +GM  + V ++ +R  +R   E         E+
Sbjct: 63  FKKCIYVGMATDLVLDDSKRLAKRKLIEENREKRRREEL 101

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	347
d1dszb_	84	Retinoid X receptor (RXR-alpha) DNA-binding domain	100.0
d2hanb1	83	Ecdysone receptor DNA-binding domain {Fruit fly (D	100.0
d1g2na_	256	Ultraspiracle protein, usp {Heliothis virescens [T	100.0
d1kb2a_	89	Vitamin D3 receptor, VDR, DNA-binding domain {Huma	100.0
d1dsza_	75	Retinoic acid receptor DNA-binding domain {Human (	100.0
d1lo1a_	90	Steroid hormone receptor Err2 DNA-binding domain {	100.0
d1a6ya_	78	Orphan nuclear receptor reverb DNA-binding domain	100.0
d2p1ta1	230	Retinoid-X receptor alpha (RXR-alpha) {Human (Homo	100.0
d2nllb_	103	Thyroid hormone receptor (TR-beta) DNA-binding dom	100.0
d1r4ia_	74	Androgen receptor {Rat (Rattus norvegicus) [TaxId:	100.0
d1lata_	71	Glucocorticoid receptor DNA-binding domain {Rat (R	100.0
d2e2ra1	223	Orphan nuclear receptor ERR3 {Human (Homo sapiens)	99.98
d1cita_	89	Orphan nuclear receptor NGFI-B DNA-binding domain	99.98
d1pzla_	233	Hepatocyte nuclear factor 4-alpha {Human (Homo sap	99.98
d1hcqa_	74	Estrogen receptor DNA-binding domain {Human and ch	99.98
d1hg4a_	265	Ultraspiracle protein, usp {Drosophila melanogaste	99.97
d1pq9a_	239	Oxysterols receptor LXR-beta {Human (Homo sapiens)	99.97
d3d24a1	227	Steroid hormone receptor ERR1 {Human (Homo sapiens	99.97
d1fcya_	236	Retinoic acid receptor gamma (RAR-gamma) {Human (H	99.97
d1n46a_	251	Thyroid hormone receptor beta (TR-beta) {Human (Ho	99.97
d1pk5a_	242	Orphan nuclear receptor NR5a2 (LRH-1) {Mouse (Mus	99.97
d1ovla_	236	Orphan nuclear receptor NURR1 {Human (Homo sapiens	99.97
d2r40d1	243	Ecdysone receptor {Noctuid moth (Heliothis viresce	99.97
d1xnxa_	232	Orphan nuclear receptor NR1I3 (CAR) {Mouse (Mus mu	99.97
d1osha_	231	Bile acid receptor FXR {Human (Homo sapiens) [TaxI	99.96
d1xvpb_	246	Orphan nuclear receptor NR1I3 (CAR) {Human (Homo s	99.96
d1pdua_	230	Nuclear hormone receptor HR38 {Fruit fly (Drosophi	99.96
d1xpca_	245	Estrogen receptor alpha {Human (Homo sapiens) [Tax	99.96
d1ie9a_	255	Vitamin D nuclear receptor {Human (Homo sapiens) [	99.96
d1t7ra_	250	Androgen receptor {Chimpanzee (Pan troglodytes) [T	99.96
d2p54a1	267	Peroxisome proliferator activated receptor alpha,	99.96
d1n83a_	251	Orphan nuclear receptor ROR-alpha {Human (Homo sap	99.96
d1sqna_	251	Progesterone receptor {Human (Homo sapiens) [TaxId	99.96
d1nhza_	247	Glucocorticoid receptor {Human (Homo sapiens) [Tax	99.96
d2qw4a1	233	Orphan nuclear receptor NR4A1 {Human (Homo sapiens	99.96
d2j7ya1	236	Estrogen receptor beta {Rat (Rattus norvegicus) [T	99.96
d2b50b1	265	Peroxisome proliferator-activated receptor delta,	99.96
d1nq7a_	244	Orphan nuclear receptor ROR-beta {Rat (Rattus norv	99.96
d2fvja1	271	Peroxisome proliferator activated receptor gamma,	99.96
d1nrla_	292	Pregnane x receptor, PXR {Human (Homo sapiens) [Ta	99.95
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	85.67

>d1dszb_ g.39.1.2 (B:) Retinoid X receptor (RXR-alpha) DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Retinoid X receptor (RXR-alpha) DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=4.9e-37  Score=217.44  Aligned_cols=80  Identities=86%  Similarity=1.634  Sum_probs=76.4

Q ss_pred             CCcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhh
Q psy3092          55 KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQR  134 (347)
Q Consensus        55 ~~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~  134 (347)
                      +++|.|||++|+|+||||.+|+|||+||||+|.++..|.|..+++|.+++..|..||+|||+|||++||++++||.+|++
T Consensus         5 ~~~C~VC~~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~c~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~Rdr   84 (84)
T d1dszb_           5 KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQR   84 (84)
T ss_dssp             CEECTTTCCEESSEETTEECCHHHHHHHHHHHHHTCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCCCCC
T ss_pred             CCcCccCCCcCCccCCCHHHHHHhHHHHHHHHhcCCCeeccCCCCcccCCCCCccCCCCccHHHHHcCCChHHcccccCC
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999999988763

>d2hanb1 g.39.1.2 (B:5-87) Ecdysone receptor DNA-binding domain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Ecdysone receptor DNA-binding domain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=100.00  E-value=2.2e-36  Score=213.85  Aligned_cols=82  Identities=51%  Similarity=1.061  Sum_probs=77.5

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhh
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRT  135 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~  135 (347)
                      ++|.|||++++|+||||.+|+|||+||||++..+..|.|+.+++|.+++..|..||+|||+||+++||++++||.+|+..
T Consensus         1 e~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~c~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~   80 (83)
T d2hanb1           1 ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECRLKKCLAVGMRPECVVPENQCA   80 (83)
T ss_dssp             CBCTTTCSBCCEEETTEEECHHHHHHHHHHHHTTCCCCCSSCSCCCCSTTGGGTCHHHHHHHHHHTTCCGGGSSCSSHHH
T ss_pred             CcCccCCCcCCccCcCHHhHhHhHHHHHHHHhcCCceeecCCCCcccCCcccccCccchHHHHHHcCCCHHHccccchhc
Confidence            36999999999999999999999999999999999999999999999999999999999999999999999999988765


Q ss_pred             hc
Q psy3092         136 KE  137 (347)
Q Consensus       136 ~~  137 (347)
                      .+
T Consensus        81 ~k   82 (83)
T d2hanb1          81 MK   82 (83)
T ss_dssp             HH
T ss_pred             cC
Confidence            43

>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=1.1e-33  Score=248.59  Aligned_cols=197  Identities=48%  Similarity=0.779  Sum_probs=168.8

Q ss_pred             CCCCcHHHHHHHHHhccCCCCCCc---------cccchhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHH
Q psy3092         150 LIEMPVERILEAEQRVDMKQEPAD---------QDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRA  220 (347)
Q Consensus       150 ~~~~~~~~l~~~~~~~~~~~~~~~---------~~~~~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~  220 (347)
                      ..+.+++++++++..+....+...         .+......+..+|+..+++++.+|+|||++|+|..|+.+||+.|||+
T Consensus         3 ~~~~~i~~l~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lc~~~~~~L~~~VewAK~lP~F~~L~~~DQi~LLk~   82 (256)
T d1g2na_           3 VQELSIERLLEMESLVADPSEEFQFLRVGPDSNVPPKFRAPVSSLCQIGNKQIAALVVWARDIPHFSQLEMEDQILLIKG   82 (256)
T ss_dssp             SCCCCHHHHHHHHHCCCCCCCCCCSBCCCTTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHH
T ss_pred             cccccHHHHHHHHHhccCCchhhhhhcCCCCCCCCCccccHHHHHHHHHHHHHHHHHHHHhcCCChhhCCHHHHHHHHHH
Confidence            356779999998876554332211         01122345789999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhcccccCC------------------CceEecCCccccccchhhcCchhhHHhhHHHHHHHHHhcCCCHh
Q psy3092         221 GWNELLIASFSHRSISVK------------------DGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKT  282 (347)
Q Consensus       221 ~~~~~~~l~~a~~s~~~~------------------~~~~~~~g~~i~~~~~~~~~~~~~~~~~~~~l~~~l~~L~l~~~  282 (347)
                      +|.+++++..+|+++...                  +...+.+|..++++.....++..++++++.+++.+|++|++|++
T Consensus        83 ~w~el~iL~~a~rs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~L~ld~~  162 (256)
T d1g2na_          83 SWNELLLFAIAWRSMEFLTEERDGVDGTGNRTTSPPQLMCLMPGMTLHRNSALQAGVGQIFDRVLSELSLKMRTLRVDQA  162 (256)
T ss_dssp             HHHHHHHHHHHHHHGGGSCCC----------CCCCCCEEEEETTEEEEHHHHHHHTCHHHHHHHHHHTHHHHHHTTCCHH
T ss_pred             HHHHHHHHHHHHHHhhhccccccccccccccccCcchhhccCCCcccCHHHHHhcchHHHHHHHHHHHHHHHHHcCCCHH
Confidence            999999999999876542                  23445667777777777778888888999999999999999999


Q ss_pred             HHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhhhhhhccC
Q psy3092         283 ELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIE  346 (347)
Q Consensus       283 E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll~~lr~i~  346 (347)
                      ||++||||+|||||++|+++...|+++|+++..+|++|+..++++.+.||++||++||+||+|+
T Consensus       163 E~~~LkaIvLfnpd~~gL~~~~~Ie~lqe~~~~aL~~y~~~~~p~~~~Rf~~LLl~Lp~LR~l~  226 (256)
T d1g2na_         163 EYVALKAIILLNPDVKGLKNRQEVEVLREKMFLCLDEYCRRSRSSEEGRFAALLLRLPALRSIS  226 (256)
T ss_dssp             HHHHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHSTTCTTHHHHHHTHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCccCCcccHHHHHHHHHHHHHHHHHHHHhcCCChhhHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999885

>d1kb2a_ g.39.1.2 (A:) Vitamin D3 receptor, VDR, DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Vitamin D3 receptor, VDR, DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=7.2e-36  Score=214.12  Aligned_cols=83  Identities=37%  Similarity=0.999  Sum_probs=78.1

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhh
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRT  135 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~  135 (347)
                      ++|.|||++|+|+||||++|+|||+||||++..+..|.|..+++|.+++..|+.||+|||+||+++||++++||.+|+..
T Consensus         1 r~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~c~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~   80 (89)
T d1kb2a_           1 RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDEEVQ   80 (89)
T ss_dssp             CBCTTTCSBCCSEETTEECCHHHHHHHHHHHHTTCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCHHHHH
T ss_pred             CCCeeCCCcCCccCCCHHHHHHHHHHHHHHHhcCCCeecCCCCccCCCCcCCccCchhhHHHHHHcCCCHhhccccchhc
Confidence            36999999999999999999999999999999999999999999999999999999999999999999999999988865


Q ss_pred             hcc
Q psy3092         136 KER  138 (347)
Q Consensus       136 ~~~  138 (347)
                      ..+
T Consensus        81 ~kr   83 (89)
T d1kb2a_          81 RKR   83 (89)
T ss_dssp             HHH
T ss_pred             hhh
Confidence            543

>d1dsza_ g.39.1.2 (A:) Retinoic acid receptor DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Retinoic acid receptor DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=2.1e-35  Score=204.95  Aligned_cols=74  Identities=55%  Similarity=1.299  Sum_probs=71.8

Q ss_pred             CcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHH
Q psy3092          58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEE  131 (347)
Q Consensus        58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~  131 (347)
                      |.|||++++|+||||.+|+|||+||||++..+..|.|..+++|.+++..|..||+|||+|||++||++++||.|
T Consensus         2 C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~c~~~~~c~~~~~~r~~Cr~CR~~KCl~~GM~~~~vq~d   75 (75)
T d1dsza_           2 CFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRND   75 (75)
T ss_dssp             CTTTCSCCCSEETTEECCHHHHHHHHHHHHTTCCCCCSSCSCCCCSTTTGGGCHHHHHHHHHHTTCCGGGSCCC
T ss_pred             CccCCCcCCccCcCHHHhhhhHHHHHHHHhcCCceecccCCccccCCccccccchhHHHHHHHhCCCHHHccCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999853

>d1lo1a_ g.39.1.2 (A:) Steroid hormone receptor Err2 DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Steroid hormone receptor Err2 DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=5.6e-36  Score=214.84  Aligned_cols=82  Identities=50%  Similarity=1.017  Sum_probs=77.9

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhh
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRT  135 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~  135 (347)
                      ++|.|||++++|+||||++|+|||+||||++..+..|.|..+++|.++...|+.|++|||+||+++||++++||.+|++.
T Consensus         5 ~~C~VCg~~~~~~hyG~~sC~aC~~FFRR~v~~~~~~~c~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~r~~~   84 (90)
T d1lo1a_           5 RLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKALKVGMLKEGVRLDRVRG   84 (90)
T ss_dssp             CEETTTTEECSEESSSSEECHHHHHHHHHHHHTTCCCCCSSCSCCCCCHHHHHHCHHHHHHHHHHHTCCGGGSCSSCCTT
T ss_pred             CcCCcCCCcCCceEcCeeechhhHHHHHHHHhcCCccchhcCCCCccCCCCccccchhhHHHHHHcCCCHHHhccccccc
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999988765


Q ss_pred             hc
Q psy3092         136 KE  137 (347)
Q Consensus       136 ~~  137 (347)
                      ..
T Consensus        85 ~r   86 (90)
T d1lo1a_          85 GR   86 (90)
T ss_dssp             CC
T ss_pred             cc
Confidence            43

>d1a6ya_ g.39.1.2 (A:) Orphan nuclear receptor reverb DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Orphan nuclear receptor reverb DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=2.2e-35  Score=206.46  Aligned_cols=76  Identities=55%  Similarity=1.223  Sum_probs=71.2

Q ss_pred             cCcccCCCCCCcccccccchhhHHHHHhhhcCCCccc-ccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHH
Q psy3092          57 LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYA-CREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEER  132 (347)
Q Consensus        57 ~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~-C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r  132 (347)
                      +|.|||++|+|+||||++|+|||+||||++..+..|. |..+++|.+++..|..||+|||+||+++||++++||.+|
T Consensus         2 iC~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~~~~~~~~c~~~~~~r~~Cr~CR~~KCl~~GM~~~~vq~~R   78 (78)
T d1a6ya_           2 LCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGR   78 (78)
T ss_dssp             BCTTTSSBCCEEETTEEECHHHHHHHHHHHSSCCCCCCCSSTTCCCCCTTTTTSCHHHHHHHHTTTTCCSTTCCCCC
T ss_pred             CCeeCCCcCCcccCcchhhhhchhhhhhhhccCCceeeeccCCCcccCCCCCccchhhHHHHHHHhCCCHHHhcCCC
Confidence            5999999999999999999999999999999999987 556789999999999999999999999999999998754

>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=8.5e-33  Score=239.22  Aligned_cols=195  Identities=70%  Similarity=1.088  Sum_probs=170.7

Q ss_pred             CCcHHHHHHHHHhccCCCCCCcc------ccchhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHH
Q psy3092         152 EMPVERILEAEQRVDMKQEPADQ------DIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNEL  225 (347)
Q Consensus       152 ~~~~~~l~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~  225 (347)
                      ++|++++++++..+++..+....      .......+..+++.+.+.++.+++|||++|+|..|+.+||+.|||++|.++
T Consensus         1 ~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~l~~~a~~~l~~~v~wak~lp~F~~L~~~DQ~~LLk~~~~el   80 (230)
T d2p1ta1           1 DMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNEL   80 (230)
T ss_dssp             CCCHHHHHHHHHHHC-------------------CHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHhcCCCCcccccccCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHcCCccccCCHHHHHHHHHHHHHHH
Confidence            46789999998777764433221      112234577899999999999999999999999999999999999999999


Q ss_pred             HHHHhhcccccCCCceEecCCccccccchhhcCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHH
Q psy3092         226 LIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQV  305 (347)
Q Consensus       226 ~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~  305 (347)
                      +++..++++...++++++.+|..+..+.....+...++++.+.+++.+|++|++|++||++|+||+||+|++.|+++...
T Consensus        81 ~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~ld~~E~~lLkaivL~~pd~~~l~~~~~  160 (230)
T d2p1ta1          81 LIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAE  160 (230)
T ss_dssp             HHHHHHHHTTTSSSEEECTTSCEEEHHHHHTTTCHHHHHHHHHHTHHHHHHTTCCHHHHHHHHHHHHSCTTCTTCSCHHH
T ss_pred             HHHHHHHHhhcCCCeEEecCCeeecHhHHHhccchHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhccccCCcccHHH
Confidence            99999999999899999999999988888777888888888889999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhhhhhhccC
Q psy3092         306 VEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIE  346 (347)
Q Consensus       306 i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll~~lr~i~  346 (347)
                      |+++|+++..+|++|+..++++.+.||++||++||+||.++
T Consensus       161 i~~~q~~~~~aL~~y~~~~~~~~~~R~~~Ll~~L~~Lr~l~  201 (230)
T d2p1ta1         161 VEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIG  201 (230)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhhCCCchhHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999875

>d2nllb_ g.39.1.2 (B:) Thyroid hormone receptor (TR-beta) DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Thyroid hormone receptor (TR-beta) DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=8.1e-35  Score=215.33  Aligned_cols=81  Identities=47%  Similarity=1.087  Sum_probs=74.4

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCccc--ccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHh
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYA--CREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQ  133 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~--C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~  133 (347)
                      ++|.|||++|+|+||||+||+|||+||||+|..+..|.  |..+++|.+++..|+.|++|||+||++|||++++||.+++
T Consensus         2 ~~C~VCg~~a~g~HfGv~sC~aCkaFFRR~v~~~~~~~~~c~~~~~c~~~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~   81 (103)
T d2nllb_           2 ELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQECRFKKCIYVGMATDLVLDDSK   81 (103)
T ss_dssp             CBCTTTCSBCCSEETTEECCHHHHHHHHHHHHTTCGGGCCCSSCTTCCCSTTTTTSCHHHHHHHHHHTTCCGGGSCCHHH
T ss_pred             CcCccCCCcCCcccCchhhhHHHHHHhHHHhhccccceeecccCCCCcCCCCccCCCccccchhHHHhhccHHhhhcccc
Confidence            56999999999999999999999999999998877654  5678899999999999999999999999999999999888


Q ss_pred             hhh
Q psy3092         134 RTK  136 (347)
Q Consensus       134 ~~~  136 (347)
                      +..
T Consensus        82 ~~~   84 (103)
T d2nllb_          82 RLA   84 (103)
T ss_dssp             HHH
T ss_pred             chh
Confidence            654

>d1r4ia_ g.39.1.2 (A:) Androgen receptor {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Androgen receptor
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=100.00  E-value=6.8e-35  Score=201.54  Aligned_cols=72  Identities=46%  Similarity=0.974  Sum_probs=69.3

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhH
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREA  127 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~  127 (347)
                      ++|.|||++|+|+||||.+|+|||+||||++..+..|.|+.+++|.+++..|+.||+|||+||+++||+.+|
T Consensus         3 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~c~~~~~C~~~~~~r~~C~~CR~~KCl~vGM~~~A   74 (74)
T d1r4ia_           3 KTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLGA   74 (74)
T ss_dssp             CBCSSSCSBEEEEETTEEEEHHHHHHHHHHHTSCCCCCCSSSSCCCCCTTTTTTCHHHHHHHHHHHTCCSCC
T ss_pred             CcCccCCCcCCccCCCHHhhHHHHHHHHHHHhcccceeeecCCCcccCCCCcccchhhhHHHHHHcCCcCCC
Confidence            569999999999999999999999999999999999999999999999999999999999999999999864

>d1lata_ g.39.1.2 (A:) Glucocorticoid receptor DNA-binding domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Glucocorticoid receptor DNA-binding domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=100.00  E-value=3.2e-34  Score=196.75  Aligned_cols=70  Identities=54%  Similarity=1.135  Sum_probs=67.9

Q ss_pred             cCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchh
Q psy3092          57 LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKRE  126 (347)
Q Consensus        57 ~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~  126 (347)
                      +|.|||++|+|+||||.+|+|||+||||++..+..|.|..+++|.+++..|+.||+|||+|||++||++|
T Consensus         2 ~C~VC~~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~c~~~~~C~~~~~~r~~Cr~CR~~KCl~~GM~~e   71 (71)
T d1lata_           2 PCLVCSDEASGCHYGVLTCEGCKAFFKRAVEGQHNYLCKYEGKCIIDKIRRKNCPACRYRKCLQAGMNLE   71 (71)
T ss_dssp             BCTTTCSBCCEEETTEEECHHHHHHHHHHHHSCCCCCCSSCSCCCCSTTTTTTCHHHHHHHHHHTTCCCC
T ss_pred             cCeeCCCcCCceEcCHhhHHHHHHHHHHHHhcCcceeeecCcccccccCccccCCccchhHHhHccCCCC
Confidence            4999999999999999999999999999999999999999999999999999999999999999999975

>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=99.98  E-value=5.2e-32  Score=232.68  Aligned_cols=169  Identities=33%  Similarity=0.570  Sum_probs=156.9

Q ss_pred             chhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhh
Q psy3092         177 VNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHE  256 (347)
Q Consensus       177 ~~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~  256 (347)
                      .....++.+++..++.++.+|+|+|++|+|..|+.+||+.|+|++|.+++++..++++...++..++++|..+.++....
T Consensus        27 ~~~~~~~~l~~~a~~~l~~~V~waK~lp~F~~L~~~DQi~LLk~~~~el~~L~~a~~s~~~~~~~~~~~~~~~~~~~~~~  106 (223)
T d2e2ra1          27 SDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDELVYADDYIMDEDQSKL  106 (223)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTSSSCEEEETTEEECHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHhCcchhhcCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeeeecCCcccchHHhhh
Confidence            34456889999999999999999999999999999999999999999999999999999988999999998888877766


Q ss_pred             cCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHH
Q psy3092         257 AGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLL  336 (347)
Q Consensus       257 ~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL  336 (347)
                      .+..++.+. +.+++.+|++|++|++||++|+||+||+||++|+++.+.|+++|+++..+|++|+..++++.+.||++||
T Consensus       107 ~~~~~~~~~-i~~~~~~l~~L~ld~~E~~lLkaivL~~pd~~~L~~~~~I~~~q~~~~~aL~~y~~~~~~~~~~rf~~LL  185 (223)
T d2e2ra1         107 AGLLDLNNA-ILQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKML  185 (223)
T ss_dssp             TTCHHHHHH-HHHHHHHHHHHTCCHHHHHHHHHHHHHTCCCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHH
T ss_pred             ccHHHHHHH-HHHHHHHHHHcCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCchhHHHHHH
Confidence            777776655 4589999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhhccC
Q psy3092         337 LRLPSLRSIE  346 (347)
Q Consensus       337 ~ll~~lr~i~  346 (347)
                      ++||.||+++
T Consensus       186 ~~Lp~Lr~l~  195 (223)
T d2e2ra1         186 MTLPLLRQTS  195 (223)
T ss_dssp             TTHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999999885

>d1cita_ g.39.1.2 (A:) Orphan nuclear receptor NGFI-B DNA-binding domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Orphan nuclear receptor NGFI-B DNA-binding domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.98  E-value=4.5e-34  Score=205.00  Aligned_cols=80  Identities=55%  Similarity=1.202  Sum_probs=75.5

Q ss_pred             cCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhhh
Q psy3092          57 LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRTK  136 (347)
Q Consensus        57 ~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~~  136 (347)
                      .|.|||++|+|+||||.+|+|||+||||++..+..|.|..+++|.++...|..||+|||+||+++||++++||.+++...
T Consensus         2 ~C~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~c~~~~~c~~~~~~r~~Cr~CR~~KCl~~GM~~~~v~~~~~~~~   81 (89)
T d1cita_           2 RCAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTDSLKGR   81 (89)
T ss_dssp             CCSSSCCCCCEEETTEEECHHHHHHHHHHHHHTCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHTTCCGGGSCCGGGTTC
T ss_pred             CCeECCCcCCccCCCcccchhhHHHHHHHHHcCCceeecCCCCccccCCccccCchhhHHHHHHcCCCHHHhcccccccc
Confidence            49999999999999999999999999999999999999999999999999999999999999999999999998766543

>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=99.98  E-value=2.5e-32  Score=236.53  Aligned_cols=167  Identities=40%  Similarity=0.644  Sum_probs=156.2

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV  259 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~  259 (347)
                      .+..++++.++++++.+++|||++|+|..|+.+||+.|+|++|.+++++..+|++...++.+++.+|..+..+.....+.
T Consensus        37 ~~~~~l~~~a~~~l~~~vewaK~ip~F~~L~~~DQ~~LLk~~~~el~lL~~a~~s~~~~~~~~l~~~~~~~~~~~~~~~~  116 (233)
T d1pzla_          37 ASIADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVLLLGNDYIVPRHCPELAEM  116 (233)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHTTCHHHHTSCHHHHHHHHHHSHHHHHHHHHHHHHTTSSSEEECTTSCEEESSCGGGGGG
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCceeecCCccccchhhhhhhh
Confidence            45788999999999999999999999999999999999999999999999999999999999999999888877666666


Q ss_pred             hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhh
Q psy3092         260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRL  339 (347)
Q Consensus       260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll  339 (347)
                      .....+.+.+++.+|++|++|.+||++|+||+||+||.+|+++.+.++++|+++..+|++|+..++++.+.||++||++|
T Consensus       117 ~~~~~~~l~~~~~~~~~L~ld~~E~~lLkaiiL~~pd~~~l~~~~~i~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LLl~L  196 (233)
T d1pzla_         117 SRVSIRILDELVLPFQELQIDDNEYAYLKAIIFFDPDAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLL  196 (233)
T ss_dssp             HHHHHHHHHHTHHHHHHHTCCHHHHHHHHHHHHCCTTCTTCSCHHHHHHHHHHHHHHHHHHHHSSSSCCTTHHHHHHTHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhcccccCCcccHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence            66666778899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhccC
Q psy3092         340 PSLRSIE  346 (347)
Q Consensus       340 ~~lr~i~  346 (347)
                      |+||+++
T Consensus       197 p~Lr~i~  203 (233)
T d1pzla_         197 PTLQSIT  203 (233)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9999875

>d1hcqa_ g.39.1.2 (A:) Estrogen receptor DNA-binding domain {Human and chicken (Homo sapiens) and (Gallus gallus) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Estrogen receptor DNA-binding domain
species: Human and chicken (Homo sapiens) and (Gallus gallus) [TaxId: 9606]

Probab=99.98  E-value=1.4e-33  Score=194.97  Aligned_cols=71  Identities=49%  Similarity=1.119  Sum_probs=68.3

Q ss_pred             CCcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcch
Q psy3092          55 KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKR  125 (347)
Q Consensus        55 ~~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~  125 (347)
                      .+.|.|||++|+|+||||++|+|||+||||++..+..|.|+.+++|.++...|+.||+|||+||+++||++
T Consensus         4 ~~~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~k   74 (74)
T d1hcqa_           4 TRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMK   74 (74)
T ss_dssp             CCBCTTTCSBCCEEETTEEECHHHHHHHHHHHSSCCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHHTCCC
T ss_pred             CCCCccCCCcCCceEcCeeehHHHHHHHHHHHHcccccccccCCCCccCCCccccchHhhHHHHHHcCCcC
Confidence            46799999999999999999999999999999999999999999999999999999999999999999974

>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=99.97  E-value=1.1e-31  Score=237.28  Aligned_cols=168  Identities=50%  Similarity=0.892  Sum_probs=150.0

Q ss_pred             hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCC-------------------
Q psy3092         179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKD-------------------  239 (347)
Q Consensus       179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~-------------------  239 (347)
                      ...+..++++....++.+|+|||++|+|..|+.+||+.|||++|.+++++..+|++.....                   
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            4568899999999999999999999999999999999999999999999999998865432                   


Q ss_pred             --------ceEecCCccccccchhhcCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHH
Q psy3092         240 --------GILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLRE  311 (347)
Q Consensus       240 --------~~~~~~g~~i~~~~~~~~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~  311 (347)
                              .+.+.+|..+.++.....+....+.+.+.+++.+|++|++|++||++||||+|||||++++++...|+++|+
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                    233444555555555566677788888999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhcCCCCchHHHHHHhhhhhhhccC
Q psy3092         312 KVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIE  346 (347)
Q Consensus       312 ~~~~~L~~y~~~~~~~~~~Rf~~LL~ll~~lr~i~  346 (347)
                      ++..+|++|+..++++.+.||++||++||.||+|+
T Consensus       198 ~~~~aL~~y~~~~~p~~~~Rf~~LLl~Lp~Lr~l~  232 (265)
T d1hg4a_         198 KVYACLDEHCRLEHPGDDGRFAQLLLRLPALRSIS  232 (265)
T ss_dssp             HHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhCCChhhHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999886

>d1pq9a_ a.123.1.1 (A:) Oxysterols receptor LXR-beta {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Oxysterols receptor LXR-beta
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=2.4e-31  Score=230.91  Aligned_cols=167  Identities=27%  Similarity=0.406  Sum_probs=154.3

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV  259 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~  259 (347)
                      ..+..+++.....+..+|+|||++|+|..|+.+||+.|||++|.+++++..++++....+.+++.+|..+.++.....++
T Consensus        47 ~~~~~~~~~~~~~i~~iVefAK~lP~F~~L~~~DQi~LLk~~~~el~ll~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~  126 (239)
T d1pq9a_          47 QRFAHFTELAIISVQEIVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETARRYNHETECITFLKDFTYSKDDFHRAGL  126 (239)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTSTTSTTSCHHHHHHHHHHHHHHHHHHHHHHTEETTTTEEEEETTEEECHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHhHhhhcCcCHHhcCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEeecCCCcccHHHHhhhhh
Confidence            44667888888999999999999999999999999999999999999999999988888899999999988888877777


Q ss_pred             hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhh
Q psy3092         260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRL  339 (347)
Q Consensus       260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll  339 (347)
                      ...+...+.+++.+|++|++|++||++|+||+||+||++|+++...|+++|+++..+|+.|+..++++.+.||++||++|
T Consensus       127 ~~~~~~~i~~~~~~l~~L~ld~~E~alLkAivL~~pd~~gl~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~rf~~LL~~L  206 (239)
T d1pq9a_         127 QVEFINPIFEFSRAMRRLGLDDAEYALLIAINIFSADRPNVQEPGRVEALQQPYVEALLSYTRIKRPQDQLRFPRMLMKL  206 (239)
T ss_dssp             CHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcCccccHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHH
Confidence            65444556689999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhccC
Q psy3092         340 PSLRSIE  346 (347)
Q Consensus       340 ~~lr~i~  346 (347)
                      |.||+|+
T Consensus       207 ~~LR~l~  213 (239)
T d1pq9a_         207 VSLRTLS  213 (239)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9999986

>d3d24a1 a.123.1.1 (A:194-420) Steroid hormone receptor ERR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Steroid hormone receptor ERR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=1.4e-31  Score=230.82  Aligned_cols=167  Identities=29%  Similarity=0.532  Sum_probs=149.2

Q ss_pred             hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcC
Q psy3092         179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG  258 (347)
Q Consensus       179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~  258 (347)
                      ...+..+++..++.++.+|+|+|++|+|..|+.+||+.|+|++|.+++++..+++++..++.+.+++|..++.+.....+
T Consensus        29 ~~~~~~l~~~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~  108 (227)
T d3d24a1          29 LPAVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQDELAFAEDLVLDEEGARAAG  108 (227)
T ss_dssp             --CHHHHHHHHHHHHHHHHHHHHHSTTTTTSCHHHHHHHHHHHHHHHHHHHHHHHHTTSSSEEEEETTEEEEHHHHHHTT
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhCcchhcCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCeeeecCCcccchhhhcccc
Confidence            34578999999999999999999999999999999999999999999999999999998999999999888877766666


Q ss_pred             chhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCC----CCchHHHH
Q psy3092         259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHS----EEPGRFAK  334 (347)
Q Consensus       259 ~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~----~~~~Rf~~  334 (347)
                      ...+.+. +.+++.+|++|++|++||++|+||+||+||++|+++...|+++|+++..+|++|+..+++    +.+.||++
T Consensus       109 ~~~~~~~-l~~~~~~~~~L~ld~~E~~lLkaivLf~pd~~gL~~~~~I~~~q~~~~~aL~~y~~~~~~~~~~~~~~Rf~~  187 (227)
T d3d24a1         109 LGELGAA-LLQLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQLREALHEALLEYEAGRAGPGGGAERRRAGR  187 (227)
T ss_dssp             CTTHHHH-HHHHHHHHHTTTCCHHHHHHHHHHHHHTCCCTTCSCHHHHHHHHHHHHHHHHHHHTC--------CHHHHHH
T ss_pred             HHHHHHH-HHHHHHHHHHcCCCHHHHHHHHHHHHhCCcCCCcccHHHHHHHHHHHHHHHHHHHHHhcCCCchhHHhHHHH
Confidence            6666655 558999999999999999999999999999999999999999999999999999987753    44679999


Q ss_pred             HHhhhhhhhccC
Q psy3092         335 LLLRLPSLRSIE  346 (347)
Q Consensus       335 LL~ll~~lr~i~  346 (347)
                      ||++||.||+++
T Consensus       188 LL~~Lp~Lr~l~  199 (227)
T d3d24a1         188 LLLTLPLLRQTA  199 (227)
T ss_dssp             HHTTHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            999999999885

>d1fcya_ a.123.1.1 (A:) Retinoic acid receptor gamma (RAR-gamma) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Retinoic acid receptor gamma (RAR-gamma)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=3e-31  Score=229.84  Aligned_cols=165  Identities=28%  Similarity=0.494  Sum_probs=154.8

Q ss_pred             HHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCch
Q psy3092         181 QATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVG  260 (347)
Q Consensus       181 ~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~~  260 (347)
                      -+..+.+.....+..+|+|||++|+|..|+.+||+.|||++|.++++++.++++....+.+.+.+|..+.++.....+..
T Consensus        45 ~~~~~~~~~~~~i~~iV~faK~ip~F~~L~~~DQi~LLk~~~~el~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~~~~~  124 (236)
T d1fcya_          45 LWDKFSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMTFSDGLTLNRTQMHNAGFG  124 (236)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETTTTEEECTTCBEEEHHHHHHHTTG
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcccCCeeeccCCceecHHHHhhcccH
Confidence            46778888899999999999999999999999999999999999999999999888888999999999998888877777


Q ss_pred             hhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhhh
Q psy3092         261 GIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLP  340 (347)
Q Consensus       261 ~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll~  340 (347)
                      .+.+.+ .+++.+|++|++|++||++|+||+||+||++||++...|+++|+++..+|++|+..++++.+.||++||++||
T Consensus       125 ~l~~~~-~~~~~~l~~L~ld~~E~alL~Ai~L~~pd~~gL~~~~~Ve~lq~~~~~aL~~y~~~~~~~~~~rf~~LL~~Lp  203 (236)
T d1fcya_         125 PLTDLV-FAFAGQLLPLEMDDTETGLLSAICLICGDRMDLEEPEKVDKLQEPLLEALRLYARRRRPSQPYMFPRMLMKIT  203 (236)
T ss_dssp             GGHHHH-HHHHHHHGGGCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHH
T ss_pred             HHHHHH-HHHHHHHHHcCCCHHHHHHHHHHhhccCCCCCcccccHHHHHHHHHHHHHHHHHHHhCCCchhHHHHHHHHHH
Confidence            777665 4899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhccC
Q psy3092         341 SLRSIE  346 (347)
Q Consensus       341 ~lr~i~  346 (347)
                      .||+|+
T Consensus       204 ~LR~l~  209 (236)
T d1fcya_         204 DLRGIS  209 (236)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            999885

>d1n46a_ a.123.1.1 (A:) Thyroid hormone receptor beta (TR-beta) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Thyroid hormone receptor beta (TR-beta)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=5.4e-31  Score=229.87  Aligned_cols=166  Identities=24%  Similarity=0.425  Sum_probs=154.5

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV  259 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~  259 (347)
                      ..+..+++.....+..+|+|||.+|+|..|+.+||+.|||++|.+++++..++++...++.+.+.+|..+.++.....++
T Consensus        57 ~~~~~~~~~~~~~i~~vV~fAK~iPgF~~L~~~DQi~LLk~~~~El~lL~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~  136 (251)
T d1n46a_          57 EAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLNGEMAVTRGQLKNGGL  136 (251)
T ss_dssp             HHHHHHHTTHHHHHHHHHHHHHTCTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTCBTTTTBEEETTTEEECHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEeCCCccccHHHHhhccc
Confidence            44778888899999999999999999999999999999999999999999999988888889999999988888777777


Q ss_pred             hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhh
Q psy3092         260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRL  339 (347)
Q Consensus       260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll  339 (347)
                      +.+.+.+. +++.+|++|++|++||+||+||+||+||++||++...|+++|+++..+|+.|+..++++.+.||++||++|
T Consensus       137 ~~~~~~i~-~f~~~l~~L~ld~~E~alL~AivL~~pdr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~rf~kLL~~L  215 (251)
T d1n46a_         137 GVVSDAIF-DLGMSLSSFNLDDTEVALLQAVLLMSSDRPGLACVERIEKYQDSFLLAFEHYINYRKHHVTHFWPKLLMKV  215 (251)
T ss_dssp             TTHHHHHH-HHHHHHGGGTCCHHHHHHHHHHHHTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCCSSTTHHHHHHHHH
T ss_pred             HHHHHHHH-HHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCCcCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHh
Confidence            77666554 89999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhccC
Q psy3092         340 PSLRSIE  346 (347)
Q Consensus       340 ~~lr~i~  346 (347)
                      |.||+|+
T Consensus       216 p~LR~l~  222 (251)
T d1n46a_         216 TDLRMIG  222 (251)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9999986

>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=99.97  E-value=2.5e-30  Score=225.18  Aligned_cols=166  Identities=34%  Similarity=0.622  Sum_probs=145.9

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccC--CCceEecCCccccccchhhc
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISV--KDGILLAPGVTVYRSSAHEA  257 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~--~~~~~~~~g~~i~~~~~~~~  257 (347)
                      ..+..+++.+++.++.+|+|||++|+|..|+.+||+.|||++|.+++++..+|+++..  .+.+.+.+|..++.+.....
T Consensus        42 ~~~~~l~~~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~iL~~a~~s~~~~~~~~~~~~~g~~~~~~~~~~~  121 (242)
T d1pk5a_          42 SAFGLLCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVAHGKEGTIFLVTGEHVDYSTIISH  121 (242)
T ss_dssp             CSHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCSSEEECTTSCEEEHHHHHHT
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHhCCCHhhcCHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCeeEecCCCcccchHHhhh
Confidence            3577889999999999999999999999999999999999999999999999988654  35577888887765544322


Q ss_pred             ---CchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHH
Q psy3092         258 ---GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAK  334 (347)
Q Consensus       258 ---~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~  334 (347)
                         ++..+. +.+.+++.+|++|++|++||++|+||+|||||++|+++...|+++|+++..+|++|+..++++.+.||++
T Consensus       122 ~~~~~~~~~-~~~~~l~~~l~~L~ld~~E~~lLkai~Lf~pd~~gL~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~  200 (242)
T d1pk5a_         122 TEVAFNNLL-SLAQELVVRLRSLQFDQREFVCLKFLVLFSSDVKNLENLQLVEGVQEQVNAALLDYTVCNYPQQTEKFGQ  200 (242)
T ss_dssp             SCHHHHHHH-HHHHHHHHHHHHTTCCHHHHHHHHHHHHSCSCCSSCTTHHHHHHHHHHHHHHHHHHHHHHCTTSTTHHHH
T ss_pred             cccchHHHH-HHHHHHHHHHHHhCCCHHHHHHHHHHHhcCCCCCCchhHHHHHHHHHHHHHHHHHHHHhhCCCcchHHHH
Confidence               222233 4456899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhhhhhhccC
Q psy3092         335 LLLRLPSLRSIE  346 (347)
Q Consensus       335 LL~ll~~lr~i~  346 (347)
                      ||++||.||+++
T Consensus       201 LLl~Lp~Lr~~~  212 (242)
T d1pk5a_         201 LLLRLPELRAIS  212 (242)
T ss_dssp             HHTTHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            999999999875

>d1ovla_ a.123.1.1 (A:) Orphan nuclear receptor NURR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NURR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=7.9e-30  Score=220.40  Aligned_cols=164  Identities=27%  Similarity=0.510  Sum_probs=148.7

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV  259 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~  259 (347)
                      ..++.+.+.....+..+++|||++|+|.+|+.+||+.|||++|.++++++.++++...++.+++.+|..+.+... ..++
T Consensus        39 ~~~~~f~~~~~~~i~~iv~fAK~iPgF~~L~~~DQi~LLk~~~~ElllL~~a~~~~~~~~~l~~~~~~~~~~~~~-~~~~  117 (236)
T d1ovla_          39 QHIQQFYDLLTGSMEIIRGWAEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIFCNGVVLHRLQC-VRGF  117 (236)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHSBTTTTEEECTTSBEEEHHHH-TTTT
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEecCCceechHhh-cccH
Confidence            356777888889999999999999999999999999999999999999999999988888899999999887665 3456


Q ss_pred             hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCC--CCchHHHHHHh
Q psy3092         260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHS--EEPGRFAKLLL  337 (347)
Q Consensus       260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~--~~~~Rf~~LL~  337 (347)
                      +++.+.+ .+++.+|++|++|++||++|+||+||+ |++|+++.+.|+++|+++..+|++|+..+++  +.+.||++||+
T Consensus       118 ~~~~~~i-~~~~~~l~~L~ld~~E~alLkAI~L~~-dr~gL~~~~~Ve~lQ~~~~~aL~~~~~~~~~~~~~~~rf~~LL~  195 (236)
T d1ovla_         118 GEWIDSI-VEFSSNLQNMNIDISAFSCIAALAMVT-ERHGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLG  195 (236)
T ss_dssp             TTHHHHH-HHHHHHHHTTCCCHHHHHHHHHHHHSS-CCTTCSCHHHHHHHHHHHHHHHHHHHHGGGTTTTSTTHHHHHHH
T ss_pred             HHHHHHH-HHHHHHHHHcCCCHHHHHHHHHHHHcC-CCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCccHHHHHHHHHH
Confidence            6666654 489999999999999999999999997 8999999999999999999999999998876  67899999999


Q ss_pred             hhhhhhccC
Q psy3092         338 RLPSLRSIE  346 (347)
Q Consensus       338 ll~~lr~i~  346 (347)
                      +||.||+|+
T Consensus       196 ~Lp~LR~l~  204 (236)
T d1ovla_         196 KLPELRTLC  204 (236)
T ss_dssp             HHHHHHHHH
T ss_pred             HhHHHHHHH
Confidence            999999985

>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=99.97  E-value=1e-29  Score=220.98  Aligned_cols=164  Identities=25%  Similarity=0.375  Sum_probs=151.3

Q ss_pred             HHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCch
Q psy3092         181 QATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVG  260 (347)
Q Consensus       181 ~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~~  260 (347)
                      .+..+++.....+..+|+|||.+|+|..|+.+||+.|||++|.+++++..++++....+.+++++|..+.++.....+++
T Consensus        49 ~~~~~~~~~~~~i~~iV~faK~lP~F~~L~~~DQi~LLk~~~~El~lL~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  128 (243)
T d2r40d1          49 PFRQITEMTILTVQLIVEFAKGLPGFAKISQSDQITLLKACSSEVMMLRVARRYDAATDSVLFANNQAYTRDNYRKAGMA  128 (243)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEETTTTEEECTTSCEECHHHHHHTTCH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCcChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCeEEecCCeeecHHHHhhcccH
Confidence            46678888888999999999999999999999999999999999999999999988889999999999998888887888


Q ss_pred             hhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCC---CchHHHHHHh
Q psy3092         261 GIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSE---EPGRFAKLLL  337 (347)
Q Consensus       261 ~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~---~~~Rf~~LL~  337 (347)
                      .+++.++ +++.+|++|++|++||++|+||+||+ |++|+++...|+++|+++..+|++|+..++++   .+.||++||+
T Consensus       129 ~~~~~l~-~f~~~l~~L~ld~~E~alL~AivL~s-d~~~L~~~~~ve~lq~~~~~aL~~y~~~~~~~~p~~~~rf~~LL~  206 (243)
T d2r40d1         129 YVIEDLL-HFCRCMYSMMMDNVHYALLTAIVIFS-DRPGLEQPLLVEEIQRYYLNTLRVYILNQNSASPRCAVIFGKILG  206 (243)
T ss_dssp             HHHHHHH-HHHHHHHTTTCCHHHHHHHHHHHHTS-CCTTCSCHHHHHHHHHHHHHHHHHHHHHHTTTCTTHHHHHHHHHH
T ss_pred             HHHHHHH-HHHHHHHHhCCCHHHHHHHHHHHhcC-CCCCCCcHHHHHHHHHHHHHHHHHHHHhhCCCCccHhHHHHHHHH
Confidence            8887766 79999999999999999999999999 88999999999999999999999999888764   4579999999


Q ss_pred             hhhhhhccC
Q psy3092         338 RLPSLRSIE  346 (347)
Q Consensus       338 ll~~lr~i~  346 (347)
                      +||+||+|+
T Consensus       207 ~L~~LR~l~  215 (243)
T d2r40d1         207 ILTEIRTLG  215 (243)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999999986

>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=99.97  E-value=4.2e-30  Score=221.69  Aligned_cols=164  Identities=22%  Similarity=0.339  Sum_probs=141.2

Q ss_pred             HHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCch
Q psy3092         181 QATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVG  260 (347)
Q Consensus       181 ~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~~  260 (347)
                      .+..+++.....+..+|+|||++|+|..|+.+||+.|||++|.++++++.++++....+.+.+.++..... +....++.
T Consensus        54 ~~~~~~~~~~~~i~~iV~faK~lP~F~~L~~eDQi~LLk~~~~El~~L~~a~~~~~~~~~~~~~~~~~~~~-~~~~~~~~  132 (232)
T d1xnxa_          54 LLTHFADINTFMVQQIIKFTKDLPLFRSLTMEDQISLLKGAAVEILHISLNTTFCLQTENFFCGPLCYKME-DAVHAGFQ  132 (232)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTCHHHHTSCHHHHHHHHHHHHHHHHHHHHGGGEETTTTEEEETTEEECHH-HHHHTTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCceeeCCcccchH-HHHhcccc
Confidence            46678888999999999999999999999999999999999999999999988777667666666554433 33334443


Q ss_pred             -hhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCC--CchHHHHHHh
Q psy3092         261 -GIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSE--EPGRFAKLLL  337 (347)
Q Consensus       261 -~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~--~~~Rf~~LL~  337 (347)
                       ++++.+ .+++.+|++|++|++||+||+||+||+||++||++...|+++|+++..+|++|+..+++.  ++.||++||+
T Consensus       133 ~~~~~~i-~~f~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~~~~~f~kLL~  211 (232)
T d1xnxa_         133 YEFLESI-LHFHKNLKGLHLQEPEYVLMAATALFSPDRPGVTQREEIDQLQEEMALILNNHIMEQQSRLQSRFLYAKLMG  211 (232)
T ss_dssp             HHHHHHH-HHHHHHHHTTCCCHHHHHHHHHHHHTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHTTTTCCSTTHHHHHHH
T ss_pred             HHHHHHH-HHHHHHHHHhCCCHHHHHHHHHHHHhcCCCCCcCCHHHHHHHHHHHHHHHHHHHHHhCCCCCcccHHHHHHH
Confidence             455554 589999999999999999999999999999999999999999999999999999988774  4456999999


Q ss_pred             hhhhhhccC
Q psy3092         338 RLPSLRSIE  346 (347)
Q Consensus       338 ll~~lr~i~  346 (347)
                      +||+||+|+
T Consensus       212 ~L~~LR~l~  220 (232)
T d1xnxa_         212 LLADLRSIN  220 (232)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999999986

>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=99.96  E-value=6.1e-30  Score=220.75  Aligned_cols=163  Identities=24%  Similarity=0.386  Sum_probs=138.8

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV  259 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~  259 (347)
                      ..+..+++..+..+..+|+|||++|+|..|+.+||+.|||++|.+++++..++++...    .+.++..+..+.....+.
T Consensus        42 ~~~~~l~~~~~~~i~~iVe~AK~iP~F~~L~~~DQi~LLk~~~~El~~L~~~~~~~~~----~~~~~~~~~~~~~~~~~~  117 (231)
T d1osha_          42 ENFLILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKK----LPSGHSDLLEERIRNSGI  117 (231)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHT----SCHHHHHHHHHHHHTSSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhcCcc----ccCCCccccHHHHHhccc
Confidence            3466788999999999999999999999999999999999999999999988765322    223334444444444444


Q ss_pred             hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhh
Q psy3092         260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRL  339 (347)
Q Consensus       260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll  339 (347)
                      ...+...+.+++.+|++|++|++||++|+||+|||||++|+++...|+++|+++..+|++|+..++++.+.||++||++|
T Consensus       118 ~~~~~~~i~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~Ve~lq~~~~~aL~~y~~~~~p~~~~rf~~LL~~L  197 (231)
T d1osha_         118 SDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRL  197 (231)
T ss_dssp             CTTTHHHHHHHHHHHHTTCCCHHHHHHHHHHHHTCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhccCCCCCccHHHHHHHHHHHHHHHHHHHHHHCCCchhHHHHHHHHH
Confidence            43233345589999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhccC
Q psy3092         340 PSLRSIE  346 (347)
Q Consensus       340 ~~lr~i~  346 (347)
                      |.||+|+
T Consensus       198 ~~LR~l~  204 (231)
T d1osha_         198 TELRTFN  204 (231)
T ss_dssp             HHHHTHH
T ss_pred             HHHHHHH
Confidence            9999986

>d1xvpb_ a.123.1.1 (B:) Orphan nuclear receptor NR1I3 (CAR) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NR1I3 (CAR)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=1.1e-29  Score=221.39  Aligned_cols=166  Identities=23%  Similarity=0.363  Sum_probs=140.5

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV  259 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~  259 (347)
                      ..+..++++....+..+|+|||++|+|..|+.+||+.|||++|.+++++.+++++....+.+.+ ++......+....+.
T Consensus        54 ~~~~~~~~~~~~~i~~iV~waK~lP~F~~L~~~DQi~LLk~~~~El~~l~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~  132 (246)
T d1xvpb_          54 PLVTHFADINTFMVLQVIKFTKDLPVFRSLPIEDQISLLKGAAVEICHIVLNTTFCLQTQNFLC-GPLRYTIEDGARVGF  132 (246)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTCHHHHHSCHHHHHHHHHHHHHHHHHHHHGGGEETTTTEEEC-SSCEECHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHhcccCCeeec-CCCccchHHHhcccc
Confidence            3467788999999999999999999999999999999999999999999999877655554444 334444444444443


Q ss_pred             hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcC--CCCchHHHHHHh
Q psy3092         260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNH--SEEPGRFAKLLL  337 (347)
Q Consensus       260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~--~~~~~Rf~~LL~  337 (347)
                      ...+.+.+.+++.+|++|++|++||++|+||+|||||++||++...|+++|+++..+|++|+..++  ++++.||++||+
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            333334556899999999999999999999999999999999999999999999999999998765  578999999999


Q ss_pred             hhhhhhccC
Q psy3092         338 RLPSLRSIE  346 (347)
Q Consensus       338 ll~~lr~i~  346 (347)
                      +||.||+|+
T Consensus       213 ~L~~LR~l~  221 (246)
T d1xvpb_         213 LLAELRSIN  221 (246)
T ss_dssp             HHHHHHHHH
T ss_pred             HhHHHHHHH
Confidence            999999986

>d1pdua_ a.123.1.1 (A:) Nuclear hormone receptor HR38 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Nuclear hormone receptor HR38
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.96  E-value=1.5e-29  Score=218.01  Aligned_cols=166  Identities=22%  Similarity=0.411  Sum_probs=149.3

Q ss_pred             hhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhc
Q psy3092         178 NEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEA  257 (347)
Q Consensus       178 ~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~  257 (347)
                      ....+..+++.....+..+|+|||.+|+|.+|+.+||+.|||++|.++++++.++++....+.+++.+|..+.++.... 
T Consensus        34 ~~~~~~~~~~~~~~~i~~ivefAK~iPgF~~L~~~DQi~LLk~~~~El~~L~~a~~~~~~~~~l~~~~g~~~~~~~~~~-  112 (230)
T d1pdua_          34 EADKVQQFYQLLTSSVDVIKQFAEKIPGYFDLLPEDQELLFQSASLELFVLRLAYRARIDDTKLIFCNGTVLHRTQCLR-  112 (230)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHCCSSCSEEECTTSBEEEHHHHHH-
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHcCCChhcCCHHHHHHHHHHHHHHHHHHHHHHhccCCCCeEEecCCccccHHHHHH-
Confidence            3455777788888999999999999999999999999999999999999999999998888999999999988776544 


Q ss_pred             CchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCC--CCchHHHHH
Q psy3092         258 GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHS--EEPGRFAKL  335 (347)
Q Consensus       258 ~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~--~~~~Rf~~L  335 (347)
                      +++++++.+. +++.+|++|++|++||++|+||+||+ |++||++.+.|+++|+++..+|++|+..+++  +.+.||++|
T Consensus       113 ~~~~~~~~i~-~~~~~~~~L~ld~~E~alL~AivL~~-d~~~L~~~~~Ve~lq~~~~~aL~~~i~~~~~~~~~~~rf~~L  190 (230)
T d1pdua_         113 SFGEWLNDIM-EFSRSLHNLEIDISAFACLCALTLIT-ERHGLREPKKVEQLQMKIIGSLRDHVTYNAEAQKKQHYFSRL  190 (230)
T ss_dssp             HHTTHHHHHH-HHHHHHHHHCCCHHHHHHHHHHHHSS-CCTTCSCHHHHHHHHHHHHHHHHHHHHHCHHHHTSTTHHHHH
T ss_pred             hHHHHHHHHH-HHHHHHHHcCCCHHHHHHHhhheeec-CcccccCHHHHHHHHHHHHHHHHHHHHHhCCCcchhhHHHHH
Confidence            4566666655 89999999999999999999999995 7899999999999999999999999998877  567899999


Q ss_pred             HhhhhhhhccC
Q psy3092         336 LLRLPSLRSIE  346 (347)
Q Consensus       336 L~ll~~lr~i~  346 (347)
                      |++||.||+|+
T Consensus       191 L~~Lp~LR~l~  201 (230)
T d1pdua_         191 LGKLPELRSLS  201 (230)
T ss_dssp             HTHHHHHHHHH
T ss_pred             HHHhHHHHHHH
Confidence            99999999986

>d1xpca_ a.123.1.1 (A:) Estrogen receptor alpha {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Estrogen receptor alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=1.6e-29  Score=220.25  Aligned_cols=167  Identities=29%  Similarity=0.505  Sum_probs=145.8

Q ss_pred             hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhh-c
Q psy3092         179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHE-A  257 (347)
Q Consensus       179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~-~  257 (347)
                      ...+..+++.+++.++.+|+|+|++|+|..|+.+||+.|||++|.+++++..++++....+.+.+++|..++++.... .
T Consensus        34 ~~~~~~l~~la~~~l~~~V~waK~ip~F~~L~~~DQi~LLk~~~~el~iL~~a~~s~~~~~~l~~~~~~~~~~~~~~~~~  113 (245)
T d1xpca_          34 ASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVE  113 (245)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTSTTEEEEETTEEEEHHHHTTST
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCccHHhcCHHHHHHHHHHHHHHHHHHHHHHHhhccCCceeecCCcccchhHHhhhc
Confidence            345788999999999999999999999999999999999999999999999999999888889999998877665543 3


Q ss_pred             CchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCC--------HHHHHHHHHHHHHHHHHHHHhcCC---
Q psy3092         258 GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKS--------QQVVEMLREKVYTSLEEYTRVNHS---  326 (347)
Q Consensus       258 ~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~--------~~~i~~~r~~~~~~L~~y~~~~~~---  326 (347)
                      ++.++.+.+ .+++.+|++|++|++||++|+||+||+||..++++        ++.|+.+|+++..+|.+|+...+.   
T Consensus       114 ~~~~~~~~~-~~~~~~~~~L~ld~~E~~lLkaI~L~~pd~~~l~~~~r~~l~~~~~v~~~q~~~~~aL~~~~~~~~~~~~  192 (245)
T d1xpca_         114 GMVEIFDML-LATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQ  192 (245)
T ss_dssp             THHHHHHHH-HHHHHHHHHHTCCHHHHHHHHHHHHHHTTTTCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCHH
T ss_pred             cHHHHHHHH-HHHHHHHHHcCCCHHHHHHHHHHHHcCCccccccccchhhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCC
Confidence            455565554 48999999999999999999999999999887753        567889999999999999976543   


Q ss_pred             CCchHHHHHHhhhhhhhccC
Q psy3092         327 EEPGRFAKLLLRLPSLRSIE  346 (347)
Q Consensus       327 ~~~~Rf~~LL~ll~~lr~i~  346 (347)
                      +.+.||++||++||.||+++
T Consensus       193 ~~~~Rf~~LL~~Lp~Lr~~~  212 (245)
T d1xpca_         193 QQHQRLAQLLLILSHIRHMS  212 (245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH
T ss_pred             CcccHHHHHHHHHHHHHHHH
Confidence            45789999999999999875

>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=99.96  E-value=4.7e-29  Score=218.33  Aligned_cols=164  Identities=21%  Similarity=0.375  Sum_probs=140.0

Q ss_pred             HhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccc-cchhhcCch
Q psy3092         182 ATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYR-SSAHEAGVG  260 (347)
Q Consensus       182 ~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~-~~~~~~~~~  260 (347)
                      +..+++.....+..+|+|||++|+|..|+.+||+.|||++|.+++++..++++....+.+.+.++..... ......+..
T Consensus        59 ~~~~~~l~~~~i~~iVefAK~iPgF~~L~~~DQi~LLK~~~~El~ll~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  138 (255)
T d1ie9a_          59 LPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVSDVTKAGHS  138 (255)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHGGGTEETTTTEEECSSGGGEECHHHHHTTTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCcccccCCHHHHHHHHHHHHHHHHHHHHHHheeCCCCeEEeCCCCeeecHHHHHhccch
Confidence            5678888999999999999999999999999999999999999999999987666556666665554443 223333333


Q ss_pred             -hhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCC--CchHHHHHHh
Q psy3092         261 -GIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSE--EPGRFAKLLL  337 (347)
Q Consensus       261 -~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~--~~~Rf~~LL~  337 (347)
                       .+.+.+ .+++.+|++|++|++||+||+||+||+||++|+++...|+++|+++..+|+.|++.++++  .+.||++||+
T Consensus       139 ~~~~~~i-~~f~~~l~~L~ld~~E~~lLkAiiL~~pdr~gL~~~~~Ve~lq~~~~~aL~~y~~~~~~~~~~~~~f~kLL~  217 (255)
T d1ie9a_         139 LELIEPL-IKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLLYAKMIQ  217 (255)
T ss_dssp             HHHHHHH-HHHHHHHHTTCCCHHHHHHHHHHHHSCSCSTTCSCHHHHHHHHHHHHHHHHHHHHHHCCTTTTTTHHHHHHH
T ss_pred             HHHHHHH-HHHHHHHHHhCCCHHHHHHHHHHHhcCCCcccccCHHHHHHHHHHHHHHHHHHHHHhCCCCCcccHHHHHHH
Confidence             455554 489999999999999999999999999999999999999999999999999999999884  5678999999


Q ss_pred             hhhhhhccC
Q psy3092         338 RLPSLRSIE  346 (347)
Q Consensus       338 ll~~lr~i~  346 (347)
                      +||.||+|+
T Consensus       218 ~L~~LR~l~  226 (255)
T d1ie9a_         218 KLADLRSLN  226 (255)
T ss_dssp             HHHHHHHHH
T ss_pred             HhHHHHHHH
Confidence            999999886

>d1t7ra_ a.123.1.1 (A:) Androgen receptor {Chimpanzee (Pan troglodytes) [TaxId: 9598]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Androgen receptor
species: Chimpanzee (Pan troglodytes) [TaxId: 9598]

Probab=99.96  E-value=2.2e-29  Score=219.89  Aligned_cols=169  Identities=22%  Similarity=0.401  Sum_probs=145.0

Q ss_pred             chhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCc--eEecCCccccccch
Q psy3092         177 VNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDG--ILLAPGVTVYRSSA  254 (347)
Q Consensus       177 ~~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~--~~~~~g~~i~~~~~  254 (347)
                      .+......++++.+++++.+|+|+|++|+|..|+.+||+.|+|++|.+++++..++++....+.  +.+.++........
T Consensus        28 ~~~~~l~~l~~~a~~~L~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~rs~~~~~~~~l~~~~~~~~~~~~~  107 (250)
T d1t7ra_          28 SFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRM  107 (250)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHhCccHHHhhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCCcccCHHHH
Confidence            3445568899999999999999999999999999999999999999999999999998765433  45566666655555


Q ss_pred             hhcCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCC-CCCCCHHHHHHHHHHHHHHHHHHHHhcCCC---Cch
Q psy3092         255 HEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDV-RGLKSQQVVEMLREKVYTSLEEYTRVNHSE---EPG  330 (347)
Q Consensus       255 ~~~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~-~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~---~~~  330 (347)
                      ...+...+++++. +++.+|++|++|++||++||||+||||+. +++++...|+.+|+++..+|..|+...+++   ++.
T Consensus       108 ~~~~~~~~~~~~~-~~~~~~~~L~ld~~E~~lLkaIvL~npd~~~~l~~~~~i~~lq~~~~~aL~~y~~~~~~~~~~~p~  186 (250)
T d1t7ra_         108 HKSRMYSQCVRMR-HLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFFDELRMNYIKELDRIIACKRKNPTSCSR  186 (250)
T ss_dssp             HHTTCHHHHHHHH-HHHHHHHHTTCCHHHHHHHHHHHHTSEEETTCCTTHHHHHHHHHHHHHHHHHHHHTTCCSHHHHHH
T ss_pred             hhchhHHHHHHHH-HHHHHHHHcCCCHHHHHHHHHHHhcCCccccCCccHHHHHHHHHHHHHHHHHHHHHhCCCCcchhh
Confidence            5555556666644 79999999999999999999999999875 789999999999999999999999987773   567


Q ss_pred             HHHHHHhhhhhhhccC
Q psy3092         331 RFAKLLLRLPSLRSIE  346 (347)
Q Consensus       331 Rf~~LL~ll~~lr~i~  346 (347)
                      ||++||++||+||+++
T Consensus       187 Rf~~LL~~Lp~lr~l~  202 (250)
T d1t7ra_         187 RFYQLTKLLDSVQPIA  202 (250)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            9999999999999875

>d2p54a1 a.123.1.1 (A:202-468) Peroxisome proliferator activated receptor alpha, PPAR-alpha {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Peroxisome proliferator activated receptor alpha, PPAR-alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=3.7e-29  Score=219.29  Aligned_cols=191  Identities=23%  Similarity=0.282  Sum_probs=146.1

Q ss_pred             cHHHHHHHHHhccCCCCCCc-cccchhHHHhhhh-HHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhh
Q psy3092         154 PVERILEAEQRVDMKQEPAD-QDIVNEQQATNIC-KATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFS  231 (347)
Q Consensus       154 ~~~~l~~~~~~~~~~~~~~~-~~~~~~~~~~~~~-~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a  231 (347)
                      .++.+.+++..+........ .....+......| ...+..+..+|+|||.+|+|.+|+.+||+.|||++|.+++++..+
T Consensus        42 ~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~iVewAK~iPgF~~L~~~DQi~LLK~~~~Ellil~~a  121 (267)
T d2p54a1          42 DMETLCMAEKTLVAKLVANGIQNKEAEVRIFHCCQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLS  121 (267)
T ss_dssp             SHHHHHHHHHHHSGGGGSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHG
T ss_pred             chHHHHHhhhhhhhhhcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHhhCcChhhCCHHHHHHHHHHHHHHHHHHHHH
Confidence            35788888876544322211 1112222333444 345677899999999999999999999999999999999999999


Q ss_pred             cccccCCCceEecCCccccccch--hhcCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHH
Q psy3092         232 HRSISVKDGILLAPGVTVYRSSA--HEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEML  309 (347)
Q Consensus       232 ~~s~~~~~~~~~~~g~~i~~~~~--~~~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~  309 (347)
                      +++....+ .+...+..+..+..  ...++..+.+. +.+++.+|++|++|++||+||+||+||+||++|+.+...|+++
T Consensus       122 ~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~L~ld~~E~alLkAIvLf~pd~~gL~~~~~Ve~l  199 (267)
T d2p54a1         122 SVMNKDGM-LVAYGNGFITREFLKSLRKPFCDIMEP-KFDFAMKFNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKM  199 (267)
T ss_dssp             GGEETTEE-EETTTTEEEEHHHHHHSCTTGGGTSHH-HHHHHHHHHTTCCCHHHHHHHHHHHHSCTTCTTCSCHHHHHHH
T ss_pred             HhccCCCC-EEEeCCCccchHHHHHhcchHHHHHHH-HHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcccHHHHHHH
Confidence            87654322 22222222222221  12334445544 4589999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhcCCCCchHHHHHHhhhhhhhccC
Q psy3092         310 REKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIE  346 (347)
Q Consensus       310 r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll~~lr~i~  346 (347)
                      |+++..+|+.|+..++++.+.||++||++||.||+|+
T Consensus       200 Qe~~~~aL~~y~~~~~p~~~~rf~kLL~~Lp~LR~l~  236 (267)
T d2p54a1         200 QEGIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQLV  236 (267)
T ss_dssp             HHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCCChhhHHHHHHHHhHHHHHHH
Confidence            9999999999999999999999999999999999885

>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=99.96  E-value=1.4e-28  Score=214.96  Aligned_cols=164  Identities=21%  Similarity=0.310  Sum_probs=147.5

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV  259 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~  259 (347)
                      ..+..+.+.....+..+|+|||.+|+|..|+.+||+.|||++|.+++++..++++ ...+..++.+|.++.++.....+.
T Consensus        58 ~~~~~~~~~~~~~i~~vV~faK~iPgF~~L~~~DQi~LLk~~~~el~ll~~a~~~-~~~~~~~~~~~~~~~~~~~~~~~~  136 (251)
T d1n83a_          58 VMWQLCAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAF-DSQNNTVYFDGKYASPDVFKSLGC  136 (251)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHSTTTTTSCHHHHHHHHHHHHHHHHHHHGGGGE-ETTTTEEEETTEEECGGGGGGGSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHh-CCCCCEEecCCeeecHHHHhhccH
Confidence            3466777788889999999999999999999999999999999999999998765 455677888898888887777777


Q ss_pred             hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhh
Q psy3092         260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRL  339 (347)
Q Consensus       260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll  339 (347)
                      +++.+.+. +++..|++|++|++||++|+||+||+||++||++.+.|+++|+++..+|+.|+..+++ ++.||++||++|
T Consensus       137 ~~~~~~~~-~~~~~~~~L~ld~~E~alL~AivL~~pd~~gL~~~~~Ve~lq~~~~~aL~~~~~~~~~-~~~rf~~Ll~~L  214 (251)
T d1n83a_         137 EDFISFVF-EFGKSLCSMHLTEDEIALFSAFVLMSADRSWLQEKVKIEKLQQKIQLALQHVLQKNHR-EDGILTKLICKV  214 (251)
T ss_dssp             HHHHHHHH-HHHHHHHTTCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCT-TSCHHHHHHHHH
T ss_pred             HHHHHHHH-HHHHHHHHcCCCHHHHHHHHHHHHHccCccccCCHHHHHHHHHHHHHHHHHHHHhcCC-CccHHHHHHHHh
Confidence            77777655 7999999999999999999999999999999999999999999999999999998877 468999999999


Q ss_pred             hhhhccC
Q psy3092         340 PSLRSIE  346 (347)
Q Consensus       340 ~~lr~i~  346 (347)
                      |.||+|+
T Consensus       215 p~LR~l~  221 (251)
T d1n83a_         215 STLRALC  221 (251)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9999875

>d1sqna_ a.123.1.1 (A:) Progesterone receptor {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Progesterone receptor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=2.2e-29  Score=219.90  Aligned_cols=169  Identities=21%  Similarity=0.411  Sum_probs=142.1

Q ss_pred             chhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCC--CceEecCCccccccch
Q psy3092         177 VNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVK--DGILLAPGVTVYRSSA  254 (347)
Q Consensus       177 ~~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~--~~~~~~~g~~i~~~~~  254 (347)
                      .....+..++++.+++++.+|+|+|++|+|.+|+.+||+.|+|++|.+++++..|+++....  +.+.+.+|........
T Consensus        29 ~~~~~~~~l~~la~r~L~~~VewaK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~rs~~~~~~~~l~~~~~~~~~~~~~  108 (251)
T d1sqna_          29 TSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRM  108 (251)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECGGGC
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHhccchhhcCHHHHHHHHHHHHHHHHHHHHHHHhhhccCcceeeccCCceecHHhh
Confidence            34456888999999999999999999999999999999999999999999999999987653  3445555655555444


Q ss_pred             hhcCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCC-CCCCCCHHHHHHHHHHHHHHHHHHHHhcCCC---Cch
Q psy3092         255 HEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD-VRGLKSQQVVEMLREKVYTSLEEYTRVNHSE---EPG  330 (347)
Q Consensus       255 ~~~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~-~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~---~~~  330 (347)
                      ...+...+.+. +.+++.+|++|++|++||++|+||++|||| .+++++...|+++|+++.++|++|+..++++   ++.
T Consensus       109 ~~~~~~~~~~~-~~~~~~~l~~L~ld~~E~~lLkAIiL~npd~~~~l~~~~~V~~lq~~~~~aL~~~~~~~~~~~~~~~~  187 (251)
T d1sqna_         109 KESSFYSLCLT-MWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSSSQ  187 (251)
T ss_dssp             CSHHHHHHHHH-HHHHHHHHHHHTCCHHHHHHHHHHHHTSEECTTCCTTHHHHHHHHHHHHHHHHHHHHTTC-CHHHHHH
T ss_pred             ccccHHHHHHH-HHHHHHHHHHcCCCHHHHHHHHHHHHcCCccccCCcCHHHHHHHHHHHHHHHHHHHHHhCCCCCcHHH
Confidence            33334444444 458999999999999999999999999996 7889999999999999999999999887654   568


Q ss_pred             HHHHHHhhhhhhhccC
Q psy3092         331 RFAKLLLRLPSLRSIE  346 (347)
Q Consensus       331 Rf~~LL~ll~~lr~i~  346 (347)
                      ||++||++||+||+++
T Consensus       188 Rf~~LL~lLp~lR~l~  203 (251)
T d1sqna_         188 RFYQLTKLLDNLHDLV  203 (251)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            9999999999999875

>d1nhza_ a.123.1.1 (A:) Glucocorticoid receptor {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Glucocorticoid receptor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=9.6e-29  Score=215.53  Aligned_cols=168  Identities=23%  Similarity=0.352  Sum_probs=144.1

Q ss_pred             hhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCC--CceEecCCccccccchh
Q psy3092         178 NEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVK--DGILLAPGVTVYRSSAH  255 (347)
Q Consensus       178 ~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~--~~~~~~~g~~i~~~~~~  255 (347)
                      +......++++.+++++.+|+|+|++|+|..|+.+||+.|+|++|.+++++..||+++..+  +.+.+.++.........
T Consensus        27 ~~~~~~~l~~la~r~L~~~IewaK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~s~~~~~~~~~~~~~~~~~~~~~~~  106 (247)
T d1nhza_          27 TWRIMTTLNMLGGRQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMSLMAFALGWRSYRQSSANLLCFAPDLIINEQRMT  106 (247)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECTTGGG
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhcccHhhcCHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCeEeccccceecHHhhc
Confidence            4455688999999999999999999999999999999999999999999999999986543  33455667666665555


Q ss_pred             hcCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCC-CCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCC---chH
Q psy3092         256 EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD-VRGLKSQQVVEMLREKVYTSLEEYTRVNHSEE---PGR  331 (347)
Q Consensus       256 ~~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~-~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~---~~R  331 (347)
                      ..+...+.+. +.+++.+|++|++|++||++|+||+||||| +.++.+.+.|+++|+++..+|.+|+..++++.   +.|
T Consensus       107 ~~~~~~~~~~-~~~~~~~l~~L~l~~~E~~lLkaIvLfnpd~~~~l~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~~~~R  185 (247)
T d1nhza_         107 LPDMYDQCKH-MLYVSSELHRLQVSYEEYLCMKTLLLLSSVPKDGLKSQELFDEIRMTYIKELGKAIVKREGNSSQNWQR  185 (247)
T ss_dssp             STTHHHHHHH-HHHHHHHHHHTTCCHHHHHHHHHHHHTSEEETTCCTTHHHHHHHHHHHHHHHHHHHHHHCCSTHHHHHH
T ss_pred             cccHHHHHHH-HHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCcccccHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHH
Confidence            4444455544 448999999999999999999999999999 67899999999999999999999999888754   459


Q ss_pred             HHHHHhhhhhhhccC
Q psy3092         332 FAKLLLRLPSLRSIE  346 (347)
Q Consensus       332 f~~LL~ll~~lr~i~  346 (347)
                      |++||++||.||.++
T Consensus       186 f~~LL~~Lp~lR~~~  200 (247)
T d1nhza_         186 FYQLTKLLDSMHEVV  200 (247)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999999875

>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=99.96  E-value=7.2e-29  Score=214.26  Aligned_cols=164  Identities=25%  Similarity=0.455  Sum_probs=145.9

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV  259 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~  259 (347)
                      ..+..+.+.....+..+++|||.+|+|..|+.+||+.|||++|.++++++.++++...++.+++.+|..+.++... .++
T Consensus        39 ~~~~~~~~~~~~~i~~iv~wAK~iPgF~~L~~~DQi~LLk~~~~el~lL~~a~~~~~~~~~l~~~~~~~~~~~~~~-~~~  117 (233)
T d2qw4a1          39 GDVQQFYDLLSGSLEVIRKWAEKIPGFAELSPADQDLLLESAFLELFILRLAYRSKPGEGKLIFCSGLVLHRLQCA-RGF  117 (233)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTSTTTTTSCHHHHHHHHHHHHHHHHHHHHHHHSBGGGTEEECTTSCEEEHHHHH-HHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhCCCCCCceeecCCeeecHHhhh-hhh
Confidence            4567788888899999999999999999999999999999999999999999999888899999999888776553 345


Q ss_pred             hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhc--CCCCchHHHHHHh
Q psy3092         260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVN--HSEEPGRFAKLLL  337 (347)
Q Consensus       260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~--~~~~~~Rf~~LL~  337 (347)
                      +.+++.+. +++.+|++|++|++||++|+||+||+ |++||++...|+++|+++..+|++|+..+  +++.+.||++||+
T Consensus       118 ~~~~~~i~-~~~~~l~~L~ld~~E~alLkAivL~~-d~~gL~~~~~Ve~lq~~~~~aL~~yi~~~~~~~~~~~rf~kLL~  195 (233)
T d2qw4a1         118 GDWIDSIL-AFSRSLHSLLVDVPAFACLSALVLIT-DRHGLQEPRRVEELQNRIASCLKEHVAAVAGEPQPASCLSRLLG  195 (233)
T ss_dssp             TTHHHHHH-HHHHHHHHHTCCHHHHHHHHHHHHSS-CCTTCSCHHHHHHHHHHHHHHHHHHHHHSCC---CCTTHHHHHT
T ss_pred             HHHHHHHH-HHHHHHHHcCCCHHHHHHHHHHHhcC-cccCccCHHHHHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHH
Confidence            66666554 89999999999999999999999998 78999999999999999999999999765  4578999999999


Q ss_pred             hhhhhhccC
Q psy3092         338 RLPSLRSIE  346 (347)
Q Consensus       338 ll~~lr~i~  346 (347)
                      +||.||+|+
T Consensus       196 ~Lp~LR~l~  204 (233)
T d2qw4a1         196 KLPELRTLC  204 (233)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999999986

>d2j7ya1 a.123.1.1 (A:217-452) Estrogen receptor beta {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Estrogen receptor beta
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.96  E-value=8.5e-28  Score=208.34  Aligned_cols=166  Identities=31%  Similarity=0.504  Sum_probs=143.5

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhc-C
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEA-G  258 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~-~  258 (347)
                      ..+..+++..++.++.+|+|+|++|+|..|+.+||+.|+|++|.+++++..+++++..++.+++.+|....++..... +
T Consensus        32 ~~~~~l~~~a~~~l~~~V~waK~lp~F~~L~~~DQi~LLk~~~~el~~L~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~  111 (236)
T d2j7ya1          32 SMMMSLTKLADKELVHMIGWAKKIPGFVELSLLDQVRLLESCWMEVLMVGLMWRSIDHPGKLIFAPDLVLDRDEGKCVEG  111 (236)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTSTTEEEEETTEEEEGGGGGGSTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCchHHHhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcEEecCCcccCHHHHHHHhh
Confidence            446788899999999999999999999999999999999999999999999999999999999999988877665433 4


Q ss_pred             chhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCC-------HHHHHHHHHHHHHHHHHHHHhcCC---CC
Q psy3092         259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKS-------QQVVEMLREKVYTSLEEYTRVNHS---EE  328 (347)
Q Consensus       259 ~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~-------~~~i~~~r~~~~~~L~~y~~~~~~---~~  328 (347)
                      +.++.+. +.+++.+|++|++|++||++|+||+|||||.+++++       .+.+..+++++..+|..|+..++.   +.
T Consensus       112 ~~~~~~~-i~~~~~~l~~L~ld~~E~~lLkaIvLf~pd~~~l~~~~~~~~~~~~v~~~~~~~~~~l~~~~~~~~~~~p~~  190 (236)
T d2j7ya1         112 ILEIFDM-LLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLASANQEAESSRKLTHLLNAVTDALVWVIAKSGISSQQQ  190 (236)
T ss_dssp             HHHHHHH-HHHHHHHHHHHTCCHHHHHHHHHHHHTTTTCCCCC------HHHHHHHHHHHHHHHHHHHHHHHTCCCHHHH
T ss_pred             HHHHHHH-HHHHHHHHHHcCCCHHHHHHHHHHHHhCCcCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcch
Confidence            5555555 458999999999999999999999999999999875       345667788888899998876553   45


Q ss_pred             chHHHHHHhhhhhhhccC
Q psy3092         329 PGRFAKLLLRLPSLRSIE  346 (347)
Q Consensus       329 ~~Rf~~LL~ll~~lr~i~  346 (347)
                      +.||++||++||.||+|+
T Consensus       191 ~~Rf~~LL~~Lp~Lr~l~  208 (236)
T d2j7ya1         191 SVRLANLLMLLSHVRHIS  208 (236)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHH
Confidence            789999999999999885

>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=99.96  E-value=4.4e-28  Score=212.38  Aligned_cols=189  Identities=26%  Similarity=0.344  Sum_probs=151.1

Q ss_pred             HHHHHHHHHhccCCCCCCccccch---hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhh
Q psy3092         155 VERILEAEQRVDMKQEPADQDIVN---EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFS  231 (347)
Q Consensus       155 ~~~l~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a  231 (347)
                      .+.+.+++.....+......+...   ...+..........+..+|+|||.+|+|.+|+.+||+.|||++|.+++++..+
T Consensus        42 m~~~~~ae~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~I~~iVefAK~iPgF~~L~~~DQi~LLK~~~~Ellil~~a  121 (265)
T d2b50b1          42 IETLWQAEKGLVWKQLVNGLPPYKEISVHVFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLA  121 (265)
T ss_dssp             HHHHHHHHTTTSCC-----CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHTSHHHHTSCHHHHHHHHHHHHHHHHHHHHG
T ss_pred             cccHHHhHHHHHHhcCCCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHhcCcChhhCCHHHHHHHHHHHHHHHHHHHHH
Confidence            478888887665443222211111   12234455566778889999999999999999999999999999999999998


Q ss_pred             cccccCCCceEecCCccccccchhhcC---chhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHH
Q psy3092         232 HRSISVKDGILLAPGVTVYRSSAHEAG---VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEM  308 (347)
Q Consensus       232 ~~s~~~~~~~~~~~g~~i~~~~~~~~~---~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~  308 (347)
                      ++.  ..++..+.+|..+.........   +..+. +.+.+++.+|++|++|++||++|+||+||+||++|+++.+.|++
T Consensus       122 ~~~--~~d~~~~~~g~~~~~~~~~~~~~~~~~~~~-~~~~~f~~~~~~L~ld~~E~alLkAiiL~~pd~~~L~~~~~Ve~  198 (265)
T d2b50b1         122 SIV--NKDGLLVANGSGFVTREFLRSLRKPFSDII-EPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEA  198 (265)
T ss_dssp             GGE--ETTEEEETTTTEEEEHHHHHTSCHHHHHHH-HHHHHHHHHHHTTCCCHHHHHHHHHHHHSCTTCTTCSCHHHHHH
T ss_pred             HHh--CCCCceEeCCcccccHHHHHHhhhhHHHHH-HHHHHHHHHHHHhCCCHHHHHHHHHHhhcccCccccccHHHHHH
Confidence            875  3577888888776654433221   22233 44568999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhcCCCCchHHHHHHhhhhhhhccC
Q psy3092         309 LREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIE  346 (347)
Q Consensus       309 ~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll~~lr~i~  346 (347)
                      +|+++..+|++|+..++++.+.||++||++||.||+|+
T Consensus       199 lQ~~~~~aL~~y~~~~~p~~~~rfakLL~~L~~LR~ls  236 (265)
T d2b50b1         199 IQDTILRALEFHLQANHPDAQQLFPKLLQKMADLRQLV  236 (265)
T ss_dssp             HHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCChhhHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999885

>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=99.96  E-value=3.2e-28  Score=211.88  Aligned_cols=164  Identities=20%  Similarity=0.352  Sum_probs=145.4

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092         180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV  259 (347)
Q Consensus       180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~  259 (347)
                      ..+..+.+.....+..+|+|||++|+|..|+.+||+.|||++|.+++++..++++...++ .++.+|.++..+.....+.
T Consensus        50 ~~~~~~~~~~~~~i~~vV~faK~lP~F~~L~~~DQi~LLk~~~~el~~l~~a~~~~~~~~-~~~~~~~~~~~~~~~~~~~  128 (244)
T d1nq7a_          50 ALWQQCAIQITHAIQYVVEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPLNN-TVLFEGKYGGMQMFKALGS  128 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCHHHHTSCHHHHHHHHHHHHHHHHHHHHGGGEETTTT-EEEETTEEEEGGGGGGGSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHccCCCC-eEeeCCccccHHHHhhccc
Confidence            457778888899999999999999999999999999999999999999999988755554 4555666777777666666


Q ss_pred             hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhh
Q psy3092         260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRL  339 (347)
Q Consensus       260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll  339 (347)
                      .++.+.+. +++.+|++|++|++||++|+||+||+||++|+++...|+++|+++..+|++|+..++++ +.||++||++|
T Consensus       129 ~~~~~~~~-~~~~~~~~L~l~~~E~all~AivL~~pd~~~l~~~~~Ve~lq~~~~~aL~~~~~~~~~~-~~rf~~LL~~L  206 (244)
T d1nq7a_         129 DDLVNEAF-DFAKNLCSLQLTEEEIALFSSAVLISPDRAWLLEPRKVQKLQEKIYFALQHVIQKNHLD-DETLAKLIAKI  206 (244)
T ss_dssp             HHHHHHHH-HHHHHHHTTCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCSC-TTHHHHHHHTH
T ss_pred             HHHHHHHH-HHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCcccHHHHHHHHHHHHHHHHHHHHhcCCC-chHHHHHHHHh
Confidence            77776654 89999999999999999999999999999999999999999999999999999999985 46999999999


Q ss_pred             hhhhccC
Q psy3092         340 PSLRSIE  346 (347)
Q Consensus       340 ~~lr~i~  346 (347)
                      |.||+|+
T Consensus       207 p~LR~l~  213 (244)
T d1nq7a_         207 PTITAVC  213 (244)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9999885

>d2fvja1 a.123.1.1 (A:207-477) Peroxisome proliferator activated receptor gamma, PPAR-gamma {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Peroxisome proliferator activated receptor gamma, PPAR-gamma
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=1.9e-28  Score=215.57  Aligned_cols=189  Identities=24%  Similarity=0.402  Sum_probs=147.6

Q ss_pred             HHHHHHHHHhccCCCCCCccc---cchhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhh
Q psy3092         155 VERILEAEQRVDMKQEPADQD---IVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFS  231 (347)
Q Consensus       155 ~~~l~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a  231 (347)
                      .+.+..++..+..+.......   ......+..++......+..+|+|||.+|+|..|+.+||+.|||++|.+++++..+
T Consensus        46 ~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~vVefAK~iP~F~~L~~~DQi~LLK~~~~ElllL~~a  125 (271)
T d2fvja1          46 MNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLA  125 (271)
T ss_dssp             HHHHHHHHHC-------------CCHHHHHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHhhhhhhcccccCCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCcChhhCCHHHHHHHHHHHHHHHHHHHHH
Confidence            577777776654432211111   11123466667778889999999999999999999999999999999999999999


Q ss_pred             cccccCCCceEecCCccccccchhh---cCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHH
Q psy3092         232 HRSISVKDGILLAPGVTVYRSSAHE---AGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEM  308 (347)
Q Consensus       232 ~~s~~~~~~~~~~~g~~i~~~~~~~---~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~  308 (347)
                      +++.  .++..+.+|..+.......   .....+.+ .+.+++.+|++|++|++||++|+||+|||||++|+.+...|++
T Consensus       126 ~~~~--~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~-~i~~f~~~~~~L~ld~~E~alLkAIvLf~pd~~gL~~~~~Ve~  202 (271)
T d2fvja1         126 SLMN--KDGVLISEGQGFMTREFLKSLRKPFGDFME-PKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIED  202 (271)
T ss_dssp             TTEE--TTEEEETTTTEEEEHHHHHTSCTTGGGSSH-HHHHHHHHHHTTCCCHHHHHHHHHHHHTCTTSTTCSCHHHHHH
T ss_pred             HHcC--CCCCeeeCCCccchHHHHHHhhhhHHHHHH-HHHHHHHHHHHhCCCHHHHHHHHHHHHHcccccCCccHHHHHH
Confidence            8753  4556666665444332221   22334444 4558999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhcCCCCchHHHHHHhhhhhhhccC
Q psy3092         309 LREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRSIE  346 (347)
Q Consensus       309 ~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll~~lr~i~  346 (347)
                      +|+++..+|++|+..++++.+.||++||++||.||+|+
T Consensus       203 lQ~~~~~aL~~y~~~~~p~~~~rf~kLL~~Lp~LR~l~  240 (271)
T d2fvja1         203 IQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIV  240 (271)
T ss_dssp             HHHHHHHHHHHHHHHHSTTSTTHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCCchhHHHHHHHHhHHHHHHH
Confidence            99999999999999999999999999999999999875

>d1nrla_ a.123.1.1 (A:) Pregnane x receptor, PXR {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Pregnane x receptor, PXR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=7.6e-28  Score=214.84  Aligned_cols=163  Identities=23%  Similarity=0.352  Sum_probs=136.2

Q ss_pred             HhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCchh
Q psy3092         182 ATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGG  261 (347)
Q Consensus       182 ~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~~~  261 (347)
                      +..+.+.....+..+|+|||.+|+|..|+.+||+.|||++|.+++++.+++++... +..++.++..+..+.... +...
T Consensus        99 l~~~~~~~~~~i~~iV~fAK~iP~F~~L~~~DQi~LLk~~~~el~~l~~a~~~~~~-~~~~~~~~~~~~~~~~~~-~~~~  176 (292)
T d1nrla_          99 LPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAE-TGTWECGRLSYCLEDTAG-GFQQ  176 (292)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHCHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTEETT-TTEEEETTEEEEECCCSS-CHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCcCHhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCC-CCeeeCCCccccHHHhhh-hhHH
Confidence            45667777888999999999999999999999999999999999999999876443 344555554444444322 2222


Q ss_pred             hHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCc--hHHHHHHhhh
Q psy3092         262 IFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEP--GRFAKLLLRL  339 (347)
Q Consensus       262 ~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~--~Rf~~LL~ll  339 (347)
                      .+.+.+.+++.+|++|++|++||+||+||+||+||++||++...|+++|+++..+|+.|+..++++.+  .||++||++|
T Consensus       177 ~~~~~~~~~~~~l~~L~ld~~E~~lLkAi~L~~pd~~gL~~~~~Ve~lq~~~~~aL~~y~~~~~p~~~~~~~f~kLL~~l  256 (292)
T d1nrla_         177 LLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLKIMAML  256 (292)
T ss_dssp             HTTSHHHHHHHHHHHTCCCHHHHHHHHHHHHTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCCSGGGTTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHhCCCCchhhHHHHHHHHH
Confidence            33345568999999999999999999999999999999999999999999999999999999998654  4799999999


Q ss_pred             hhhhccC
Q psy3092         340 PSLRSIE  346 (347)
Q Consensus       340 ~~lr~i~  346 (347)
                      |.||+|+
T Consensus       257 ~~LR~l~  263 (292)
T d1nrla_         257 TELRSIN  263 (292)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9999885

>d1we9a_ g.50.1.2 (A:) PHD finger protein At5g26210 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein At5g26210
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=85.67  E-value=0.097  Score=33.04  Aligned_cols=52  Identities=17%  Similarity=0.508  Sum_probs=32.6

Q ss_pred             CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhH
Q psy3092          56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQ  116 (347)
Q Consensus        56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~  116 (347)
                      ..|.||++....-++ .+.|..|..+|...-..        -..=.+.....+.|..|+-+
T Consensus         7 ~~C~~C~~~~~~~~~-~I~Cd~C~~w~H~~C~~--------~~~~~~~~~~~w~C~~C~~~   58 (64)
T d1we9a_           7 GQCGACGESYAADEF-WICCDLCEMWFHGKCVK--------ITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             CCCSSSCCCCCSSSC-EEECSSSCCEEETTTTT--------CCTTGGGGCSSCCCHHHHTT
T ss_pred             CcCcCcCCCCCCCCC-EEEcCCCCccCCcccCC--------cChHHCCCCCeEECcCCcCc
Confidence            359999987544432 46899999888765332        11112222345899999854