Psyllid ID: psy2636

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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-----
Protein Sequence
TQLGRSSSSESPKLRHSAPLSSASSSPGCDTSRPTPPSPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEcccEEEcccccccccccccccccHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccEEEEcccEEEHHHHHHHHcHHHHHHHHHHHHHcccccccHHHHHHHHHHHHc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccEccccccEcccEccccEccHHHHHHHHHHHHcccccccccccccccccccccccHHHHHHHHHHHccccccccccHcccHHHHHHcccccccccccccccHcccHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccHHHccHHHHHHHHHHHHHHHHEcccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccHHHccHHHHHHHHHHHHHHHHHHHHHHHccccccEEEccccEEEEHHHHHHHHcccHHHHHHHHHHHHHHHcccHHHHHHHHHHHHc
Coil and Loop (DISEMBL)
tqlgrssssespklrhsaplssassspgcdtsrptppspsqlcavcgdiaacqhygvrtcegckgffkrtvqkgskyvcladkacpvdkrrrnrcqfcrfqkclQVGMVKEvvrtdslkgrrgrlpskpkspqesppsppvslitalyrepnpleppiaepeKIQQFYSLLTTSVDVIRHFadkipgfsdlCKEDQELLFQSASLelfyrepnpleppiaepeKIQQFYSLLTTSVDVIRHFadkipgfsdlCKEDQELLFQSASLELFVLRLAYRtraedtklifcNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI
Flexible Loop (DISEMBL)
tqlgrssssespklrhsaplssassspgcDTSRPTPPSPSQLCAVCGDIAACQHYGVRTCEGCKGFFKrtvqkgskyvcladkacpvdkrrrnRCQFCrfqkclqvgmvkevvrtdslkgrrgrlpskpkspqesppspPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI
Low Complexity Region (SEG)
TQLGRSSSSESPKLRHsaplssassspGCDTSRPTPPSPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDkrrrnrcqfcrfqkCLQVGMVKEVVRTDSLKGRRGRLpskpkspqesppsppvsLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI
Disordered region (IsUnstruct)
*****************************************LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVR************************************************KIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFYRE***********EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTL*
Disordered Region (DISOPRED)
*******************************************AVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKE******************************************************************IRHFADKIPGFSDLCKEDQELLFQSASL******************KIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI
Disordered Region (DISEMBL)
***************************************SQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLK*********************VSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI
Disordered Region (DISPRO)
***************************************SQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRT*************************************PLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
TQLGRSSSSESPKLRHSAPLSSASSSPGCDTSRPTPPSPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI
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	335	2.2.26 [Sep-21-2011]
P49870	360	Probable nuclear hormone	N/A	N/A	0.802	0.747	0.641	1e-107
P49869	1073	Probable nuclear hormone	yes	N/A	0.743	0.232	0.667	2e-96
Q04913	577	Nuclear receptor subfamil	N/A	N/A	0.758	0.440	0.544	8e-83
Q0V8F0	598	Nuclear receptor subfamil	yes	N/A	0.791	0.443	0.524	2e-82
P12813	601	Nuclear receptor subfamil	yes	N/A	0.734	0.409	0.552	7e-82
P51666	598	Nuclear receptor subfamil	yes	N/A	0.856	0.479	0.510	4e-81
P22829	597	Nuclear receptor subfamil	yes	N/A	0.844	0.474	0.504	5e-81
P22736	598	Nuclear receptor subfamil	yes	N/A	0.823	0.461	0.516	1e-80
Q92570	626	Nuclear receptor subfamil	no	N/A	0.743	0.397	0.527	3e-78
Q9QZB6	627	Nuclear receptor subfamil	no	N/A	0.743	0.397	0.527	7e-78

>sp|P49870|HR38_BOMMO Probable nuclear hormone receptor HR38 (Fragment) OS=Bombyx mori GN=HR38 PE=2 SV=1

 Score =  390 bits (1001), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 204/318 (64%), Positives = 230/318 (72%), Gaps = 49/318 (15%)

Query: 23  ASSSPGCDTS-----RPTPPSPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKY 77
            SSSPG   +     R  P SPSQLCAVCGD AACQHYGVRTCEGCKGFFKRTVQKGSKY
Sbjct: 1   GSSSPGVAPADNTGPRAAPSSPSQLCAVCGDTAACQHYGVRTCEGCKGFFKRTVQKGSKY 60

Query: 78  VCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPP 137
           VCLA+K+CPVDKRRRNRCQFC FQKCL VGMVKEVVRTDSLKGRRGRLPSKPK PQESPP
Sbjct: 61  VCLAEKSCPVDKRRRNRCQFCWFQKCLAVGMVKEVVRTDSLKGRRGRLPSKPKCPQESPP 120

Query: 138 SPPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQE 197
           SPP+SLITAL                              +R   D  P F++L      
Sbjct: 121 SPPISLITAL------------------------------VRAHVDTSPDFANLDYSQ-- 148

Query: 198 LLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQ 257
                      YREP+PLEPP+++ E IQQFYSLLTTS+D+I+ FA+K+PG+ DLC ED+
Sbjct: 149 -----------YREPSPLEPPMSDLEVIQQFYSLLTTSIDMIKLFAEKVPGYGDLCPEDR 197

Query: 258 ELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLH 317
           E LF SA LELFVLRLAYRT  EDTKL F NG VL+K+QCQRSFG DWL+A+L+F  + +
Sbjct: 198 EQLFASARLELFVLRLAYRTALEDTKLTFSNGSVLDKRQCQRSFG-DWLHAVLDFSNTSY 256

Query: 318 LMEIDISAFACLCALTLI 335
            M+IDIS FACLCALTLI
Sbjct: 257 SMDIDISTFACLCALTLI 274

Bombyx mori (taxid: 7091)

>sp|P49869|HR38_DROME Probable nuclear hormone receptor HR38 OS=Drosophila melanogaster GN=Hr38 PE=1 SV=3

 Score =  352 bits (904), Expect = 2e-96,   Method: Compositional matrix adjust.
 Identities = 199/298 (66%), Positives = 216/298 (72%), Gaps = 49/298 (16%)

Query: 38  SPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQF 97
           +PSQLCAVCGD AACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADK CPVDKRRRNRCQF
Sbjct: 739 APSQLCAVCGDTAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKNCPVDKRRRNRCQF 798

Query: 98  CRFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVSLITALYREPNPLEPP 157
           CRFQKCL VGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPP+SLITAL          
Sbjct: 799 CRFQKCLVVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPISLITAL---------- 848

Query: 158 IAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFYREPNPLEP 217
                               +R   D  P  S L     E                  E 
Sbjct: 849 --------------------VRSHVDTTPDPSCLDYSHYE------------------EQ 870

Query: 218 PIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRT 277
            ++E +K+QQFY LLT+SVDVI+ FA+KIPG+ DL  EDQELLFQSASLELFVLRLAYR 
Sbjct: 871 SMSEADKVQQFYQLLTSSVDVIKQFAEKIPGYFDLLPEDQELLFQSASLELFVLRLAYRA 930

Query: 278 RAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
           R +DTKLIFCNG VL + QC RSFG +WLN I+EF +SLH +EIDISAFACLCALTLI
Sbjct: 931 RIDDTKLIFCNGTVLHRTQCLRSFG-EWLNDIMEFSRSLHNLEIDISAFACLCALTLI 987

Binds to NGFI-B response elements. Plays an important role in late stages of epidermal metamorphosis.

Drosophila melanogaster (taxid: 7227)

>sp|Q04913|NR4A1_XENLA Nuclear receptor subfamily 4 group A member 1 OS=Xenopus laevis GN=nr4a1 PE=2 SV=1

 Score =  307 bits (786), Expect = 8e-83,   Method: Compositional matrix adjust.
 Identities = 164/301 (54%), Positives = 196/301 (65%), Gaps = 47/301 (15%)

Query: 35  TPPSPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNR 94
           +P S    CAVCGD A+CQHYGVRTCEGCKGFFKRTVQK +KY+CLA+K CPVDKRRRNR
Sbjct: 238 SPSSNEGRCAVCGDNASCQHYGVRTCEGCKGFFKRTVQKNAKYICLANKDCPVDKRRRNR 297

Query: 95  CQFCRFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVSLITALYREPNPL 154
           CQFCRFQKCL VGMVKEVVRTDSLKGRRGRLPSKPK   ES P   V LI +L       
Sbjct: 298 CQFCRFQKCLVVGMVKEVVRTDSLKGRRGRLPSKPKQIAESSP---VDLINSL------- 347

Query: 155 EPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFYREPNP 214
                                  +R   D IP  S L                 ++E  P
Sbjct: 348 -----------------------VRAHIDSIPSSSKLDYSK-------------FQETVP 371

Query: 215 LEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLA 274
           L+        +QQFY LL+ S++VIR +A+KI GF DL KEDQ+LL +SA LELF+LRLA
Sbjct: 372 LQLEKESSVDVQQFYDLLSGSLEVIRKWAEKIQGFVDLPKEDQDLLLESAFLELFILRLA 431

Query: 275 YRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
           YR+R E+ KLIFCNGVVL + QC R FG +W+++I+EF  SL  M ID+ +F+CL AL +
Sbjct: 432 YRSRPEEGKLIFCNGVVLHRTQCVRGFG-EWIDSIIEFSHSLQRMNIDVPSFSCLSALVI 490

Query: 335 I 335
           +
Sbjct: 491 V 491

Probable nuclear receptor.

Xenopus laevis (taxid: 8355)

>sp|Q0V8F0|NR4A1_BOVIN Nuclear receptor subfamily 4 group A member 1 OS=Bos taurus GN=NR4A1 PE=2 SV=1

 Score =  306 bits (783), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 170/324 (52%), Positives = 208/324 (64%), Gaps = 59/324 (18%)

Query: 15  RHSAPLSSA---SSSPGCDTSRPTPPSPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTV 71
           R  AP++SA   S +PG    R         CAVCGD A+CQHYGVRTCEGCKGFFKRTV
Sbjct: 245 RLDAPVTSAKARSGAPGGSEGR---------CAVCGDNASCQHYGVRTCEGCKGFFKRTV 295

Query: 72  QKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPKS 131
           QK +KY+CLA+K CPVDKRRRNRCQFCRFQKCL VGMVKEVVRTDSLKGRRGRLPSKPK 
Sbjct: 296 QKNAKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTDSLKGRRGRLPSKPKQ 355

Query: 132 PQESPPSPPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDL 191
           P E+ P+    L+T+L                              +R   D  P  S L
Sbjct: 356 PPETSPA---HLLTSL------------------------------VRAHLDSGPSTSKL 382

Query: 192 CKEDQELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSD 251
                   FQ  +L  F +E         +   +QQFY LL+ S++VIR +A+KIPGF++
Sbjct: 383 DYSK----FQELALPHFGKE---------DAGDVQQFYDLLSGSLEVIRKWAEKIPGFAE 429

Query: 252 LCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILE 311
           L   DQ+LL +SA LELF+LRLAYR++  + KLIFC+G+VL + QC R FG DW+++IL 
Sbjct: 430 LSPGDQDLLLESAFLELFILRLAYRSKPAEGKLIFCSGLVLHRLQCARGFG-DWIDSILA 488

Query: 312 FCQSLHLMEIDISAFACLCALTLI 335
           F +SLH + +DI AFACL AL LI
Sbjct: 489 FSRSLHSLVVDIPAFACLSALVLI 512

Orphan nuclear receptor. May act concomitantly with NURR1 in regulating the expression of delayed-early genes during liver regeneration. Binds the NGFI-B response element (NBRE) 5'-AAAAGGTCA-3'. May inhibit NF-kappa-B transactivation of IL2.

Bos taurus (taxid: 9913)

>sp|P12813|NR4A1_MOUSE Nuclear receptor subfamily 4 group A member 1 OS=Mus musculus GN=Nr4a1 PE=2 SV=1

 Score =  304 bits (778), Expect = 7e-82,   Method: Compositional matrix adjust.
 Identities = 162/293 (55%), Positives = 194/293 (66%), Gaps = 47/293 (16%)

Query: 43  CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
           CAVCGD A+CQHYGVRTCEGCKGFFKRTVQK +KY+CLA+K CPVDKRRRNRCQFCRFQK
Sbjct: 270 CAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQK 329

Query: 103 CLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVSLITALYREPNPLEPPIAEPE 162
           CL VGMVKEVVRTDSLKGRRGRLPSKPK P   P + P +L+T+L               
Sbjct: 330 CLAVGMVKEVVRTDSLKGRRGRLPSKPKQP---PDASPTNLLTSL--------------- 371

Query: 163 KIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFYREPNPLEPPIAEP 222
                          IR   D  P  + L        FQ   L  F +E         + 
Sbjct: 372 ---------------IRAHLDSGPSTAKLDYSK----FQELVLPRFGKE---------DA 403

Query: 223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT 282
             +QQFY LL+ S+DVIR +A+KIPGF +LC  DQ+LL +SA LELF+LRLAYR++  + 
Sbjct: 404 GDVQQFYDLLSGSLDVIRKWAEKIPGFIELCPGDQDLLLESAFLELFILRLAYRSKPGEG 463

Query: 283 KLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
           KLIFC+G+VL + QC R FG DW++ IL F +SLH + +D+ AFACL AL LI
Sbjct: 464 KLIFCSGLVLHQLQCARGFG-DWIDNILAFSRSLHSLGVDVPAFACLSALVLI 515

Orphan nuclear receptor. May act concomitantly with NURR1 in regulating the expression of delayed-early genes during liver regeneration. Binds the NGFI-B response element (NBRE) 5'-AAAAGGTCA-3'. May inhibit NF-kappa-B transactivation of IL2.

Mus musculus (taxid: 10090)

>sp|P51666|NR4A1_CANFA Nuclear receptor subfamily 4 group A member 1 OS=Canis familiaris GN=NR4A1 PE=2 SV=1

 Score =  301 bits (772), Expect = 4e-81,   Method: Compositional matrix adjust.
 Identities = 175/343 (51%), Positives = 213/343 (62%), Gaps = 56/343 (16%)

Query: 2   QLG-RSSSSESPKLRHSAPLSSASSSPG-------CDTSRPTPPSPSQ-LCAVCGDIAAC 52
           QLG R S S S      AP S     PG          +R   PS S+  CAVCGD A+C
Sbjct: 217 QLGERESYSISTAFPGLAPTSPHLDGPGMLDAPVPSAKARSGAPSGSEGRCAVCGDNASC 276

Query: 53  QHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEV 112
           QHYGVRTCEGCKGFFKRTVQK +KY+CLA+K CPVDKRRRNRCQFCRFQKCL VGMVKEV
Sbjct: 277 QHYGVRTCEGCKGFFKRTVQKNAKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEV 336

Query: 113 VRTDSLKGRRGRLPSKPKSPQESPPSPPVSLITALYREPNPLEPPIAEPEKIQQFYSLLT 172
           VRTDSLKGRRGRLPSKPK P   P + P +L+T+L                         
Sbjct: 337 VRTDSLKGRRGRLPSKPKQP---PDASPANLLTSL------------------------- 368

Query: 173 TSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLL 232
                +R   D  P  + L        FQ   L  F +E         +   +QQFY LL
Sbjct: 369 -----VRAHLDSGPSTAKLDYSK----FQELVLPHFGKE---------DAGDVQQFYDLL 410

Query: 233 TTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVL 292
           + S++VIR +A+KIPGF++L   DQ+LL +SA LELF+LRLAYR++  + KLIFC+G+VL
Sbjct: 411 SGSLEVIRKWAEKIPGFAELSPGDQDLLLESAFLELFILRLAYRSKPAEGKLIFCSGLVL 470

Query: 293 EKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            + QC R FG DW+++IL F +SLH + +D+ AFACL AL LI
Sbjct: 471 HRLQCARGFG-DWIDSILAFSRSLHGLVVDVPAFACLSALVLI 512

Orphan nuclear receptor. May act concomitantly with NURR1 in regulating the expression of delayed-early genes during liver regeneration. Binds the NGFI-B response element (NBRE) 5'-AAAAGGTCA-3'. May inhibit NF-kappa-B transactivation of IL2.

Canis familiaris (taxid: 9615)

>sp|P22829|NR4A1_RAT Nuclear receptor subfamily 4 group A member 1 OS=Rattus norvegicus GN=Nr4a1 PE=1 SV=2

 Score =  301 bits (771), Expect = 5e-81,   Method: Compositional matrix adjust.
 Identities = 175/347 (50%), Positives = 212/347 (61%), Gaps = 64/347 (18%)

Query: 2   QLGRSSSSESPKLRHSAPLSSASSSPGCDTS----RPTPPSPSQL---------CAVCGD 48
           QLG   S   P    +A    A +SP CDTS     P   + ++          CAVCGD
Sbjct: 216 QLGEGESYSVP----AAFPGLAPTSPNCDTSGILDAPVTSTKARSGSSGGSEGRCAVCGD 271

Query: 49  IAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGM 108
            A+CQHYGVRTCEGCKGFFKRTVQK +KY+CLA+K CPVDKRRRNRCQFCRFQKCL VGM
Sbjct: 272 NASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGM 331

Query: 109 VKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVSLITALYREPNPLEPPIAEPEKIQQFY 168
           VKEVVRTDSLKGRRGRLPSKPK P   P + P +L+T+L                     
Sbjct: 332 VKEVVRTDSLKGRRGRLPSKPKQP---PDASPTNLLTSL--------------------- 367

Query: 169 SLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFYREPNPLEPPIAEPEKIQQF 228
                    IR   D  P  + L        FQ   L  F +E         +   +QQF
Sbjct: 368 ---------IRAHLDSGPNTAKLDYSK----FQELVLPRFGKE---------DAGDVQQF 405

Query: 229 YSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCN 288
           Y LL+ S+DVIR +A+KIPGF +L   DQ+LL +SA LELF+LRLAYR++  + KLIFC+
Sbjct: 406 YDLLSGSLDVIRKWAEKIPGFIELSPGDQDLLLESAFLELFILRLAYRSKPGEGKLIFCS 465

Query: 289 GVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
           G+VL + QC R FG DW++ IL F +SLH + +D+ AFACL AL LI
Sbjct: 466 GLVLHRLQCARGFG-DWIDNILAFSRSLHSLGVDVPAFACLSALVLI 511

Orphan nuclear receptor. May act concomitantly with NURR1 in regulating the expression of delayed-early genes during liver regeneration. Binds the NGFI-B response element (NBRE) 5'-AAAAGGTCA-3'. May inhibit NF-kappa-B transactivation of IL2.

Rattus norvegicus (taxid: 10116)

>sp|P22736|NR4A1_HUMAN Nuclear receptor subfamily 4 group A member 1 OS=Homo sapiens GN=NR4A1 PE=1 SV=1

 Score =  300 bits (768), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 168/325 (51%), Positives = 207/325 (63%), Gaps = 49/325 (15%)

Query: 11  SPKLRHSAPLSSASSSPGCDTSRPTPPSPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRT 70
           SP L  S  L +  +S    +  P        CAVCGD A+CQHYGVRTCEGCKGFFKRT
Sbjct: 237 SPHLEGSGILDTPVTSTKARSGAPG--GSEGRCAVCGDNASCQHYGVRTCEGCKGFFKRT 294

Query: 71  VQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPK 130
           VQK +KY+CLA+K CPVDKRRRNRCQFCRFQKCL VGMVKEVVRTDSLKGRRGRLPSKPK
Sbjct: 295 VQKNAKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTDSLKGRRGRLPSKPK 354

Query: 131 SPQESPPSPPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSD 190
            P   P + P +L+T+L R      P  A+ +   +F  L      V+ HF         
Sbjct: 355 QP---PDASPANLLTSLVRAHLDSGPSTAKLD-YSKFQEL------VLPHFG-------- 396

Query: 191 LCKEDQELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFS 250
             KED                             +QQFY LL+ S++VIR +A+KIPGF+
Sbjct: 397 --KEDAG--------------------------DVQQFYDLLSGSLEVIRKWAEKIPGFA 428

Query: 251 DLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAIL 310
           +L   DQ+LL +SA LELF+LRLAYR++  + KLIFC+G+VL + QC R FG DW+++IL
Sbjct: 429 ELSPADQDLLLESAFLELFILRLAYRSKPGEGKLIFCSGLVLHRLQCARGFG-DWIDSIL 487

Query: 311 EFCQSLHLMEIDISAFACLCALTLI 335
            F +SLH + +D+ AFACL AL LI
Sbjct: 488 AFSRSLHSLLVDVPAFACLSALVLI 512

Orphan nuclear receptor. May act concomitantly with NURR1 in regulating the expression of delayed-early genes during liver regeneration. Binds the NGFI-B response element (NBRE) 5'-AAAAGGTCA-3' (By similarity). May inhibit NF-kappa-B transactivation of IL2.

Homo sapiens (taxid: 9606)

>sp|Q92570|NR4A3_HUMAN Nuclear receptor subfamily 4 group A member 3 OS=Homo sapiens GN=NR4A3 PE=2 SV=3

 Score =  292 bits (747), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 156/296 (52%), Positives = 189/296 (63%), Gaps = 47/296 (15%)

Query: 43  CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
           CAVCGD AACQHYGVRTCEGCKGFFKRTVQK +KYVCLA+K CPVDKRRRNRCQ+CRFQK
Sbjct: 292 CAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQK 351

Query: 103 CLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVSLITALYREPNPLEPPIAEPE 162
           CL VGMVKEVVRTDSLKGRRGRLPSKPKSP                     L+   ++P 
Sbjct: 352 CLSVGMVKEVVRTDSLKGRRGRLPSKPKSP---------------------LQQEPSQPS 390

Query: 163 KIQQFYSLLTTSVDVIRHFADKIP---GFSDLCKEDQELLFQSASLELFYREPNPLEPPI 219
                  ++     ++R   D  P    +S  C  DQ      A                
Sbjct: 391 PPSPPICMMNA---LVRALTDSTPRDLDYSRYCPTDQAAAGTDA---------------- 431

Query: 220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRA 279
              E +QQFY+LLT S+DV R +A+KIPGF+DL KEDQ LL +SA LELFVLRL+ R+  
Sbjct: 432 ---EHVQQFYNLLTASIDVSRSWAEKIPGFTDLPKEDQTLLIESAFLELFVLRLSIRSNT 488

Query: 280 EDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            + K +FCNG+VL + QC R FG +WL++I +F  +L  + +DI A ACL AL++I
Sbjct: 489 AEDKFVFCNGLVLHRLQCLRGFG-EWLDSIKDFSLNLQSLNLDIQALACLSALSMI 543

Binds to the B1A response-element.

Homo sapiens (taxid: 9606)

>sp|Q9QZB6|NR4A3_MOUSE Nuclear receptor subfamily 4 group A member 3 OS=Mus musculus GN=Nr4a3 PE=2 SV=1

 Score =  291 bits (744), Expect = 7e-78,   Method: Compositional matrix adjust.
 Identities = 156/296 (52%), Positives = 189/296 (63%), Gaps = 47/296 (15%)

Query: 43  CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
           CAVCGD AACQHYGVRTCEGCKGFFKRTVQK +KYVCLA+K CPVDKRRRNRCQ+CRFQK
Sbjct: 293 CAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQK 352

Query: 103 CLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVSLITALYREPNPLEPPIAEPE 162
           CL VGMVKEVVRTDSLKGRRGRLPSKPKSP                     L+   ++P 
Sbjct: 353 CLSVGMVKEVVRTDSLKGRRGRLPSKPKSP---------------------LQQEPSQPS 391

Query: 163 KIQQFYSLLTTSVDVIRHFADKIP---GFSDLCKEDQELLFQSASLELFYREPNPLEPPI 219
                  ++     ++R   D  P    +S  C  DQ      A                
Sbjct: 392 PPSPPICMMNA---LVRALTDATPRDLDYSRYCPTDQATAGTDA---------------- 432

Query: 220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRA 279
              E +QQFY+LLT S+DV R +A+KIPGF+DL KEDQ LL +SA LELFVLRL+ R+  
Sbjct: 433 ---EHVQQFYNLLTASIDVSRSWAEKIPGFTDLPKEDQTLLIESAFLELFVLRLSIRSNT 489

Query: 280 EDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            + K +FCNG+VL + QC R FG +WL++I +F  +L  + +DI A ACL AL++I
Sbjct: 490 AEDKFVFCNGLVLHRLQCLRGFG-EWLDSIKDFSLNLQSLNLDIQALACLSALSMI 544

Binds to the B1A response-element.

Mus musculus (taxid: 10090)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	335
357602873	572	hypothetical protein KGM_00033 [Danaus p	0.782	0.458	0.666	1e-111
242016902	595	retinoid X receptor, putative [Pediculus	0.773	0.435	0.732	1e-110
383857638	793	PREDICTED: uncharacterized protein LOC10	0.853	0.360	0.676	1e-108
189237801	633	PREDICTED: similar to AGAP008334-PA [Tri	0.770	0.407	0.725	1e-108
270008126	744	hormone receptor in 38-like protein [Tri	0.770	0.346	0.725	1e-107
332019521	803	Putative nuclear hormone receptor HR38 [	0.850	0.354	0.659	1e-107
193712543	728	PREDICTED: hypothetical protein LOC10016	0.853	0.392	0.641	1e-106
157135212	790	expressed protein (AHR38) [Aedes aegypti	0.770	0.326	0.708	1e-106
158296777	732	AGAP008334-PA [Anopheles gambiae str. PE	0.770	0.352	0.701	1e-106
1708293	360	RecName: Full=Probable nuclear hormone r	0.802	0.747	0.641	1e-106

>gi|357602873|gb|EHJ63549.1| hypothetical protein KGM_00033 [Danaus plexippus]

 Score =  409 bits (1050), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 204/306 (66%), Positives = 232/306 (75%), Gaps = 44/306 (14%)

Query: 30  DTSRPTPPSPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDK 89
           + SR  PPSPSQLCAVCGD AACQHYGVRTCEGCKGFFKRTVQKGSKYVCLA+K+CPVDK
Sbjct: 224 NASRAAPPSPSQLCAVCGDTAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLAEKSCPVDK 283

Query: 90  RRRNRCQFCRFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVSLITALYR 149
           RRRNRCQFCRFQKCL VGMVKEVVRTDSLKGRRGRLPSKPK PQESPPSPP+SLITAL  
Sbjct: 284 RRRNRCQFCRFQKCLAVGMVKEVVRTDSLKGRRGRLPSKPKCPQESPPSPPISLITAL-- 341

Query: 150 EPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFY 209
                                       +R   D  P F++L                 Y
Sbjct: 342 ----------------------------VRAHVDTSPDFANLDYSQ-------------Y 360

Query: 210 REPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELF 269
           REPNP+EPPI++ E IQQFY+LL+TS+D+I+ FA+K+PG+ DLC ED+E LF SA LELF
Sbjct: 361 REPNPMEPPISDIEVIQQFYTLLSTSIDMIKVFAEKVPGYGDLCPEDREQLFASARLELF 420

Query: 270 VLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACL 329
           VLRLAYRTR +DTKL FCNG+VL+K+QCQRSFG DWL+A+L+F  +LH M+IDIS FACL
Sbjct: 421 VLRLAYRTRPDDTKLTFCNGLVLDKRQCQRSFG-DWLHAVLDFSNTLHSMDIDISTFACL 479

Query: 330 CALTLI 335
           CALTLI
Sbjct: 480 CALTLI 485

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242016902|ref|XP_002428935.1| retinoid X receptor, putative [Pediculus humanus corporis] gi|212513751|gb|EEB16197.1| retinoid X receptor, putative [Pediculus humanus corporis]

 Score =  403 bits (1036), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 222/303 (73%), Positives = 237/303 (78%), Gaps = 44/303 (14%)

Query: 33  RPTPPSPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRR 92
           RP P SPSQLCAVCGD AACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADK+CPVDKRRR
Sbjct: 220 RPAPQSPSQLCAVCGDTAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKSCPVDKRRR 279

Query: 93  NRCQFCRFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVSLITALYREPN 152
           NRCQFCRFQKCL VGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVSLITAL     
Sbjct: 280 NRCQFCRFQKCLAVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVSLITAL----- 334

Query: 153 PLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFYREP 212
                                    +R   D  P  ++L                 YREP
Sbjct: 335 -------------------------VRAHVDTTPDLANLDFSQ-------------YREP 356

Query: 213 NPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLR 272
            P EPP++E EKIQQFYSLLTTSVDVIRHFADKIPGF++L KEDQ+LLFQSASLELFVLR
Sbjct: 357 IPGEPPMSEAEKIQQFYSLLTTSVDVIRHFADKIPGFTELTKEDQDLLFQSASLELFVLR 416

Query: 273 LAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCAL 332
           LAYRT+A+DTKL FCNGVVL+K QCQRSFG DWL+AIL+FCQSLH M+IDISAFACLCAL
Sbjct: 417 LAYRTKADDTKLTFCNGVVLDKHQCQRSFG-DWLHAILDFCQSLHAMDIDISAFACLCAL 475

Query: 333 TLI 335
           TLI
Sbjct: 476 TLI 478

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383857638|ref|XP_003704311.1| PREDICTED: uncharacterized protein LOC100884030 [Megachile rotundata]

 Score =  397 bits (1021), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 226/334 (67%), Positives = 250/334 (74%), Gaps = 48/334 (14%)

Query: 6   SSSSESPKLRHSAPLSSA---SSSPGCDTSRP-TPPSPSQLCAVCGDIAACQHYGVRTCE 61
           S S+ESPK R  +  + +   S SPG   S    PPSPSQLCAVCGD AACQHYGVRTCE
Sbjct: 418 SGSTESPKARGGSGSTGSSVNSPSPGSGASNERAPPSPSQLCAVCGDTAACQHYGVRTCE 477

Query: 62  GCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLKGR 121
           GCKGFFKRTVQKGSKYVCLA+KACPVDKRRRNRCQFCRFQKCL VGMVKEVVRTDSLKGR
Sbjct: 478 GCKGFFKRTVQKGSKYVCLAEKACPVDKRRRNRCQFCRFQKCLMVGMVKEVVRTDSLKGR 537

Query: 122 RGRLPSKPKSPQESPPSPPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHF 181
           RGRLPSKPKSPQESPPSPPVSLITAL                              +R  
Sbjct: 538 RGRLPSKPKSPQESPPSPPVSLITAL------------------------------VRAH 567

Query: 182 ADKIPGFSDLCKEDQELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRH 241
            D  P        DQ  L  S      YR+P P +PPI E EK QQFY+LLTTS+DVIR+
Sbjct: 568 LDTTP--------DQASLDYSQ-----YRQPRPGDPPITEAEKTQQFYNLLTTSIDVIRN 614

Query: 242 FADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSF 301
           FADKIPGF+DL +EDQELLFQSASLELFVLRLAYRT+ EDTKL FCNGVVL  +QCQRSF
Sbjct: 615 FADKIPGFTDLVREDQELLFQSASLELFVLRLAYRTKPEDTKLTFCNGVVLALEQCQRSF 674

Query: 302 GDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
           G DWL++ILEFC++LH++++DISAFACLCALTL+
Sbjct: 675 G-DWLHSILEFCRALHVLDVDISAFACLCALTLV 707

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189237801|ref|XP_001814072.1| PREDICTED: similar to AGAP008334-PA [Tribolium castaneum]

 Score =  396 bits (1018), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 219/302 (72%), Positives = 233/302 (77%), Gaps = 44/302 (14%)

Query: 34  PTPPSPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRN 93
           PTPPSPSQLCAVCGD AACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRN
Sbjct: 290 PTPPSPSQLCAVCGDTAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRN 349

Query: 94  RCQFCRFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVSLITALYREPNP 153
           RCQFCRFQKCL VGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVSLITAL      
Sbjct: 350 RCQFCRFQKCLAVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVSLITAL------ 403

Query: 154 LEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFYREPN 213
                                   +R   D  P  ++L                 Y EP+
Sbjct: 404 ------------------------VRAHVDTTPDLANLDYSQ-------------YLEPS 426

Query: 214 PLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRL 273
           P+EP I+E EKIQQFY+LLTTSVDVI++FADKIPGF +LC ED+ELLFQSASLELFVLRL
Sbjct: 427 PIEPVISEAEKIQQFYTLLTTSVDVIKNFADKIPGFQELCPEDRELLFQSASLELFVLRL 486

Query: 274 AYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALT 333
           AYRT   DTKL FCNGVVL+KQQCQRSFG DWL+AI+EFC SL  MEIDISAFACLCALT
Sbjct: 487 AYRTHPNDTKLTFCNGVVLDKQQCQRSFG-DWLHAIMEFCSSLMAMEIDISAFACLCALT 545

Query: 334 LI 335
           LI
Sbjct: 546 LI 547

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270008126|gb|EFA04574.1| hormone receptor in 38-like protein [Tribolium castaneum]

 Score =  393 bits (1010), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 219/302 (72%), Positives = 233/302 (77%), Gaps = 44/302 (14%)

Query: 34  PTPPSPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRN 93
           PTPPSPSQLCAVCGD AACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRN
Sbjct: 306 PTPPSPSQLCAVCGDTAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRN 365

Query: 94  RCQFCRFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVSLITALYREPNP 153
           RCQFCRFQKCL VGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVSLITAL      
Sbjct: 366 RCQFCRFQKCLAVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVSLITAL------ 419

Query: 154 LEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFYREPN 213
                                   +R   D  P  ++L                 Y EP+
Sbjct: 420 ------------------------VRAHVDTTPDLANLDYSQ-------------YLEPS 442

Query: 214 PLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRL 273
           P+EP I+E EKIQQFY+LLTTSVDVI++FADKIPGF +LC ED+ELLFQSASLELFVLRL
Sbjct: 443 PIEPVISEAEKIQQFYTLLTTSVDVIKNFADKIPGFQELCPEDRELLFQSASLELFVLRL 502

Query: 274 AYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALT 333
           AYRT   DTKL FCNGVVL+KQQCQRSFG DWL+AI+EFC SL  MEIDISAFACLCALT
Sbjct: 503 AYRTHPNDTKLTFCNGVVLDKQQCQRSFG-DWLHAIMEFCSSLMAMEIDISAFACLCALT 561

Query: 334 LI 335
           LI
Sbjct: 562 LI 563

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332019521|gb|EGI60000.1| Putative nuclear hormone receptor HR38 [Acromyrmex echinatior]

 Score =  393 bits (1010), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 221/335 (65%), Positives = 248/335 (74%), Gaps = 50/335 (14%)

Query: 6   SSSSESPKLRHSAPLSSAS----SSPGCDTSRPTPPSPSQLCAVCGDIAACQHYGVRTCE 61
           S S++SPK R     +S++    S     +    PPSPSQLCAVCGD AACQHYGVRTCE
Sbjct: 428 SGSTDSPKPRGGGGTASSTVSSPSPGSGTSGERAPPSPSQLCAVCGDTAACQHYGVRTCE 487

Query: 62  GCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLKGR 121
           GCKGFFKRTVQKGSKYVCLA+KACPVDKRRRNRCQFCRFQKCL VGMVKEVVRTDSLKGR
Sbjct: 488 GCKGFFKRTVQKGSKYVCLAEKACPVDKRRRNRCQFCRFQKCLMVGMVKEVVRTDSLKGR 547

Query: 122 RGRLPSKPKSPQESPPSPPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHF 181
           RGRLPSKPKSPQESPPSPPVSLITAL                              +R  
Sbjct: 548 RGRLPSKPKSPQESPPSPPVSLITAL------------------------------VRAH 577

Query: 182 ADKIPGFSDLCKEDQELLFQSASLELF-YREPNPLEPPIAEPEKIQQFYSLLTTSVDVIR 240
            D  P                ASL+   YR+P P +PPI E EKIQQFY+LLTTS+DVIR
Sbjct: 578 LDTTP--------------DKASLDYSQYRQPRPGDPPITEAEKIQQFYNLLTTSIDVIR 623

Query: 241 HFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRS 300
           +FADKIPGF+DL +EDQELLFQSASLELFVLRLAYRT  +DTKL+FCNGVVL  +QCQRS
Sbjct: 624 NFADKIPGFTDLVREDQELLFQSASLELFVLRLAYRTHPDDTKLVFCNGVVLALEQCQRS 683

Query: 301 FGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
           FG DWL++IL+FC++LH +E+DISAFACLCALTL+
Sbjct: 684 FG-DWLHSILDFCKALHFLEVDISAFACLCALTLV 717

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193712543|ref|XP_001944711.1| PREDICTED: hypothetical protein LOC100162780 [Acyrthosiphon pisum]

 Score =  391 bits (1005), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 222/346 (64%), Positives = 241/346 (69%), Gaps = 60/346 (17%)

Query: 6   SSSSESPKLRH-------SAPLSSASSSPGCDTSRP---------TPPSPSQLCAVCGDI 49
           +S+S SPKLRH       + P+  +  +P      P          P SPSQLCAVCGD 
Sbjct: 340 ASNSLSPKLRHCINTLSVTVPVECSPPTPDAACIMPQRNATAVATAPSSPSQLCAVCGDT 399

Query: 50  AACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMV 109
           AACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADK CPVDKRRRNRCQFCRFQKCLQVGMV
Sbjct: 400 AACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKNCPVDKRRRNRCQFCRFQKCLQVGMV 459

Query: 110 KEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVSLITALYREPNPLEPPIAEPEKIQQFYS 169
           KEVVRTDSLKGRRGRLPSKPKSP  SPPSPPVSLITA                       
Sbjct: 460 KEVVRTDSLKGRRGRLPSKPKSPHGSPPSPPVSLITA----------------------- 496

Query: 170 LLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFYREPNPLEPPIAEPEKIQQFY 229
                  ++R   D  P FS L                 Y EP P EP I E EKIQQF+
Sbjct: 497 -------IVRAHVDTNPDFSSLDYSQ-------------YHEPKPFEPLITEAEKIQQFF 536

Query: 230 SLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNG 289
            LLTTSV+VIRHFA+KIPGF  LCK DQ+LLFQSASLELFVLRLAYRT+  DTKLIFCNG
Sbjct: 537 GLLTTSVEVIRHFAEKIPGFKTLCKSDQDLLFQSASLELFVLRLAYRTKYADTKLIFCNG 596

Query: 290 VVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
           VVL+KQQC RSFG DWL AIL+F QSLH ++IDIS+F+CLCALTLI
Sbjct: 597 VVLDKQQCHRSFG-DWLQAILDFSQSLHSLDIDISSFSCLCALTLI 641

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157135212|ref|XP_001663431.1| expressed protein (AHR38) [Aedes aegypti] gi|108870261|gb|EAT34486.1| AAEL013270-PA [Aedes aegypti]

 Score =  391 bits (1005), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 214/302 (70%), Positives = 228/302 (75%), Gaps = 44/302 (14%)

Query: 34  PTPPSPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRN 93
           PTP SPSQLCAVCGD AACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRN
Sbjct: 447 PTPQSPSQLCAVCGDTAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRN 506

Query: 94  RCQFCRFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVSLITALYREPNP 153
           RCQFCRFQKCL VGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVS+ITAL      
Sbjct: 507 RCQFCRFQKCLAVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVSMITAL------ 560

Query: 154 LEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFYREPN 213
                                   +R   D  P  + L                 YREP 
Sbjct: 561 ------------------------VRAHVDTTPDLASLDYSQ-------------YREPG 583

Query: 214 PLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRL 273
             EP I+E EK+QQFY+LLTTSVDVI+ FADK+PGFSDL  +DQELLFQSASLELFVLRL
Sbjct: 584 QNEPIISEAEKVQQFYNLLTTSVDVIKQFADKLPGFSDLSSDDQELLFQSASLELFVLRL 643

Query: 274 AYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALT 333
           +YR R +DTK+ FCNGVVL K QCQRSFG DWLNAILEF +SLH MEIDISAFACLCALT
Sbjct: 644 SYRARIDDTKMTFCNGVVLHKHQCQRSFG-DWLNAILEFSKSLHSMEIDISAFACLCALT 702

Query: 334 LI 335
           L+
Sbjct: 703 LV 704

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|158296777|ref|XP_317123.4| AGAP008334-PA [Anopheles gambiae str. PEST] gi|157014874|gb|EAA12420.4| AGAP008334-PA [Anopheles gambiae str. PEST]

 Score =  391 bits (1005), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 212/302 (70%), Positives = 229/302 (75%), Gaps = 44/302 (14%)

Query: 34  PTPPSPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRN 93
           PTP SPSQLCAVCGD AACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRN
Sbjct: 389 PTPVSPSQLCAVCGDTAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRN 448

Query: 94  RCQFCRFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVSLITALYREPNP 153
           RCQFCRFQKCL VGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVS+ITAL      
Sbjct: 449 RCQFCRFQKCLAVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVSMITAL------ 502

Query: 154 LEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFYREPN 213
                                   +R   D  P  + L                 YREP 
Sbjct: 503 ------------------------VRAHVDTTPDLASLDYSQ-------------YREPG 525

Query: 214 PLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRL 273
             EP I E EK+QQFY+LLTTSVDVI+HFADK+PG++DL  EDQELLFQSASLELFVLRL
Sbjct: 526 QNEPIITEAEKVQQFYNLLTTSVDVIKHFADKLPGYNDLSVEDQELLFQSASLELFVLRL 585

Query: 274 AYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALT 333
           +YR R++DTK+ FCNGVVL + QCQRSFG DWLNAILEF +SLH M+IDISAFACLCALT
Sbjct: 586 SYRARSDDTKMTFCNGVVLHRHQCQRSFG-DWLNAILEFSKSLHAMQIDISAFACLCALT 644

Query: 334 LI 335
           L+
Sbjct: 645 LV 646

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|1708293|sp|P49870.1|HR38_BOMMO RecName: Full=Probable nuclear hormone receptor HR38; Short=bHR38; AltName: Full=Nuclear receptor subfamily 4 group A member 4 gi|929003|emb|CAA61535.1| BHR38 [Bombyx mori]

 Score =  390 bits (1001), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 204/318 (64%), Positives = 230/318 (72%), Gaps = 49/318 (15%)

Query: 23  ASSSPGCDTS-----RPTPPSPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKY 77
            SSSPG   +     R  P SPSQLCAVCGD AACQHYGVRTCEGCKGFFKRTVQKGSKY
Sbjct: 1   GSSSPGVAPADNTGPRAAPSSPSQLCAVCGDTAACQHYGVRTCEGCKGFFKRTVQKGSKY 60

Query: 78  VCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPP 137
           VCLA+K+CPVDKRRRNRCQFC FQKCL VGMVKEVVRTDSLKGRRGRLPSKPK PQESPP
Sbjct: 61  VCLAEKSCPVDKRRRNRCQFCWFQKCLAVGMVKEVVRTDSLKGRRGRLPSKPKCPQESPP 120

Query: 138 SPPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQE 197
           SPP+SLITAL                              +R   D  P F++L      
Sbjct: 121 SPPISLITAL------------------------------VRAHVDTSPDFANLDYSQ-- 148

Query: 198 LLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQ 257
                      YREP+PLEPP+++ E IQQFYSLLTTS+D+I+ FA+K+PG+ DLC ED+
Sbjct: 149 -----------YREPSPLEPPMSDLEVIQQFYSLLTTSIDMIKLFAEKVPGYGDLCPEDR 197

Query: 258 ELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLH 317
           E LF SA LELFVLRLAYRT  EDTKL F NG VL+K+QCQRSFG DWL+A+L+F  + +
Sbjct: 198 EQLFASARLELFVLRLAYRTALEDTKLTFSNGSVLDKRQCQRSFG-DWLHAVLDFSNTSY 256

Query: 318 LMEIDISAFACLCALTLI 335
            M+IDIS FACLCALTLI
Sbjct: 257 SMDIDISTFACLCALTLI 274

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

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	335
UNIPROTKB|Q6NXU0	535	NR4A2 "Nuclear receptor subfam	0.286	0.179	0.712	1.5e-67
UNIPROTKB|Q08E53	598	NR4A2 "Nuclear receptor subfam	0.286	0.160	0.712	7.2e-67
UNIPROTKB|P43354	598	NR4A2 "Nuclear receptor subfam	0.286	0.160	0.712	7.2e-67
UNIPROTKB|F1RPU1	598	NR4A2 "Uncharacterized protein	0.286	0.160	0.712	7.2e-67
UNIPROTKB|Q5R5Y4	598	NR4A2 "Nuclear receptor subfam	0.286	0.160	0.712	7.2e-67
MGI|MGI:1352456	598	Nr4a2 "nuclear receptor subfam	0.286	0.160	0.712	7.2e-67
RGD|3202	598	Nr4a2 "nuclear receptor subfam	0.286	0.160	0.712	7.2e-67
UNIPROTKB|E2RBX8	609	NR4A2 "Uncharacterized protein	0.286	0.157	0.712	8.6e-67
UNIPROTKB|F5H4G9	609	NR4A2 "Nuclear receptor subfam	0.286	0.157	0.712	8.6e-67
UNIPROTKB|E1C6K9	598	NR4A2 "Uncharacterized protein	0.340	0.190	0.591	2e-66

UNIPROTKB|Q6NXU0 NR4A2 "Nuclear receptor subfamily 4, group A, member 2" [Homo sapiens (taxid:9606)]

 Score = 355 (130.0 bits), Expect = 1.5e-67, Sum P(2) = 1.5e-67
 Identities = 72/101 (71%), Positives = 75/101 (74%)

Query:    30 DTSRPTPPS---PSQ--LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKA 84
             DT  P+PPS   PS   LCAVCGD AACQHYGVRTCEGCKGFFKRTVQK +KYVCLA+K 
Sbjct:   182 DTQVPSPPSRGSPSNEGLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKN 241

Query:    85 CPVDXXXXXXXXXXXXXXCLQVGMVKEVVRTDSLKGRRGRL 125
             CPVD              CL VGMVKEVVRTDSLKGRRGRL
Sbjct:   242 CPVDKRRRNRCQYCRFQKCLAVGMVKEVVRTDSLKGRRGRL 282

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

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0001666 "response to hypoxia" evidence=IEA

GO:0001764 "neuron migration" evidence=IEA

GO:0001975 "response to amphetamine" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0008344 "adult locomotory behavior" evidence=IEA

GO:0009791 "post-embryonic development" evidence=IEA

GO:0010035 "response to inorganic substance" evidence=IEA

GO:0016265 "death" evidence=IEA

GO:0017085 "response to insecticide" evidence=IEA

GO:0021952 "central nervous system projection neuron axonogenesis" evidence=IEA

GO:0021986 "habenula development" evidence=IEA

GO:0033554 "cellular response to stress" evidence=IEA

GO:0042053 "regulation of dopamine metabolic process" evidence=IEA

GO:0042416 "dopamine biosynthetic process" evidence=IEA

GO:0042551 "neuron maturation" evidence=IEA

GO:0043085 "positive regulation of catalytic activity" evidence=IEA

GO:0043524 "negative regulation of neuron apoptotic process" evidence=IEA

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

GO:0043576 "regulation of respiratory gaseous exchange" evidence=IEA

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

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0071542 "dopaminergic neuron differentiation" evidence=IEA

UNIPROTKB|Q08E53 NR4A2 "Nuclear receptor subfamily 4 group A member 2" [Bos taurus (taxid:9913)]

 Score = 355 (130.0 bits), Expect = 7.2e-67, Sum P(2) = 7.2e-67
 Identities = 72/101 (71%), Positives = 75/101 (74%)

Query:    30 DTSRPTPPS---PSQ--LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKA 84
             DT  P+PPS   PS   LCAVCGD AACQHYGVRTCEGCKGFFKRTVQK +KYVCLA+K 
Sbjct:   245 DTQVPSPPSRGSPSNEGLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKN 304

Query:    85 CPVDXXXXXXXXXXXXXXCLQVGMVKEVVRTDSLKGRRGRL 125
             CPVD              CL VGMVKEVVRTDSLKGRRGRL
Sbjct:   305 CPVDKRRRNRCQYCRFQKCLAVGMVKEVVRTDSLKGRRGRL 345

GO:0071542 "dopaminergic neuron differentiation" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISS

GO:0046982 "protein heterodimerization activity" evidence=IEA

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

GO:0043576 "regulation of respiratory gaseous exchange" evidence=IEA

GO:0043524 "negative regulation of neuron apoptotic process" evidence=IEA

GO:0043085 "positive regulation of catalytic activity" evidence=IEA

GO:0042551 "neuron maturation" evidence=IEA

GO:0042416 "dopamine biosynthetic process" evidence=IEA

GO:0042053 "regulation of dopamine metabolic process" evidence=IEA

GO:0033554 "cellular response to stress" evidence=IEA

GO:0031668 "cellular response to extracellular stimulus" evidence=IEA

GO:0021986 "habenula development" evidence=IEA

GO:0021952 "central nervous system projection neuron axonogenesis" evidence=IEA

GO:0016265 "death" evidence=IEA

GO:0009791 "post-embryonic development" evidence=IEA

GO:0008344 "adult locomotory behavior" evidence=IEA

GO:0001975 "response to amphetamine" evidence=IEA

GO:0001764 "neuron migration" evidence=IEA

GO:0001666 "response to hypoxia" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

UNIPROTKB|P43354 NR4A2 "Nuclear receptor subfamily 4 group A member 2" [Homo sapiens (taxid:9606)]

 Score = 355 (130.0 bits), Expect = 7.2e-67, Sum P(2) = 7.2e-67
 Identities = 72/101 (71%), Positives = 75/101 (74%)

Query:    30 DTSRPTPPS---PSQ--LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKA 84
             DT  P+PPS   PS   LCAVCGD AACQHYGVRTCEGCKGFFKRTVQK +KYVCLA+K 
Sbjct:   245 DTQVPSPPSRGSPSNEGLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKN 304

Query:    85 CPVDXXXXXXXXXXXXXXCLQVGMVKEVVRTDSLKGRRGRL 125
             CPVD              CL VGMVKEVVRTDSLKGRRGRL
Sbjct:   305 CPVDKRRRNRCQYCRFQKCLAVGMVKEVVRTDSLKGRRGRL 345

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

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0001666 "response to hypoxia" evidence=IEA

GO:0001764 "neuron migration" evidence=IEA

GO:0001975 "response to amphetamine" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0008344 "adult locomotory behavior" evidence=IEA

GO:0009791 "post-embryonic development" evidence=IEA

GO:0010035 "response to inorganic substance" evidence=IEA

GO:0016265 "death" evidence=IEA

GO:0017085 "response to insecticide" evidence=IEA

GO:0021952 "central nervous system projection neuron axonogenesis" evidence=IEA

GO:0021986 "habenula development" evidence=IEA

GO:0033554 "cellular response to stress" evidence=IEA

GO:0042053 "regulation of dopamine metabolic process" evidence=IEA

GO:0042416 "dopamine biosynthetic process" evidence=IEA

GO:0042551 "neuron maturation" evidence=IEA

GO:0043085 "positive regulation of catalytic activity" evidence=IEA

GO:0043524 "negative regulation of neuron apoptotic process" evidence=IEA

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

GO:0043576 "regulation of respiratory gaseous exchange" evidence=IEA

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

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

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

GO:0071542 "dopaminergic neuron differentiation" evidence=ISS

GO:0007165 "signal transduction" evidence=NAS

GO:0031668 "cellular response to extracellular stimulus" 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:0005515 "protein binding" evidence=IPI

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

UNIPROTKB|F1RPU1 NR4A2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 355 (130.0 bits), Expect = 7.2e-67, Sum P(2) = 7.2e-67
 Identities = 72/101 (71%), Positives = 75/101 (74%)

Query:    30 DTSRPTPPS---PSQ--LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKA 84
             DT  P+PPS   PS   LCAVCGD AACQHYGVRTCEGCKGFFKRTVQK +KYVCLA+K 
Sbjct:   245 DTQVPSPPSRGSPSNEGLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKN 304

Query:    85 CPVDXXXXXXXXXXXXXXCLQVGMVKEVVRTDSLKGRRGRL 125
             CPVD              CL VGMVKEVVRTDSLKGRRGRL
Sbjct:   305 CPVDKRRRNRCQYCRFQKCLAVGMVKEVVRTDSLKGRRGRL 345

GO:0071542 "dopaminergic neuron differentiation" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

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

GO:0043576 "regulation of respiratory gaseous exchange" evidence=IEA

GO:0043524 "negative regulation of neuron apoptotic process" evidence=IEA

GO:0043085 "positive regulation of catalytic activity" evidence=IEA

GO:0042551 "neuron maturation" evidence=IEA

GO:0042416 "dopamine biosynthetic process" evidence=IEA

GO:0042053 "regulation of dopamine metabolic process" evidence=IEA

GO:0033554 "cellular response to stress" evidence=IEA

GO:0031668 "cellular response to extracellular stimulus" evidence=IEA

GO:0021986 "habenula development" evidence=IEA

GO:0021952 "central nervous system projection neuron axonogenesis" evidence=IEA

GO:0016265 "death" evidence=IEA

GO:0009791 "post-embryonic development" evidence=IEA

GO:0008344 "adult locomotory behavior" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0001975 "response to amphetamine" evidence=IEA

GO:0001764 "neuron migration" evidence=IEA

GO:0001666 "response to hypoxia" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

UNIPROTKB|Q5R5Y4 NR4A2 "Nuclear receptor subfamily 4 group A member 2" [Pongo abelii (taxid:9601)]

 Score = 355 (130.0 bits), Expect = 7.2e-67, Sum P(2) = 7.2e-67
 Identities = 72/101 (71%), Positives = 75/101 (74%)

Query:    30 DTSRPTPPS---PSQ--LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKA 84
             DT  P+PPS   PS   LCAVCGD AACQHYGVRTCEGCKGFFKRTVQK +KYVCLA+K 
Sbjct:   245 DTQVPSPPSRGSPSNEGLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKN 304

Query:    85 CPVDXXXXXXXXXXXXXXCLQVGMVKEVVRTDSLKGRRGRL 125
             CPVD              CL VGMVKEVVRTDSLKGRRGRL
Sbjct:   305 CPVDKRRRNRCQYCRFQKCLAVGMVKEVVRTDSLKGRRGRL 345

GO:0005634 "nucleus" evidence=ISS

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

GO:0071542 "dopaminergic neuron differentiation" evidence=ISS

MGI|MGI:1352456 Nr4a2 "nuclear receptor subfamily 4, group A, member 2" [Mus musculus (taxid:10090)]

 Score = 355 (130.0 bits), Expect = 7.2e-67, Sum P(2) = 7.2e-67
 Identities = 72/101 (71%), Positives = 75/101 (74%)

Query:    30 DTSRPTPPS---PSQ--LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKA 84
             DT  P+PPS   PS   LCAVCGD AACQHYGVRTCEGCKGFFKRTVQK +KYVCLA+K 
Sbjct:   245 DTQVPSPPSRGSPSNEGLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKN 304

Query:    85 CPVDXXXXXXXXXXXXXXCLQVGMVKEVVRTDSLKGRRGRL 125
             CPVD              CL VGMVKEVVRTDSLKGRRGRL
Sbjct:   305 CPVDKRRRNRCQYCRFQKCLAVGMVKEVVRTDSLKGRRGRL 345

GO:0001666 "response to hypoxia" evidence=IMP

GO:0001764 "neuron migration" evidence=IMP

GO:0001975 "response to amphetamine" evidence=IMP

GO:0003677 "DNA binding" evidence=IDA

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

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO;IDA

GO:0005737 "cytoplasm" evidence=ISO

GO:0006351 "transcription, DNA-dependent" evidence=ISO;IDA

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

GO:0006950 "response to stress" evidence=IMP

GO:0007399 "nervous system development" evidence=IMP

GO:0008270 "zinc ion binding" evidence=IEA

GO:0008344 "adult locomotory behavior" evidence=IMP

GO:0009791 "post-embryonic development" evidence=IMP

GO:0010035 "response to inorganic substance" evidence=ISO

GO:0010467 "gene expression" evidence=IMP

GO:0016265 "death" evidence=IMP

GO:0017085 "response to insecticide" evidence=ISO

GO:0021952 "central nervous system projection neuron axonogenesis" evidence=IMP

GO:0021953 "central nervous system neuron differentiation" evidence=IMP

GO:0021986 "habenula development" evidence=IMP

GO:0030182 "neuron differentiation" evidence=IMP

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

GO:0031668 "cellular response to extracellular stimulus" evidence=ISO;IDA

GO:0033554 "cellular response to stress" evidence=IMP

GO:0042053 "regulation of dopamine metabolic process" evidence=IDA

GO:0042416 "dopamine biosynthetic process" evidence=IMP

GO:0042417 "dopamine metabolic process" evidence=IMP

GO:0042551 "neuron maturation" evidence=IMP

GO:0043085 "positive regulation of catalytic activity" evidence=IMP

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

GO:0043524 "negative regulation of neuron apoptotic process" evidence=IMP

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

GO:0043576 "regulation of respiratory gaseous exchange" evidence=IMP

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

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

GO:0046872 "metal ion binding" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IPI

GO:0071542 "dopaminergic neuron differentiation" evidence=IDA

RGD|3202 Nr4a2 "nuclear receptor subfamily 4, group A, member 2" [Rattus norvegicus (taxid:10116)]

 Score = 355 (130.0 bits), Expect = 7.2e-67, Sum P(2) = 7.2e-67
 Identities = 72/101 (71%), Positives = 75/101 (74%)

Query:    30 DTSRPTPPS---PSQ--LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKA 84
             DT  P+PPS   PS   LCAVCGD AACQHYGVRTCEGCKGFFKRTVQK +KYVCLA+K 
Sbjct:   245 DTQVPSPPSRGSPSNEGLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKN 304

Query:    85 CPVDXXXXXXXXXXXXXXCLQVGMVKEVVRTDSLKGRRGRL 125
             CPVD              CL VGMVKEVVRTDSLKGRRGRL
Sbjct:   305 CPVDKRRRNRCQYCRFQKCLAVGMVKEVVRTDSLKGRRGRL 345

GO:0001666 "response to hypoxia" evidence=IEA;ISO

GO:0001764 "neuron migration" evidence=IEA;ISO

GO:0001975 "response to amphetamine" evidence=IEA;ISO

GO:0003677 "DNA binding" evidence=ISO;TAS

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

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

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

GO:0005634 "nucleus" evidence=IEA;ISO;IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0006351 "transcription, DNA-dependent" evidence=ISO;ISS

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

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

GO:0006950 "response to stress" evidence=ISO

GO:0007399 "nervous system development" evidence=ISO

GO:0008270 "zinc ion binding" evidence=IEA

GO:0008344 "adult locomotory behavior" evidence=IEA;ISO

GO:0009791 "post-embryonic development" evidence=IEA;ISO

GO:0010035 "response to inorganic substance" evidence=IDA

GO:0010467 "gene expression" evidence=ISO

GO:0016265 "death" evidence=IEA;ISO

GO:0017085 "response to insecticide" evidence=IDA

GO:0021952 "central nervous system projection neuron axonogenesis" evidence=IEA;ISO

GO:0021953 "central nervous system neuron differentiation" evidence=ISO

GO:0021986 "habenula development" evidence=IEA;ISO

GO:0030182 "neuron differentiation" evidence=ISO

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

GO:0031668 "cellular response to extracellular stimulus" evidence=IEA;ISO

GO:0033554 "cellular response to stress" evidence=IEA;ISO

GO:0042053 "regulation of dopamine metabolic process" evidence=IEA;ISO

GO:0042416 "dopamine biosynthetic process" evidence=IEA;ISO

GO:0042417 "dopamine metabolic process" evidence=ISO

GO:0042551 "neuron maturation" evidence=IEA;ISO

GO:0043085 "positive regulation of catalytic activity" evidence=IEA;ISO

GO:0043524 "negative regulation of neuron apoptotic process" evidence=IEA;ISO

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

GO:0043576 "regulation of respiratory gaseous exchange" evidence=IEA;ISO

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

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

GO:0046982 "protein heterodimerization activity" evidence=IEA;ISO

GO:0071542 "dopaminergic neuron differentiation" evidence=ISO;ISS

UNIPROTKB|E2RBX8 NR4A2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 355 (130.0 bits), Expect = 8.6e-67, Sum P(2) = 8.6e-67
 Identities = 72/101 (71%), Positives = 75/101 (74%)

Query:    30 DTSRPTPPS---PSQ--LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKA 84
             DT  P+PPS   PS   LCAVCGD AACQHYGVRTCEGCKGFFKRTVQK +KYVCLA+K 
Sbjct:   256 DTQVPSPPSRGSPSNEGLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKN 315

Query:    85 CPVDXXXXXXXXXXXXXXCLQVGMVKEVVRTDSLKGRRGRL 125
             CPVD              CL VGMVKEVVRTDSLKGRRGRL
Sbjct:   316 CPVDKRRRNRCQYCRFQKCLAVGMVKEVVRTDSLKGRRGRL 356

GO:0071542 "dopaminergic neuron differentiation" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

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

GO:0043576 "regulation of respiratory gaseous exchange" evidence=IEA

GO:0043524 "negative regulation of neuron apoptotic process" evidence=IEA

GO:0043085 "positive regulation of catalytic activity" evidence=IEA

GO:0042551 "neuron maturation" evidence=IEA

GO:0042416 "dopamine biosynthetic process" evidence=IEA

GO:0042053 "regulation of dopamine metabolic process" evidence=IEA

GO:0033554 "cellular response to stress" evidence=IEA

GO:0031668 "cellular response to extracellular stimulus" evidence=IEA

GO:0021986 "habenula development" evidence=IEA

GO:0021952 "central nervous system projection neuron axonogenesis" evidence=IEA

GO:0016265 "death" evidence=IEA

GO:0009791 "post-embryonic development" evidence=IEA

GO:0008344 "adult locomotory behavior" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0001975 "response to amphetamine" evidence=IEA

GO:0001764 "neuron migration" evidence=IEA

GO:0001666 "response to hypoxia" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

UNIPROTKB|F5H4G9 NR4A2 "Nuclear receptor subfamily 4 group A member 2" [Homo sapiens (taxid:9606)]

 Score = 355 (130.0 bits), Expect = 8.6e-67, Sum P(2) = 8.6e-67
 Identities = 72/101 (71%), Positives = 75/101 (74%)

Query:    30 DTSRPTPPS---PSQ--LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKA 84
             DT  P+PPS   PS   LCAVCGD AACQHYGVRTCEGCKGFFKRTVQK +KYVCLA+K 
Sbjct:   256 DTQVPSPPSRGSPSNEGLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKN 315

Query:    85 CPVDXXXXXXXXXXXXXXCLQVGMVKEVVRTDSLKGRRGRL 125
             CPVD              CL VGMVKEVVRTDSLKGRRGRL
Sbjct:   316 CPVDKRRRNRCQYCRFQKCLAVGMVKEVVRTDSLKGRRGRL 356

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|E1C6K9 NR4A2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 353 (129.3 bits), Expect = 2.0e-66, Sum P(2) = 2.0e-66
 Identities = 68/115 (59%), Positives = 91/115 (79%)

Query:   221 EPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAE 280
             + + IQQFY LLT S+++IR +A+KIPGF+DL K DQ+LLF+SA LELFVLRLAYR+   
Sbjct:   399 DTQHIQQFYDLLTGSMEIIRGWAEKIPGFTDLPKTDQDLLFESAFLELFVLRLAYRSNPV 458

Query:   281 DTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
             + KLIFCNGVVL + QC R FG+ W+++I+EF  +L  M IDISAF+C+ AL ++
Sbjct:   459 EGKLIFCNGVVLHRLQCVRGFGE-WIDSIVEFSSNLQNMNIDISAFSCIAALAMV 512

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0001666 "response to hypoxia" evidence=IEA

GO:0001764 "neuron migration" evidence=IEA

GO:0001975 "response to amphetamine" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0008344 "adult locomotory behavior" evidence=IEA

GO:0009791 "post-embryonic development" evidence=IEA

GO:0016265 "death" evidence=IEA

GO:0021952 "central nervous system projection neuron axonogenesis" evidence=IEA

GO:0021986 "habenula development" evidence=IEA

GO:0031668 "cellular response to extracellular stimulus" evidence=IEA

GO:0033554 "cellular response to stress" evidence=IEA

GO:0042053 "regulation of dopamine metabolic process" evidence=IEA

GO:0042416 "dopamine biosynthetic process" evidence=IEA

GO:0042551 "neuron maturation" evidence=IEA

GO:0043085 "positive regulation of catalytic activity" evidence=IEA

GO:0043524 "negative regulation of neuron apoptotic process" evidence=IEA

GO:0043576 "regulation of respiratory gaseous exchange" evidence=IEA

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

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0071542 "dopaminergic neuron differentiation" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P51666	NR4A1_CANFA	No assigned EC number	0.5102	0.8567	0.4799	yes	N/A
P12813	NR4A1_MOUSE	No assigned EC number	0.5529	0.7343	0.4093	yes	N/A
P22736	NR4A1_HUMAN	No assigned EC number	0.5169	0.8238	0.4615	yes	N/A
Q0V8F0	NR4A1_BOVIN	No assigned EC number	0.5246	0.7910	0.4431	yes	N/A
P22829	NR4A1_RAT	No assigned EC number	0.5043	0.8447	0.4740	yes	N/A
P49869	HR38_DROME	No assigned EC number	0.6677	0.7432	0.2320	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	335
cd07072	239	cd07072, NR_LBD_DHR38_like, Ligand binding domain	2e-77
cd07348	238	cd07348, NR_LBD_NGFI-B, The ligand binding domain	1e-51
cd06969	75	cd06969, NR_DBD_NGFI-B, DNA-binding domain of the	3e-51
cd06945	239	cd06945, NR_LBD_Nurr1_like, The ligand binding dom	1e-50
cd07071	238	cd07071, NR_LBD_Nurr1, The ligand binding domain o	6e-42
cd06916	72	cd06916, NR_DBD_like, DNA-binding domain of nuclea	2e-41
pfam00105	70	pfam00105, zf-C4, Zinc finger, C4 type (two domain	4e-40
cd06961	85	cd06961, NR_DBD_TR, DNA-binding domain of thyroid	2e-33
cd07167	93	cd07167, NR_DBD_Lrh-1_like, The DNA-binding domain	2e-32
cd06956	77	cd06956, NR_DBD_RXR, DNA-binding domain of retinoi	3e-32
cd07168	90	cd07168, NR_DBD_DHR4_like, DNA-binding domain of e	3e-32
smart00399	70	smart00399, ZnF_C4, c4 zinc finger in nuclear horm	1e-31
cd07170	97	cd07170, NR_DBD_ERR, DNA-binding domain of estroge	2e-31
cd06960	76	cd06960, NR_DBD_HNF4A, DNA-binding domain of hepto	1e-30
cd06967	87	cd06967, NR_DBD_TR2_like, DNA-binding domain of th	2e-29
cd06964	85	cd06964, NR_DBD_RAR, DNA-binding domain of retinoi	3e-29
cd07169	90	cd07169, NR_DBD_GCNF_like, DNA-binding domain of G	5e-29
cd07155	75	cd07155, NR_DBD_ER_like, DNA-binding domain of est	5e-28
cd07165	81	cd07165, NR_DBD_DmE78_like, DNA-binding domain of	7e-28
cd07164	78	cd07164, NR_DBD_PNR_like_1, DNA-binding domain of	1e-27
cd07166	89	cd07166, NR_DBD_REV_ERB, DNA-binding domain of REV	2e-27
cd07171	82	cd07171, NR_DBD_ER, DNA-binding domain of estrogen	3e-27
cd06958	73	cd06958, NR_DBD_COUP_TF, DNA-binding domain of chi	8e-27
cd07154	73	cd07154, NR_DBD_PNR_like, The DNA-binding domain o	3e-26
cd07158	73	cd07158, NR_DBD_Ppar_like, The DNA-binding domain	3e-26
cd06970	92	cd06970, NR_DBD_PNR, DNA-binding domain of the pho	1e-24
cd06965	84	cd06965, NR_DBD_Ppar, DNA-binding domain of peroxi	2e-24
cd06968	95	cd06968, NR_DBD_ROR, DNA-binding domain of Retinoi	2e-24
cd06957	82	cd06957, NR_DBD_PNR_like_2, DNA-binding domain of	3e-24
cd07163	92	cd07163, NR_DBD_TLX, DNA-binding domain of Tailles	5e-24
cd07179	74	cd07179, 2DBD_NR_DBD2, The second DNA-binding doma	7e-24
cd06157	168	cd06157, NR_LBD, The ligand binding domain of nucl	2e-23
cd07156	72	cd07156, NR_DBD_VDR_like, The DNA-binding domain o	8e-23
cd07161	91	cd07161, NR_DBD_EcR, DNA-binding domain of Ecdyson	4e-22
cd07160	101	cd07160, NR_DBD_LXR, DNA-binding domain of Liver X	5e-22
cd06959	73	cd06959, NR_DBD_EcR_like, The DNA-binding domain o	7e-22
cd06945	239	cd06945, NR_LBD_Nurr1_like, The ligand binding dom	8e-21
cd07162	87	cd07162, NR_DBD_PXR, DNA-binding domain of pregnan	2e-20
cd06962	84	cd06962, NR_DBD_FXR, DNA-binding domain of Farneso	2e-20
cd06955	107	cd06955, NR_DBD_VDR, DNA-binding domain of vitamin	3e-20
cd07172	78	cd07172, NR_DBD_GR_PR, DNA-binding domain of gluco	4e-20
cd07157	86	cd07157, 2DBD_NR_DBD1, The first DNA-binding domai	5e-18
cd06963	73	cd06963, NR_DBD_GR_like, The DNA binding domain of	6e-18
cd06966	94	cd06966, NR_DBD_CAR, DNA-binding domain of constit	7e-17
smart00430	163	smart00430, HOLI, Ligand binding domain of hormone	9e-17
cd07173	82	cd07173, NR_DBD_AR, DNA-binding domain of androgen	1e-16
cd07348	238	cd07348, NR_LBD_NGFI-B, The ligand binding domain	2e-16
cd07071	238	cd07071, NR_LBD_Nurr1, The ligand binding domain o	2e-14
cd06929	174	cd06929, NR_LBD_F1, Ligand-binding domain of nucle	5e-14
pfam00104	186	pfam00104, Hormone_recep, Ligand-binding domain of	5e-13
cd06937	231	cd06937, NR_LBD_RAR, The ligand binding domain (LB	5e-12
cd07068	221	cd07068, NR_LBD_ER_like, The ligand binding domain	8e-12
cd06941	195	cd06941, NR_LBD_DmE78_like, The ligand binding dom	3e-11
cd06954	236	cd06954, NR_LBD_LXR, The ligand binding domain of	4e-11
cd06940	189	cd06940, NR_LBD_REV_ERB, The ligand binding domain	5e-11
cd06930	165	cd06930, NR_LBD_F2, Ligand-binding domain of nucle	6e-10
cd06938	231	cd06938, NR_LBD_EcR, The ligand binding domain (LB	9e-10
cd06949	235	cd06949, NR_LBD_ER, Ligand binding domain of Estro	2e-09
cd06935	243	cd06935, NR_LBD_TR, The ligand binding domain of t	6e-09
cd06946	221	cd06946, NR_LBD_ERR, The ligand binding domain of	5e-08
cd06939	241	cd06939, NR_LBD_ROR_like, The ligand binding domai	1e-07
cd06950	206	cd06950, NR_LBD_Tlx_PNR_like, The ligand binding d	3e-05
cd06929	174	cd06929, NR_LBD_F1, Ligand-binding domain of nucle	2e-04
cd06933	238	cd06933, NR_LBD_VDR, The ligand binding domain of	2e-04
cd06941	195	cd06941, NR_LBD_DmE78_like, The ligand binding dom	3e-04
cd06939	241	cd06939, NR_LBD_ROR_like, The ligand binding domai	8e-04
cd06949	235	cd06949, NR_LBD_ER, Ligand binding domain of Estro	0.001
cd07076	247	cd07076, NR_LBD_GR, Ligand binding domain of the g	0.001
cd06933	238	cd06933, NR_LBD_VDR, The ligand binding domain of	0.004

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

 Score =  237 bits (605), Expect = 2e-77
 Identities = 121/197 (61%), Positives = 135/197 (68%), Gaps = 44/197 (22%)

Query: 139 PPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQEL 198
           PPVSLITAL                              +R   D  P F++L   D   
Sbjct: 1   PPVSLITAL------------------------------VRAHVDTSPDFANL---DYSQ 27

Query: 199 LFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQE 258
                     YREP+PLEPP++E EK+QQFYSLLT+S+DVI+ FA+KIPGF DLCKEDQE
Sbjct: 28  ----------YREPSPLEPPMSEAEKVQQFYSLLTSSIDVIKTFAEKIPGFPDLCKEDQE 77

Query: 259 LLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHL 318
           LLFQSASLELFVLRLAYRT  EDTKL FCNGVVL KQQCQRSFG DWL+AILEF +SLH 
Sbjct: 78  LLFQSASLELFVLRLAYRTAPEDTKLTFCNGVVLHKQQCQRSFG-DWLHAILEFSKSLHA 136

Query: 319 MEIDISAFACLCALTLI 335
           M+IDISAFACLCALTLI
Sbjct: 137 MDIDISAFACLCALTLI 153

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

 Score =  170 bits (433), Expect = 1e-51
 Identities = 75/127 (59%), Positives = 96/127 (75%), Gaps = 1/127 (0%)

Query: 209 YREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL 268
           ++E         +   IQQFY LL+ S++VIR +A+KIPGFSD CKEDQELL +SA +EL
Sbjct: 27  FQESVSPLFEKEDASDIQQFYDLLSGSLEVIRKWAEKIPGFSDFCKEDQELLLESAFVEL 86

Query: 269 FVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFAC 328
           F+LRLAYR+  E+ KLIFCNGVVL + QC R FG DW+++ILEF QSLH M +D+SAF+C
Sbjct: 87  FILRLAYRSNPEEGKLIFCNGVVLHRTQCVRGFG-DWIDSILEFSQSLHRMNLDVSAFSC 145

Query: 329 LCALTLI 335
           L AL +I
Sbjct: 146 LAALVII 152

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

 Score =  164 bits (416), Expect = 3e-51
 Identities = 68/75 (90%), Positives = 71/75 (94%)

Query: 41  QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRF 100
            LCAVCGD AACQHYGVRTCEGCKGFFKRTVQK +KYVCLA+K CPVDKRRRNRCQ+CRF
Sbjct: 1   GLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRF 60

Query: 101 QKCLQVGMVKEVVRT 115
           QKCLQVGMVKEVVRT
Sbjct: 61  QKCLQVGMVKEVVRT 75

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

 Score =  167 bits (426), Expect = 1e-50
 Identities = 74/128 (57%), Positives = 92/128 (71%), Gaps = 2/128 (1%)

Query: 209 YREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL 268
            +E     PP  + +++QQFY LLT SVDVIR +A+KIPGF DL +EDQ+LL +SA LEL
Sbjct: 27  IQENVDPVPPKPDSQQVQQFYDLLTGSVDVIRQWAEKIPGFKDLHREDQDLLLESAFLEL 86

Query: 269 FVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLH-LMEIDISAFA 327
           FVLRLAYR+   D KL+FCNG+VL + QC R FG +WL++IL F  SL  L+  DISAF 
Sbjct: 87  FVLRLAYRSNPVDGKLVFCNGLVLHRLQCVRGFG-EWLDSILAFSSSLQSLLLDDISAFC 145

Query: 328 CLCALTLI 335
           CL  L LI
Sbjct: 146 CLALLLLI 153

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

 Score =  145 bits (367), Expect = 6e-42
 Identities = 68/115 (59%), Positives = 91/115 (79%), Gaps = 1/115 (0%)

Query: 221 EPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAE 280
           + + IQQFY LLT S+++IR +A+KIPGF+DL K DQ+LLF+SA LELFVLRLAYR+   
Sbjct: 39  DTQHIQQFYDLLTGSMEIIRGWAEKIPGFTDLPKADQDLLFESAFLELFVLRLAYRSNPV 98

Query: 281 DTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
           + KLIFCNGVVL + QC R FG +W+++I+EF  +L  M IDISAF+C+ AL ++
Sbjct: 99  EGKLIFCNGVVLHRLQCVRGFG-EWIDSIVEFSSNLQNMNIDISAFSCIAALAMV 152

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

 Score =  138 bits (351), Expect = 2e-41
 Identities = 46/72 (63%), Positives = 54/72 (75%)

Query: 43  CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
           CAVCGD A+  HYGV TCEGCKGFF+R+V++  +Y C A   C +DKR RNRCQ CR +K
Sbjct: 1   CAVCGDKASGYHYGVLTCEGCKGFFRRSVRRNLEYTCPAGGNCVIDKRNRNRCQACRLKK 60

Query: 103 CLQVGMVKEVVR 114
           CL VGM KE VR
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|201004 pfam00105, zf-C4, Zinc finger, C4 type (two domains)

 Score =  135 bits (341), Expect = 4e-40
 Identities = 44/70 (62%), Positives = 54/70 (77%)

Query: 41  QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRF 100
           +LC VCGD A+  HYGV TCEGCKGFF+R++QK   Y C  +K C +DKR RNRCQ+CR 
Sbjct: 1   ELCKVCGDKASGYHYGVLTCEGCKGFFRRSIQKNIVYTCPFNKDCVIDKRNRNRCQYCRL 60

Query: 101 QKCLQVGMVK 110
           +KCL+VGM K
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|143519 cd06961, NR_DBD_TR, DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers

 Score =  118 bits (297), Expect = 2e-33
 Identities = 44/84 (52%), Positives = 55/84 (65%)

Query: 42  LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQ 101
            C VCGD A   HY   TCEGCKGFF+RTVQK   Y C  +  C +DK  RN+CQ CRF+
Sbjct: 1   PCVVCGDKATGYHYRCITCEGCKGFFRRTVQKKLSYSCKGEGKCEIDKVTRNQCQECRFK 60

Query: 102 KCLQVGMVKEVVRTDSLKGRRGRL 125
           KC+ VGM K++V  D  +G + +L
Sbjct: 61  KCIAVGMAKDLVLDDRKRGAKRKL 84

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|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 =  116 bits (291), Expect = 2e-32
 Identities = 45/82 (54%), Positives = 57/82 (69%)

Query: 43  CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
           C VCGD  +  HYG+ TCE CKGFFKRTVQ   +Y C+ ++ C +DK +R RC +CRFQK
Sbjct: 1   CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKRYTCIENQNCQIDKTQRKRCPYCRFQK 60

Query: 103 CLQVGMVKEVVRTDSLKGRRGR 124
           CL VGM  E VR D ++G R +
Sbjct: 61  CLSVGMKLEAVRADRMRGGRNK 82

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

 Score =  114 bits (288), Expect = 3e-32
 Identities = 45/73 (61%), Positives = 59/73 (80%)

Query: 42  LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQ 101
           +CA+CGD A+ +HYGV +CEGCKGFFKRTV+K   Y C  +K C +DKR+RNRCQ+CR+Q
Sbjct: 2   ICAICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQ 61

Query: 102 KCLQVGMVKEVVR 114
           KCL +GM +E V+
Sbjct: 62  KCLAMGMKREAVQ 74

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|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 =  115 bits (289), Expect = 3e-32
 Identities = 44/83 (53%), Positives = 57/83 (68%)

Query: 40  SQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCR 99
            +LC++C D A   HYG+ TCEGCKGFFKRTVQ    Y C+ D  C + K +RNRCQ+CR
Sbjct: 6   PKLCSICEDKATGLHYGIITCEGCKGFFKRTVQNKRVYTCVGDGRCEITKAQRNRCQYCR 65

Query: 100 FQKCLQVGMVKEVVRTDSLKGRR 122
           F+KC++ GM+   VR D + G R
Sbjct: 66  FRKCIRKGMMLAAVREDRMPGGR 88

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

 Score =  113 bits (284), Expect = 1e-31
 Identities = 36/70 (51%), Positives = 44/70 (62%)

Query: 42  LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQ 101
           LC VCGD A+  H+GV +C  CK FF+RTV    KY C     C ++KR R RC+ CR +
Sbjct: 1   LCCVCGDHASGFHFGVCSCRACKAFFRRTVNLRYKYRCDRKNNCSINKRYRCRCRACRLK 60

Query: 102 KCLQVGMVKE 111
           KCL VGM  E
Sbjct: 61  KCLGVGMDPE 70

Length = 70

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

 Score =  113 bits (284), Expect = 2e-31
 Identities = 49/93 (52%), Positives = 62/93 (66%)

Query: 39  PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFC 98
           P +LC VCGDIA+  HYGV +CE CK FFKRT+Q   +Y C A   C + KRRR  CQ C
Sbjct: 3   PKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQAC 62

Query: 99  RFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPKS 131
           RF KCL+VGM+KE VR D ++G R +   +  +
Sbjct: 63  RFMKCLKVGMLKEGVRLDRVRGGRQKYKRRIDA 95

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

 Score =  110 bits (278), Expect = 1e-30
 Identities = 41/74 (55%), Positives = 53/74 (71%)

Query: 43  CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
           CAVCGD A  +HYGV +C GCKGFF+R+V+K   Y C     C VDK +RN C++CRF+K
Sbjct: 1   CAVCGDRATGKHYGVLSCNGCKGFFRRSVRKNRTYTCRFGGNCVVDKDKRNACRYCRFKK 60

Query: 103 CLQVGMVKEVVRTD 116
           CL+VGM  E V+ +
Sbjct: 61  CLEVGMDPEAVQNE 74

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 =  107 bits (270), Expect = 2e-29
 Identities = 41/76 (53%), Positives = 54/76 (71%)

Query: 39  PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFC 98
           P +LC VCGD A+ +HYG  +CEGCKGFFKR+++K   Y C   K C ++K  RNRCQ+C
Sbjct: 2   PVELCVVCGDKASGRHYGAVSCEGCKGFFKRSIRKNLGYSCRGSKDCVINKHHRNRCQYC 61

Query: 99  RFQKCLQVGMVKEVVR 114
           R QKCL +GM  + V+
Sbjct: 62  RLQKCLAMGMKSDSVQ 77

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

 Score =  107 bits (268), Expect = 3e-29
 Identities = 45/85 (52%), Positives = 56/85 (65%)

Query: 37  PSPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQ 96
           P   + C VC D ++  HYGV  CEGCKGFF+R++QK   Y C  DK C ++K  RNRCQ
Sbjct: 1   PRIYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQ 60

Query: 97  FCRFQKCLQVGMVKEVVRTDSLKGR 121
           +CR QKC +VGM KE VR D  K +
Sbjct: 61  YCRLQKCFEVGMSKESVRNDRNKKK 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|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 =  106 bits (267), Expect = 5e-29
 Identities = 40/82 (48%), Positives = 56/82 (68%)

Query: 43  CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
           C +CGD A   HYG+ +CEGCKGFFKR++     Y C  DK C + +++RNRCQ+CR  K
Sbjct: 9   CLICGDRATGLHYGIISCEGCKGFFKRSICNKRVYRCSRDKNCVMSRKQRNRCQYCRLLK 68

Query: 103 CLQVGMVKEVVRTDSLKGRRGR 124
           CLQ+GM ++ +R D + G R +
Sbjct: 69  CLQMGMNRKAIREDGMPGGRNK 90

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|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 =  103 bits (259), Expect = 5e-28
 Identities = 45/74 (60%), Positives = 52/74 (70%)

Query: 43  CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
           C VCGDIA+  HYGV +CE CK FFKRT+Q    Y C +   C VDK+RR  CQ CR QK
Sbjct: 1   CLVCGDIASGYHYGVASCEACKAFFKRTIQGNLGYSCPSTSECEVDKKRRKSCQACRLQK 60

Query: 103 CLQVGMVKEVVRTD 116
           CL+VGM+KE VR D
Sbjct: 61  CLKVGMLKEGVRLD 74

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|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 =  103 bits (259), Expect = 7e-28
 Identities = 45/88 (51%), Positives = 60/88 (68%), Gaps = 7/88 (7%)

Query: 43  CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
           C VCGD A+  HYGV +CEGCKGFF+R++QK  +Y CL D  C + +  RNRCQ+CRF+K
Sbjct: 1   CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYRCLRDGKCEIIRLNRNRCQYCRFKK 60

Query: 103 CLQVGMVKEVVRTDSLKGRRGRLPSKPK 130
           CL  GM K+ V       R GR+P++ +
Sbjct: 61  CLAAGMSKDSV-------RYGRIPNRQR 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|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 =  102 bits (257), Expect = 1e-27
 Identities = 39/72 (54%), Positives = 55/72 (76%)

Query: 43  CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
           C VCGD A+ +HYGV +C+GC+GFFKR++++   YVC  + +C VD  RRN+CQ CRF+K
Sbjct: 1   CRVCGDRASGKHYGVPSCDGCRGFFKRSIRRNLAYVCKENGSCVVDVARRNQCQACRFKK 60

Query: 103 CLQVGMVKEVVR 114
           CLQV M ++ V+
Sbjct: 61  CLQVNMNRDAVQ 72

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

 Score =  103 bits (257), Expect = 2e-27
 Identities = 44/91 (48%), Positives = 61/91 (67%), Gaps = 8/91 (8%)

Query: 42  LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKY-VCLADKACPVDKRRRNRCQFCRF 100
           LC VCGD A+  HYGV  CEGCKGFF+R++Q+  +Y  C  ++ C + +  RNRCQ+CRF
Sbjct: 5   LCKVCGDKASGFHYGVHACEGCKGFFRRSIQQKIQYRKCTKNETCSIMRINRNRCQYCRF 64

Query: 101 QKCLQVGMVKEVVRTDSLKGRRGRLPSKPKS 131
           +KCL VGM ++ VR        GR+P + K+
Sbjct: 65  KKCLAVGMSRDAVRF-------GRIPKREKA 88

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

 Score =  101 bits (254), Expect = 3e-27
 Identities = 42/85 (49%), Positives = 55/85 (64%), Gaps = 4/85 (4%)

Query: 39  PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFC 98
            +  CAVC D A+  HYGV +CEGCK FFKR++Q  + Y+C A   C +DK RR  CQ C
Sbjct: 2   DTHFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQAC 61

Query: 99  RFQKCLQVGMVKEVVRTDSLKGRRG 123
           R +KC +VGM+K  +R    + RRG
Sbjct: 62  RLRKCYEVGMMKGGIR----RERRG 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|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 =  100 bits (250), Expect = 8e-27
 Identities = 38/72 (52%), Positives = 54/72 (75%)

Query: 43  CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
           C VCGD ++ +HYG  TCEGCK FFKR+V++   Y C  ++ CP+D+  RN+CQ+CR +K
Sbjct: 1   CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRGNRNCPIDQHHRNQCQYCRLKK 60

Query: 103 CLQVGMVKEVVR 114
           CL+VGM +E V+
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|143529 cd07154, NR_DBD_PNR_like, The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family

 Score = 98.8 bits (246), Expect = 3e-26
 Identities = 38/73 (52%), Positives = 53/73 (72%), Gaps = 1/73 (1%)

Query: 43  CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLA-DKACPVDKRRRNRCQFCRFQ 101
           C VCGD ++ +HYGV  C+GC GFFKR++++   Y C A + +C VDK RRN+CQ CR +
Sbjct: 1   CKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNLLYTCKAGNGSCVVDKARRNQCQACRLK 60

Query: 102 KCLQVGMVKEVVR 114
           KCL+V M K+ V+
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 = 98.8 bits (246), Expect = 3e-26
 Identities = 41/73 (56%), Positives = 51/73 (69%), Gaps = 1/73 (1%)

Query: 43  CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYV-CLADKACPVDKRRRNRCQFCRFQ 101
           C VCGD A+  HYGV +CEGCKGFF+RT+Q    Y  CL    C + ++ RNRCQ+CRF+
Sbjct: 1   CKVCGDKASGFHYGVHSCEGCKGFFRRTIQHNLTYRRCLNGGKCVIQRKNRNRCQYCRFK 60

Query: 102 KCLQVGMVKEVVR 114
           KCL VGM +  VR
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|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 = 95.4 bits (237), Expect = 1e-24
 Identities = 41/83 (49%), Positives = 54/83 (65%), Gaps = 1/83 (1%)

Query: 35  TPPSPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKA-CPVDKRRRN 93
              +P  LC VCGD ++ +HYG+  C GC GFFKR+V++   Y C A    CPVDK  RN
Sbjct: 1   KGLNPGLLCRVCGDTSSGKHYGIYACNGCSGFFKRSVRRKLIYRCQAGTGMCPVDKAHRN 60

Query: 94  RCQFCRFQKCLQVGMVKEVVRTD 116
           +CQ CR +KCLQ GM K+ V+ +
Sbjct: 61  QCQACRLKKCLQAGMNKDAVQNE 83

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

 Score = 94.8 bits (236), Expect = 2e-24
 Identities = 43/86 (50%), Positives = 54/86 (62%), Gaps = 10/86 (11%)

Query: 42  LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKY-VCLADKACPVDKRRRNRCQFCRF 100
            C VCGD A+  HYGV  CEGCKGFF+RT++    Y  C  D +C + K+ RN+CQ+CRF
Sbjct: 1   ECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLVYKPC--DLSCKIHKKSRNKCQYCRF 58

Query: 101 QKCLQVGMVKEVVRTDSLKGRRGRLP 126
           QKCL VGM    +R        GR+P
Sbjct: 59  QKCLNVGMSHNAIRF-------GRMP 77

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

 Score = 94.9 bits (236), Expect = 2e-24
 Identities = 38/72 (52%), Positives = 49/72 (68%)

Query: 43  CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
           C +CGD ++  HYGV TCEGCKGFF+R+ Q    Y C   K C +D+  RNRCQ CR QK
Sbjct: 8   CKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVSYSCPRQKNCLIDRTNRNRCQHCRLQK 67

Query: 103 CLQVGMVKEVVR 114
           CL +GM ++ V+
Sbjct: 68  CLALGMSRDAVK 79

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|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 = 94.1 bits (234), Expect = 3e-24
 Identities = 40/75 (53%), Positives = 49/75 (65%), Gaps = 1/75 (1%)

Query: 43  CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADK-ACPVDKRRRNRCQFCRFQ 101
           C VCGD +  +HYGV  C+GC  FFKR+V+KG  Y C+A    C VDK RRN C FCR Q
Sbjct: 1   CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKGIIYTCIAGNGNCVVDKARRNWCPFCRLQ 60

Query: 102 KCLQVGMVKEVVRTD 116
           KC  VGM +  V+ +
Sbjct: 61  KCFAVGMNRAAVQEE 75

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

 Score = 93.7 bits (233), Expect = 5e-24
 Identities = 36/74 (48%), Positives = 53/74 (71%), Gaps = 2/74 (2%)

Query: 43  CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADK--ACPVDKRRRNRCQFCRF 100
           C VCGD ++ +HYG+  C+GC GFFKR++++  +YVC +     CPVDK  RN+C+ CR 
Sbjct: 9   CKVCGDRSSGKHYGIYACDGCSGFFKRSIRRNRQYVCKSKGQGGCPVDKTHRNQCRACRL 68

Query: 101 QKCLQVGMVKEVVR 114
           +KC +VGM K+ V+
Sbjct: 69  KKCFEVGMNKDAVQ 82

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|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 = 92.6 bits (230), Expect = 7e-24
 Identities = 34/72 (47%), Positives = 44/72 (61%)

Query: 43  CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
           C VCG  ++  H+G  TCEGCKGFF+RT    + YVC   + C +    RN C+ CRF++
Sbjct: 1   CRVCGGKSSGFHFGALTCEGCKGFFRRTELSSNSYVCPGGQNCAITPATRNACKSCRFRR 60

Query: 103 CLQVGMVKEVVR 114
           CL VGM K   R
Sbjct: 61  CLAVGMSKTGSR 72

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

 Score = 94.7 bits (236), Expect = 2e-23
 Identities = 32/113 (28%), Positives = 53/113 (46%), Gaps = 4/113 (3%)

Query: 226 QQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLI 285
           +    L T  + +I  +A  IPGF +L  EDQ +L +S  LEL VL LAYR+      L+
Sbjct: 1   ELLCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLL 60

Query: 286 FCNGVVL----EKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
                      ++ + +     + +  + EF   L  +++D   +A L A+ L
Sbjct: 61  LAPNGGHTDDDKEDEMKLLLKGELIRLLFEFVNPLRALKLDDEEYALLKAIVL 113

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|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 = 89.7 bits (223), Expect = 8e-23
 Identities = 32/71 (45%), Positives = 47/71 (66%)

Query: 43  CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
           C VCGD A   H+   TCEGCKGFF+R++++ +++ C  +  C + K  R  CQ CR +K
Sbjct: 1   CGVCGDRATGYHFNAMTCEGCKGFFRRSMKRKARFTCPFNGDCEITKDNRRHCQACRLKK 60

Query: 103 CLQVGMVKEVV 113
           CL +GM KE++
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|143535 cd07161, NR_DBD_EcR, DNA-binding domain of Ecdysone receptor (ECR) family is composed of two C4-type zinc fingers

 Score = 88.4 bits (219), Expect = 4e-22
 Identities = 40/77 (51%), Positives = 50/77 (64%)

Query: 41  QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRF 100
           +LC VCGD A+  HY   TCEGCKGFF+R+V K + Y C   +AC +D   R +CQ CR 
Sbjct: 2   ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYHCKYGRACEMDMYMRRKCQECRL 61

Query: 101 QKCLQVGMVKEVVRTDS 117
           +KCL VGM  E V  +S
Sbjct: 62  KKCLSVGMRPECVVPES 78

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

 Score = 88.4 bits (219), Expect = 5e-22
 Identities = 39/88 (44%), Positives = 58/88 (65%), Gaps = 4/88 (4%)

Query: 33  RPTPPSP----SQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVD 88
           R   P+P    +++C+VCGD A+  HY V +CEGCKGFF+R+V KG++YVC     C +D
Sbjct: 7   RKKGPAPKMLGNEVCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAQYVCKNGGKCQMD 66

Query: 89  KRRRNRCQFCRFQKCLQVGMVKEVVRTD 116
              R +CQ CR +KC + GM ++ V ++
Sbjct: 67  MYMRRKCQECRLRKCREAGMREQCVLSE 94

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|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 = 87.5 bits (217), Expect = 7e-22
 Identities = 35/72 (48%), Positives = 45/72 (62%)

Query: 42  LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQ 101
            C VCGD A+  HYGV +CEGCKGFF+R+V KG+ Y C     C +D   R +CQ CR +
Sbjct: 1   NCVVCGDKASGFHYGVLSCEGCKGFFRRSVTKGAVYACKFGNKCEMDMYMRRKCQECRLR 60

Query: 102 KCLQVGMVKEVV 113
           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|132743 cd06945, NR_LBD_Nurr1_like, The ligand binding domain of Nurr1 and related nuclear receptor proteins, members of nuclear receptor superfamily

 Score = 89.4 bits (222), Expect = 8e-21
 Identities = 43/87 (49%), Positives = 53/87 (60%), Gaps = 18/87 (20%)

Query: 140 PVSLITAL------------------YREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHF 181
           PVSLITAL                   +E     PP  + +++QQFY LLT SVDVIR +
Sbjct: 1   PVSLITALVRAHVDSTPRKTDLDYSKIQENVDPVPPKPDSQQVQQFYDLLTGSVDVIRQW 60

Query: 182 ADKIPGFSDLCKEDQELLFQSASLELF 208
           A+KIPGF DL +EDQ+LL +SA LELF
Sbjct: 61  AEKIPGFKDLHREDQDLLLESAFLELF 87

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

 Score = 83.8 bits (207), Expect = 2e-20
 Identities = 35/81 (43%), Positives = 51/81 (62%)

Query: 42  LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQ 101
           +C VCGD A   H+   TCEGCKGFF+R +++ ++  C   K C + K  R +CQ CR +
Sbjct: 1   ICRVCGDRATGYHFNAMTCEGCKGFFRRAMKRNARLCCPFQKGCVITKSNRRQCQACRLR 60

Query: 102 KCLQVGMVKEVVRTDSLKGRR 122
           KCL +GM KE++ +D    +R
Sbjct: 61  KCLSIGMKKELIMSDEAVEKR 81

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

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

 Score = 83.5 bits (206), Expect = 2e-20
 Identities = 35/76 (46%), Positives = 49/76 (64%)

Query: 41  QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRF 100
           +LC VCGD A+  HY   TCEGCKGFF+R++ K + Y C     C +D   R +CQ CR 
Sbjct: 2   ELCVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCEMDMYMRRKCQECRL 61

Query: 101 QKCLQVGMVKEVVRTD 116
           +KC ++GM+ E + T+
Sbjct: 62  RKCKEMGMLAECLLTE 77

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

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

 Score = 84.2 bits (208), Expect = 3e-20
 Identities = 35/91 (38%), Positives = 55/91 (60%)

Query: 41  QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRF 100
           ++C VCGD A   H+   TCEGCKGFF+R++++ + + C  +  C + K  R  CQ CR 
Sbjct: 7   RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRL 66

Query: 101 QKCLQVGMVKEVVRTDSLKGRRGRLPSKPKS 131
           ++C+ +GM+KE + TD    R+  +  K K 
Sbjct: 67  KRCVDIGMMKEFILTDEEVQRKREMILKRKE 97

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 = 83.0 bits (205), Expect = 4e-20
 Identities = 35/71 (49%), Positives = 42/71 (59%)

Query: 39  PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFC 98
           P ++C VC D A+  HYGV TC  CK FFKR V+    Y+C     C +DK RR  C  C
Sbjct: 1   PQKICLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPAC 60

Query: 99  RFQKCLQVGMV 109
           R +KCLQ GM 
Sbjct: 61  RLRKCLQAGMN 71

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|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 = 77.5 bits (191), Expect = 5e-18
 Identities = 31/72 (43%), Positives = 40/72 (55%), Gaps = 2/72 (2%)

Query: 41  QLCAVCGDIAACQHYGVRTCEGCKGFFKRTV--QKGSKYVCLADKACPVDKRRRNRCQFC 98
           Q C VCG+ AA  H+G   CE CK FF R+      +   C     C +DK+ R +CQ C
Sbjct: 1   QTCQVCGEPAAGFHHGAYVCEACKKFFMRSSNAISFTISECPNGGKCIIDKKNRTKCQAC 60

Query: 99  RFQKCLQVGMVK 110
           R++KCL VGM  
Sbjct: 61  RYRKCLNVGMSL 72

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

 Score = 76.9 bits (189), Expect = 6e-18
 Identities = 32/73 (43%), Positives = 39/73 (53%)

Query: 43  CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
           C +CGD A+  HYGV TC  CK FFKR  +    Y+C     C +DK RR  C  CR +K
Sbjct: 1   CLICGDEASGCHYGVLTCGSCKVFFKRAAEGQHNYLCAGRNDCIIDKIRRKNCPACRLRK 60

Query: 103 CLQVGMVKEVVRT 115
           C Q GM     + 
Sbjct: 61  CYQAGMTLGARKL 73

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 = 74.4 bits (183), Expect = 7e-17
 Identities = 29/92 (31%), Positives = 49/92 (53%)

Query: 43  CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
           C VCGD A   ++   TCE CK FF+R   K  ++ C  +++C ++   R  CQ CR  K
Sbjct: 3   CGVCGDKALGYNFNAITCESCKAFFRRNALKNKEFKCPFNESCEINVVTRRFCQKCRLDK 62

Query: 103 CLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQE 134
           C  +GM KE + ++  K  + +   + ++ + 
Sbjct: 63  CFAIGMKKEWIMSEEDKSEKRQKIEENRAKKR 94

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

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

 Score = 76.3 bits (188), Expect = 9e-17
 Identities = 26/100 (26%), Positives = 44/100 (44%), Gaps = 4/100 (4%)

Query: 239 IRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVL----EK 294
              +A   PGF +L  EDQ +L +S   EL +L LAYR+     +L+             
Sbjct: 8   TVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKELLLAPDGTYIRPDAV 67

Query: 295 QQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
            + ++ F       + E  + L  +++D   +A L A+ L
Sbjct: 68  LELRKLFSPFLDRILSELVKPLRELKLDDEEYALLKAIVL 107

Length = 163

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

 Score = 73.4 bits (180), Expect = 1e-16
 Identities = 32/71 (45%), Positives = 41/71 (57%)

Query: 38  SPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQF 97
            P + C +CGD A+  HYG  TC  CK FFKR  +   KY+C +   C +DK RR  C  
Sbjct: 1   PPQKTCLICGDEASGCHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPS 60

Query: 98  CRFQKCLQVGM 108
           CR +KC + GM
Sbjct: 61  CRLRKCFEAGM 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|132762 cd07348, NR_LBD_NGFI-B, The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors

 Score = 76.8 bits (189), Expect = 2e-16
 Identities = 43/87 (49%), Positives = 54/87 (62%), Gaps = 18/87 (20%)

Query: 140 PVSLITALYR---EPNP------------LEPPIAEPEK---IQQFYSLLTTSVDVIRHF 181
           PV+LI +L R   + NP               P+ E E    IQQFY LL+ S++VIR +
Sbjct: 1   PVNLIASLVRAHIDSNPSSAKLDYSKFQESVSPLFEKEDASDIQQFYDLLSGSLEVIRKW 60

Query: 182 ADKIPGFSDLCKEDQELLFQSASLELF 208
           A+KIPGFSD CKEDQELL +SA +ELF
Sbjct: 61  AEKIPGFSDFCKEDQELLLESAFVELF 87

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 = 71.6 bits (175), Expect = 2e-14
 Identities = 45/100 (45%), Positives = 58/100 (58%), Gaps = 24/100 (24%)

Query: 140 PVSLITALYREPNPLEPPIA------------------EPEKIQQFYSLLTTSVDVIRHF 181
           PVSLI+AL R      P +                   + + IQQFY LLT S+++IR +
Sbjct: 1   PVSLISALVRAHVDSNPAMTSLDYSRFQANPDYQMSGDDTQHIQQFYDLLTGSMEIIRGW 60

Query: 182 ADKIPGFSDLCKEDQELLFQSASLELF-----YREPNPLE 216
           A+KIPGF+DL K DQ+LLF+SA LELF     YR  NP+E
Sbjct: 61  AEKIPGFTDLPKADQDLLFESAFLELFVLRLAYRS-NPVE 99

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

 Score = 68.8 bits (169), Expect = 5e-14
 Identities = 30/114 (26%), Positives = 56/114 (49%)

Query: 222 PEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAED 281
            EK   F  ++T ++  +  FA +IPGF +L +EDQ  L +    E+ +LR A     E 
Sbjct: 1   QEKFDHFTEIMTVAIRRVVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATLYDPEK 60

Query: 282 TKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
             L F +G    +         +++  + EF + ++ +++D + +A L A+ L 
Sbjct: 61  NSLTFGDGKGNSRDVLLNGGFGEFIEPLFEFAEKMNKLQLDDNEYALLTAIVLF 114

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

 Score = 66.3 bits (162), Expect = 5e-13
 Identities = 28/98 (28%), Positives = 48/98 (48%), Gaps = 4/98 (4%)

Query: 241 HFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRT-RAEDTKLIFCNGVVLEKQQCQR 299
            +A + PGF +L  +DQ  L +S+  E   L LA R+   E   L+F NG+ L++ + + 
Sbjct: 18  EWAKRFPGFRELSLDDQLALLKSSWFEWLRLELASRSAECEKDDLLFSNGLYLDRDELKS 77

Query: 300 SFGD---DWLNAILEFCQSLHLMEIDISAFACLCALTL 334
              +   + +  + E  Q L  +++     A L AL L
Sbjct: 78  IEVNYINEQIRQLFELVQPLKELKLTDEELAALKALLL 115

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

>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 = 64.4 bits (157), Expect = 5e-12
 Identities = 31/110 (28%), Positives = 53/110 (48%)

Query: 226 QQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLI 285
            +F  L T  +  I  FA ++PGF+ L   DQ  L ++A L++ +LR+  R   E   + 
Sbjct: 41  DKFSELSTKCIIKIVEFAKRLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMT 100

Query: 286 FCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
           F +G+ L + Q   +      + +  F   L  +E+D +    L A+ LI
Sbjct: 101 FSDGLTLNRTQMHNAGFGPLTDLVFTFANQLLPLEMDDTEIGLLSAICLI 150

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

 Score = 63.4 bits (155), Expect = 8e-12
 Identities = 36/130 (27%), Positives = 61/130 (46%), Gaps = 6/130 (4%)

Query: 211 EPNPL--EPPIAEPEKIQQFYSLLTTSVD----VIRHFADKIPGFSDLCKEDQELLFQSA 264
           EP+ L        P+      + L+   D     I  +A  IPGFSDL   DQ  L QSA
Sbjct: 9   EPDKLYAMNDPTGPDTEVSLLATLSDLADRELVHIISWAKHIPGFSDLSLNDQMHLLQSA 68

Query: 265 SLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDIS 324
            LE+ +L L +R+     KL+F   ++L+++Q +     +  + +L+  +    + +   
Sbjct: 69  WLEILMLGLVWRSLPHPGKLVFAPDLLLDREQARVEGLLEIFDMLLQLVRRFRELGLQRE 128

Query: 325 AFACLCALTL 334
            + CL A+ L
Sbjct: 129 EYVCLKAIIL 138

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

 Score = 61.3 bits (149), Expect = 3e-11
 Identities = 33/109 (30%), Positives = 61/109 (55%)

Query: 226 QQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLI 285
           QQ    LT SV  +  FA +IPGF DL ++DQ LL ++   E++++R++    ++   + 
Sbjct: 5   QQLSEALTPSVQRVVEFAKRIPGFCDLSQDDQLLLIKAGFFEVWLVRISRLINSKSGSIT 64

Query: 286 FCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
           F +G+ + +QQ    +  D++ A+ EF  S + + +  +  A  CA+ L
Sbjct: 65  FDDGISISRQQLDIIYDSDFVKALFEFSDSFNSLGLSDTEVALFCAVVL 113

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

 Score = 61.7 bits (150), Expect = 4e-11
 Identities = 31/108 (28%), Positives = 56/108 (51%), Gaps = 1/108 (0%)

Query: 228 FYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFC 287
           F  L   SV  I  FA ++PGF  L +EDQ  L +++++E+ +L  A R   E   + F 
Sbjct: 48  FTELAILSVQEIVDFAKQLPGFLTLTREDQIALLKASTIEVMLLETARRYNPESEAITFL 107

Query: 288 NGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISAFACLCALTL 334
                 +    R+    +++N I EF +S+  +++D + +A L A+ +
Sbjct: 108 KDFPYSRDDFARAGLQVEFINPIFEFSKSMRELQLDDAEYALLIAINI 155

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

 Score = 60.6 bits (147), Expect = 5e-11
 Identities = 33/126 (26%), Positives = 59/126 (46%), Gaps = 7/126 (5%)

Query: 214 PLEPPIAEPEKIQQFYSL-LTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLR 272
           P   P     +I + +S+  T +V  +  FA +IPGF DL + DQ  L ++ + E+ ++R
Sbjct: 2   PYVDPPKSGHEIWEEFSMSFTPAVREVVEFAKRIPGFRDLSQHDQVTLLKAGTFEVLMVR 61

Query: 273 LAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFC---QSLHLMEIDISAFACL 329
            A    A++  + F +G              D LN++ +F     SL L + ++  F   
Sbjct: 62  FASLFDAKERSVTFLSGQKYSVDDLHSMGAGDLLNSMFDFSEKLNSLQLSDEEMGLF--- 118

Query: 330 CALTLI 335
            A+ L+
Sbjct: 119 TAVVLV 124

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

 Score = 56.9 bits (138), Expect = 6e-10
 Identities = 24/96 (25%), Positives = 46/96 (47%), Gaps = 2/96 (2%)

Query: 241 HFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT--KLIFCNGVVLEKQQCQ 298
            +A  +P F +L  +DQ  L Q++  EL +L LA R+   +    L+    +V+  ++  
Sbjct: 17  DWAKNLPAFRNLPLDDQLTLLQNSWAELLLLGLAQRSVHFELSELLLPSPLLVILTEREA 76

Query: 299 RSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
                + +  + E    L  +++D   +ACL A+ L
Sbjct: 77  LLGLAELVQRLQELLSKLRSLQLDPKEYACLKAIVL 112

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

 Score = 57.8 bits (140), Expect = 9e-10
 Identities = 29/110 (26%), Positives = 58/110 (52%)

Query: 223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT 282
            + +    +   +V +I  FA ++PGF  L +EDQ  L ++ S E+ +LR+A R  A+  
Sbjct: 39  MRFRHITEMTILTVQLIVEFAKRLPGFDKLSREDQITLLKACSSEVMMLRVARRYDAKTD 98

Query: 283 KLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCAL 332
            ++F N     +   +++   D    +  FC+++  M++D + +A L A+
Sbjct: 99  SIVFANNQPYTRDSYRKAGMGDSAEDLFRFCRAMCSMKVDNAEYALLTAI 148

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

 Score = 56.7 bits (137), Expect = 2e-09
 Identities = 35/132 (26%), Positives = 60/132 (45%), Gaps = 7/132 (5%)

Query: 211 EPNPL------EPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSA 264
           EP  +        P  E   +    +L    +  + ++A KIPGF DL   DQ  L +SA
Sbjct: 14  EPPHIYSEYDPTRPFTEASLMMLLTNLADRELVHMINWAKKIPGFVDLSLHDQVHLLESA 73

Query: 265 SLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFG-DDWLNAILEFCQSLHLMEIDI 323
            LEL +L L +R+     KL+F   ++L++ Q     G  +  + +L        +++  
Sbjct: 74  WLELLMLGLVWRSMEHPGKLLFAPDLLLDRNQGSCVEGMVEIFDMLLATASRFRELQLQR 133

Query: 324 SAFACLCALTLI 335
             + CL A+ L+
Sbjct: 134 EEYVCLKAIILL 145

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

 Score = 55.6 bits (134), Expect = 6e-09
 Identities = 30/113 (26%), Positives = 53/113 (46%)

Query: 223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT 282
           E    F  ++T ++  +  FA K+P F++L  EDQ +L +   +E+  LR A R   E  
Sbjct: 52  EAFSHFTKIITPAITRVVDFAKKLPMFTELPCEDQIILLKGCCMEIMSLRAAVRYDPESE 111

Query: 283 KLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            L     + + ++Q +        +AI +   SL    +D +  A L A+ L+
Sbjct: 112 TLTLSGEMAVTREQLKNGGLGVVSDAIFDLGVSLSSFNLDDTEVALLQAVLLM 164

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

 Score = 52.4 bits (126), Expect = 5e-08
 Identities = 36/130 (27%), Positives = 64/130 (49%), Gaps = 6/130 (4%)

Query: 211 EPNPL--EPPIAEPEKIQQFYSLLTTSVD----VIRHFADKIPGFSDLCKEDQELLFQSA 264
           EP+ L   P  A P+   +  + L+   D    VI  +A  IPGFS L   DQ  L QSA
Sbjct: 9   EPDKLFAMPDPALPDSDIKALTTLSDLADRELVVIIGWAKHIPGFSSLSLNDQMSLLQSA 68

Query: 265 SLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDIS 324
            +E+  L + +R+   + +L+F    +L+++  + +   +  +A L+  + L  + ++  
Sbjct: 69  WMEILTLGVVFRSLPFNGELVFAEDFILDEELAREAGLLELYSACLQLVRRLQRLRLEKE 128

Query: 325 AFACLCALTL 334
            +  L AL L
Sbjct: 129 EYVLLKALAL 138

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

 Score = 51.2 bits (123), Expect = 1e-07
 Identities = 38/113 (33%), Positives = 62/113 (54%), Gaps = 19/113 (16%)

Query: 232 LTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVV 291
           +T ++  +  FA +IPGF +LC+ DQ +L ++ SLE+ ++R++   RA +      N  V
Sbjct: 57  ITEAIQYVVEFAKRIPGFMELCQNDQIVLLKAGSLEVVLVRMS---RAFNPS----NNTV 109

Query: 292 L--EK---QQCQRSFG-DDWLNAILEFCQS---LHLMEIDISAFACLCALTLI 335
           L   K       +S G DD ++A+ +F +S   L L E +I+ F    AL LI
Sbjct: 110 LFDGKYAPIDLFKSLGCDDLISAVFDFAKSLCELKLTEDEIALF---SALVLI 159

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

 Score = 43.8 bits (104), Expect = 3e-05
 Identities = 37/132 (28%), Positives = 58/132 (43%), Gaps = 14/132 (10%)

Query: 210 REPNPLEP---PIAEPEKIQQFYS-LLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSAS 265
           R P P          PE + +  + LL  +V     +A  IP FS L   DQ +L + + 
Sbjct: 13  RPPFPYGTISSYEVSPESVCESAARLLFMAV----KWAKSIPAFSTLPFRDQLILLEESW 68

Query: 266 LELFVLRLAYRTRAED-TKLIFCNGVVLEKQQCQRSFGDD--WLNAILEFCQSLHLMEID 322
            ELF+L  A  +   D   L+   G+  +  + +R+F  +   L   L   + L +   D
Sbjct: 69  SELFLLGAAQWSLPLDSCPLLAVPGLSPDNTEAERTFLSEVRALQETLSRFRQLRV---D 125

Query: 323 ISAFACLCALTL 334
            + FACL A+ L
Sbjct: 126 ATEFACLKAIVL 137

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

 Score = 41.1 bits (97), Expect = 2e-04
 Identities = 16/47 (34%), Positives = 26/47 (55%)

Query: 161 PEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL 207
            EK   F  ++T ++  +  FA +IPGF +L +EDQ  L +    E+
Sbjct: 1   QEKFDHFTEIMTVAIRRVVEFAKRIPGFRELSQEDQIALLKGGCFEI 47

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

 Score = 41.5 bits (97), Expect = 2e-04
 Identities = 22/64 (34%), Positives = 35/64 (54%), Gaps = 1/64 (1%)

Query: 209 YREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL 268
           Y + N   PP+     +     L++ S+  +  FA  IPGF DL  EDQ  L +S+++E+
Sbjct: 24  YSDFNKFRPPVRLS-MLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEV 82

Query: 269 FVLR 272
            +LR
Sbjct: 83  IMLR 86

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

 Score = 40.8 bits (96), Expect = 3e-04
 Identities = 19/43 (44%), Positives = 26/43 (60%)

Query: 165 QQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL 207
           QQ    LT SV  +  FA +IPGF DL ++DQ LL ++   E+
Sbjct: 5   QQLSEALTPSVQRVVEFAKRIPGFCDLSQDDQLLLIKAGFFEV 47

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

 Score = 40.0 bits (94), Expect = 8e-04
 Identities = 32/111 (28%), Positives = 46/111 (41%), Gaps = 24/111 (21%)

Query: 171 LTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFY----REPNPLEPPIAEPEK-- 224
           +T ++  +  FA +IPGF +LC+ DQ +L ++ SLE+      R  NP    +    K  
Sbjct: 57  ITEAIQYVVEFAKRIPGFMELCQNDQIVLLKAGSLEVVLVRMSRAFNPSNNTVLFDGKYA 116

Query: 225 -IQQFYSLLTTSVDVIRHFADKIPGFSDLCK--------EDQELLFQSASL 266
            I  F SL            D I    D  K        ED+  LF +  L
Sbjct: 117 PIDLFKSLGC---------DDLISAVFDFAKSLCELKLTEDEIALFSALVL 158

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

 Score = 39.3 bits (92), Expect = 0.001
 Identities = 25/76 (32%), Positives = 34/76 (44%), Gaps = 7/76 (9%)

Query: 139 PPVSLITALY-REPNPL------EPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDL 191
               LI+AL   EP  +        P  E   +    +L    +  + ++A KIPGF DL
Sbjct: 2   SAEQLISALLEAEPPHIYSEYDPTRPFTEASLMMLLTNLADRELVHMINWAKKIPGFVDL 61

Query: 192 CKEDQELLFQSASLEL 207
              DQ  L +SA LEL
Sbjct: 62  SLHDQVHLLESAWLEL 77

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

 Score = 39.9 bits (93), Expect = 0.001
 Identities = 23/96 (23%), Positives = 44/96 (45%), Gaps = 2/96 (2%)

Query: 242 FADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRT--RAEDTKLIFCNGVVLEKQQCQR 299
           +A  IPGF +L  +DQ  L Q + + L    L +R+  ++    L F   +++ +Q+   
Sbjct: 47  WAKAIPGFRNLHLDDQMTLLQYSWMFLMAFALGWRSYRQSNGNLLCFAPDLIINEQRMTL 106

Query: 300 SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
               D    +L     LH +++    + C+  L L+
Sbjct: 107 PCMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLL 142

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

 Score = 38.0 bits (88), Expect = 0.004
 Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 1/66 (1%)

Query: 148 YREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL 207
           Y + N   PP+     +     L++ S+  +  FA  IPGF DL  EDQ  L +S+++E+
Sbjct: 24  YSDFNKFRPPVRLS-MLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEV 82

Query: 208 FYREPN 213
                N
Sbjct: 83  IMLRSN 88

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	335
KOG4217|consensus	605		100.0
KOG4215|consensus	432		100.0
KOG4216|consensus	479		100.0
KOG4218|consensus	475		100.0
KOG4846|consensus	538		100.0
cd07170	97	NR_DBD_ERR DNA-binding domain of estrogen related	100.0
cd06964	85	NR_DBD_RAR DNA-binding domain of retinoic acid rec	100.0
cd06962	84	NR_DBD_FXR DNA-binding domain of Farnesoid X recep	100.0
cd07160	101	NR_DBD_LXR DNA-binding domain of Liver X receptors	100.0
cd06970	92	NR_DBD_PNR DNA-binding domain of the photoreceptor	100.0
cd06956	77	NR_DBD_RXR DNA-binding domain of retinoid X recept	100.0
cd06961	85	NR_DBD_TR DNA-binding domain of thyroid hormone re	100.0
cd06967	87	NR_DBD_TR2_like DNA-binding domain of the TR2 and	100.0
cd07171	82	NR_DBD_ER DNA-binding domain of estrogen receptors	100.0
cd06969	75	NR_DBD_NGFI-B DNA-binding domain of the orphan nuc	100.0
cd07155	75	NR_DBD_ER_like DNA-binding domain of estrogen rece	100.0
cd07163	92	NR_DBD_TLX DNA-binding domain of Tailless (TLX) is	100.0
cd06957	82	NR_DBD_PNR_like_2 DNA-binding domain of the photor	100.0
cd07168	90	NR_DBD_DHR4_like DNA-binding domain of ecdysone-in	100.0
cd07161	91	NR_DBD_EcR DNA-binding domain of Ecdysone receptor	100.0
cd07172	78	NR_DBD_GR_PR DNA-binding domain of glucocorticoid	100.0
cd07169	90	NR_DBD_GCNF_like DNA-binding domain of Germ cell n	100.0
cd07166	89	NR_DBD_REV_ERB DNA-binding domain of REV-ERB recep	100.0
cd06955	107	NR_DBD_VDR DNA-binding domain of vitamin D recepto	100.0
cd07154	73	NR_DBD_PNR_like The DNA-binding domain of the phot	100.0
cd06959	73	NR_DBD_EcR_like The DNA-binding domain of Ecdysone	100.0
cd07156	72	NR_DBD_VDR_like The DNA-binding domain of vitamin	100.0
cd07167	93	NR_DBD_Lrh-1_like The DNA-binding domain of Lrh-1	100.0
cd06960	76	NR_DBD_HNF4A DNA-binding domain of heptocyte nucle	100.0
cd06958	73	NR_DBD_COUP_TF DNA-binding domain of chicken ovalb	100.0
cd06916	72	NR_DBD_like DNA-binding domain of nuclear receptor	100.0
cd07164	78	NR_DBD_PNR_like_1 DNA-binding domain of the photor	100.0
cd06963	73	NR_DBD_GR_like The DNA binding domain of GR_like n	100.0
cd06966	94	NR_DBD_CAR DNA-binding domain of constitutive andr	100.0
cd07173	82	NR_DBD_AR DNA-binding domain of androgen receptor	100.0
cd06968	95	NR_DBD_ROR DNA-binding domain of Retinoid-related	100.0
cd07179	74	2DBD_NR_DBD2 The second DNA-binding domain (DBD) o	100.0
cd07157	86	2DBD_NR_DBD1 The first DNA-binding domain (DBD) of	100.0
cd07165	81	NR_DBD_DmE78_like DNA-binding domain of Drosophila	100.0
cd07162	87	NR_DBD_PXR DNA-binding domain of pregnane X recept	100.0
cd07158	73	NR_DBD_Ppar_like The DNA-binding domain of peroxis	100.0
cd06965	84	NR_DBD_Ppar DNA-binding domain of peroxisome proli	100.0
smart00399	70	ZnF_C4 c4 zinc finger in nuclear hormone receptors	99.98
PF00105	70	zf-C4: Zinc finger, C4 type (two domains); InterPr	99.97
cd07072	239	NR_LBD_DHR38_like Ligand binding domain of DHR38_l	99.95
cd07348	238	NR_LBD_NGFI-B The ligand binding domain of Nurr1,	99.92
cd07071	238	NR_LBD_Nurr1 The ligand binding domain of Nurr1, a	99.92
cd06940	189	NR_LBD_REV_ERB The ligand binding domain of REV-ER	99.91
cd07076	247	NR_LBD_GR Ligand binding domain of the glucocortic	99.91
cd06935	243	NR_LBD_TR The ligand binding domain of thyroid hor	99.9
cd07075	248	NR_LBD_MR Ligand binding domain of the mineralocor	99.9
cd06945	239	NR_LBD_Nurr1_like The ligand binding domain of Nur	99.9
cd06941	195	NR_LBD_DmE78_like The ligand binding domain of Dro	99.89
cd06937	231	NR_LBD_RAR The ligand binding domain (LBD) of reti	99.89
cd06947	246	NR_LBD_GR_Like Ligand binding domain of nuclear ho	99.89
cd07074	248	NR_LBD_PR Ligand binding domain of the progesteron	99.88
cd06939	241	NR_LBD_ROR_like The ligand binding domain of Retin	99.88
cd06949	235	NR_LBD_ER Ligand binding domain of Estrogen recept	99.88
cd07073	246	NR_LBD_AR Ligand binding domain of the nuclear rec	99.88
cd06954	236	NR_LBD_LXR The ligand binding domain of Liver X re	99.87
cd06929	174	NR_LBD_F1 Ligand-binding domain of nuclear recepto	99.87
cd06934	226	NR_LBD_PXR_like The ligand binding domain of xenob	99.86
cd06938	231	NR_LBD_EcR The ligand binding domain (LBD) of the	99.86
cd06944	237	NR_LBD_Ftz-F1_like The ligand binding domain of FT	99.85
cd06942	191	NR_LBD_Sex_1_like The ligand binding domain of Cae	99.85
cd06946	221	NR_LBD_ERR The ligand binding domain of estrogen r	99.85
cd07069	241	NR_LBD_Lrh-1 The ligand binding domain of the live	99.85
cd07070	237	NR_LBD_SF-1 The ligand binding domain of nuclear r	99.85
cd06933	238	NR_LBD_VDR The ligand binding domain of vitamin D	99.85
cd06932	259	NR_LBD_PPAR The ligand binding domain of peroxisom	99.84
cd07068	221	NR_LBD_ER_like The ligand binding domain of estrog	99.84
cd06930	165	NR_LBD_F2 Ligand-binding domain of nuclear recepto	99.84
cd06943	207	NR_LBD_RXR_like The ligand binding domain of the r	99.84
cd06950	206	NR_LBD_Tlx_PNR_like The ligand binding domain of T	99.84
cd06953	213	NR_LBD_DHR4_like The ligand binding domain of orph	99.82
cd06931	222	NR_LBD_HNF4_like The ligand binding domain of hept	99.81
cd06951	222	NR_LBD_Dax1_like The ligand binding domain of DAX1	99.81
cd06936	221	NR_LBD_Fxr The ligand binding domain of Farnesoid	99.8
cd07349	222	NR_LBD_SHP The ligand binding domain of DAX1 prote	99.79
cd07350	232	NR_LBD_Dax1 The ligand binding domain of DAX1 prot	99.79
cd06948	236	NR_LBD_COUP-TF Ligand binding domain of chicken ov	99.79
cd06952	222	NR_LBD_TR2_like The ligand binding domain of the o	99.72
PF00104	203	Hormone_recep: Ligand-binding domain of nuclear ho	99.72
cd06157	168	NR_LBD The ligand binding domain of nuclear recept	99.71
smart00430	163	HOLI Ligand binding domain of hormone receptors.	99.68
KOG4217|consensus	605		94.65
KOG3277|consensus	165		85.67
cd07072	239	NR_LBD_DHR38_like Ligand binding domain of DHR38_l	84.2
PF10764	46	Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700	82.76

>KOG4217|consensus

Probab=100.00  E-value=6.8e-64  Score=430.61  Aligned_cols=251  Identities=66%  Similarity=1.115  Sum_probs=224.0

Q ss_pred             CCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeeccc
Q psy2636          39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSL  118 (335)
Q Consensus        39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~  118 (335)
                      .+..|.||||.|.--||||-+||||||||+|||++|.+|+|.+|++|.|||..||+||||||||||+|||-+|.|+.|..
T Consensus       268 ~e~~CAVCgDnAaCqHYGvRTCEGCKGFFKRTVQKnaKYvClanKnCPVDKRrRnRCQyCRfQKCL~VGMVKEVVRtdSL  347 (605)
T KOG4217|consen  268 AEGLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLAVGMVKEVVRTDSL  347 (605)
T ss_pred             ccceeeecCChHHhhhcCccccccchHHHHHHHhcCCeeEeecCCCCCcchhhhhhchhhhHhHHHHhhhhhhheecccc
Confidence            36789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCCCCCCCCCCCCCCCcchhhhhhcCCCCCCCCCCChhHHHHHHHhhcchhhhhhhcccCCCCCCCCCHHHHHH
Q psy2636         119 KGRRGRLPSKPKSPQESPPSPPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQEL  198 (335)
Q Consensus       119 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~i~~~~~~~p~~~~l~~~~~~~  198 (335)
                      ++||+|.+++++++++.++++|..+++++.+++.+..                              |+...+.      
T Consensus       348 kGRRGRLpSKpKs~q~sppSpPi~LltalvrAh~Dst------------------------------p~~~~ld------  391 (605)
T KOG4217|consen  348 KGRRGRLPSKPKSRQPSPPSPPISLLTALVRAHVDST------------------------------PSTMTLD------  391 (605)
T ss_pred             ccccCCCCCCCCCCCCCCCCCchHHHHHHHHHhhcCC------------------------------CCcchhh------
Confidence            9999999999999999899999999988887764322                              2211111      


Q ss_pred             HHhhhhhccccCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhc
Q psy2636         199 LFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTR  278 (335)
Q Consensus       199 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~  278 (335)
                       +      ..| .+........+...+++|+++++-++..+..||..||+|.+|+.+||-+||.++++|+++|+.|||+.
T Consensus       392 -y------s~~-q~~~~~~~~tdA~~vqqfy~lLtgsl~virk~aekiPgf~el~paDq~lLlesaflelfvlRlAyRs~  463 (605)
T KOG4217|consen  392 -Y------SRF-QELVPHFSGTDALHVQQFYDLLTGSLEVIRKWAEKIPGFAELPPADQDLLLESAFLELFVLRLAYRSN  463 (605)
T ss_pred             -H------HHh-ccccccccccHHHHHHHHHHHhhhhHHHHHHHHHhCcCcccCChhhHHHHHHHHHHHHHHHHHHHhcC
Confidence             0      000 01011112467788999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCeEEeeCCeEeeHHhhhhhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHc
Q psy2636         279 AEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTL  334 (335)
Q Consensus       279 ~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l  334 (335)
                      ..+++++|.+|..+++-++..+|| +|++.+.+|...|..|.+|..-|+||.||.+
T Consensus       464 ~~e~kliFcsG~vlhr~qC~rgfg-ewidsi~~FS~~l~~l~idi~AfacL~aLa~  518 (605)
T KOG4217|consen  464 PSEDKLIFCSGLVLHRLQCLRGFG-EWIDSIREFSRSLHSLNIDISAFACLSALAL  518 (605)
T ss_pred             CCCCeEEEecchhhhHHHHHHHHH-HHHHHHHHHHHHhhhchhhHHHHHHHHHHHh
Confidence            999999999999999999999999 9999999999999999999999999999986

>KOG4215|consensus

Probab=100.00  E-value=1.2e-62  Score=411.45  Aligned_cols=250  Identities=27%  Similarity=0.515  Sum_probs=179.8

Q ss_pred             CCCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636          38 SPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS  117 (335)
Q Consensus        38 ~~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~  117 (335)
                      ....+|.||||+|+|.||||.+|+||||||||+|+++..|+|+++.+|.|||+.||.|||||||||+++||+++|||.+|
T Consensus        17 ~~~~~CaICGDkaTGKHYGA~SCdGCKGFFRRSVrk~~~YtCRF~k~C~VDKdkRNaCRyCRfqKC~~aGMK~eAiQnER   96 (432)
T KOG4215|consen   17 GVAEFCAICGDKATGKHYGAISCDGCKGFFRRSVRKNHQYTCRFNKQCVVDKDKRNACRYCRFQKCVRAGMKREAIQNER   96 (432)
T ss_pred             cccchhheeCCcccccccceeecCcchHHHHHHHHhcceeeeeccccccccchhhhhhhHhhHHHHHHhcccHHhhhccc
Confidence            34567999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             ccccCCCCCCCCCCCCCCCCCCCcchhhhhhcCCCCCCCCCCChhHHHHHHHhhcchhhhhhhcccCCCCCCCCCHHHHH
Q psy2636         118 LKGRRGRLPSKPKSPQESPPSPPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQE  197 (335)
Q Consensus       118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~i~~~~~~~p~~~~l~~~~~~  197 (335)
                      ++.+..+ +....    .  ......+.++..+.                        ...+...............+  
T Consensus        97 DrIg~Rr-~~~~~----~--n~~~~~id~L~~aE------------------------~~~~q~~~srs~~~~~~~~d--  143 (432)
T KOG4215|consen   97 DRIGSRR-PSYEA----G--NENSPSIDALVQAE------------------------ALVRQLRSSRSGGVPGIDGD--  143 (432)
T ss_pred             ccccccC-CCCCC----C--CCCchhHHHHHhHH------------------------HHHhhhhccccccCcCcchh--
Confidence            6654311 11000    0  01111122221111                        00000000000000000000  


Q ss_pred             HHHhhhhhccccCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhh
Q psy2636         198 LLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRT  277 (335)
Q Consensus       198 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~  277 (335)
                               .++..+      ...........+.+.+.+..+|||||.+|.|.+|+.+||++|||++..++++|..|||+
T Consensus       144 ---------~r~~~~------n~~~at~~Dv~eSm~qqLlllVEWAK~i~~F~el~l~DqvaLLk~~a~~hllLg~a~RS  208 (432)
T KOG4215|consen  144 ---------IRQGPP------NKKIATENDVCESMKQQLLLLVEWAKYIPPFCELPLDDQVALLKAHAGQHLLLGAAFRS  208 (432)
T ss_pred             ---------hhcCcc------ccccccHHHHHHHHHHHHHHHHHHHHhccchhcCCchhHHHHHHccchhhhhhhhhhcc
Confidence                     000000      11122234556677888889999999999999999999999999999999999999999


Q ss_pred             ccCCCeEEeeCCeEeeHHhhhh-hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         278 RAEDTKLIFCNGVVLEKQQCQR-SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       278 ~~~~~~~~~~~g~~~~~~~~~~-~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ....+.+++.|...+..+..+. ....-..+.+.|++.+|++|++|+.||++||||+||
T Consensus       209 m~l~~v~ll~N~~v~~~~~~~~~eis~v~~RIiDElv~Pmr~L~md~~Ey~cLKAi~Ff  267 (432)
T KOG4215|consen  209 MHLKDVCLLNNTYVLHRHAPDLPEISRVAPRIIDELVNPMRRLQMDEIEYVCLKAIAFF  267 (432)
T ss_pred             ccccceEEecCceeeccCCCChHHHHHHHHHHHHHHhhHHHHhccchHHHHHHHHHHhc
Confidence            9888888888877777654433 223233455669999999999999999999999987

>KOG4216|consensus

Probab=100.00  E-value=9.8e-55  Score=366.17  Aligned_cols=294  Identities=25%  Similarity=0.453  Sum_probs=182.3

Q ss_pred             CCCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636          38 SPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS  117 (335)
Q Consensus        38 ~~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~  117 (335)
                      ++..+|+||||+++|.||||++||||||||||+.+.+..|.|.++.+|.||+.+||+||+||+||||++||.++||...|
T Consensus        44 IEvIPCKiCGDKSSGiHYGVITCEGCKGFFRRSQ~s~a~YsCpRqknC~iDRtnRNRCQ~CRLqKClaLGMSRDAVKFGR  123 (479)
T KOG4216|consen   44 IEIIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQSNANYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGR  123 (479)
T ss_pred             eEEEeeeeccCCCCcceeeeEeeccchHhhhhhhhccccccCCcccCCcccccccchhhHHHHHHHHHhccchhhHHhcc
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999998765


Q ss_pred             cccc-CC---------------C---CCCCC-CCCCCCCCCCCcchhhh-----hhc----CC-CCCCC-CCCChhHH-H
Q psy2636         118 LKGR-RG---------------R---LPSKP-KSPQESPPSPPVSLITA-----LYR----EP-NPLEP-PIAEPEKI-Q  165 (335)
Q Consensus       118 ~~~~-~~---------------~---~~~~~-~~~~~~~~~~~~~~~~~-----~~~----~~-~~~~~-~~~~~~~~-~  165 (335)
                      ..++ |.               .   .+... ...+.++..++...-..     ...    .. ..... ...+|..- .
T Consensus       124 MSKKQRdsl~aEVq~h~~q~q~q~~a~~~~~~y~~s~p~~~~~l~~~~s~y~~g~~p~~~k~~~s~Ys~~~q~tPdq~~~  203 (479)
T KOG4216|consen  124 MSKKQRDSLYAEVQKHRMQQQQQDEAEPLTPTYDISPPNGLTELHDDLSNYSDGHSPEGSKADSSFYSLDIQPTPDQSGL  203 (479)
T ss_pred             ccHhhHHHHHHHHHHHHHHHHhhhhcCCcccccccCCCCCccccccCcccccCCcCCCCCCCCCCcceeccccCCCcccc
Confidence            3211 00               0   00000 00000000000000000     000    00 00000 00000000 0


Q ss_pred             HHHHhhcchh---hhhhhcc----cCCCCCCCCCHHHHHHHHhhh---------hhccc----cCCCC----CCCCCCCh
Q psy2636         166 QFYSLLTTSV---DVIRHFA----DKIPGFSDLCKEDQELLFQSA---------SLELF----YREPN----PLEPPIAE  221 (335)
Q Consensus       166 ~~~~~l~~~~---~~i~~~~----~~~p~~~~l~~~~~~~l~~~~---------~~~~~----~~~~~----~~~~~~~~  221 (335)
                      .++..+..+.   .....-+    ...|. ..+.  +.+.+.++.         .++..    +..+.    +.......
T Consensus       204 d~~g~~~d~t~~~~~~~~~s~~~~~~~p~-~~~~--e~d~laq~i~ksh~etq~~~e~lh~~~~~~~~~e~I~~yq~k~~  280 (479)
T KOG4216|consen  204 DINGPICDSTPGSGYFPYCSFTNGETSPT-VSMA--ELDHLAQNIIKSHLETQYLLEELHQITWQTFDQEEIENYQNKGR  280 (479)
T ss_pred             ccCCCcccCCCCCCcccccccCCCCCCCC-Cchh--HHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHhhhH
Confidence            0000000000   0000000    00111 1111  111111110         00000    00000    00111234


Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhhhh
Q psy2636         222 PEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSF  301 (335)
Q Consensus       222 ~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~~~  301 (335)
                      .+.|+.++.-++..|+.||||||.|+||.+|+++||++|||.+.+|+.+++++..++...+.+.+ .|.+...+.+...-
T Consensus       281 e~mWe~cA~~lt~~IQ~vVEFAK~I~GFM~L~Q~dQI~LLKaGsfEv~lvrm~r~~~v~~ntV~~-e~~~~g~~~f~a~~  359 (479)
T KOG4216|consen  281 EEMWELCAIKLTPAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSFEVVLVRMCRAFDVDNNTVYF-EGKYAGPEVFYALG  359 (479)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhHhhccCccceEEeeecCceeeeHHHHHHhhcccccceee-cccccchhheeccC
Confidence            45677777788999999999999999999999999999999999999999999998887776666 56666655444433


Q ss_pred             cHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         302 GDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       302 ~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ..+++..++++...|..|++++.|.||+.|+||+
T Consensus       360 ~~elis~vf~~~ksL~~Lq~te~EiAL~~alVL~  393 (479)
T KOG4216|consen  360 CEELISRVFEFGKSLCSLQLTEDEIALFSALVLM  393 (479)
T ss_pred             hHHHHHHHHhhhHHHHhhccCcHHHHHHHHHHhh
Confidence            3479999999999999999999999999999984

>KOG4218|consensus

Probab=100.00  E-value=2.3e-49  Score=328.57  Aligned_cols=294  Identities=29%  Similarity=0.481  Sum_probs=182.5

Q ss_pred             CCCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636          38 SPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS  117 (335)
Q Consensus        38 ~~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~  117 (335)
                      ..++.|.||||+.+|||||..+||+|||||+|||++|+.|+|..+.+|.||+..|.+|.+|||||||.|||+-+||+.||
T Consensus        13 dl~ElCPVCGDkVSGYHYGLLTCESCKGFFKRTVQNnK~YtC~e~qnC~iDkTqRKRCP~CRFQKCLtvGMklEAVRADR   92 (475)
T KOG4218|consen   13 DLGELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKQYTCSEEQNCHIDKTQRKRCPSCRFQKCLTVGMKLEAVRADR   92 (475)
T ss_pred             ccccccccccCccccceeeeeehhhhhhHHHHHhhcCcceecccccccccchHhhccCCchhHHHHhhhhhhHHHHHHhh
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccccCCCCCCC------------C----------CCCCC--CCCCCCc---chhhh--------h-------hcCCCCCC
Q psy2636         118 LKGRRGRLPSK------------P----------KSPQE--SPPSPPV---SLITA--------L-------YREPNPLE  155 (335)
Q Consensus       118 ~~~~~~~~~~~------------~----------~~~~~--~~~~~~~---~~~~~--------~-------~~~~~~~~  155 (335)
                      .++.|.+...-            .          .-+.+  ....++.   +....        +       ..++-++.
T Consensus        93 MRGGRNKFGpmYKrDRAlkqQkkAqirAng~KlE~~~~~~~~~~psp~~~ss~~q~lh~~~~kgL~~~~aa~pp~~~~l~  172 (475)
T KOG4218|consen   93 MRGGRNKFGPMYKRDRALKQQKKAQIRANGIKLEYIKTEYDAHLPSPTLSSSTNQQLHVSDFKGLAVLLAATPPDPLQLN  172 (475)
T ss_pred             hcccccccCchhhhhHHHHHHHHHHhhhcceeeeccccccCCCCCCCcccccccccccCCCcccchhhhccCCCCCcccc
Confidence            87766543220            0          00000  0000000   00000        0       00000000


Q ss_pred             CCCCCh-hH----HH---HHHHhhcch-hhhhh---------------------hcccCCCCCCCCCHHHHHHHHhhhh-
Q psy2636         156 PPIAEP-EK----IQ---QFYSLLTTS-VDVIR---------------------HFADKIPGFSDLCKEDQELLFQSAS-  204 (335)
Q Consensus       156 ~~~~~~-~~----~~---~~~~~l~~~-~~~i~---------------------~~~~~~p~~~~l~~~~~~~l~~~~~-  204 (335)
                      .....+ +.    +.   +-|...+.. .+++.                     ..+...|.+..+.-.    +.+... 
T Consensus       173 ~f~~~p~~ms~p~~HgsL~gY~tY~~fp~raikseyP~py~Sspqs~~~ygym~~~ss~sP~lP~lil~----llk~epd  248 (475)
T KOG4218|consen  173 EFKQEPFDMSEPFIHGSLHGYPTYTSFPTRAIKSEYPMPYVSSPQSLVTYGYMTEASSTSPILPLLILP----LLKTEPD  248 (475)
T ss_pred             cccCCCccccCccCCCcccCCcccCCCcchhhhhcCCCCcCCCCcccccccccCccccCCCCccccchh----hhccCCh
Confidence            000000 00    00   000000000 00000                     000001110000000    000000 


Q ss_pred             -------hccccCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhh
Q psy2636         205 -------LELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRT  277 (335)
Q Consensus       205 -------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~  277 (335)
                             ...+..++.......+.++++.-........+..||+||++--.|.+|+.+||++||+++|.++.|++..|+.
T Consensus       249 E~qv~a~i~a~lq~~~ts~s~~~kp~~fgl~c~mAdqtl~sIV~WAr~~~~F~eL~vdDQM~LLQncWselli~Dhiyrq  328 (475)
T KOG4218|consen  249 EMQVTAPIDAQLQRIFTSVSGTSKPEKFGLSCQMADQTLKSIVIWARNDQLFSELSVDDQMILLQNCWSELLIVDHIYRQ  328 (475)
T ss_pred             hhhhcchhHHHHhhhhhcccCCCchhhhhhhhhhhHhHHHHHHHHHhhhhHHHhcchhhHHHHHHHhhHHHHHHHHHHHH
Confidence                   0000000000111112233333334455667788999999999999999999999999999999999999998


Q ss_pred             ccCC--CeEEeeCCeEeeHHhhhhh---hcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         278 RAED--TKLIFCNGVVLEKQQCQRS---FGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       278 ~~~~--~~~~~~~g~~~~~~~~~~~---~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      +..+  ..+.+.+|+.+........   ....++....+++.+|+.|++|..||++||-|+||
T Consensus       329 V~hgkegsi~lvtGqeV~~~~vA~qags~l~tlvs~aqelV~~Lr~lqfd~~efvclkFl~LF  391 (475)
T KOG4218|consen  329 VHHGKEGSIKLVTGQEVPVGLVALQAGSLLQTLVSSAQELVIRLRNLQFDNFEFVCLKFLALF  391 (475)
T ss_pred             HhcCcccceEEecCCcccchhHhhhhhhHHHHHHHHHHHHHHHHHhcCCccchhhHHHHHHHH
Confidence            8754  4688888887765432211   22467778889999999999999999999999987

>KOG4846|consensus

Probab=100.00  E-value=1.6e-44  Score=306.55  Aligned_cols=283  Identities=26%  Similarity=0.396  Sum_probs=165.1

Q ss_pred             CcccccCCCCCccccCCccccccccceecccccCCee-ecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecccc
Q psy2636          41 QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKY-VCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLK  119 (335)
Q Consensus        41 ~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y-~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~~  119 (335)
                      .+|+||||+|+||||||.+||||||||||+|+.++.| .|.++++|.|.+++||+||+|||+|||+|||.+++|+..+.+
T Consensus       133 ~lCkVCgDkASGfHYGV~aCEGCKGFFRRSIQqkI~YrrClk~e~C~I~R~nRNRCQ~CRfKKCL~vGMSrDaVRFG~m~  212 (538)
T KOG4846|consen  133 SLCKVCGDKASGFHYGVTACEGCKGFFRRSIQQKIDYRRCLKQEVCEIKRENRNRCQYCRFKKCLDVGMSRDAVRFGQMK  212 (538)
T ss_pred             EeehhhccccccceeceeecccchHHHHHHHHHhhhHHHHhhhhceehhhhccchhhhhhHHHHHhcccchhhhhhcccc
Confidence            5799999999999999999999999999999999999 799999999999999999999999999999999999987655


Q ss_pred             ccCCCCCCCCCCCCCCCCCCCc-----------chhhhhhcCCCCCCCCCCChhHHHHHHHh--------hcchhhhhhh
Q psy2636         120 GRRGRLPSKPKSPQESPPSPPV-----------SLITALYREPNPLEPPIAEPEKIQQFYSL--------LTTSVDVIRH  180 (335)
Q Consensus       120 ~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------l~~~~~~i~~  180 (335)
                      .|.+......+.+ ....++..           ..+..+.+++..+...  ...++...+..        ...-......
T Consensus       213 ~rnka~M~~~~~p-~~V~sp~~sq~~~Q~env~~V~~~V~rAh~t~~~y--~~~k~gsi~~~~fnv~~n~~s~P~~~~~~  289 (538)
T KOG4846|consen  213 FRNKAAMRDDKSP-DSVFSPEISQLERQEENVDAVYEAVLRAHTTFSFY--TDIKIGSIVARPFNVRINEDSKPMNRLNA  289 (538)
T ss_pred             cccccccCCCCCC-CCCCChhhhhhhhhhccHHHHHHHHHHhhcchhhe--ehhhcCcccCCCcccccccCCccccchhH
Confidence            4431110000001 00011111           1122222322111000  00000000000        0000011122


Q ss_pred             cccC-CCCCCCCCHHHHHHHHhhhhh---------------------ccccCCCCCCCC--------CCChhHHHHHHHH
Q psy2636         181 FADK-IPGFSDLCKEDQELLFQSASL---------------------ELFYREPNPLEP--------PIAEPEKIQQFYS  230 (335)
Q Consensus       181 ~~~~-~p~~~~l~~~~~~~l~~~~~~---------------------~~~~~~~~~~~~--------~~~~~~~~~~~~~  230 (335)
                      |... .|.+.+..++...-+.++...                     ...++.+..+.+        .......|+.+-.
T Consensus       290 w~n~~~pa~~di~qe~~n~l~q~pvfd~~~~~~g~a~~s~h~~n~~pty~~~~~~g~~Pn~~~~~rsgR~~qlp~~~~~l  369 (538)
T KOG4846|consen  290 WQNYAHPADVDIKQEVVNFLKQIPVFDKFNFINGNAKASLHRKNAFPTYLLRIVRGMSPNRGLMLRSGRLIQLPFKSLQL  369 (538)
T ss_pred             HhhcCCCCcccchHHHHHHHHhCccccccccCCCccchhhhcCCCcchhhhhhcccCCcccccccccccccccCcchhhh
Confidence            2222 455555555554444443311                     111111211111        0111122444555


Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCC-HHHHHHHHHHhHHHHHHHHHhhhhccCCCeE-EeeCCeEeeHHhh-hhhhcHHHHH
Q psy2636         231 LLTTSVDVIRHFADKIPGFSDLC-KEDQELLFQSASLELFVLRLAYRTRAEDTKL-IFCNGVVLEKQQC-QRSFGDDWLN  307 (335)
Q Consensus       231 ~~~~~i~~vvefAk~~P~F~~L~-~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~-~~~~g~~~~~~~~-~~~~~~~~~~  307 (335)
                      +....+..+++||+++++|..++ .-++.++|+.+-.......++-.+......+ +|.--..+..+.+ ..+.+ +...
T Consensus       370 l~~~av~e~~~fa~hi~~~~~~~~~~~~~~~L~~~q~l~t~~~f~t~f~~~~Q~~~mfl~~~~~~~Q~~~~~~~g-d~~~  448 (538)
T KOG4846|consen  370 LYGSAVDEMLAFANHIITIGCTDGDIALFIVLILCQPLTTEQQFSTNFKSQLQLLEMFLFYKKVLFQKMTCRIDG-DTYK  448 (538)
T ss_pred             hhhHHHHHHHHhhhccCCccccccchhHHHHHhccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhch-HHHH
Confidence            56677888999999999999998 7899999999888877766654433222111 1100011111122 22445 7778


Q ss_pred             HHHHHHHHhhcCCCCHHHHH
Q psy2636         308 AILEFCQSLHLMEIDISAFA  327 (335)
Q Consensus       308 ~~~~~~~~l~~l~l~~~E~~  327 (335)
                      .++.+++++..|....+|.+
T Consensus       449 a~~~~~~~ln~L~~~~~~~~  468 (538)
T KOG4846|consen  449 ALMKCIHELNRLNELHKQQL  468 (538)
T ss_pred             HHHHhhcchhhcCchHHHHH
Confidence            88899999999998888763

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

Probab=100.00  E-value=2.1e-37  Score=219.89  Aligned_cols=85  Identities=58%  Similarity=1.125  Sum_probs=78.8

Q ss_pred             CCCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636          38 SPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS  117 (335)
Q Consensus        38 ~~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~  117 (335)
                      ++..+|.|||++++|+||||++|+|||+||||+|..+..|.|..+++|.|++..|..||+|||+|||+|||++++||.++
T Consensus         2 ~~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~vq~~r   81 (97)
T cd07170           2 IPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDR   81 (97)
T ss_pred             CCCCCCeecCCcCcceEECceeehhhhHHHHHHhccCCceeecCCCccccCcccCccCCccccchhhhcCCCHHHccccc
Confidence            35567999999999999999999999999999999999999999999999999999999999999999999999999887


Q ss_pred             ccccC
Q psy2636         118 LKGRR  122 (335)
Q Consensus       118 ~~~~~  122 (335)
                      ....+
T Consensus        82 ~~~~~   86 (97)
T cd07170          82 VRGGR   86 (97)
T ss_pred             CCCCC
Confidence            55444

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

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

Probab=100.00  E-value=1.1e-36  Score=211.81  Aligned_cols=80  Identities=55%  Similarity=1.089  Sum_probs=75.7

Q ss_pred             CCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecccc
Q psy2636          40 SQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLK  119 (335)
Q Consensus        40 ~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~~  119 (335)
                      ..+|.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|++..|..||+|||+|||+|||++++||.++.+
T Consensus         4 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~R~~   83 (85)
T cd06964           4 YKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNK   83 (85)
T ss_pred             CCCCcccCCcCcccEECcceeeeeeeEEeeeecCCCCeECCCCCccccCCcccccCccchhhhhhhhCCCHHHhhccccC
Confidence            35799999999999999999999999999999999999999999999999999999999999999999999999987643

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

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

Probab=100.00  E-value=1.1e-36  Score=211.17  Aligned_cols=79  Identities=44%  Similarity=0.937  Sum_probs=75.2

Q ss_pred             CcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecccc
Q psy2636          41 QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLK  119 (335)
Q Consensus        41 ~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~~  119 (335)
                      ++|.||||+++|+||||.+|+|||+||||+|.++..|.|..+++|.|+...|..||+|||+|||+|||++++|+.++..
T Consensus         2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~~   80 (84)
T cd06962           2 ELCVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCEMDMYMRRKCQECRLRKCKEMGMLAECLLTEIQC   80 (84)
T ss_pred             CCCeecCCcCcceEECcceeecceeeeeeeeccCCceecCCCCcCccCccccccCccchhhHHHHhCCChHHccCHHHH
Confidence            5699999999999999999999999999999999999999999999999999999999999999999999999987543

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

>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=1.5e-36  Score=216.79  Aligned_cols=80  Identities=45%  Similarity=0.976  Sum_probs=76.1

Q ss_pred             CCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeeccc
Q psy2636          39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSL  118 (335)
Q Consensus        39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~  118 (335)
                      ...+|.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|++..|..||+|||+|||+|||++++||.++.
T Consensus        17 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~~   96 (101)
T cd07160          17 GNEVCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAQYVCKNGGKCQMDMYMRRKCQECRLRKCREAGMREQCVLSEEQ   96 (101)
T ss_pred             CCCCCeecCCcCcceEECcceehhhhhhhhhcccccCccccCCCCccccCCcccccCccchhHHHHHhCCCHHHhcChhh
Confidence            35679999999999999999999999999999999999999999999999999999999999999999999999998754

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

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

Probab=100.00  E-value=2e-36  Score=212.97  Aligned_cols=81  Identities=51%  Similarity=1.092  Sum_probs=75.6

Q ss_pred             CCCCcccccCCCCCccccCCccccccccceecccccCCeeecCCC-CCCcccccccccccchhhHHHHhcCceeeeeeec
Q psy2636          38 SPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLAD-KACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTD  116 (335)
Q Consensus        38 ~~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~-~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~  116 (335)
                      .|..+|.||||+++|+||||.+|+|||+||||+|..+..|.|..+ ++|.|++..|..||+|||+|||+|||++++||.+
T Consensus         4 ~p~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~   83 (92)
T cd06970           4 NPGLLCRVCGDTSSGKHYGIYACNGCSGFFKRSVRRKLIYRCQAGTGMCPVDKAHRNQCQACRLKKCLQAGMNKDAVQNE   83 (92)
T ss_pred             CCCCCCeecCCcCcccEECccEEeeeeeEeeeeeecCCCceeecCCCcCccCCCccccCccchhhHhhHhCCCHHHcccc
Confidence            345579999999999999999999999999999999999999985 8999999999999999999999999999999987


Q ss_pred             cc
Q psy2636         117 SL  118 (335)
Q Consensus       117 ~~  118 (335)
                      +.
T Consensus        84 R~   85 (92)
T cd06970          84 RQ   85 (92)
T ss_pred             cC
Confidence            54

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

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

Probab=100.00  E-value=8.2e-37  Score=209.18  Aligned_cols=76  Identities=59%  Similarity=1.262  Sum_probs=73.4

Q ss_pred             cccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636          42 LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS  117 (335)
Q Consensus        42 ~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~  117 (335)
                      +|.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|++..|..||+|||+|||+|||++++||.+|
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            6999999999999999999999999999999999999999999999999999999999999999999999998763

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

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

Probab=100.00  E-value=1.1e-36  Score=212.09  Aligned_cols=80  Identities=54%  Similarity=1.053  Sum_probs=76.1

Q ss_pred             cccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecccccc
Q psy2636          42 LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLKGR  121 (335)
Q Consensus        42 ~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~~~~  121 (335)
                      +|.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|++..|+.||+|||+|||+|||++++||.++.+..
T Consensus         1 ~C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~~   80 (85)
T cd06961           1 PCVVCGDKATGYHYRCITCEGCKGFFRRTVQKKLSYSCKGEGKCEIDKVTRNQCQECRFKKCIAVGMAKDLVLDDRKRGA   80 (85)
T ss_pred             CCceeCCcCcceEEChhhhhhhhHhhHhhhccCCccccCCCCccccCccccccCccchhhhhhhccCCHHHcccccCccc
Confidence            59999999999999999999999999999999999999999999999999999999999999999999999999876543

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

>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=100.00  E-value=3.5e-36  Score=210.34  Aligned_cols=81  Identities=51%  Similarity=1.112  Sum_probs=76.7

Q ss_pred             CCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeeccc
Q psy2636          39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSL  118 (335)
Q Consensus        39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~  118 (335)
                      |.++|.||||+++|+||||.+|+|||+||||+|.++..|.|.++++|.|++..|..||+|||+|||+|||++++||.++.
T Consensus         2 ~~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~R~   81 (87)
T cd06967           2 PVELCVVCGDKASGRHYGAVSCEGCKGFFKRSIRKNLGYSCRGSKDCVINKHHRNRCQYCRLQKCLAMGMKSDSVQCERK   81 (87)
T ss_pred             CCCCCeecCCcCCcCEeCcceEeeeeeEeeeeeeCCCCcccCCCCccccCccccccCccchhhhhhHcCCCHHHhccccC
Confidence            45679999999999999999999999999999999999999999999999999999999999999999999999998764


Q ss_pred             c
Q psy2636         119 K  119 (335)
Q Consensus       119 ~  119 (335)
                      .
T Consensus        82 ~   82 (87)
T cd06967          82 P   82 (87)
T ss_pred             C
Confidence            3

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

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

Probab=100.00  E-value=1.9e-36  Score=208.88  Aligned_cols=79  Identities=49%  Similarity=1.074  Sum_probs=75.0

Q ss_pred             CCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636          39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS  117 (335)
Q Consensus        39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~  117 (335)
                      +.++|.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|+...|..||+|||+|||+|||++++|+.++
T Consensus         2 ~~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~~   80 (82)
T cd07171           2 DTHFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRRER   80 (82)
T ss_pred             CCCCCeecCCcCcceEECceeehhhHHhHHHHeeCCCceeCCCCCccccCCcccccCccchhHHHhHhcCCHHHHHHhh
Confidence            3467999999999999999999999999999999999999999999999999999999999999999999999998764

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

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

Probab=100.00  E-value=4.9e-36  Score=204.25  Aligned_cols=75  Identities=91%  Similarity=1.615  Sum_probs=71.9

Q ss_pred             CcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeee
Q psy2636          41 QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRT  115 (335)
Q Consensus        41 ~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~  115 (335)
                      .+|.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|++..|..||+|||+|||++||++++||.
T Consensus         1 ~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~   75 (75)
T cd06969           1 GLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLQVGMVKEVVRT   75 (75)
T ss_pred             CCCeecCCcCcceEECcceeeeeeeeeeeeeecCCcccCCcCCccccCCcccccCcccHhHHHHHhCCCHHHccC
Confidence            369999999999999999999999999999999999999999999999999999999999999999999999973

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

>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=100.00  E-value=3.4e-36  Score=205.25  Aligned_cols=75  Identities=60%  Similarity=1.146  Sum_probs=72.5

Q ss_pred             ccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636          43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS  117 (335)
Q Consensus        43 C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~  117 (335)
                      |.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|++..|..||+|||+|||+|||++++||.++
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            899999999999999999999999999999999999999999999999999999999999999999999998764

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

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

Probab=100.00  E-value=1e-35  Score=210.22  Aligned_cols=80  Identities=45%  Similarity=1.068  Sum_probs=75.0

Q ss_pred             CCCcccccCCCCCccccCCccccccccceecccccCCeeecCC--CCCCcccccccccccchhhHHHHhcCceeeeeeec
Q psy2636          39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLA--DKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTD  116 (335)
Q Consensus        39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~  116 (335)
                      ++.+|.|||++++|+||||.+|+|||+||||+|..+..|.|..  +++|.|++..|..||+|||+||++|||++++||.+
T Consensus         5 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~   84 (92)
T cd07163           5 LDIPCKVCGDRSSGKHYGIYACDGCSGFFKRSIRRNRQYVCKSKGQGGCPVDKTHRNQCRACRLKKCFEVGMNKDAVQHE   84 (92)
T ss_pred             cCCCCcccCCcCcccEECceeeeeeeeEEeeeecCCCCcCCCCCCCCCCccCCCccccCccchhhhhhhhcCCHHHhhcc
Confidence            4667999999999999999999999999999999999999987  47899999999999999999999999999999986


Q ss_pred             cc
Q psy2636         117 SL  118 (335)
Q Consensus       117 ~~  118 (335)
                      +.
T Consensus        85 r~   86 (92)
T cd07163          85 RG   86 (92)
T ss_pred             cC
Confidence            54

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).

>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=100.00  E-value=9.3e-36  Score=206.30  Aligned_cols=76  Identities=51%  Similarity=1.089  Sum_probs=72.3

Q ss_pred             ccccCCCCCccccCCccccccccceecccccCCeeecC-CCCCCcccccccccccchhhHHHHhcCceeeeeeeccc
Q psy2636          43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCL-ADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSL  118 (335)
Q Consensus        43 C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~-~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~  118 (335)
                      |.||||+++|+||||++|+|||+||||+|.++..|.|. .+++|.|++..|+.||+|||+|||+|||++++||.++.
T Consensus         1 C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~   77 (82)
T cd06957           1 CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKGIIYTCIAGNGNCVVDKARRNWCPFCRLQKCFAVGMNRAAVQEERG   77 (82)
T ss_pred             CCccCccCcceEECcceEeeeeeEEEEeecCCCceEccCccCCCccCCCccCcccCcchhhcccccCCHHHhccccC
Confidence            89999999999999999999999999999999999999 56899999999999999999999999999999998653

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

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

Probab=100.00  E-value=7.9e-36  Score=209.94  Aligned_cols=83  Identities=52%  Similarity=1.114  Sum_probs=77.4

Q ss_pred             CCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeeccc
Q psy2636          39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSL  118 (335)
Q Consensus        39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~  118 (335)
                      ...+|.|||++++|+||||++|+|||+||||++..+..|.|..+++|.|++..|..||+|||+|||+|||++++||.++.
T Consensus         5 ~~~~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R~   84 (90)
T cd07168           5 SPKLCSICEDKATGLHYGIITCEGCKGFFKRTVQNKRVYTCVGDGRCEITKAQRNRCQYCRFRKCIRKGMMLAAVREDRM   84 (90)
T ss_pred             cCCCCcccCCcCcceEECceehhhhhHhhhhhhcCCCCccCCCCCCccccccccccccccchhhhhhcCCCHHHhhcccC
Confidence            34569999999999999999999999999999999999999999999999999999999999999999999999998775


Q ss_pred             ccc
Q psy2636         119 KGR  121 (335)
Q Consensus       119 ~~~  121 (335)
                      +..
T Consensus        85 ~~~   87 (90)
T cd07168          85 PGG   87 (90)
T ss_pred             CCC
Confidence            543

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

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

Probab=100.00  E-value=6e-36  Score=210.44  Aligned_cols=78  Identities=51%  Similarity=0.998  Sum_probs=74.8

Q ss_pred             CcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeeccc
Q psy2636          41 QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSL  118 (335)
Q Consensus        41 ~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~  118 (335)
                      ++|.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|+...|..||+|||+|||+|||++++||.++.
T Consensus         2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~   79 (91)
T cd07161           2 ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYHCKYGRACEMDMYMRRKCQECRLKKCLSVGMRPECVVPESQ   79 (91)
T ss_pred             CCCeeCCCcCcceEECceeehhhHHHHHHHhccCCceecCCCCccccCccccccCccchhhHHhHcCCCHHHcCchhh
Confidence            569999999999999999999999999999999999999999999999999999999999999999999999998753

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

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

Probab=100.00  E-value=1.1e-35  Score=203.34  Aligned_cols=76  Identities=46%  Similarity=0.951  Sum_probs=72.1

Q ss_pred             CCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeee
Q psy2636          39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVR  114 (335)
Q Consensus        39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq  114 (335)
                      |..+|.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|++..|+.||+|||+|||+|||+..++.
T Consensus         1 ~~~~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~   76 (78)
T cd07172           1 PQKICLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCLQAGMNLGARK   76 (78)
T ss_pred             CCCCCeecCCcCcceEECceeehhhHHhHHHHeeCCCceeCCCCCccccCCcccccCccchhHHHHHhCCCccccc
Confidence            3467999999999999999999999999999999999999999999999999999999999999999999988774

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

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

Probab=100.00  E-value=8.5e-36  Score=209.49  Aligned_cols=84  Identities=48%  Similarity=1.077  Sum_probs=78.0

Q ss_pred             CCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeeccc
Q psy2636          39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSL  118 (335)
Q Consensus        39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~  118 (335)
                      ...+|.|||++++|+||||++|+|||+||||+|..+..|.|..+++|.|+...|..||+|||+|||+|||++++||.++.
T Consensus         5 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~   84 (90)
T cd07169           5 EQRTCLICGDRATGLHYGIISCEGCKGFFKRSICNKRVYRCSRDKNCVMSRKQRNRCQYCRLLKCLQMGMNRKAIREDGM   84 (90)
T ss_pred             cCCCCeecCCcCcceEECcceehhhHHHHHHHhcCCCceecCCCCcccccccccccccccchhhhccccCCHHHhccccC
Confidence            34569999999999999999999999999999999999999999999999999999999999999999999999999876


Q ss_pred             cccC
Q psy2636         119 KGRR  122 (335)
Q Consensus       119 ~~~~  122 (335)
                      ++.+
T Consensus        85 ~~~~   88 (90)
T cd07169          85 PGGR   88 (90)
T ss_pred             CCCC
Confidence            5443

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).

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

Probab=100.00  E-value=9.8e-36  Score=209.01  Aligned_cols=80  Identities=50%  Similarity=1.113  Sum_probs=75.7

Q ss_pred             CCcccccCCCCCccccCCccccccccceecccccCCee-ecCCCCCCcccccccccccchhhHHHHhcCceeeeeeeccc
Q psy2636          40 SQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKY-VCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSL  118 (335)
Q Consensus        40 ~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y-~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~  118 (335)
                      ..+|.||||+++|+||||.+|+|||+||||+|..+..| .|..+++|.|++..|..||+|||+|||+|||++++||.++.
T Consensus         3 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~   82 (89)
T cd07166           3 VVLCKVCGDKASGFHYGVHACEGCKGFFRRSIQQKIQYRKCTKNETCSIMRINRNRCQYCRFKKCLAVGMSRDAVRFGRI   82 (89)
T ss_pred             CCCCcccCccCcceEEChhhhhhHhhEecceeEcCCcchhhccCCcccccccccccccchhhhhcccccCCHHHhcCCCC
Confidence            45799999999999999999999999999999999999 59999999999999999999999999999999999998765


Q ss_pred             c
Q psy2636         119 K  119 (335)
Q Consensus       119 ~  119 (335)
                      +
T Consensus        83 ~   83 (89)
T cd07166          83 P   83 (89)
T ss_pred             C
Confidence            4

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

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

Probab=100.00  E-value=9.2e-36  Score=214.79  Aligned_cols=78  Identities=41%  Similarity=1.006  Sum_probs=74.4

Q ss_pred             CCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636          40 SQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS  117 (335)
Q Consensus        40 ~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~  117 (335)
                      ..+|.|||++++|+||||.+|+|||+||||+|..+..|.|..+++|.|++..|+.||+|||+|||+|||++++|+.++
T Consensus         6 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~   83 (107)
T cd06955           6 PRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDE   83 (107)
T ss_pred             CCCCeecCCcCcccEECcceeeeecceecceeccCCccccCCCCccccccCCccccccchhHHHHHcCCCchhccCHH
Confidence            356999999999999999999999999999999999999999999999999999999999999999999999999863

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

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

Probab=100.00  E-value=2.2e-35  Score=200.44  Aligned_cols=72  Identities=51%  Similarity=1.151  Sum_probs=69.6

Q ss_pred             ccccCCCCCccccCCccccccccceecccccCCeeecC-CCCCCcccccccccccchhhHHHHhcCceeeeee
Q psy2636          43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCL-ADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVR  114 (335)
Q Consensus        43 C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~-~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq  114 (335)
                      |.||||+++|+||||.+|+|||+||||+|..+..|.|. .+++|.|++..|..||+|||+|||+|||++++||
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 6889999999999999999999999999999885

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

>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=100.00  E-value=1.4e-35  Score=201.12  Aligned_cols=73  Identities=48%  Similarity=1.012  Sum_probs=70.4

Q ss_pred             cccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeee
Q psy2636          42 LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVR  114 (335)
Q Consensus        42 ~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq  114 (335)
                      +|.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|++..|..||+|||+|||+|||+++.|+
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            5999999999999999999999999999999999999999999999999999999999999999999999874

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

>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=100.00  E-value=2e-35  Score=199.83  Aligned_cols=72  Identities=44%  Similarity=1.066  Sum_probs=69.8

Q ss_pred             ccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeee
Q psy2636          43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVR  114 (335)
Q Consensus        43 C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq  114 (335)
                      |.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|++..|..||+|||+|||+|||++++|+
T Consensus         1 C~VC~~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   72 (72)
T cd07156           1 CGVCGDRATGYHFNAMTCEGCKGFFRRSMKRKARFTCPFNGDCEITKDNRRHCQACRLKKCLDIGMKKEMIL   72 (72)
T ss_pred             CCccCccCcccEECcceehhhhhhhchhccCcCccccCCCCccccCCcccccCccchhHHHHHhCCCHHHcC
Confidence            899999999999999999999999999999999999999999999999999999999999999999999873

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

>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=100.00  E-value=1.2e-35  Score=209.21  Aligned_cols=80  Identities=56%  Similarity=1.204  Sum_probs=75.7

Q ss_pred             ccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeeccccccC
Q psy2636          43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLKGRR  122 (335)
Q Consensus        43 C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~~~~~  122 (335)
                      |.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|+...|+.||+|||+|||+|||++++||.++..+.+
T Consensus         1 C~VCg~~a~g~hyGv~sC~aCk~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~Vq~~r~~~~~   80 (93)
T cd07167           1 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMRGGR   80 (93)
T ss_pred             CcccCccCcceEECchhhhhHHHHHHHHeeCCCccccCCCCccccCccccCcCCCcccchhhhccCCHHHhhhcccCCCc
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999998754433

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

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

Probab=100.00  E-value=2.9e-35  Score=201.68  Aligned_cols=75  Identities=55%  Similarity=1.178  Sum_probs=72.6

Q ss_pred             ccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636          43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS  117 (335)
Q Consensus        43 C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~  117 (335)
                      |.||||+++|+||||++|+|||+||||+|..+..|.|..+++|.|+...|..||+|||+|||++||++++||.++
T Consensus         1 C~vCg~~~~~~hygv~~C~aC~~FFrR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r   75 (76)
T cd06960           1 CAVCGDRATGKHYGVLSCNGCKGFFRRSVRKNRTYTCRFGGNCVVDKDKRNACRYCRFKKCLEVGMDPEAVQNER   75 (76)
T ss_pred             CCccCccCcccEECcceeeeehheeCccccCCCceeCCCCCcccccCcccccCccchhhhhhhcCCCHHHcccCC
Confidence            899999999999999999999999999999999999999999999999999999999999999999999999765

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

>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=100.00  E-value=2.4e-35  Score=200.03  Aligned_cols=72  Identities=53%  Similarity=1.232  Sum_probs=70.3

Q ss_pred             ccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeee
Q psy2636          43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVR  114 (335)
Q Consensus        43 C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq  114 (335)
                      |.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|++..|..||+|||+|||+|||++++||
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            899999999999999999999999999999999999999999999999999999999999999999999986

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

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

Probab=100.00  E-value=3.3e-35  Score=198.97  Aligned_cols=72  Identities=64%  Similarity=1.245  Sum_probs=70.1

Q ss_pred             ccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeee
Q psy2636          43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVR  114 (335)
Q Consensus        43 C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq  114 (335)
                      |.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|+...|..||+|||+|||++||++++||
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            899999999999999999999999999999999999999999999999999999999999999999999885

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

>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=100.00  E-value=2.4e-35  Score=202.73  Aligned_cols=76  Identities=51%  Similarity=1.142  Sum_probs=73.4

Q ss_pred             ccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeeccc
Q psy2636          43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSL  118 (335)
Q Consensus        43 C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~  118 (335)
                      |.||||+++|+||||.+|+|||+||||++..+..|.|..+++|.|++..|..||+|||+|||+|||++++||.++.
T Consensus         1 C~VCg~~~~g~hyG~~~C~~C~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~   76 (78)
T cd07164           1 CRVCGDRASGKHYGVPSCDGCRGFFKRSIRRNLAYVCKENGSCVVDVARRNQCQACRFKKCLQVNMNRDAVQHERA   76 (78)
T ss_pred             CcccCccCcceEECcchhhhhhhhhhhhccCCCCccCCCCCcccccCcccccCccchhhhhhHhcCCHHHhccCCC
Confidence            8999999999999999999999999999999999999999999999999999999999999999999999998764

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

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

Probab=100.00  E-value=2.9e-35  Score=199.11  Aligned_cols=72  Identities=44%  Similarity=0.951  Sum_probs=69.7

Q ss_pred             ccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeee
Q psy2636          43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVR  114 (335)
Q Consensus        43 C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq  114 (335)
                      |.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|++..|+.||+|||+|||++||+++++.
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            899999999999999999999999999999999999999999999999999999999999999999999873

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

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

Probab=100.00  E-value=2e-35  Score=209.33  Aligned_cols=80  Identities=36%  Similarity=0.826  Sum_probs=75.8

Q ss_pred             CcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeeccccc
Q psy2636          41 QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLKG  120 (335)
Q Consensus        41 ~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~~~  120 (335)
                      .+|.|||++++|+||||++|+||++||||+|..+..|.|..+++|.|+...|..|++|||+|||+|||++++||.++...
T Consensus         1 ~~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~r~~~   80 (94)
T cd06966           1 KICGVCGDKALGYNFNAITCESCKAFFRRNALKNKEFKCPFNESCEINVVTRRFCQKCRLDKCFAIGMKKEWIMSEEDKS   80 (94)
T ss_pred             CCCeeCCCcCcceEECcceeeeehheehhcccCCCccccCCCCccccCccccccCccchhhhCcccCCCHHHccchhhhh
Confidence            36999999999999999999999999999999999999999999999999999999999999999999999999886543

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

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

Probab=100.00  E-value=3e-35  Score=202.65  Aligned_cols=76  Identities=42%  Similarity=0.947  Sum_probs=71.5

Q ss_pred             CCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeee
Q psy2636          39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVR  114 (335)
Q Consensus        39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq  114 (335)
                      +..+|.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|++..|+.||+|||+|||+|||+++...
T Consensus         2 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~~~   77 (82)
T cd07173           2 PQKTCLICGDEASGCHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCFEAGMTLGARK   77 (82)
T ss_pred             CCCCCeecCCcCcceEECcchhhhHHHHHHHHhcCCCceecCCCCccccCCCccCcCcchhhhhhhhcCCCcChHH
Confidence            4567999999999999999999999999999999999999999999999999999999999999999999977553

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

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

Probab=100.00  E-value=3.1e-35  Score=208.53  Aligned_cols=81  Identities=47%  Similarity=1.021  Sum_probs=76.1

Q ss_pred             CCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeeccc
Q psy2636          39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSL  118 (335)
Q Consensus        39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~  118 (335)
                      ...+|.||||+++|+||||.+|+||++||||+|..+..|.|..+++|.|+...|..||+|||+||++|||++++||.++.
T Consensus         4 ~~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~V~~~r~   83 (95)
T cd06968           4 EVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVSYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRM   83 (95)
T ss_pred             cccCCcccCCcCcceEECceeehhhHHhhHHheeCCCceecCCCcccccccCCceeccccchhhcccccCChhhcccCcC
Confidence            34579999999999999999999999999999999999999999999999999999999999999999999999998754


Q ss_pred             c
Q psy2636         119 K  119 (335)
Q Consensus       119 ~  119 (335)
                      .
T Consensus        84 ~   84 (95)
T cd06968          84 S   84 (95)
T ss_pred             C
Confidence            4

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

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

Probab=100.00  E-value=3.5e-35  Score=199.51  Aligned_cols=73  Identities=47%  Similarity=1.021  Sum_probs=70.9

Q ss_pred             ccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeee
Q psy2636          43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRT  115 (335)
Q Consensus        43 C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~  115 (335)
                      |.||||+++|+||||++|+|||+||||++..+..|.|..+++|.|++..|..||+|||+|||++||++++|+.
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            8999999999999999999999999999999999999999999999999999999999999999999999974

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.

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

Probab=100.00  E-value=1.1e-34  Score=202.30  Aligned_cols=76  Identities=42%  Similarity=0.789  Sum_probs=71.3

Q ss_pred             cccccCCCCCccccCCccccccccceecccccCC--eeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636          42 LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGS--KYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS  117 (335)
Q Consensus        42 ~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~--~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~  117 (335)
                      +|.|||++++|+||||++|+|||+||||++..+.  .|.|.++++|.|+...|+.||+|||+|||+|||+++.++.++
T Consensus         2 ~C~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~~~~   79 (86)
T cd07157           2 TCQVCGEPAAGFHHGAYVCEACKKFFMRSSNAISFTISECPNGGKCIIDKKNRTKCQACRYRKCLNVGMSLGGPRYGR   79 (86)
T ss_pred             CCcccCCcCcccEECcceeeEeeeEEecceecCCCccccCCCCCccccCccccccCccchhhHHhHcCCCcccccccc
Confidence            5999999999999999999999999999998664  899999999999999999999999999999999999987654

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.

>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=100.00  E-value=5.3e-35  Score=202.29  Aligned_cols=77  Identities=55%  Similarity=1.156  Sum_probs=74.1

Q ss_pred             ccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecccc
Q psy2636          43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLK  119 (335)
Q Consensus        43 C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~~  119 (335)
                      |.|||++++|+||||.+|+||++||||+|..+..|.|..+++|.|++..|..||+|||+|||+|||++++||.++.+
T Consensus         1 C~VCg~~~~g~hyG~~sC~aC~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~V~~~r~~   77 (81)
T cd07165           1 CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYRCLRDGKCEIIRLNRNRCQYCRFKKCLAAGMSKDSVRYGRIP   77 (81)
T ss_pred             CCccCccCcceEECchhhhhHHHHHHhHhccCCceeCCCCCCccccccccccccchhhhhcccccCCHHHcccCCCC
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999987654

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,

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

Probab=100.00  E-value=6.5e-35  Score=204.46  Aligned_cols=76  Identities=45%  Similarity=1.041  Sum_probs=73.3

Q ss_pred             cccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636          42 LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS  117 (335)
Q Consensus        42 ~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~  117 (335)
                      +|.||||+++|+||||.+|+||++||||++..+..|.|..+++|.|++..|+.||+|||+|||++||++++|+.++
T Consensus         1 ~C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~   76 (87)
T cd07162           1 ICRVCGDRATGYHFNAMTCEGCKGFFRRAMKRNARLCCPFQKGCVITKSNRRQCQACRLRKCLSIGMKKELIMSDE   76 (87)
T ss_pred             CCcccCCcCcceEECcceehhhHHHHHhhhccCceeEcCCCCceecCCcccccCccchhhHHhHhCCCHHHccCHH
Confidence            4999999999999999999999999999999999999999999999999999999999999999999999999874

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

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

Probab=100.00  E-value=7e-35  Score=198.19  Aligned_cols=72  Identities=57%  Similarity=1.257  Sum_probs=69.9

Q ss_pred             ccccCCCCCccccCCccccccccceecccccCCee-ecCCCCCCcccccccccccchhhHHHHhcCceeeeee
Q psy2636          43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKY-VCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVR  114 (335)
Q Consensus        43 C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y-~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq  114 (335)
                      |.||||+++|+||||.+|+|||+||||+|..+..| .|..+++|.|++..|..||+|||+|||+|||++++|+
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 8999999999999999999999999999999999885

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

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

Probab=100.00  E-value=1.1e-34  Score=201.63  Aligned_cols=76  Identities=51%  Similarity=1.104  Sum_probs=71.0

Q ss_pred             cccccCCCCCccccCCccccccccceecccccCCeee-cCCCCCCcccccccccccchhhHHHHhcCceeeeeeecccc
Q psy2636          42 LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYV-CLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLK  119 (335)
Q Consensus        42 ~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~-C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~~  119 (335)
                      +|.||||+++|+||||.+|+|||+||||+|..+..|. |..+  |.|++..|+.||+|||+|||+|||++++||.++.+
T Consensus         1 ~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~~C~~~--C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~~   77 (84)
T cd06965           1 ECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLVYKPCDLS--CKIHKKSRNKCQYCRFQKCLNVGMSHNAIRFGRMP   77 (84)
T ss_pred             CCcccCccCcceEEChhhhhhhhhheeeeeecCCCccccccC--CCcCccccccccchhhhhhhhccCCHHHcccCCCC
Confidence            4999999999999999999999999999999999995 9753  99999999999999999999999999999987654

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

>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors

Probab=99.98  E-value=1.5e-33  Score=190.46  Aligned_cols=70  Identities=51%  Similarity=1.047  Sum_probs=67.4

Q ss_pred             cccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceee
Q psy2636          42 LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKE  111 (335)
Q Consensus        42 ~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~  111 (335)
                      +|.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|++..|..||+|||+|||++||+++
T Consensus         1 ~C~vC~~~~~~~hygv~~C~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~   70 (70)
T smart00399        1 LCCVCGDHASGFHFGVCSCRACKAFFRRTVNLRYKYRCDRKNNCSINKRYRCRCRACRLKKCLGVGMDPE   70 (70)
T ss_pred             CCeEeCCcCcccEeCCcEechhhhhhhhheeCCCCeecCCCcccccCCCccccCccCcChhHhhccCcCC
Confidence            4999999999999999999999999999999999999999999999999999999999999999999864

>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=99.97  E-value=1.9e-32  Score=185.73  Aligned_cols=70  Identities=51%  Similarity=1.086  Sum_probs=62.9

Q ss_pred             CcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCcee
Q psy2636          41 QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVK  110 (335)
Q Consensus        41 ~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~  110 (335)
                      ++|+||||+++|+||||.+|++|+.||||++..+..|.|..+++|.|++..+..|++|||+|||+|||++
T Consensus         1 ~~C~VCg~~~~~~~ygv~sC~~C~~FFrR~~~~~~~~~C~~~~~C~i~~~~~~~C~~CRf~KCl~~GM~k   70 (70)
T PF00105_consen    1 KKCKVCGDPASGYHYGVLSCNACKMFFRRSVKKKKPYKCKKNGNCKIDKDNRRKCRSCRFQKCLEVGMKK   70 (70)
T ss_dssp             -BSTTTSSBESEEETTEEEEHHHHHHHHHHHHTTCG-STSSSST---STTTTTTSHHHHHHHHHHTTBSG
T ss_pred             CCCeECCCccCcccccccccccceeeeeecccccccccccccccccccccCCCEeCcchHHHHHHHCCcC
Confidence            4699999999999999999999999999999999999999999999999999999999999999999974

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 ....

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

Probab=99.95  E-value=7.5e-27  Score=196.11  Aligned_cols=127  Identities=83%  Similarity=1.350  Sum_probs=116.3

Q ss_pred             ccCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEee
Q psy2636         208 FYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFC  287 (335)
Q Consensus       208 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~  287 (335)
                      +|.++.+.++...+.+.|++++++.+..|+.+|+|||++|||.+|+.+||++|||++|+|+++|+.||++.+.++++++.
T Consensus        27 ~~~~~~~~~~~~~~~~~~~~~~~l~t~~i~~iv~wAK~IPgF~~L~~~DQi~LLk~~w~Ell~L~~a~r~~~~~~~l~~~  106 (239)
T cd07072          27 QYREPSPLEPPMSEAEKVQQFYSLLTSSIDVIKTFAEKIPGFPDLCKEDQELLFQSASLELFVLRLAYRTAPEDTKLTFC  106 (239)
T ss_pred             ccCCCCcccCCcchHHHHHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHHHHHHhHHHHHHHHHHHHccCCCCeEEee
Confidence            34555555666788899999999999999999999999999999999999999999999999999999999988899999


Q ss_pred             CCeEeeHHhhhhhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         288 NGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       288 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      +|..+.+.+...+++ ++++.+++|+.+|++|++|.+||+|||||+||
T Consensus       107 ~g~~~~~~~~~~~~~-~~~~~i~ef~~~l~~L~ld~~E~a~LkAivLf  153 (239)
T cd07072         107 NGVVLHKQQCQRSFG-DWLHAILEFSKSLHAMDIDISAFACLCALTLI  153 (239)
T ss_pred             CCeeecHHHHHhhHH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence            999998887766777 68999999999999999999999999999986

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).

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

Probab=99.92  E-value=1.4e-24  Score=182.31  Aligned_cols=116  Identities=64%  Similarity=1.139  Sum_probs=107.5

Q ss_pred             CChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhh
Q psy2636         219 IAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQ  298 (335)
Q Consensus       219 ~~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~  298 (335)
                      ..+...++++++..+..++.+|+|||++|||.+|+.+||++|||++|.|+++|+.||++.+.+++++|.+|..+.+.+..
T Consensus        37 ~~~~~~~~~~~el~t~~l~~iVewAK~iPgF~~L~~~DQi~LLk~~w~El~vL~~a~r~~~~~~~l~f~~~~~~~r~~~~  116 (238)
T cd07348          37 KEDASDIQQFYDLLSGSLEVIRKWAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNPEEGKLIFCNGVVLHRTQCV  116 (238)
T ss_pred             ccchHHHHHHHHHHHHHHHHHHHHHccCCCccCCChHHHHHHHHHHHHHHHHHHHHHHcCCCCCeEEeeCCeeecHHHHH
Confidence            34557789999999999999999999999999999999999999999999999999999999899999999999887655


Q ss_pred             hhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         299 RSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       299 ~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      .+++ ++++.+++|+.+|++|+||.+||+|||||+||
T Consensus       117 ~~~~-~~~~~i~ef~~~l~~L~ld~~E~a~LkAIvLf  152 (238)
T cd07348         117 RGFG-DWIDSILEFSQSLHRMNLDVSAFSCLAALVII  152 (238)
T ss_pred             hhHH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence            5676 88999999999999999999999999999987

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

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

Probab=99.92  E-value=2.9e-24  Score=180.59  Aligned_cols=114  Identities=60%  Similarity=1.076  Sum_probs=105.7

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhhh
Q psy2636         221 EPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRS  300 (335)
Q Consensus       221 ~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~~  300 (335)
                      ....++++++..+..++.+|+|||++|||.+|+.+||++|||++|+|+++|+.|+++...++.+++.+|..+.+.+...+
T Consensus        39 ~~~~~~~~~e~~~~~i~~iVewAK~iPgF~~L~~~DQi~LLk~~~~Ell~L~~a~~~~~~~~~l~~~~g~~~~~~~~~~~  118 (238)
T cd07071          39 DTQHIQQFYDLLTGSMEIIRGWAEKIPGFTDLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIFCNGVVLHRLQCVRG  118 (238)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCCceEeeCCceechhhhhhc
Confidence            45778899999999999999999999999999999999999999999999999999999889999999999887665456


Q ss_pred             hcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         301 FGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       301 ~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ++ ++++.+++|+.+|++|+||.+||+|||||+||
T Consensus       119 ~~-~~~~~i~ef~~~l~~L~ld~~E~alLkAIvLf  152 (238)
T cd07071         119 FG-EWIDSIVEFSSNLQNMNIDISAFSCIAALAMV  152 (238)
T ss_pred             HH-HHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHc
Confidence            66 78899999999999999999999999999986

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).

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

Probab=99.91  E-value=2.2e-23  Score=170.16  Aligned_cols=116  Identities=25%  Similarity=0.461  Sum_probs=106.3

Q ss_pred             CChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhh
Q psy2636         219 IAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQ  298 (335)
Q Consensus       219 ~~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~  298 (335)
                      ....+.|++|...++..|+.+|+|||++|+|.+|+.+||++|||++|+++++++.|+++....+.+.+.+|..++.+...
T Consensus         8 ~~~~~~~~~~~~~~~~~i~~~V~waK~iPgF~~L~~~DQi~LLk~~w~Ell~L~~a~~~~~~~~~l~~~~~~~~~~~~~~   87 (189)
T cd06940           8 KSGHEIWEEFSMSFTPAVREVVEFAKRIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFDAKERSVTFLSGQKYSVDDLH   87 (189)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCChhhHHHHHHHhhHHHHHHHHHHHhccCCCeEEecCCcEEcHHHHH
Confidence            45667899999999999999999999999999999999999999999999999999998888888999999999887754


Q ss_pred             h-hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         299 R-SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       299 ~-~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      . +++ ++++.+++|+.+|++|++|.+||++||||+||
T Consensus        88 ~~~~~-~~~~~~~~~~~~l~~L~ld~~E~a~LkAivLf  124 (189)
T cd06940          88 SMGAG-DLLNSMFDFSEKLNSLQLSDEEMGLFTAVVLV  124 (189)
T ss_pred             HcCcH-HHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHh
Confidence            4 444 78899999999999999999999999999986

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

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

Probab=99.91  E-value=3.8e-23  Score=173.57  Aligned_cols=116  Identities=22%  Similarity=0.338  Sum_probs=101.8

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCC--eEEeeCCeEeeHHhh
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT--KLIFCNGVVLEKQQC  297 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~--~~~~~~g~~~~~~~~  297 (335)
                      +....+..+.++..+.+..+|+|||++|+|.+|+.+||++|||++|.++++++.||++....+  .+++++|..++.+..
T Consensus        25 ~~~~~~~~l~~la~r~L~~~VeWAK~IPgF~~L~l~DQi~LLk~sW~Ellvl~~a~rs~~~~~~~~l~fa~~~~~~~~~~  104 (247)
T cd07076          25 STWRIMSTLNMLGGRQVVAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMAFALGWRSYRQSNGNLLCFAPDLIINEQRM  104 (247)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHhccCCCCCceEEecCCeeecHHHH
Confidence            445666778888899999999999999999999999999999999999999999999886443  488999999988765


Q ss_pred             hhhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         298 QRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       298 ~~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ......++.+.+++++.+|++|++|.+||+|||||+||
T Consensus       105 ~~~~~~~~~~~l~e~~~~~r~L~ld~~EfacLKAIvLf  142 (247)
T cd07076         105 TLPCMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLL  142 (247)
T ss_pred             hhhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhC
Confidence            54444467788899999999999999999999999997

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

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

Probab=99.90  E-value=6.1e-23  Score=173.97  Aligned_cols=115  Identities=27%  Similarity=0.437  Sum_probs=106.1

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR  299 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~  299 (335)
                      .+.+.|.++++..+..++.+|+|||++|||.+|+.+||++|||++|+++++|+.|+++...++.+.+++|..+..+....
T Consensus        49 ~~~~~~~~~~~~~~~~l~~iVefAK~iPgF~~L~~~DQi~LLk~~~~ElliL~~a~~~~~~~~~~~~~~~~~~~~~~~~~  128 (243)
T cd06935          49 VDLEAFSHFTKIITPAITRVVDFAKKLPMFTELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLSGEMAVTREQLKN  128 (243)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHhcCCccccCChHHHHHHHHHhHHHHHHHHHHHHhCcCCCeEEeeCCeEeeHHHHHh
Confidence            35677889999999999999999999999999999999999999999999999999998888899999999988877644


Q ss_pred             -hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 -SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 -~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                       +++ ++.+.+++|+.+|++|+||++||+||+||+||
T Consensus       129 ~~~~-~~~~~i~~f~~~l~~L~ld~~E~alLkAivLf  164 (243)
T cd06935         129 GGLG-VVSDAIFDLGVSLSSFNLDDTEVALLQAVLLM  164 (243)
T ss_pred             cChH-HHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHh
Confidence             555 78999999999999999999999999999986

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

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

Probab=99.90  E-value=7.6e-23  Score=171.82  Aligned_cols=115  Identities=17%  Similarity=0.295  Sum_probs=101.7

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCC--CeEEeeCCeEeeHHhh
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAED--TKLIFCNGVVLEKQQC  297 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~--~~~~~~~g~~~~~~~~  297 (335)
                      .....+..+++..++.+..+|+|||++|||.+|+.+||++|||++|.|+++++.||++...+  +.+.+.+|..++.+..
T Consensus        25 ~~~~~~~~l~ela~~~L~~iVeWAK~IPgF~~L~~~DQi~LLk~~w~EllvL~~a~rs~~~~~~~~l~fa~~~~~~~~~~  104 (248)
T cd07075          25 TAENLLSTLNRLAGKQMIQVVKWAKVLPGFRNLPLEDQITLIQYSWMCLSSFALSWRSYKHTNSQFLYFAPDLVFNEERM  104 (248)
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhccCCCCCceEEecCCccccHHHH
Confidence            44566788899999999999999999999999999999999999999999999999987643  3588899998887765


Q ss_pred             hh-hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         298 QR-SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       298 ~~-~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      .. +.+ ++.+.+++++.+|++|+||.+||+|||||+||
T Consensus       105 ~~~~~~-~~~~~~~e~~~~l~~L~Ld~~E~acLKAIvLf  142 (248)
T cd07075         105 HQSAMY-ELCQGMHQISLQFVRLQLTFEEYTIMKVLLLL  142 (248)
T ss_pred             hhccHH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence            44 555 67888999999999999999999999999997

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

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

Probab=99.90  E-value=7.6e-23  Score=172.80  Aligned_cols=116  Identities=56%  Similarity=0.959  Sum_probs=107.1

Q ss_pred             CChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhh
Q psy2636         219 IAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQ  298 (335)
Q Consensus       219 ~~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~  298 (335)
                      ..+...+..+++..+..+..+|+|||++|||.+|+.+||++|||++|+|+++|+.|+++.+.++.+++++|..+.+.+..
T Consensus        37 ~~~~~~~~~~~~~~~~~l~~iv~wAK~IPgF~~L~~~DQi~LLk~~w~El~~L~~a~r~~~~~~~l~~~~~~~~~~~~~~  116 (239)
T cd06945          37 KPDSQQVQQFYDLLTGSVDVIRQWAEKIPGFKDLHREDQDLLLESAFLELFVLRLAYRSNPVDGKLVFCNGLVLHRLQCV  116 (239)
T ss_pred             CcchHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCceEeeCCceecHHHHH
Confidence            34467788899999999999999999999999999999999999999999999999999998889999999999887765


Q ss_pred             hhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         299 RSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       299 ~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      .+++ ++++.+++|+.+|++|++|++||++||||+||
T Consensus       117 ~~~~-~~~~~i~~f~~~l~~L~ld~~E~~~LkaivL~  152 (239)
T cd06945         117 RGFG-EWLDSILAFSSSLQSLLLDDISAFCCLALLLL  152 (239)
T ss_pred             HhHH-HHHHHHHHHHHHHHHHhCChHHHHHHHHHHHh
Confidence            5666 88999999999999999999999999999986

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

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

Probab=99.89  E-value=1.1e-22  Score=167.57  Aligned_cols=112  Identities=29%  Similarity=0.563  Sum_probs=103.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhhhhcH
Q psy2636         224 KIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD  303 (335)
Q Consensus       224 ~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~~~~~  303 (335)
                      .|.++++..+..++.+|+|||++|+|.+|+.+||++|||++|+++++++.++++....+.+.+.+|..+..+....+.+.
T Consensus         3 ~w~~~~~~~~~~l~~iI~waK~iP~F~~L~~~DQi~LLk~~~~el~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (195)
T cd06941           3 LWQQLSEALTPSVQRVVEFAKRIPGFCDLSQDDQLLLIKAGFFEVWLVRISRLINSKSGSITFDDGISISRQQLDIIYDS   82 (195)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHcCCCCeEEecCCeEeeHHHHHhccch
Confidence            47788999999999999999999999999999999999999999999999998888778899999999988776555666


Q ss_pred             HHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         304 DWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       304 ~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ++.+.+++|+.+|++|++|++||+|||||+||
T Consensus        83 ~~~~~~~~~~~~l~~L~ld~~E~allkAi~Lf  114 (195)
T cd06941          83 DFVKALFEFSDSFNSLGLSDTEVALFCAVVLL  114 (195)
T ss_pred             HHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHc
Confidence            78899999999999999999999999999987

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

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

Probab=99.89  E-value=2.9e-22  Score=168.53  Aligned_cols=115  Identities=29%  Similarity=0.515  Sum_probs=104.6

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR  299 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~  299 (335)
                      .+...+.++++..+..+..+|+|||++|||.+|+.+||++|||++|+|+++|+.|+++.+..+.+.+.+|..+..+....
T Consensus        35 ~~~~~~~~l~e~~~~~l~~~V~wAK~iPgF~~L~~~DQi~LLk~~w~El~~L~~a~~~~~~~~~l~~~~~~~~~~~~~~~  114 (231)
T cd06937          35 LDLGLWDKFSELSTKCIIKIVEFAKRLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMHN  114 (231)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhcCCccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEecCCceecHHHHhh
Confidence            35567788889999999999999999999999999999999999999999999999999888899999999888776544


Q ss_pred             -hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 -SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 -~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                       +++ .+.+.+++|+.+|++|+||.+||+|||||+||
T Consensus       115 ~~~~-~~~~~~~~~~~~l~~L~ld~~E~alLkAivLf  150 (231)
T cd06937         115 AGFG-PLTDLVFTFANQLLPLEMDDTEIGLLSAICLI  150 (231)
T ss_pred             cChH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence             455 77888999999999999999999999999997

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

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

Probab=99.89  E-value=6.3e-22  Score=167.08  Aligned_cols=115  Identities=20%  Similarity=0.362  Sum_probs=99.8

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCC--CeEEeeCCeEeeHHhh
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAED--TKLIFCNGVVLEKQQC  297 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~--~~~~~~~g~~~~~~~~  297 (335)
                      .....+..++++.++.+..+|+|||++|+|.+|+.+||++|||++|+|+++|+.||++....  +.+.+.+|..+..+..
T Consensus        25 ~~~~~~~~l~ela~~~L~~~VeWAK~iPgF~~L~~~DQi~LLk~~w~ElliL~~a~rs~~~~~~~~l~~~~~~~~~~~~~  104 (246)
T cd06947          25 TTARLLSSLNRLGERQLVSVVKWAKALPGFRNLHLDDQMTLIQYSWMSLMVFALGWRSYKHVNSQMLYFAPDLVFNEQRM  104 (246)
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHhhccCCCCCeEEecCCeeecHHHh
Confidence            34556778899999999999999999999999999999999999999999999999987543  3477888888887765


Q ss_pred             hh-hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         298 QR-SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       298 ~~-~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      .. +.+ ++.+.+.+++.+|++|++|.+||+|||||+||
T Consensus       105 ~~~~~~-~~~~~~~e~~~~l~~L~ld~~E~acLKAIvLf  142 (246)
T cd06947         105 HQSAMY-SLCLGMRQISQEFVRLQVTYEEFLCMKVLLLL  142 (246)
T ss_pred             hhccHH-HHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHc
Confidence            33 455 57778889999999999999999999999997

The ligand binding domain of GR_like nuclear receptors: This family of NRs includes four distinct, but closely related nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). These four receptors play key roles in some of the most fundamental physiological functions such as the stress response, metabolism, electrolyte homeostasis, immune function, growth, development, and reproduction. The NRs in this family use multiple signaling pathways and share similar functional mechanisms. The dominant signaling pathway is via direct DNA binding and transcriptional regulation of target genes. Another mechanism is via protein-protein interactions, mainly with other transcription factors such as nuclear factor-kappaB and activator prote

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

Probab=99.88  E-value=7e-22  Score=165.80  Aligned_cols=115  Identities=22%  Similarity=0.392  Sum_probs=97.9

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccC--CCeEEeeCCeEeeHHhh
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAE--DTKLIFCNGVVLEKQQC  297 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~--~~~~~~~~g~~~~~~~~  297 (335)
                      .....+..+.++..+.+..+|||||++|||.+|+.+||++|||++|+++++|+.||++...  ++.+.|.+|..+..+..
T Consensus        25 ~~~~~~~~l~~la~r~L~~vVeWAK~lPgF~~L~~~DQi~LLk~sw~ellvL~~a~rS~~~~~~~~l~fa~d~~~~~~~~  104 (248)
T cd07074          25 TPSSLLTSLNQLCERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRM  104 (248)
T ss_pred             CchhhHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCeEEecCCcccchhhh
Confidence            4455567778888899999999999999999999999999999999999999999998764  34578878888777654


Q ss_pred             hh-hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         298 QR-SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       298 ~~-~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      .. +.. ++...+++++.+|++|++|.+||+|||||+||
T Consensus       105 ~~~~~~-~~~~~m~e~~~~~~~L~ld~~Ey~cLKAIvLf  142 (248)
T cd07074         105 KESSFY-SLCLTMWQIPQEFVKLQVSQEEFLCMKALLLL  142 (248)
T ss_pred             hhccHH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHC
Confidence            33 333 46777889999999999999999999999997

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

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

Probab=99.88  E-value=5.4e-22  Score=167.65  Aligned_cols=114  Identities=26%  Similarity=0.495  Sum_probs=100.9

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR  299 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~  299 (335)
                      ...+.|.++...++..|+.+|+|||++|||.+|+.+||++|||++|+|+++++.|+++...++.+.+ +|.++..+....
T Consensus        45 ~~~~~~~~~~~~~t~~i~~vVefAK~IPgF~~L~~~DQi~LLk~~~~Ellll~~a~~~~~~~~~~~~-~~~~~~~~~~~~  123 (241)
T cd06939          45 SREEMWQLCAEKITEAIQYVVEFAKRIPGFMELCQNDQIVLLKAGSLEVVLVRMSRAFNPSNNTVLF-DGKYAPIDLFKS  123 (241)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhCCCCCEEEE-CCccccHHHHHH
Confidence            3557889999999999999999999999999999999999999999999999999888877777777 566666665443


Q ss_pred             -hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 -SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 -~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                       +.+ ++++.+++|+.+|+.|+||++||+||+||+||
T Consensus       124 ~~~~-~~~~~~~~f~~~l~~L~ld~~E~all~AivL~  159 (241)
T cd06939         124 LGCD-DLISAVFDFAKSLCELKLTEDEIALFSALVLI  159 (241)
T ss_pred             cCcH-HHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHh
Confidence             444 78899999999999999999999999999986

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

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

Probab=99.88  E-value=2e-21  Score=163.94  Aligned_cols=116  Identities=27%  Similarity=0.472  Sum_probs=103.4

Q ss_pred             CChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhh
Q psy2636         219 IAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQ  298 (335)
Q Consensus       219 ~~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~  298 (335)
                      .+..+.+..++++..+.+..+|+|||++|||.+|+.+||++|||++|+++++|+.||++....+.+++.+|..+..+...
T Consensus        28 ~~~~~~~~~l~~la~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w~el~~L~~a~rs~~~~~~~~~~~~~~~~~~~~~  107 (235)
T cd06949          28 FTEASLMMLLTNLADRELVHMINWAKKIPGFVDLSLHDQVHLLESAWLELLMLGLVWRSMEHPGKLLFAPDLLLDRNQGS  107 (235)
T ss_pred             CChHHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcCCCCeEEeeCCceecHHHhh
Confidence            35567778889999999999999999999999999999999999999999999999999888788999999888876543


Q ss_pred             --hhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         299 --RSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       299 --~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                        .+. .++.+.+++++.+|++|++|.+||+|||||+||
T Consensus       108 ~~~~~-~~~~~~~~~~~~~l~~L~ld~~EyalLKAIvLf  145 (235)
T cd06949         108 CVEGM-VEIFDMLLATASRFRELQLQREEYVCLKAIILL  145 (235)
T ss_pred             hcccH-HHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHc
Confidence              233 367888999999999999999999999999987

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

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

Probab=99.88  E-value=1.8e-21  Score=164.25  Aligned_cols=114  Identities=19%  Similarity=0.332  Sum_probs=98.4

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccC--CCeEEeeCCeEeeHHhhh
Q psy2636         221 EPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAE--DTKLIFCNGVVLEKQQCQ  298 (335)
Q Consensus       221 ~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~--~~~~~~~~g~~~~~~~~~  298 (335)
                      ....+..++++..+.+..+|+|||++|+|.+|+.+||++|||++|.|+++|+.||++...  .+.+.+.+|..++.+...
T Consensus        26 ~~~~~~~l~~la~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~w~ElliL~~a~rs~~~~~~~~l~~~~~~~l~~~~~~  105 (246)
T cd07073          26 FAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMH  105 (246)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHcCCCccCCCHHHHHHHHHHHHHHHHHHHHHHhccccCCCCeEEecCCeeechhhhc
Confidence            445567788889999999999999999999999999999999999999999999998764  446999999888866543


Q ss_pred             h-hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         299 R-SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       299 ~-~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      . +.. +....+++++.+|++|++|.+||+|||||+||
T Consensus       106 ~~~~~-~~~~~l~~~~~~l~~L~ld~~EyacLKAIiLf  142 (246)
T cd07073         106 KSRMY-SQCVRMRHLSQEFGWLQITPQEFLCMKALLLF  142 (246)
T ss_pred             cccHH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence            3 333 55566789999999999999999999999997

The ligand binding domain of the androgen receptor (AR): AR is a member of the nuclear receptor family. It is activated by binding either of the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for male primary sexual characteristics and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of an androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR-regulated genes and modulates their expression. Another mode of action is independent of their interactions with DNA. The receptors interact directly with signal transduction proteins in the cytoplasm, causing rapid changes in cell funct

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

Probab=99.87  E-value=1e-21  Score=166.65  Aligned_cols=113  Identities=27%  Similarity=0.503  Sum_probs=103.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhh-hhh
Q psy2636         223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQ-RSF  301 (335)
Q Consensus       223 ~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~-~~~  301 (335)
                      ..+.+++++.+..++.+|+|||++|+|.+|+.+||++|||++|+++++|+.|+++....+.+.+++|..+.+++.. .+.
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            5677888999999999999999999999999999999999999999999999999888889999999988877654 344


Q ss_pred             cHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         302 GDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       302 ~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ..++.+.+.+|+.+|++|++|.+||+||+||+||
T Consensus       123 ~~~~~~~i~~~~~~l~~L~ld~~E~~lL~aivLf  156 (236)
T cd06954         123 QVEFINPIFEFSKSMRELQLDDAEYALLIAINIF  156 (236)
T ss_pred             hHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhhc
Confidence            5588999999999999999999999999999987

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

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

Probab=99.87  E-value=2.1e-21  Score=157.60  Aligned_cols=113  Identities=27%  Similarity=0.489  Sum_probs=101.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhhhhc
Q psy2636         223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFG  302 (335)
Q Consensus       223 ~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~~~~  302 (335)
                      +.|..+++..+..+..+|+|||++|+|.+|+.+||++|||++|+++++++.|+++....+.+.+++|.....+.......
T Consensus         2 ~~~~~~~~~~~~~l~~~v~~ak~ip~F~~L~~~Dq~~Llk~~~~~l~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (174)
T cd06929           2 EKFDHFTEIMTVAIRRVVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATLYDPEKNSLTFGDGKGNSRDVLLNGGF   81 (174)
T ss_pred             cHHHHHHHHHHHHHHHHHhhccCCcCcccCChhHHHHHHHhcHHHHHHHHHHHHhcccCCeEEecCCceecHHHHHHccc
Confidence            35778888899999999999999999999999999999999999999999999888888889999999877665444334


Q ss_pred             HHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         303 DDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       303 ~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ..+.+.+.+++.+|++|++|.+||++||||+||
T Consensus        82 ~~~~~~~~~~~~~l~~L~l~~~E~~llkai~l~  114 (174)
T cd06929          82 GEFIEPLFEFAEKMNKLQLDDNEYALLTAIVLF  114 (174)
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence            578899999999999999999999999999986

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).

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

Probab=99.86  E-value=2.1e-21  Score=162.83  Aligned_cols=113  Identities=21%  Similarity=0.304  Sum_probs=96.3

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHh-hhhh
Q psy2636         222 PEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQ-CQRS  300 (335)
Q Consensus       222 ~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~-~~~~  300 (335)
                      ...+.++++..+..++.+|+|||++|||.+|+.+||++|||++|+|+++++.++++....+.+.+ +|..+...+ ...+
T Consensus        34 ~~~~~~~~~~~~~~l~~iV~wAK~iPgF~~L~~~DQi~LLk~~~~Ellil~~~~~~~~~~~~~~~-~~~~~~~~~~~~~g  112 (226)
T cd06934          34 FSLLPHFADLTTYMIKQIIKFAKDLPYFRSLPIEDQISLLKGATFEICQIRFNTVFNEETGTWEC-GPLTYCIEDAARAG  112 (226)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHhcCCcccccCCcchHHHHHHHhHHHHHHHHHHHHhcccCCeEee-CCEeecHHHHHHcc
Confidence            45577888888999999999999999999999999999999999999999999988876665555 555555443 3345


Q ss_pred             hcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         301 FGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       301 ~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ++..+.+.+++|+.+|++|++|.+||+|||||+||
T Consensus       113 ~~~~~~~~~~~~~~~l~~L~ld~~E~alLkAivLf  147 (226)
T cd06934         113 FQQLLLEPLLRFHYTLRKLQLQEEEYVLMQAMSLF  147 (226)
T ss_pred             chHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence            66567888999999999999999999999999987

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

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

Probab=99.86  E-value=4e-21  Score=162.15  Aligned_cols=113  Identities=27%  Similarity=0.549  Sum_probs=102.2

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh-h
Q psy2636         222 PEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR-S  300 (335)
Q Consensus       222 ~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~-~  300 (335)
                      ...+.+++++.+..++.+|+|||++|+|.+|+.+||++|||++|+++++|+.|+++....+.+.+++|..+.++.... +
T Consensus        38 ~~~~~~~~~~~~~~i~~iIefaK~lp~F~~L~~~DQi~LLK~~~~el~~L~~a~~~~~~~~~~~f~~g~~~~~~~~~~~~  117 (231)
T cd06938          38 DMRFRHITEMTILTVQLIVEFAKRLPGFDKLSREDQITLLKACSSEVMMLRVARRYDAKTDSIVFANNQPYTRDSYRKAG  117 (231)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHhcCCccccCChhHHHHHHHHHHHHHHHHHHHHHhCCCCCeEEeeCCEEecHHHHhhcC
Confidence            356778888889999999999999999999999999999999999999999999988888889999999988876533 4


Q ss_pred             hcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         301 FGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       301 ~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      .+ ++.+.+++|+.+|++|+||++||++|+||+||
T Consensus       118 ~~-~~~~~l~~~~~~l~~L~ld~~E~~lL~AI~Lf  151 (231)
T cd06938         118 MG-DSAEDLFRFCRAMCSMKVDNAEYALLTAIVIF  151 (231)
T ss_pred             HH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence            44 77888999999999999999999999999986

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

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

Probab=99.85  E-value=7.7e-21  Score=160.81  Aligned_cols=114  Identities=21%  Similarity=0.318  Sum_probs=98.7

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCC--CeEEeeCCeEeeHHhhhh
Q psy2636         222 PEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAED--TKLIFCNGVVLEKQQCQR  299 (335)
Q Consensus       222 ~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~--~~~~~~~g~~~~~~~~~~  299 (335)
                      .+.+..+..+....+..+|||||++|+|.+|+.+||++|||++|+++++|+.||++...+  +.+.+++|..+.......
T Consensus        37 ~~~~~~~~~~a~~~l~~~VewaK~lp~F~~L~~~DQi~LLk~~w~el~~L~~a~rs~~~~~~~~l~~~~g~~~~~~~~~~  116 (237)
T cd06944          37 LDTFGLMCKMADQTLFSIVEWARNSVFFKELKVDDQMKLLQNCWSELLVLDHIYRQVHHGKEDSILLVTGQEVDLSTLAS  116 (237)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHhCCChhcCCHHHHHHHHHHHhHHHHHHHHHHHhcccCCCCceeecCCCccchhhhhh
Confidence            445667777888889999999999999999999999999999999999999999988654  679999999888775432


Q ss_pred             --hhc-HHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 --SFG-DDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 --~~~-~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                        +.+ .++++.+.+++.+|++|++|.+||+|||||+||
T Consensus       117 ~~~~~~~~~~~~i~~~~~~l~~L~ld~~E~~lLkaIiL~  155 (237)
T cd06944         117 QAGLGLSSLVDRAQELVNKLRELQFDRQEFVCLKFLILF  155 (237)
T ss_pred             hccccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence              222 367888899999999999999999999999986

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

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

Probab=99.85  E-value=8.6e-21  Score=155.60  Aligned_cols=109  Identities=24%  Similarity=0.455  Sum_probs=95.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhh-h-hh
Q psy2636         224 KIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQ-R-SF  301 (335)
Q Consensus       224 ~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~-~-~~  301 (335)
                      .|.++.+..+..++.+|+|||++|||.+|+.+||++|||++|+++++++.++++..+  .+++++|..+..+... . +.
T Consensus         3 ~w~~~~~~~~~~i~~~IefaK~iPgF~~L~~~DQi~LLk~~~~e~~ll~~~~~~~~~--~~~~~~g~~~~~~~~~~~~~~   80 (191)
T cd06942           3 AWGHFAHEFEMHIQEIVQFVKSIPGFNQLSGEDRAQLLKGNMFPLYLLRLSRDYNNE--GTVLCDFRPVEFASLLSQLLH   80 (191)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCcccCChhHHHHHHHHHHHHHHHHHHHHHhCcC--CeEEeCCccccHHHHHHhcch
Confidence            577888899999999999999999999999999999999999999999988766655  5778889888776542 2 23


Q ss_pred             cHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         302 GDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       302 ~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      + ++++.+.+++.+|++|+||++||+||+||+||
T Consensus        81 ~-~~~~~~~~~~~~l~~L~l~~~E~~lL~Aivl~  113 (191)
T cd06942          81 G-KLIDEMLQFANKILTLNLTNAELALLCAAELL  113 (191)
T ss_pred             H-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence            3 77888899999999999999999999999986

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).

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

Probab=99.85  E-value=2.5e-20  Score=156.59  Aligned_cols=116  Identities=25%  Similarity=0.405  Sum_probs=100.4

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR  299 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~  299 (335)
                      ...+.+..++++.+..+..+|+|||++|||.+|+.+||++|||++|+++++|+.||++.+.++.+++.+|.+........
T Consensus        24 ~~~~~~~~~~~~~~~~l~~~Ve~aK~lp~F~~L~~~DQi~LLk~~~~el~lL~~a~~s~~~~~~~~~~~~~~~~~~~~~~  103 (221)
T cd06946          24 SDIKALTTLSDLADRELVVIIGWAKHIPGFSSLSLNDQMSLLQSAWMEILTLGVVFRSLPFNGELVFAEDFILDEELARE  103 (221)
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHccCCCCceeecCCeEEcHHHHhh
Confidence            34566788899999999999999999999999999999999999999999999999999887788888887776554332


Q ss_pred             hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 ~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      .....+.+.+.+++.+|++|++|.+||+|||||+||
T Consensus       104 ~~~~~~~~~~~~~~~~l~~L~l~~~E~~lLkai~L~  139 (221)
T cd06946         104 AGLLELYSACLQLVRRLQRLRLEKEEYVLLKALALA  139 (221)
T ss_pred             cCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence            222366778889999999999999999999999986

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=99.85  E-value=8.4e-21  Score=160.41  Aligned_cols=113  Identities=20%  Similarity=0.302  Sum_probs=95.9

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccC--CCeEEeeCCeEeeHHhh--
Q psy2636         222 PEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAE--DTKLIFCNGVVLEKQQC--  297 (335)
Q Consensus       222 ~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~--~~~~~~~~g~~~~~~~~--  297 (335)
                      .+.+..++++....+..+|+|||++|+|.+|+.+||++|||++|.++++++.||++...  .+.+++.+|..++....  
T Consensus        39 ~~~~~~i~~~a~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~w~EllvL~~a~~s~~~~~~~~~ll~~~~~~~~~~~~~  118 (241)
T cd07069          39 LSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIAS  118 (241)
T ss_pred             cchHHHHHHHHHHHHHHHHHHHhhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCeeEecCCCccCchhhhh
Confidence            44566778888889999999999999999999999999999999999999999998753  45788999987665331  


Q ss_pred             hh--hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         298 QR--SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       298 ~~--~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ..  ++. .+++.+.+++.+|++|++|.+||+|||||+||
T Consensus       119 ~~~~~~~-~~~~~~~e~~~~lr~L~ld~~E~a~LKaivLf  157 (241)
T cd07069         119 QAGATLN-NLMSHAQELVAKLRSLQFDQREFVCLKFLVLF  157 (241)
T ss_pred             hhhhHHH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence            11  233 56788889999999999999999999999997

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

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

Probab=99.85  E-value=1.3e-20  Score=159.14  Aligned_cols=115  Identities=23%  Similarity=0.338  Sum_probs=97.1

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccC--CCeEEeeCCeEeeHHhhh
Q psy2636         221 EPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAE--DTKLIFCNGVVLEKQQCQ  298 (335)
Q Consensus       221 ~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~--~~~~~~~~g~~~~~~~~~  298 (335)
                      ..+.+..++++....+..+|+|||++|+|.+|+.+||++|||++|.++++|+.||++...  .+.+++++|..+..+...
T Consensus        36 ~~~~~~~l~~~a~~~L~~~VeWaK~lP~F~~L~~~DQi~LLk~~w~el~vL~~a~rs~~~~~~~~l~~~~g~~~~~~~~~  115 (237)
T cd07070          36 QPAPFGLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQHGKEGSILLVTGQEVELSTVA  115 (237)
T ss_pred             cccHHHHHHHHHHHHHHHHHHHHHhCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCceeecCCCeechhHHH
Confidence            445567788888899999999999999999999999999999999999999999998753  467999999988866543


Q ss_pred             hhhc---HHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         299 RSFG---DDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       299 ~~~~---~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ...+   ..++..+.+++.+|++|++|.+||+|||||+||
T Consensus       116 ~~~~~~~~~~~~~~~e~~~kl~~L~ld~~Ey~~LkaIiLf  155 (237)
T cd07070         116 AQAGSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILF  155 (237)
T ss_pred             HHHhHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHhc
Confidence            2222   234455678999999999999999999999997

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).

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

Probab=99.85  E-value=1.8e-20  Score=158.45  Aligned_cols=115  Identities=21%  Similarity=0.334  Sum_probs=95.8

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCC-eEeeHHhhh-
Q psy2636         221 EPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNG-VVLEKQQCQ-  298 (335)
Q Consensus       221 ~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g-~~~~~~~~~-  298 (335)
                      ....+.++++..+..++.+|+|||++|||.+|+.+||++|||++|+|+++++.++.+..++..+.+.++ ..+..++.. 
T Consensus        35 ~~~l~~~l~~l~~~~l~~iI~wAK~iPgF~~L~~~DQi~LLk~~~~ElliL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  114 (238)
T cd06933          35 RLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEVIMLRSNQSFSLDDMSWTCGSPDFKYKVSDVTK  114 (238)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCCCccccCChHHHHHHHHHhHHHHHHHHHHHhcCcCCCeeEecCCceeecHHHHHH
Confidence            355678889999999999999999999999999999999999999999999999876555555665543 334444432 


Q ss_pred             hhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         299 RSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       299 ~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      .+...++++.+++|+.+|++|++|.+||+|||||+||
T Consensus       115 ~g~~~~~~~~l~~~~~~l~~L~ld~~E~alLkAivLf  151 (238)
T cd06933         115 AGHSLELLEPLVKFQVGLKKLNLHEEEHVLLMAICIL  151 (238)
T ss_pred             ccCcHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHH
Confidence            3445578899999999999999999999999999986

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

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

Probab=99.84  E-value=3.3e-20  Score=158.34  Aligned_cols=114  Identities=22%  Similarity=0.357  Sum_probs=95.7

Q ss_pred             CChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCC-eEeeHHhh
Q psy2636         219 IAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNG-VVLEKQQC  297 (335)
Q Consensus       219 ~~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g-~~~~~~~~  297 (335)
                      ..+.+.|..+....+..|+.+|||||++|||.+|+.+||++|||++|+|++++..|.++.  .+.+.+.+| .++.++..
T Consensus        59 ~~~~~~~~~~~~~~~~~i~~vVewAK~IPgF~~L~~~DQi~LLk~~~~Ellil~~a~~~~--~~~~~~~~~~~~~~~~~~  136 (259)
T cd06932          59 TIRIRLFQRCQVRSVETIRELTEFAKSLPGFRNLDLNDQVTLLKYGVHEVIFTMLASLYN--KDGLLFPEGNGYVTREFL  136 (259)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCChhHHHHHHHHhhHHHHHHHHHHhcC--CCCeEEeCCCEEeeHHHH
Confidence            346677888888888999999999999999999999999999999999999999997754  334666655 55666654


Q ss_pred             hh---hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         298 QR---SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       298 ~~---~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ..   +++ ++++.+++|+.+|++|+||++||+|||||+||
T Consensus       137 ~~~~~~~~-~~~~~~~e~~~~l~~L~ld~~E~alLkAivLf  176 (259)
T cd06932         137 ESLRKPFC-DIMEPKFEFAEKFNALELTDSELALFCAVIIL  176 (259)
T ss_pred             HHhcccHH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence            33   233 67888999999999999999999999999997

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

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

Probab=99.84  E-value=3.6e-20  Score=155.53  Aligned_cols=116  Identities=28%  Similarity=0.474  Sum_probs=102.2

Q ss_pred             CChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhh
Q psy2636         219 IAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQ  298 (335)
Q Consensus       219 ~~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~  298 (335)
                      ....+.+..++.+..+.+..+|||||++|+|.+|+.+||++|||++|++++++..||++...++.+.+.+|..+..+...
T Consensus        23 ~~~~~~~~~~~~~a~~~l~~~vewaK~lp~F~~L~~~DQi~LLk~~~~~~~~l~~a~~s~~~~~~~~~~~~~~~~~~~~~  102 (221)
T cd07068          23 DTEVSLLATLSDLADRELVHIISWAKHIPGFSDLSLNDQMHLLQSAWLEILMLGLVWRSLPHPGKLVFAPDLLLDREQAR  102 (221)
T ss_pred             CCchHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHhhHHHHHHHHHHhhcCCCCeEEeCCCceECHHHHh
Confidence            34567788889999999999999999999999999999999999999999999999999887778999898887765433


Q ss_pred             -hhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         299 -RSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       299 -~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                       .++. ++.+.+.+++.+|++|++|++||++||||+||
T Consensus       103 ~~~~~-~~~~~~~~~~~~l~~L~ld~~E~~lLkaIil~  139 (221)
T cd07068         103 VEGLL-EIFDMLLQLVRRFRELGLQREEYVCLKAIILA  139 (221)
T ss_pred             hccHH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence             2443 66778889999999999999999999999986

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

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

Probab=99.84  E-value=1.9e-20  Score=150.79  Aligned_cols=109  Identities=23%  Similarity=0.285  Sum_probs=95.1

Q ss_pred             HHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccC--CCeEEeeCCeEeeHHhhhhhhcHH
Q psy2636         227 QFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAE--DTKLIFCNGVVLEKQQCQRSFGDD  304 (335)
Q Consensus       227 ~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~~  304 (335)
                      .+.++..+.+..+|||||++|+|.+|+.+||++|||++|.++++|+.||++...  .+.+.+++|..+..+........+
T Consensus         3 ~~~~~~~~~l~~~ie~ak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (165)
T cd06930           3 SLCELADRVLFKTVDWAKNLPAFRNLPLDDQLTLLQNSWAELLLLGLAQRSVHFELSELLLPSPLLVILTEREALLGLAE   82 (165)
T ss_pred             hHHHHHHHHHHHHHHHHHcCCccccCChHHHHHHHHHHHHHHHHHHHHHHHhccCCCcceeecCCcccchhhhhhhhHHH
Confidence            345667788889999999999999999999999999999999999999999865  456899999988876654433336


Q ss_pred             HHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         305 WLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       305 ~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      +.+.+.+++.+|++|++|++||++||||+||
T Consensus        83 ~~~~~~~~~~~l~~L~l~~~E~~lLkai~l~  113 (165)
T cd06930          83 LVQRLQELLSKLRSLQLDPKEYACLKAIVLF  113 (165)
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence            7888899999999999999999999999986

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

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

Probab=99.84  E-value=3e-20  Score=154.85  Aligned_cols=111  Identities=21%  Similarity=0.401  Sum_probs=96.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhh-hhhc
Q psy2636         224 KIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQ-RSFG  302 (335)
Q Consensus       224 ~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~-~~~~  302 (335)
                      .+..++.+....+..+|+|||++|+|.+|+.+||++|||++|++++++..||++....+.+++.+|..+..+... .+++
T Consensus        31 ~~~~~~~~~~~~l~~~Iewak~lp~F~~L~~~DQ~~LLk~~~~e~~~l~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~~  110 (207)
T cd06943          31 PVSNICQAADKQLFQLVEWAKRIPHFSELPLDDQVILLRAGWNELLIAAFAHRSIAVKDGILLATGLHLHRNSAHQAGVG  110 (207)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHhCchhhccChhhhHHHHHHHHHHHHHHHHHHHccCCCCeeEecCCceeccchhhhccch
Confidence            356778888899999999999999999999999999999999999999999999887778889999888765542 2444


Q ss_pred             HHHHHH-HHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         303 DDWLNA-ILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       303 ~~~~~~-~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                       .+... +.+++.+|++|+||++||++||||+||
T Consensus       111 -~~~~~~~~~~~~~l~~L~ld~~E~~lLkaI~L~  143 (207)
T cd06943         111 -AIFDRILTELVVKMRDLKMDRTELGCLRAIILF  143 (207)
T ss_pred             -HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhc
Confidence             44445 458999999999999999999999987

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

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

Probab=99.84  E-value=3.2e-20  Score=153.77  Aligned_cols=111  Identities=22%  Similarity=0.224  Sum_probs=88.4

Q ss_pred             HHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhhhhcHH
Q psy2636         225 IQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDD  304 (335)
Q Consensus       225 ~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~  304 (335)
                      +..++++..+.+..+|+|||++|+|.+|+.+||++|||++|.++++|+.|+++...+...++.++...............
T Consensus        28 ~~~~~~~a~~~L~~~VewaK~ip~F~~L~~~DQi~LLk~~w~el~iL~~a~~s~~~~~~~ll~~~~~~~~~~~~~~~~~~  107 (206)
T cd06950          28 PESVCESAARLLFMAVKWAKSIPAFSTLPFRDQLILLEESWSELFLLGAAQWSLPLDSCPLLAVPGLSPDNTEAERTFLS  107 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCcceeecCCcccccccchhhHHHH
Confidence            45677788888999999999999999999999999999999999999999998876655555443322221111112224


Q ss_pred             HHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         305 WLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       305 ~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ..+.+.+++.+|++|+||.+||++||||+||
T Consensus       108 ~~~~i~~~~~~~~~L~ld~~EyalLKai~L~  138 (206)
T cd06950         108 EVRALQETLSRFRQLRVDATEFACLKAIVLF  138 (206)
T ss_pred             HHHHHHHHHHHHHHhCCCHHHHHHHHHHHHh
Confidence            4567889999999999999999999999986

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

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

Probab=99.82  E-value=1.3e-19  Score=150.89  Aligned_cols=115  Identities=14%  Similarity=0.178  Sum_probs=90.6

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCe-----EEeeCCeEeeH
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTK-----LIFCNGVVLEK  294 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~-----~~~~~g~~~~~  294 (335)
                      +..+.+..+++.....+..+|+|||++|+|.+|+.+||++|||++|+++++|+.|+++......     +....|.....
T Consensus        24 ~~~~~~~~l~~la~~~l~~~I~waK~lp~F~~L~~~DQi~LLk~~w~el~iL~~a~~s~~~~~~~l~~~~~~~~~~~~~~  103 (213)
T cd06953          24 DQAELFALLCRLGDELLFRQIQWTKKLPFFTELSIKDHTHLLTTKWAELILLSTITVASLQNLGLLQDCLSKYLPSEDEL  103 (213)
T ss_pred             chhhHHHHHHHHHHHHHHHHHHHHhcCCchhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHhhhccCCchhhH
Confidence            3446677788888899999999999999999999999999999999999999999999864321     11122222111


Q ss_pred             HhhhhhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         295 QQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       295 ~~~~~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      .+.....+ ++++.+.+++.+|++|++|.+||+|||||+||
T Consensus       104 ~~~~~~~~-~~~~~i~~l~~~l~~L~ld~eEy~lLkAIvLf  143 (213)
T cd06953         104 ERFGDEGG-EVVERLTYLLAKFRQLKVSNEEYVCLKVINFL  143 (213)
T ss_pred             HHHHhhHH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence            11222233 67888899999999999999999999999986

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

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

Probab=99.81  E-value=1.6e-19  Score=152.02  Aligned_cols=111  Identities=23%  Similarity=0.351  Sum_probs=95.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhhhhcH
Q psy2636         224 KIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD  303 (335)
Q Consensus       224 ~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~~~~~  303 (335)
                      .+..+...+...+..+++|||.||+|.+|+.+||++|||++|+++++++.||++....+.+++++|..+..+.....++ 
T Consensus        33 ~~~~~~~~~~~~l~~~vewak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~s~~~~~~l~~~~g~~~~~~~~~~~~~-  111 (222)
T cd06931          33 SINDVCESMKQQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGVARRSMPYKDILLLGNDLIIPRHCPEPEIS-  111 (222)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHhCCccccCChHHHHHHHHHHHHHHHHHHHHHhccCCCCeeeeCCCcccccccccchHH-
Confidence            3566777888999999999999999999999999999999999999999999998877889999998877654433444 


Q ss_pred             HHHHH-HHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         304 DWLNA-ILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       304 ~~~~~-~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      .+... +.+++.+|++|++|++||++||||+||
T Consensus       112 ~~~~~~~~~~~~~l~~L~l~~~E~~lLkaiil~  144 (222)
T cd06931         112 RVANRILDELVLPLRDLNIDDNEYACLKAIVFF  144 (222)
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence            34444 458999999999999999999999987

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

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

Probab=99.81  E-value=1.1e-19  Score=151.92  Aligned_cols=111  Identities=18%  Similarity=0.151  Sum_probs=86.7

Q ss_pred             HHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCe----------EEeeCCeEeeH
Q psy2636         225 IQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTK----------LIFCNGVVLEK  294 (335)
Q Consensus       225 ~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~----------~~~~~g~~~~~  294 (335)
                      +..+++...+.+..+|+|||++|+|.+|+.+||++|||++|.|+++|+.|+++.+.+..          ++..++..+..
T Consensus        21 ~~~~ce~a~~~L~~~V~wAK~iP~F~~L~~~DQi~LLk~~w~El~iL~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~  100 (222)
T cd06951          21 PQMVCRAASQVLLKTIRFVRNLPCFTYLPPDDQLRLLRRSWAPLLLLGLAQDKVPFDTVEVPAPSILCEILTGAEMHWGG  100 (222)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCcccCChHHHHHHHHHHhHHHHHHHHHHHhccccccccccchHHHHHHhcccccccc
Confidence            45567777888999999999999999999999999999999999999999998765432          22333333322


Q ss_pred             Hhh---hhh--hcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         295 QQC---QRS--FGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       295 ~~~---~~~--~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ...   ..+  ....+++.+++|+.+|++|+||.+||++||||+||
T Consensus       101 ~~~~~~~~~~~~~~~~~~~l~e~~~~l~~L~ld~~Eya~LkAivLf  146 (222)
T cd06951         101 TPPPTLTMPPCIPLADVQDIQQFLMKCWSLDLDCKEYAYLKGAVLF  146 (222)
T ss_pred             ccccccccchhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence            110   111  12245788899999999999999999999999997

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.

>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=99.80  E-value=6.3e-19  Score=147.46  Aligned_cols=109  Identities=23%  Similarity=0.404  Sum_probs=90.0

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeH-Hhhh-h
Q psy2636         222 PEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEK-QQCQ-R  299 (335)
Q Consensus       222 ~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~-~~~~-~  299 (335)
                      .+.+..+++|.+..+..+|+|||++|||.+|+.+||++|||++|+++++|+.|+++...     +++|..+.. +... .
T Consensus        35 ~~~~~~~~e~a~~~l~~~IefaK~iP~F~~L~~~DQi~LLk~~~~el~iL~~a~~~~~~-----~~~~~~~~~~~~~~~~  109 (221)
T cd06936          35 EENFLILTEMATSHVQVLVEFTKGLPGFETLDHEDQIALLKGSAVEAMFLRSAQIYNKK-----LPAGHADLLEERIRSS  109 (221)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHhCCCchhhCChhHHHHHHHHhHHHHHHHHHHHHhccc-----ccCCCchhhHHHHHhc
Confidence            46678889999999999999999999999999999999999999999999999765421     444543222 2222 2


Q ss_pred             hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 ~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      +...++++.+++|+.+|++|+||.+||+||+||+||
T Consensus       110 ~~~~e~~~~i~~~~~kl~~L~l~~~E~~lLkaIvL~  145 (221)
T cd06936         110 GISDEFITPMFNFYKSMGELKMTQEEYALLTAITIL  145 (221)
T ss_pred             cchHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence            334578999999999999999999999999999986

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

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

Probab=99.79  E-value=3.9e-19  Score=148.13  Aligned_cols=110  Identities=16%  Similarity=0.135  Sum_probs=83.6

Q ss_pred             HHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCe----------EEeeCCeEeeH
Q psy2636         225 IQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTK----------LIFCNGVVLEK  294 (335)
Q Consensus       225 ~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~----------~~~~~g~~~~~  294 (335)
                      +..+++...+.+..+|+|||++|+|.+|+.+||++|||++|.|+++|+.||++.+.+..          +.+. |.....
T Consensus        21 ~~~ice~a~~~L~~~V~WAK~iP~F~~L~~~DQi~LLk~~W~EL~iL~laq~s~~~~~~~~~~~~~~~~~l~~-~~~~~~   99 (222)
T cd07349          21 PHRTCREASDVLVKTVAFMRNLPSFWQLPPQDQLLLLQNCWGPLFLLGLAQDRVTFEVAEAPVPSMLKKILLE-GQSSSG   99 (222)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCcccCChHHHHHHHHHccHHHHHHHHHHHccccccccccchhHHHHHHhc-cccccc
Confidence            44556666788889999999999999999999999999999999999999998654321          2222 222111


Q ss_pred             Hh-h--hhhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         295 QQ-C--QRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       295 ~~-~--~~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      .. .  ..+.....++.+.+|+.+|++|++|.+||++||||+||
T Consensus       100 ~~~~~~~~~~~~~~~~~l~e~~~~l~~L~ld~~Eya~LkaivLf  143 (222)
T cd07349         100 GSGQPDRPQPSLAAVQWLQCCLNKFWSLDLSPKEYAYLKGTILF  143 (222)
T ss_pred             ccchhhhhhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence            10 0  11222345667789999999999999999999999997

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.

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

Probab=99.79  E-value=5.5e-19  Score=148.10  Aligned_cols=111  Identities=22%  Similarity=0.174  Sum_probs=84.5

Q ss_pred             HHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEE---------eeCCeEeeHH
Q psy2636         225 IQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLI---------FCNGVVLEKQ  295 (335)
Q Consensus       225 ~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~---------~~~g~~~~~~  295 (335)
                      +..+++...+.+..+|+|||++|+|.+|+.+||++|||++|.|+++|+.|+++.+.+...+         +.++......
T Consensus        21 ~~~~ce~a~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~W~El~iL~~a~~s~~~~~~~~~~~~~~~~~l~~~~~~~~~  100 (232)
T cd07350          21 PQVTCKAASAVLVKTLRFVKGVPCFQELPLDDQLVLVRSCWAPLLVLGLAQDGVDFETVETSEPSMLQRILTTRPPPTSG  100 (232)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCcCcccCChHHHHHHHHHhhHHHHHHHHHHHcCCCccccccchhHHHHHHhcccccccc
Confidence            4566777788889999999999999999999999999999999999999999876543221         2222111000


Q ss_pred             -------------hhhhh--hcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         296 -------------QCQRS--FGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       296 -------------~~~~~--~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                                   ....+  .....++.+++|+.+|+.|+||.+||++||||+||
T Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~e~~~~l~~L~ld~~E~a~LkAivLf  155 (232)
T cd07350         101 AEPGEPQALPQMPQAEASHLPSAADIRAIKAFLAKCWSLDISTKEYAYLKGTVLF  155 (232)
T ss_pred             cccccccccccccchhhccccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence                         00111  11235677889999999999999999999999997

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.

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

Probab=99.79  E-value=7.8e-19  Score=148.60  Aligned_cols=112  Identities=25%  Similarity=0.295  Sum_probs=91.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCC-eEEeeCCeEeeHHhhhhhh
Q psy2636         223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT-KLIFCNGVVLEKQQCQRSF  301 (335)
Q Consensus       223 ~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~-~~~~~~g~~~~~~~~~~~~  301 (335)
                      ..+..++++..+.+..+|+|||++|+|.+|+.+||++|||++|+++++|+.|+++..... .+.+++|..+..... ...
T Consensus        30 ~~~~~l~~~a~~~L~~~VewaK~lp~F~~L~~~DQi~LLk~~w~el~lL~~a~~s~~~~~~~~~~~~g~~~~~~~~-~~~  108 (236)
T cd06948          30 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLSWSELFVLNAAQCCMPLHVAPLLAAAGLHASPMSA-DRV  108 (236)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHhhHHHHHHHHHHHcccccchhhhhccccccCccch-hhH
Confidence            446778888899999999999999999999999999999999999999999999876443 477778887653321 111


Q ss_pred             c--HHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         302 G--DDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       302 ~--~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      .  .+.++.+.+++.+|++|+||++||++||||+||
T Consensus       109 ~~~~~~~~~~~~l~~~l~~L~ld~~E~~lLkaiiL~  144 (236)
T cd06948         109 VAFMDHIRIFQEQVEKLKALHVDSAEFSCLKAIVLF  144 (236)
T ss_pred             hHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence            1  133445668999999999999999999999986

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

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

Probab=99.72  E-value=2.9e-17  Score=138.17  Aligned_cols=111  Identities=23%  Similarity=0.297  Sum_probs=82.5

Q ss_pred             HHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCC-eEEeeCCeEeeHH----hhh-
Q psy2636         225 IQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT-KLIFCNGVVLEKQ----QCQ-  298 (335)
Q Consensus       225 ~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~-~~~~~~g~~~~~~----~~~-  298 (335)
                      +..+.++..+.+..+++|||++|+|.+|+.+||++|||++|.++++++.++++...+. .+....+.++...    ... 
T Consensus        23 ~~~~~~~a~~~l~~~v~wak~iP~F~~L~~~DQ~~LLk~~w~el~lL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  102 (222)
T cd06952          23 VHYICESASRLLFLSIHWARSIPAFQALGAETQTSLVRACWPELFTLGLAQCSQQLSLPTILAAIINHLQTSIQQDKLSA  102 (222)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCchhhCChHHHHHHHHHHhHHHHHHHHHHHhcccCchHHhhhhhhhhhhhHhcCCCch
Confidence            4556777788899999999999999999999999999999999999999877654332 2332333322111    110 


Q ss_pred             hhhc--HHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         299 RSFG--DDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       299 ~~~~--~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ...+  .+.+..+.+++.+|++|++|.+||++||||+||
T Consensus       103 ~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~~~LkaiiLf  141 (222)
T cd06952         103 DKVKQVMEHINKLQEFVNSMQKLDVDDHEYAYLKAIVLF  141 (222)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence            0111  133445678999999999999999999999997

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

>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=99.72  E-value=1.8e-16  Score=131.86  Aligned_cols=116  Identities=28%  Similarity=0.498  Sum_probs=101.4

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhc-cCCCeEEeeCCeEeeHHhhh
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTR-AEDTKLIFCNGVVLEKQQCQ  298 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~-~~~~~~~~~~g~~~~~~~~~  298 (335)
                      .....+..+..++...+..+++|||++|+|.+|+.+||++|||++|+++++|+.++++. ...+.+.+.+|..+..+...
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            45666788888899999999999999999999999999999999999999999999988 56678999999999877654


Q ss_pred             hh---hcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         299 RS---FGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       299 ~~---~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ..   ...+..+.+.+++.+|.+|++|.+||++|+||+||
T Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~l~l~~~E~~~l~~l~l~  133 (203)
T PF00104_consen   94 DFITGIFSEFIQYMNEVLRPFRRLKLDEEEFALLKALILF  133 (203)
T ss_dssp             HTSTTTHHHHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHS
T ss_pred             cccccccccchhHHHHHHHHHHHhhhhhHHHHHHHHHhhh
Confidence            32   34477888999999999999999999999999987

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 ....

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

Probab=99.71  E-value=1e-16  Score=129.27  Aligned_cols=108  Identities=31%  Similarity=0.461  Sum_probs=88.5

Q ss_pred             HHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCe-EEeeCCeE---eeHHhhhhhhcH
Q psy2636         228 FYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTK-LIFCNGVV---LEKQQCQRSFGD  303 (335)
Q Consensus       228 ~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~-~~~~~g~~---~~~~~~~~~~~~  303 (335)
                      +..++...+..+++|||++|+|.+|+.+||+.|||++|+++++|+.+|++...... ...+++..   ...+.....+.+
T Consensus         3 ~~~~~~~~~~~~i~~~~~~~~f~~L~~~dq~~Llk~~~~~~~~L~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (168)
T cd06157           3 LCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLLLAPNGGHTDDDKEDEMKLLLKG   82 (168)
T ss_pred             HHHHHHHHHHHHHHHHHcCCchhcCChHHHHHHHHHHhHHHHHHHHHHHHHhcCCCcEEeecccccccCchHHHHHhHHH
Confidence            45567788889999999999999999999999999999999999999999876543 44444442   223333344555


Q ss_pred             HHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         304 DWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       304 ~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      .+.+.+.+++.+|.+|++|++||++|+||+||
T Consensus        83 ~~~~~~~~~~~~~~~L~l~~~E~~~l~ai~l~  114 (168)
T cd06157          83 ELIRLLFEFVNPLRALKLDDEEYALLKAIVLF  114 (168)
T ss_pred             HHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHh
Confidence            77788889999999999999999999999987

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=99.68  E-value=2.2e-16  Score=126.56  Aligned_cols=102  Identities=22%  Similarity=0.371  Sum_probs=86.3

Q ss_pred             HHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCC-eEEeeCCeEeeHHhhh---hhhcHHHHHHH
Q psy2636         234 TSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT-KLIFCNGVVLEKQQCQ---RSFGDDWLNAI  309 (335)
Q Consensus       234 ~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~-~~~~~~g~~~~~~~~~---~~~~~~~~~~~  309 (335)
                      ..+..+++|||++|+|.+|+.+||+.|||++|+++++|+.++++...+. .+.+++|.++..+...   ..+.+.+.+.+
T Consensus         3 ~~~~~~~~~~~~~~~f~~L~~~dq~~Llk~~~~~~~~l~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (163)
T smart00430        3 RDLLLAVEWAKTFPFFRELSQEDKLILLKHFWFEWLLLESAYRSAKMKKSLLLLPDGTFIDNDKVDLLRKLFSPFLDRIL   82 (163)
T ss_pred             hHHHHHHHHHHhChhHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEeCCCcccCcchhHHHHHHHHHHHHHHH
Confidence            4567789999999999999999999999999999999999999987655 5666777666544322   34555777888


Q ss_pred             HHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         310 LEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       310 ~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      .+++.+|++|++|++||++|+||++|
T Consensus        83 ~~~~~~l~~L~l~~~E~~~l~ai~l~  108 (163)
T smart00430       83 QELVKPLRELKLDDEEYALLKAILLF  108 (163)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence            89999999999999999999999986

>KOG4217|consensus

Probab=94.65  E-value=0.074  Score=48.18  Aligned_cols=49  Identities=55%  Similarity=0.887  Sum_probs=44.2

Q ss_pred             CChhHHHHHHHhhcchhhhhhhcccCCCCCCCCCHHHHHHHHhhhhhcc
Q psy2636         159 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL  207 (335)
Q Consensus       159 ~~~~~~~~~~~~l~~~~~~i~~~~~~~p~~~~l~~~~~~~l~~~~~~~~  207 (335)
                      .....+++||++++.+.++++.|...+|.|.++.++|+++|+..+.+++
T Consensus       405 tdA~~vqqfy~lLtgsl~virk~aekiPgf~el~paDq~lLlesaflel  453 (605)
T KOG4217|consen  405 TDALHVQQFYDLLTGSLEVIRKWAEKIPGFAELPPADQDLLLESAFLEL  453 (605)
T ss_pred             cHHHHHHHHHHHhhhhHHHHHHHHHhCcCcccCChhhHHHHHHHHHHHH
Confidence            3457899999999999999999999999999999999999998887653

>KOG3277|consensus

Probab=85.67  E-value=0.62  Score=35.74  Aligned_cols=26  Identities=35%  Similarity=0.752  Sum_probs=21.0

Q ss_pred             cccccCCCCCc------cccCCc--cccccccce
Q psy2636          42 LCAVCGDIAAC------QHYGVR--TCEGCKGFF   67 (335)
Q Consensus        42 ~C~VCgd~a~g------~HyGv~--sC~gCk~FF   67 (335)
                      .|.|||-+.+.      ||=||.  +|.||+.+.
T Consensus        81 TCkvCntRs~ktisk~AY~~GvVivqC~gC~~~H  114 (165)
T KOG3277|consen   81 TCKVCNTRSTKTISKQAYEKGVVIVQCPGCKNHH  114 (165)
T ss_pred             EeeccCCccccccChhhhhCceEEEECCCCccce
Confidence            59999988754      888874  699999864

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

Probab=84.20  E-value=2  Score=36.54  Aligned_cols=51  Identities=80%  Similarity=1.291  Sum_probs=43.7

Q ss_pred             CCCCChhHHHHHHHhhcchhhhhhhcccCCCCCCCCCHHHHHHHHhhhhhc
Q psy2636         156 PPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLE  206 (335)
Q Consensus       156 ~~~~~~~~~~~~~~~l~~~~~~i~~~~~~~p~~~~l~~~~~~~l~~~~~~~  206 (335)
                      ++....+.+++++...+.....+..|++.+|.|.+|..+|+..+++.+..+
T Consensus        36 ~~~~~~~~~~~~~~l~t~~i~~iv~wAK~IPgF~~L~~~DQi~LLk~~w~E   86 (239)
T cd07072          36 PPMSEAEKVQQFYSLLTSSIDVIKTFAEKIPGFPDLCKEDQELLFQSASLE   86 (239)
T ss_pred             CCcchHHHHHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHHHHHHhHHH
Confidence            345566788899999888888889999999999999999999999888644

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).

>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development

Probab=82.76  E-value=0.46  Score=28.73  Aligned_cols=23  Identities=35%  Similarity=0.908  Sum_probs=19.4

Q ss_pred             cccccCCCC-Cccc-cCCccccccc
Q psy2636          42 LCAVCGDIA-ACQH-YGVRTCEGCK   64 (335)
Q Consensus        42 ~C~VCgd~a-~g~H-yGv~sC~gCk   64 (335)
                      .|.|||..- .|.| ||..-|..|-
T Consensus         1 ~CiiC~~~~~~GI~I~~~fIC~~CE   25 (46)
T PF10764_consen    1 KCIICGKEKEEGIHIYGKFICSDCE   25 (46)
T ss_pred             CeEeCCCcCCCCEEEECeEehHHHH
Confidence            499999775 5988 9999999985

Gin is also known as CsfB [].

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	335
1pdu_A	244	Ligand-Binding Domain Of Drosophila Orphan Nuclear		5e-46
1ovl_A	271	Crystal Structure Of Nurr1 Lbd Length = 271		1e-33
1ovl_B	271	Crystal Structure Of Nurr1 Lbd Length = 271		2e-33
2qw4_A	273	Human Nr4a1 Ligand-Binding Domain Length = 273		4e-33
1yje_A	264	Crystal Structure Of The Rngfi-B Ligand-Binding Dom		5e-33
3v3e_B	257	Crystal Structure Of The Human Nur77 Ligand-Binding		6e-33
1cit_A	89	Dna-Binding Mechanism Of The Monomeric Orphan Nucle		4e-29
3dzu_A	467	Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp		5e-18
2a66_A	113	Human Liver Receptor Homologue Dna-Binding Domain (		2e-15
1lo1_A	98	Estrogen Related Receptor 2 Dna Binding Domain In C		6e-15
2ff0_A	102	Solution Structure Of Steroidogenic Factor 1 Dna Bi		2e-14
1ynw_B	99	Crystal Structure Of Vitamin D Receptor And 9-Cis R		4e-14
1dsz_B	85	Structure Of The RxrRAR DNA-Binding Domain Heterodi		9e-14
2ebl_A	89	Solution Structure Of The Zinc Finger, C4-type Doma		2e-13
2han_A	93	Structural Basis Of Heterodimeric Ecdysteroid Recep		3e-13
1r0n_A	81	Crystal Structure Of Heterodimeric Ecdsyone Recepto		4e-13
1by4_A	82	Structure And Mechanism Of The Homodimeric Assembly		4e-13
1hcq_A	84	The Crystal Structure Of The Estrogen Receptor Dna-		4e-13
1dsz_A	86	Structure Of The RxrRAR DNA-Binding Domain Heterodi		5e-13
1r0o_A	86	Crystal Structure Of The Heterodimeric Ecdysone Rec		6e-13
1rxr_A	83	High Resolution Solution Structure Of The Retinoid		8e-13
1hra_A	80	The Solution Structure Of The Human Retinoic Acid R		5e-12
3cbb_A	78	Crystal Structure Of Hepatocyte Nuclear Factor 4alp		5e-12
1hcp_A	76	Dna Recognition By The Oestrogen Receptor: From Sol		8e-12
1hlz_A	94	Crystal Structure Of The Orphan Nuclear Receptor Re		1e-11
4aa6_E	71	The Oestrogen Receptor Recognizes An Imperfectly Pa		1e-11
2nll_A	66	Retinoid X Receptor-Thyroid Hormone Receptor Dna-Bi		1e-11
4aa6_A	71	The Oestrogen Receptor Recognizes An Imperfectly Pa		2e-11
1r0n_B	109	Crystal Structure Of Heterodimeric Ecdsyone Recepto		4e-11
2han_B	119	Structural Basis Of Heterodimeric Ecdysteroid Recep		5e-11
1ynw_A	110	Crystal Structure Of Vitamin D Receptor And 9-Cis R		1e-10
2nll_B	103	Retinoid X Receptor-Thyroid Hormone Receptor Dna-Bi		2e-10
1z5x_E	310	Hemipteran Ecdysone Receptor Ligand-Binding Domain		3e-10
1lat_A	82	Glucocorticoid Receptor MutantDNA COMPLEX Length =		4e-10
3m9e_A	105	Thyroid Hormone Beta Dna Binding Domain Homodimer W		1e-09
1kb2_A	110	Crystal Structure Of Vdr Dna-Binding Domain Bound T		1e-09
1vjb_A	251	Crystal Structure Of The Ligand-Binding Domain Of T		2e-09
1s9q_A	251	Crystal Structure Of The Ligand-Binding Domain Of T		2e-09
2e2r_A	244	Crystal Structure Of Human Estrogen-Related Recepto		2e-09
4hn6_A	114	Gr Dna Binding Domain R460d/d462r - Tslp Ngre Compl		2e-09
1kv6_A	230	X-Ray Structure Of The Orphan Nuclear Receptor Err3		2e-09
1s9p_A	227	Crystal Structure Of The Ligand-Binding Domain Of T		3e-09
2ewp_A	226	Crystal Structure Of Estrogen Related Receptor-3 (E		3e-09
3dzu_D	419	Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp		3e-09
3g9p_B	90	Gr Dna Binding Domain:sgk 16bp Complex-7 Length = 9		1e-08
2nxx_E	248	Crystal Structure Of The Ligand-Binding Domains Of		1e-08
3l0e_A	253	X-Ray Crystal Structure Of A Potent Liver X Recepto		1e-08
2c7a_A	78	Structure Of The Progesterone Receptor-Dna Complex		1e-08
1r4o_A	92	Crystallographic Analysis Of The Interaction Of The		2e-08
4hn5_A	117	Gr Dna Binding Domain - Tslp Ngre Complex Length =		2e-08
1r4r_B	92	Crystallographic Analysis Of The Interaction Of The		2e-08
1glu_A	81	Crystallographic Analysis Of The Interaction Of The		2e-08
1upv_A	257	Crystal Structure Of The Human Liver X Receptor Bet		3e-08
1pq6_A	253	Human Lxr Beta Hormone Receptor / Gw3965 Complex Le		3e-08
1p8d_A	250	X-Ray Crystal Structure Of Lxr Ligand Binding Domai		3e-08
4dk8_A	247	Crystal Structure Of Lxr Ligand Binding Domain In C		3e-08
2env_A	88	Solution Sturcture Of The C4-Type Zinc Finger Domai		3e-08
1xdk_B	303	Crystal Structure Of The RarbetaRXRALPHA LIGAND BIN		6e-08
1r20_D	265	Crystal Structure Of The Ligand-Binding Domains Of		7e-08
1xap_A	267	Structure Of The Ligand Binding Domain Of The Retin		7e-08
3g6t_A	91	Gr Gamma Dna-Binding Domain:fkbp5 16bp Complex-34 L		9e-08
3cqv_A	199	Crystal Structure Of Reverb Beta In Complex With He		1e-07
2gda_A	72	Refined Solution Structure Of The Glucocorticoid Re		1e-07
1gdc_A	72	Refined Solution Structure Of The Glucocorticoid Re		1e-07
4dk7_A	247	Crystal Structure Of Lxr Ligand Binding Domain In C		1e-07
2v7c_A	194	Crystal Structure Of Rev-Erb Beta Length = 194		1e-07
2lbd_A	267	Ligand-Binding Domain Of The Human Retinoic Acid Re		1e-07
1fcy_A	236	Isotype Selectivity Of The Human Retinoic Acid Nucl		2e-07
1fcx_A	235	Isotype Selectivity Of The Human Retinoic Acid Nucl		2e-07
1exa_A	246	Enantiomer Discrimination Illustrated By Crystal St		2e-07
1r4i_A	105	Crystal Structure Of Androgen Receptor Dna-Binding		2e-07
1r1k_D	266	Crystal Structure Of The Ligand-Binding Domains Of		2e-07
3fc6_B	266	Hrxralpha & Mlxralpha With An Indole Pharmacophore,		2e-07
3ipq_A	283	X-Ray Structure Of Gw3965 Synthetic Agonist Bound T		2e-07
1uhl_B	242	Crystal Structure Of The Lxralfa-Rxrbeta Lbd Hetero		3e-07
2acl_B	244	Liver X-Receptor Alpha Ligand Binding Domain With S		3e-07
1rgd_A	71	Structure Refinement Of The Glucocorticoid Receptor		3e-07
2v0v_A	194	Crystal Structure Of Rev-Erb Beta Length = 194		5e-07
2h79_A	269	Crystal Structure Of Human Tr Alpha Bound T3 In Ort		5e-07
3hzf_A	269	Structure Of Tr-alfa Bound To Selective Thyromimeti		5e-07
1uom_A	254	The Structure Of Estrogen Receptor In Complex With		5e-07
3jzb_A	267	Crystal Structure Of Tr-Alfa Bound To The Selective		5e-07
3kmr_A	266	Crystal Structure Of Raralpha Ligand Binding Domain		6e-07
1qkt_A	248	Mutant Estrogen Nuclear Receptor Ligand Binding Dom		7e-07
2yat_A	252	Crystal Structure Of Estradiol Derived Metal Chelat		7e-07
1pcg_A	244	Helix-Stabilized Cyclic Peptides As Selective Inhib		7e-07
4dqm_A	234	Revealing A Marine Natural Product As A Novel Agoni		7e-07
1dkf_B	235	Crystal Structure Of A Heterodimeric Complex Of Rar		7e-07
3os8_A	258	Estrogen Receptor Length = 258		8e-07
3a9e_B	269	Crystal Structure Of A Mixed Agonist-Bound Rar-Alph		8e-07
2ocf_A	298	Human Estrogen Receptor Alpha Ligand-Binding Domain		9e-07
1nav_A	263	Thyroid Receptor Alpha In Complex With An Agonist S		1e-06
3n00_A	245	Crystal Structure Of A Deletion Mutant Of Human Rev		2e-06
2h77_A	269	Crystal Structure Of Human Tr Alpha Bound T3 In Mon		2e-06
3q95_B	260	Crystal Structure Of Human Estrogen Receptor Alpha		2e-06
3uu7_A	251	Crystal Structure Of Hera-Lbd (Y537s) In Complex Wi		2e-06
3q97_A	260	Crystal Structure Of Human Estrogen Receptor Alpha		2e-06
1zky_A	257	Human Estrogen Receptor Alpha Ligand-Binding Domain		2e-06
3uu7_B	251	Crystal Structure Of Hera-Lbd (Y537s) In Complex Wi		2e-06
3hm1_A	253	Crystal Structure Of Human Estrogen Receptor Alpha		2e-06
2jfa_B	252	Estrogen Receptor Alpha Lbd In Complex With An Affi		2e-06
3os8_C	258	Estrogen Receptor Length = 258		3e-06
1l2i_A	261	Human Estrogen Receptor Alpha Ligand-Binding Domain		3e-06
3uvv_A	265	Crystal Structure Of The Ligand Binding Domains Of		3e-06
3d24_A	253	Crystal Structure Of Ligand-Binding Domain Of Estro		4e-06
2pjl_A	247	Crystal Structure Of Human Estrogen-Related Recepto		4e-06
2qa8_B	258	Crystal Structure Of The Estrogen Receptor Alpha Li		6e-06
3q95_A	260	Crystal Structure Of Human Estrogen Receptor Alpha		6e-06
2qzo_B	258	Crystal Structure Of The Estrogen Receptor Alpha Li		6e-06
1err_A	253	Human Estrogen Receptor Ligand-Binding Domain In Co		6e-06
3uuc_A	251	Crystal Structure Of Hera-Lbd (Wt) In Complex With		6e-06
3uua_A	251	Crystal Structure Of Hera-Lbd (Y537s) In Complex Wi		7e-06
2bj4_A	252	Estrogen Receptor Alpha Lbd In Complex With A Phage		7e-06
3uua_B	251	Crystal Structure Of Hera-Lbd (Y537s) In Complex Wi		7e-06
1xb7_A	247	X-Ray Structure Of Erralpha Lbd In Complex With A P		8e-06
3k6p_A	248	Estrogen Related Receptor Alpha In Complex With An		9e-06
3erd_A	261	Human Estrogen Receptor Alpha Ligand-Binding Domain		9e-06
2p15_A	258	Crystal Structure Of The Er Alpha Ligand Binding Do		9e-06
2iok_A	254	Human Estrogen Receptor Alpha Ligand-binding Domain		1e-05
3dt3_A	255	Human Estrogen Receptor Alpha Lbd With Gw368 Length		1e-05
1ere_A	253	Human Estrogen Receptor Ligand-Binding Domain In Co		1e-05
2iog_A	246	Human Estrogen Receptor Alpha Ligand-Binding Domain		1e-05
1a52_A	258	Estrogen Receptor Alpha Ligand-Binding Domain Compl		1e-05
1x7e_A	245	Crystal Structure Of Estrogen Receptor Alpha Comple		1e-05
1sj0_A	248	Human Estrogen Receptor Alpha Ligand-binding Domain		1e-05
2qa8_A	258	Crystal Structure Of The Estrogen Receptor Alpha Li		1e-05
1gwq_A	248	Human Oestrogen Receptor Alpha Ligand-Binding Domai		1e-05
3hlv_A	253	Crystal Structure Of Human Estrogen Receptor Alpha		1e-05
2qxs_A	258	Crystal Structure Of Antagonizing Mutant 536s Of Th		1e-05
1qku_A	250	Wild Type Estrogen Nuclear Receptor Ligand Binding		1e-05
1g50_A	247	Crystal Structure Of A Wild Type Her Alpha Lbd At 2		1e-05
3l03_A	253	Crystal Structure Of Human Estrogen Receptor Alpha		1e-05
1gwr_A	245	Human Oestrogen Receptor Alpha Ligand-Binding Domai		1e-05
4dma_A	247	Crystal Structure Of Era Lbd In Complex With Ru1001		2e-05
3l0l_A	248	Crystal Structure Of Orphan Nuclear Receptor Rorgam		2e-05
1n83_A	270	Crystal Structure Of The Complex Between The Orphan		2e-05
3kyt_A	243	Crystal Structure Of Orphan Nuclear Receptor Rorgam		2e-05
3jzc_A	263	Crystal Structure Of Tr-Beta Bound To The Selective		5e-05
2gl8_A	241	Human Retinoic Acid Receptor Rxr-Gamma Ligand-Bindi		5e-05
1n4h_A	259	Characterization Of Ligands For The Orphan Nuclear		8e-05
1k4w_A	252	X-Ray Structure Of The Orphan Nuclear Receptor Ror		1e-04
2j4a_A	253	Human Thyroid Hormone Receptor Beta Ligand Binding		1e-04
1nq2_A	264	Two Rth Mutants With Impaired Hormone Binding Lengt		1e-04
1xzx_X	281	Thyroxine-Thyroid Hormone Receptor Interactions Len		2e-04
3gws_X	259	Crystal Structure Of T3-Bound Thyroid Hormone Recep		2e-04
1nq7_A	244	Characterization Of Ligands For The Orphan Nuclear		2e-04
3imy_A	261	Structure Of Tr-Beta Bound To Selective Thyromimeti		2e-04
1nax_A	252	Thyroid Receptor Beta1 In Complex With A Beta-Selec		2e-04
1q4x_A	253	Crystal Structure Of Human Thyroid Hormone Receptor		2e-04
1r6g_A	259	Crystal Structure Of The Thyroid Hormone Receptor B		2e-04
1n46_A	258	Crystal Structure Of Human Tr Beta Ligand-Binding D		2e-04
1nq0_A	263	Tr Receptor Mutations Conferring Hormone Resistance		2e-04
1nq1_A	263	Tr Receptor Mutations Conferring Hormone Resistance		2e-04
1bsx_A	260	Structure And Specificity Of Nuclear Receptor-Coact		2e-04
3d57_A	266	Tr Variant D355r Length = 266		2e-04
2pin_A	253	Thyroid Receptor Beta In Complex With Inhibitor Len		3e-04
3p88_A	229	Fxr Bound To Isoquinolinecarboxylic Acid Length = 2		4e-04
3gd2_A	229	Isoxazole Ligand Bound To Farnesoid X Receptor (Fxr		4e-04
3hc6_A	232	Fxr With Src1 And Gsk088 Length = 232		4e-04
3l1b_A	233	Complex Structure Of Fxr Ligand-Binding Domain With		4e-04
3hc5_A	232	Fxr With Src1 And Gsk826 Length = 232		4e-04
3bej_A	238	Structure Of Human Fxr In Complex With Mfa-1 And Co		4e-04
1osh_A	232	A Chemical, Genetic, And Structural Analysis Of The		4e-04
3fli_A	231	Discovery Of Xl335, A Highly Potent, Selective And		5e-04
3dct_A	235	Fxr With Src1 And Gw4064 Length = 235		5e-04
3p89_A	229	Fxr Bound To A Quinolinecarboxylic Acid Length = 22		5e-04
3rut_A	229	Fxr With Src1 And Gsk359 Length = 229		5e-04
2fsz_A	246	A Second Binding Site For Hydroxytamoxifen Within T		6e-04
1lbd_A	282	Ligand-Binding Domain Of The Human Nuclear Receptor		6e-04
3fxv_A	233	Identification Of An N-Oxide Pyridine Gw4064 Analog		7e-04
3e94_A	244	Crystal Structure Of Rxralpha Ligand Binding Domain		8e-04
3uvv_B	244	Crystal Structure Of The Ligand Binding Domains Of		9e-04
3a9e_A	240	Crystal Structure Of A Mixed Agonist-Bound Rar-Alph		9e-04

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

Iteration: 1
 Score =  181 bits (459), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 88/120 (73%), Positives = 102/120 (85%), Gaps = 1/120 (0%)
Query: 216 EPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAY 275
           E  ++E +K+QQFY LLT+SVDVI+ FA+KIPG+ DL  EDQELLFQSASLELFVLRLAY
Sbjct: 40  EQSMSEADKVQQFYQLLTSSVDVIKQFAEKIPGYFDLLPEDQELLFQSASLELFVLRLAY 99
Query: 276 RTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
           R R +DTKLIFCNG VL + QC RSFG +WLN I+EF +SLH +EIDISAFACLCALTLI
Sbjct: 100 RARIDDTKLIFCNGTVLHRTQCLRSFG-EWLNDIMEFSRSLHNLEIDISAFACLCALTLI 158

>pdb|1OVL|A Chain A, Crystal Structure Of Nurr1 Lbd Length = 271

Iteration: 1
 Score =  140 bits (352), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 67/115 (58%), Positives = 89/115 (77%), Gaps = 1/115 (0%)
Query: 221 EPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAE 280
           + + IQQFY LLT S+++IR +A+KIPGF+DL K DQ+LLF+SA LELFVLRLAYR+   
Sbjct: 72  DTQHIQQFYDLLTGSMEIIRGWAEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSNPV 131
Query: 281 DTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
           + KLIFCNGVVL + QC R FG +W+++I+EF  +L    IDISAF+C+ AL  +
Sbjct: 132 EGKLIFCNGVVLHRLQCVRGFG-EWIDSIVEFSSNLQNXNIDISAFSCIAALAXV 185

>pdb|1OVL|B Chain B, Crystal Structure Of Nurr1 Lbd Length = 271

Iteration: 1
 Score =  139 bits (351), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 67/115 (58%), Positives = 88/115 (76%), Gaps = 1/115 (0%)
Query: 221 EPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAE 280
           + + IQQFY LLT S ++IR +A+KIPGF+DL K DQ+LLF+SA LELFVLRLAYR+   
Sbjct: 72  DTQHIQQFYDLLTGSXEIIRGWAEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSNPV 131
Query: 281 DTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
           + KLIFCNGVVL + QC R FG +W+++I+EF  +L    IDISAF+C+ AL  +
Sbjct: 132 EGKLIFCNGVVLHRLQCVRGFG-EWIDSIVEFSSNLQNXNIDISAFSCIAALAXV 185

>pdb|2QW4|A Chain A, Human Nr4a1 Ligand-Binding Domain Length = 273

Iteration: 1
 Score =  138 bits (348), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 81/184 (44%), Positives = 113/184 (61%), Gaps = 23/184 (12%)
Query: 152 NPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFYRE 211
            P +PP A P       +LLT+   ++R   D  P  + L        FQ   L  F +E
Sbjct: 27  KPKQPPDASPA------NLLTS---LVRAHLDSGPSTAKLDYSK----FQELVLPHFGKE 73
Query: 212 PNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVL 271
                    +   +QQFY LL+ S++VIR +A+KIPGF++L   DQ+LL +SA LELF+L
Sbjct: 74  ---------DAGDVQQFYDLLSGSLEVIRKWAEKIPGFAELSPADQDLLLESAFLELFIL 124
Query: 272 RLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCA 331
           RLAYR++  + KLIFC+G+VL + QC R FG DW+++IL F +SLH + +D+ AFACL A
Sbjct: 125 RLAYRSKPGEGKLIFCSGLVLHRLQCARGFG-DWIDSILAFSRSLHSLLVDVPAFACLSA 183
Query: 332 LTLI 335
           L LI
Sbjct: 184 LVLI 187

>pdb|1YJE|A Chain A, Crystal Structure Of The Rngfi-B Ligand-Binding Domain Length = 264

Iteration: 1
 Score =  138 bits (347), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 82/182 (45%), Positives = 111/182 (60%), Gaps = 23/182 (12%)
Query: 154 LEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFYREPN 213
           ++PP A P       +LLT+   +IR   D  P  + L        FQ   L  F +E  
Sbjct: 20  MQPPDASPT------NLLTS---LIRAHLDSGPNTAKLDYSK----FQELVLPRFGKE-- 64
Query: 214 PLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRL 273
                  +   +QQFY LL+ S+DVIR +A+KIPGF +L   DQ+LL +SA LELF+LRL
Sbjct: 65  -------DAGDVQQFYDLLSGSLDVIRKWAEKIPGFIELSPGDQDLLLESAFLELFILRL 117
Query: 274 AYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALT 333
           AYR++  + KLIFC+G+VL + QC R FG DW++ IL F +SLH + +D+ AFACL AL 
Sbjct: 118 AYRSKPGEGKLIFCSGLVLHRLQCARGFG-DWIDNILAFSRSLHSLGVDVPAFACLSALV 176
Query: 334 LI 335
           LI
Sbjct: 177 LI 178

>pdb|3V3E|B Chain B, Crystal Structure Of The Human Nur77 Ligand-Binding Domain Length = 257

Iteration: 1
 Score =  137 bits (346), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 81/184 (44%), Positives = 113/184 (61%), Gaps = 23/184 (12%)
Query: 152 NPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFYRE 211
            P +PP A P       +LLT+   ++R   D  P  + L        FQ   L  F +E
Sbjct: 3   KPKQPPDASPA------NLLTS---LVRAHLDSGPSTAKLDYSK----FQELVLPHFGKE 49
Query: 212 PNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVL 271
                    +   +QQFY LL+ S++VIR +A+KIPGF++L   DQ+LL +SA LELF+L
Sbjct: 50  ---------DAGDVQQFYDLLSGSLEVIRKWAEKIPGFAELSPADQDLLLESAFLELFIL 100
Query: 272 RLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCA 331
           RLAYR++  + KLIFC+G+VL + QC R FG DW+++IL F +SLH + +D+ AFACL A
Sbjct: 101 RLAYRSKPGEGKLIFCSGLVLHRLQCARGFG-DWIDSILAFSRSLHSLLVDVPAFACLSA 159
Query: 332 LTLI 335
           L LI
Sbjct: 160 LVLI 163

>pdb|1CIT|A Chain A, Dna-Binding Mechanism Of The Monomeric Orphan Nuclear Receptor Ngfi-B Length = 89

Iteration: 1
 Score =  125 bits (313), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 61/83 (73%), Positives = 65/83 (78%)
Query: 43  CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXXXXXX 102
           CAVCGD A+CQHYGVRTCEGCKGFFKRTVQK +KY+CLA+K CPVD              
Sbjct: 3   CAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQK 62
Query: 103 CLQVGMVKEVVRTDSLKGRRGRL 125
           CL VGMVKEVVRTDSLKGRRGRL
Sbjct: 63  CLAVGMVKEVVRTDSLKGRRGRL 85

>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 = 88.2 bits (217), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 72/295 (24%), Positives = 123/295 (41%), Gaps = 53/295 (17%)
Query: 41  QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXXXX 100
            +CA+CGD ++ +HYGV +CEGCKGFFKRTV+K   Y C  +K C +D            
Sbjct: 138 HICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRY 197
Query: 101 XXCLQVGMVKEVVRTDSLKGRRGRLXXXXXXXXXXXXXXXXXLITALYREPNPLEPPIAE 160
             CL +GM +E V+ +    +RG+                        R  N +E   + 
Sbjct: 198 QKCLAMGMKREAVQEER---QRGK-----------------------DRNENEVESTSSA 231
Query: 161 PEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFYREPNPLEPPIA 220
            E +          V+ I          ++L  E +   +  A++ L    PN     I 
Sbjct: 232 NEDM---------PVERILE--------AELAVEPKTETYVEANMGLNPSSPNDPVTNIC 274
Query: 221 EPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAE 280
           +    Q F          +  +A +IP FS+L  +DQ +L ++   EL +   ++R+ A 
Sbjct: 275 QAADKQLF---------TLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAV 325
Query: 281 DTKLIFCNGVVLEKQQCQRS-FGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
              ++   G+ + +     +  G  +   + E    +  M++D +   CL A+ L
Sbjct: 326 KDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVL 380

>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 = 79.7 bits (195), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 37/85 (43%), Positives = 48/85 (56%)
Query: 41  QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXXXX 100
           +LC VCGD  +  HYG+ TCE CKGFFKRTVQ   +Y C+ ++ C +D            
Sbjct: 10  ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQNCQIDKTQRKRCPYCRF 69
Query: 101 XXCLQVGMVKEVVRTDSLKGRRGRL 125
             CL VGM  E VR D ++G R + 
Sbjct: 70  QKCLSVGMKLEAVRADRMRGGRNKF 94

>pdb|1LO1|A Chain A, Estrogen Related Receptor 2 Dna Binding Domain In Complex With Dna Length = 98

Iteration: 1
 Score = 78.2 bits (191), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 38/86 (44%), Positives = 49/86 (56%)
Query: 39  PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXX 98
           P +LC VCGDIA+  HYGV +CE CK FFKRT+Q   +Y C A   C +           
Sbjct: 3   PKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQAC 62
Query: 99  XXXXCLQVGMVKEVVRTDSLKGRRGR 124
                L+VGM+KE VR D ++G R +
Sbjct: 63  RFMKALKVGMLKEGVRLDRVRGGRQK 88

>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 = 76.6 bits (187), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 37/85 (43%), Positives = 46/85 (54%)
Query: 41  QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXXXX 100
           +LC VCGD  +  HYG+ TCE CKGFFKRTVQ    Y C   ++C +D            
Sbjct: 2   ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKHYTCTESQSCKIDKTQRKRCPFCRF 61
Query: 101 XXCLQVGMVKEVVRTDSLKGRRGRL 125
             CL VGM  E VR D ++G R + 
Sbjct: 62  QKCLTVGMRLEAVRADRMRGGRNKF 86

>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 = 75.5 bits (184), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 34/81 (41%), Positives = 49/81 (60%)
Query: 41  QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXXXX 100
            +CA+CGD ++ +HYGV +CEGCKGFFKRTV+K   Y C  +K C +D            
Sbjct: 4   HICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRY 63
Query: 101 XXCLQVGMVKEVVRTDSLKGR 121
             CL +GM +E V+ +  +G+
Sbjct: 64  QKCLAMGMKREAVQEERQRGK 84

>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 = 74.3 bits (181), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 34/80 (42%), Positives = 48/80 (60%)
Query: 41  QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXXXX 100
            +CA+CGD ++ +HYGV +CEGCKGFFKRTV+K   Y C  +K C +D            
Sbjct: 6   HICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRY 65
Query: 101 XXCLQVGMVKEVVRTDSLKG 120
             CL +GM +E V+ +  +G
Sbjct: 66  QKCLAMGMKREAVQEERQRG 85

>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 = 72.8 bits (177), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 33/75 (44%), Positives = 45/75 (60%)
Query: 43  CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXXXXXX 102
           C VCGD ++ +HYG  TCEGCK FFKR+V++   Y C A++ CP+D              
Sbjct: 10  CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRANRNCPIDQHHRNQCQYCRLKK 69
Query: 103 CLQVGMVKEVVRTDS 117
           CL+VGM +E V+  S
Sbjct: 70  CLKVGMRREAVQRGS 84

>pdb|2HAN|A Chain A, Structural Basis Of Heterodimeric Ecdysteroid Receptor Interaction With Natural Response Element Hsp27 Gene Promoter Length = 93

Iteration: 1
 Score = 72.4 bits (176), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 33/76 (43%), Positives = 45/76 (59%)
Query: 41  QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXXXX 100
            LC++CGD A+ +HYGV +CEGCKGFFKRTV+K   Y C  ++ C +D            
Sbjct: 11  HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYACRENRNCIIDKRQRNRCQYCRY 70
Query: 101 XXCLQVGMVKEVVRTD 116
             CL  GM +E V+ +
Sbjct: 71  QKCLTCGMKREAVQEE 86

>pdb|1R0N|A Chain A, Crystal Structure Of Heterodimeric Ecdsyone Receptor Dna Binding Complex Length = 81

Iteration: 1
 Score = 72.4 bits (176), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 33/74 (44%), Positives = 45/74 (60%)
Query: 41  QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXXXX 100
            +CA+CGD ++ +HYGV +CEGCKGFFKRTV+K   Y C  +K C +D            
Sbjct: 4   HICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRY 63
Query: 101 XXCLQVGMVKEVVR 114
             CL +GM +E V+
Sbjct: 64  QKCLAMGMKREAVQ 77

>pdb|1BY4|A Chain A, Structure And Mechanism Of The Homodimeric Assembly Of The Rxr On Dna Length = 82

Iteration: 1
 Score = 72.4 bits (176), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 33/76 (43%), Positives = 46/76 (60%)
Query: 41  QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXXXX 100
            +CA+CGD ++ +HYGV +CEGCKGFFKRTV+K   Y C  +K C +D            
Sbjct: 6   HICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRY 65
Query: 101 XXCLQVGMVKEVVRTD 116
             CL +GM +E V+ +
Sbjct: 66  QKCLAMGMKREAVQEE 81

>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 = 72.4 bits (176), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 35/84 (41%), Positives = 47/84 (55%), Gaps = 4/84 (4%)
Query: 40  SQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXXX 99
           ++ CAVC D A+  HYGV +CEGCK FFKR++Q  + Y+C A   C +D           
Sbjct: 4   TRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACR 63
Query: 100 XXXCLQVGMVKEVVRTDSLKGRRG 123
              C +VGM+K  +R D    RRG
Sbjct: 64  LRKCYEVGMMKGGIRKD----RRG 83

>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 = 72.0 bits (175), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 35/86 (40%), Positives = 46/86 (53%)
Query: 37  PSPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXX 96
           P   + C VC D ++  HYGV  CEGCKGFF+R++QK   Y C  DK C ++        
Sbjct: 1   PRIYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQ 60
Query: 97  XXXXXXCLQVGMVKEVVRTDSLKGRR 122
                 C +VGM KE VR D  K ++
Sbjct: 61  YCRLQKCFEVGMSKESVRNDRNKKKK 86

>pdb|1R0O|A Chain A, Crystal Structure Of The Heterodimeric Ecdysone Receptor Dna-Binding Complex Length = 86

Iteration: 1
 Score = 71.6 bits (174), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 33/76 (43%), Positives = 45/76 (59%)
Query: 41  QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXXXX 100
            LC++CGD A+ +HYGV +CEGCKGFFKRTV+K   Y C  ++ C +D            
Sbjct: 9   HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYACRENRNCIIDKRQRNRCQYCRY 68
Query: 101 XXCLQVGMVKEVVRTD 116
             CL  GM +E V+ +
Sbjct: 69  QKCLTCGMKREAVQEE 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 = 71.2 bits (173), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 33/80 (41%), Positives = 47/80 (58%)
Query: 41  QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXXXX 100
            +CA+CGD ++ +HYGV +CEGCKGFFKRTV+K   Y C  +K C +D            
Sbjct: 4   HICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRY 63
Query: 101 XXCLQVGMVKEVVRTDSLKG 120
              L +GM +E V+ +  +G
Sbjct: 64  QKALAMGMKREAVQEERQRG 83

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

Iteration: 1
 Score = 68.6 bits (166), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 33/78 (42%), Positives = 42/78 (53%)
Query: 37  PSPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXX 96
           P   + C VC D ++  HYGV  CEGCKGFF+R++QK   Y C  DK C ++        
Sbjct: 2   PRVYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMIYTCHRDKNCVINKVTRNRCQ 61
Query: 97  XXXXXXCLQVGMVKEVVR 114
                 C +VGM KE VR
Sbjct: 62  YCRLQKCFEVGMSKESVR 79

>pdb|3CBB|A Chain A, Crystal Structure Of Hepatocyte Nuclear Factor 4alpha In Complex With Dna: Diabetes Gene Product Length = 78

Iteration: 1
 Score = 68.6 bits (166), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 31/75 (41%), Positives = 42/75 (56%)
Query: 42  LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXXXXX 101
           LCA+CGD A  +HYG  +C+GCKGFF+R+V+K   Y C   + C VD             
Sbjct: 2   LCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLK 61
Query: 102 XCLQVGMVKEVVRTD 116
            C + GM KE V+ +
Sbjct: 62  KCFRAGMKKEAVQNE 76

>pdb|1HCP|A Chain A, Dna Recognition By The Oestrogen Receptor: From Solution To The Crystal Length = 76

Iteration: 1
 Score = 67.8 bits (164), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 30/71 (42%), Positives = 41/71 (57%)
Query: 40  SQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXXX 99
           ++ CAVC D A+  HYGV +CEGCK FFKR++Q  + Y+C A   C +D           
Sbjct: 4   TRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACR 63
Query: 100 XXXCLQVGMVK 110
              C +VGM+K
Sbjct: 64  LRKCYEVGMMK 74

>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 = 67.4 bits (163), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 33/81 (40%), Positives = 46/81 (56%), Gaps = 1/81 (1%)
Query: 42  LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYV-CLADKACPVDXXXXXXXXXXXX 100
           LC VCGD+A+  HYGV  CEGCKGFF+R++Q+  +Y  CL ++ C +             
Sbjct: 9   LCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRF 68
Query: 101 XXCLQVGMVKEVVRTDSLKGR 121
             CL VGM ++ VR   +  R
Sbjct: 69  KKCLSVGMSRDAVRFGRIPKR 89

>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 = 67.0 bits (162), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 30/71 (42%), Positives = 41/71 (57%)
Query: 40  SQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXXX 99
           ++ CAVC D A+  HYGV +CEGCK FFKR++Q  + Y+C A   C +D           
Sbjct: 1   TRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACR 60
Query: 100 XXXCLQVGMVK 110
              C +VGM+K
Sbjct: 61  LRKCYEVGMMK 71

>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 = 67.0 bits (162), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 31/66 (46%), Positives = 40/66 (60%)
Query: 43  CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXXXXXX 102
           CA+CGD ++ +HYGV +CEGCKGFFKRTV+K   Y C  +K C +D              
Sbjct: 1   CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQK 60
Query: 103 CLQVGM 108
           CL +GM
Sbjct: 61  CLAMGM 66

>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 = 66.6 bits (161), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 30/68 (44%), Positives = 39/68 (57%)
Query: 43  CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXXXXXX 102
           CAVC D A+  HYGV +CEGCK FFKR++Q  + Y+C A   C +D              
Sbjct: 4   CAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRK 63
Query: 103 CLQVGMVK 110
           C +VGM+K
Sbjct: 64  CYEVGMMK 71

>pdb|1R0N|B Chain B, Crystal Structure Of Heterodimeric Ecdsyone Receptor Dna Binding Complex Length = 109

Iteration: 1
 Score = 65.9 bits (159), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 34/79 (43%), Positives = 41/79 (51%)
Query: 35  TPPSPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXX 94
            P    +LC VCGD A+  HY   TCEGCKGFF+R+V K + Y C   +AC +D      
Sbjct: 1   APRVQEELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRACEMDMYMRRK 60
Query: 95  XXXXXXXXCLQVGMVKEVV 113
                   CL VGM  E V
Sbjct: 61  CQECRLKKCLAVGMRPECV 79

>pdb|2HAN|B Chain B, Structural Basis Of Heterodimeric Ecdysteroid Receptor Interaction With Natural Response Element Hsp27 Gene Promoter Length = 119

Iteration: 1
 Score = 65.5 bits (158), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 34/79 (43%), Positives = 41/79 (51%)
Query: 35  TPPSPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXX 94
            P    +LC VCGD A+  HY   TCEGCKGFF+R+V K + Y C   +AC +D      
Sbjct: 3   APRVQEELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRACEMDMYMRRK 62
Query: 95  XXXXXXXXCLQVGMVKEVV 113
                   CL VGM  E V
Sbjct: 63  CQECRLKKCLAVGMRPECV 81

>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 = 63.5 bits (153), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 28/82 (34%), Positives = 45/82 (54%)
Query: 41  QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXXXX 100
           ++C VCGD A   H+   TCEGCKGFF+R++++ + + C A+  C +             
Sbjct: 7   RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCAANGDCRITKDNRRACQACRL 66
Query: 101 XXCLQVGMVKEVVRTDSLKGRR 122
             C+ +GM+KE + TD    R+
Sbjct: 67  KRCVDIGMMKEFILTDEEVQRK 88

>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 = 63.2 bits (152), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 34/87 (39%), Positives = 45/87 (51%), Gaps = 2/87 (2%)
Query: 41  QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKG--SKYVCLADKACPVDXXXXXXXXXX 98
           +LC VCGD A   HY   TCEGCKGFF+RT+QK     Y C  +  C +D          
Sbjct: 2   ELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQEC 61
Query: 99  XXXXCLQVGMVKEVVRTDSLKGRRGRL 125
               C+ VGM  ++V  DS +  + +L
Sbjct: 62  RFKKCIYVGMATDLVLDDSKRLAKRKL 88

>pdb|1Z5X|E Chain E, Hemipteran Ecdysone Receptor Ligand-Binding Domain Complexed With Ponasterone A Length = 310

Iteration: 1
 Score = 62.8 bits (151), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 39/161 (24%), Positives = 76/161 (47%), Gaps = 12/161 (7%)
Query: 185 IPGFSDLCKEDQELLFQSASLELFYREPNPL-----------EPPIAEPEKIQQFYSLLT 233
           + G   +  E +EL+ +    +  Y  P+P            E  +AE E+ +    +  
Sbjct: 68  VNGVKPITPEQEELIHRLVYFQNEYEHPSPEDIKRIVNAAPEEENVAE-ERFRHITEITI 126
Query: 234 TSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLE 293
            +V +I  F+ ++PGF  L +EDQ  L ++ S E+ + R+A R  AE   ++F       
Sbjct: 127 LTVQLIVEFSKRLPGFDKLIREDQIALLKACSSEVMMFRMARRYDAETDSILFATNQPYT 186
Query: 294 KQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
           ++    +   D +  +L FC+ +  M++D + +A L A+ +
Sbjct: 187 RESYTVAGMGDTVEDLLRFCRHMCAMKVDNAEYALLTAIVI 227

>pdb|1LAT|A Chain A, Glucocorticoid Receptor MutantDNA COMPLEX Length = 82

Iteration: 1
 Score = 62.0 bits (149), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 32/77 (41%), Positives = 40/77 (51%)
Query: 39  PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXX 98
           P++ C VC D A+  HYGV TCEGCK FFKR V+    Y+C  +  C +D          
Sbjct: 3   PARPCLVCSDEASGCHYGVLTCEGCKAFFKRAVEGQHNYLCKYEGKCIIDKIRRKNCPAC 62
Query: 99  XXXXCLQVGMVKEVVRT 115
               CLQ GM  E  +T
Sbjct: 63  RYRKCLQAGMNLEARKT 79

>pdb|3M9E|A Chain A, Thyroid Hormone Beta Dna Binding Domain Homodimer With Inverted Palindrome Tre Length = 105

Iteration: 1
 Score = 60.8 bits (146), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 33/82 (40%), Positives = 41/82 (50%), Gaps = 2/82 (2%)
Query: 38  SPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKG--SKYVCLADKACPVDXXXXXXX 95
              +LC VCGD A   HY   TCEGCKGFF+RT+QK     Y C  +  C +D       
Sbjct: 1   GSDELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKSLHPSYSCKYEGKCIIDKVTRNQC 60
Query: 96  XXXXXXXCLQVGMVKEVVRTDS 117
                  C+ VGM  ++V  DS
Sbjct: 61  QECRFKKCIYVGMATDLVLDDS 82

>pdb|1KB2|A Chain A, Crystal Structure Of Vdr Dna-Binding Domain Bound To Mouse Osteopontin (Spp) Response Element Length = 110

Iteration: 1
 Score = 60.5 bits (145), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 27/82 (32%), Positives = 44/82 (53%)
Query: 41  QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXXXX 100
           ++C VCGD A   H+   TCEGCKGFF+R++++ + + C  +  C +             
Sbjct: 7   RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRL 66
Query: 101 XXCLQVGMVKEVVRTDSLKGRR 122
             C+ +GM+KE + TD    R+
Sbjct: 67  KRCVDIGMMKEFILTDEEVQRK 88

>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 = 60.1 bits (144), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 41/132 (31%), Positives = 66/132 (50%), Gaps = 16/132 (12%)
Query: 219 IAEPEKIQQF---------YSLLTTSVD-------VIRHFADKIPGFSDLCKEDQELLFQ 262
           +AEPEKI               LTT  D       VI  +A  IPGFS L   DQ  L Q
Sbjct: 36  VAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQ 95
Query: 263 SASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEID 322
           SA +E+ +L + YR+ + + +L++ +  ++++ Q + +   D  NAIL+  +    M+++
Sbjct: 96  SAWMEILILGVVYRSLSFEDELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLE 155
Query: 323 ISAFACLCALTL 334
              F  L A+ L
Sbjct: 156 KEEFVTLKAIAL 167

>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 = 60.1 bits (144), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 41/132 (31%), Positives = 66/132 (50%), Gaps = 16/132 (12%)
Query: 219 IAEPEKIQQF---------YSLLTTSVD-------VIRHFADKIPGFSDLCKEDQELLFQ 262
           +AEPEKI               LTT  D       VI  +A  IPGFS L   DQ  L Q
Sbjct: 36  VAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQ 95
Query: 263 SASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEID 322
           SA +E+ +L + YR+ + + +L++ +  ++++ Q + +   D  NAIL+  +    M+++
Sbjct: 96  SAWMEILILGVVYRSLSFEDELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLE 155
Query: 323 ISAFACLCALTL 334
              F  L A+ L
Sbjct: 156 KEEFVTLKAIAL 167

>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 = 60.1 bits (144), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 41/132 (31%), Positives = 66/132 (50%), Gaps = 16/132 (12%)
Query: 219 IAEPEKIQQF---------YSLLTTSVD-------VIRHFADKIPGFSDLCKEDQELLFQ 262
           +AEPEKI               LTT  D       VI  +A  IPGFS L   DQ  L Q
Sbjct: 28  VAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQ 87
Query: 263 SASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEID 322
           SA +E+ +L + YR+ + + +L++ +  ++++ Q + +   D  NAIL+  +    M+++
Sbjct: 88  SAWMEILILGVVYRSLSFEDELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLE 147
Query: 323 ISAFACLCALTL 334
              F  L A+ L
Sbjct: 148 KEEFVTLKAIAL 159

>pdb|4HN6|A Chain A, Gr Dna Binding Domain R460d/d462r - Tslp Ngre Complex Length = 114

Iteration: 1
 Score = 60.1 bits (144), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 32/78 (41%), Positives = 39/78 (50%)
Query: 38  SPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXX 97
           +P +LC VC D A+  HYGV TC  CK FFKR V+    Y+C  D  C +D         
Sbjct: 24  APPKLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGDNRCIIDKIRRKNCPA 83
Query: 98  XXXXXCLQVGMVKEVVRT 115
                CLQ GM  E  +T
Sbjct: 84  CRYRKCLQAGMNLEARKT 101

>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 = 60.1 bits (144), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 41/132 (31%), Positives = 66/132 (50%), Gaps = 16/132 (12%)
Query: 219 IAEPEKIQQF---------YSLLTTSVD-------VIRHFADKIPGFSDLCKEDQELLFQ 262
           +AEPEKI               LTT  D       VI  +A  IPGFS L   DQ  L Q
Sbjct: 15  VAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQ 74
Query: 263 SASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEID 322
           SA +E+ +L + YR+ + + +L++ +  ++++ Q + +   D  NAIL+  +    M+++
Sbjct: 75  SAWMEILILGVVYRSLSFEDELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLE 134
Query: 323 ISAFACLCALTL 334
              F  L A+ L
Sbjct: 135 KEEFVTLKAIAL 146

>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 = 59.7 bits (143), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 41/132 (31%), Positives = 66/132 (50%), Gaps = 16/132 (12%)
Query: 219 IAEPEKIQQF---------YSLLTTSVD-------VIRHFADKIPGFSDLCKEDQELLFQ 262
           +AEPEKI               LTT  D       VI  +A  IPGFS L   DQ  L Q
Sbjct: 12  VAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQ 71
Query: 263 SASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEID 322
           SA +E+ +L + YR+ + + +L++ +  ++++ Q + +   D  NAIL+  +    M+++
Sbjct: 72  SAWMEILILGVVYRSLSFEDELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLE 131
Query: 323 ISAFACLCALTL 334
              F  L A+ L
Sbjct: 132 KEEFVTLKAIAL 143

>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 = 59.7 bits (143), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 41/132 (31%), Positives = 66/132 (50%), Gaps = 16/132 (12%)
Query: 219 IAEPEKIQQF---------YSLLTTSVD-------VIRHFADKIPGFSDLCKEDQELLFQ 262
           +AEPEKI               LTT  D       VI  +A  IPGFS L   DQ  L Q
Sbjct: 11  VAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQ 70
Query: 263 SASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEID 322
           SA +E+ +L + YR+ + + +L++ +  ++++ Q + +   D  NAIL+  +    M+++
Sbjct: 71  SAWMEILILGVVYRSLSFEDELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLE 130
Query: 323 ISAFACLCALTL 334
              F  L A+ L
Sbjct: 131 KEEFVTLKAIAL 142

>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 = 59.3 bits (142), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 73/305 (23%), Positives = 117/305 (38%), Gaps = 34/305 (11%)
Query: 43  CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKY-VCLADKACPVDXXXXXXXXXXXXX 101
           C VCGD A+  HYGV  CEGCKGFF+RT++    Y  C  D  C +              
Sbjct: 53  CRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLIYDRC--DLNCRIHKKSRNKCQYCRFQ 110
Query: 102 XCLQVGMVKEVVRTDSLKGRRGRLXXXXXXXXXXXXXXXXXLITALYREPNPLEPPIAEP 161
            CL VGM    +R        GR+                 L+  +  + + L P  A+ 
Sbjct: 111 KCLAVGMSHNAIRF-------GRM----------PQAEKEKLLAEISSDIDQLNPESADL 153
Query: 162 EKI-QQFYSLLTTSVDVIRHFA-----DKIPGFSDLCKEDQELLFQSASLELFYREPNPL 215
             + +  Y     S  + +  A      K    S     D   L      ++ ++   PL
Sbjct: 154 RALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGED-KIKFKHITPL 212
Query: 216 EPPIAEPEKIQQFYSLLTTSVDVIR---HFADKIPGFSDLCKEDQELLFQSASLELFVLR 272
           +    E   I+ F      SV+ ++    +A  IPGF +L   DQ  L +    E+    
Sbjct: 213 QEQSKEV-AIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTM 271
Query: 273 LAYRTRAEDTKLIFCNGVVLEK--QQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLC 330
           LA     +   +    G +  +  +  ++ FG D++    EF    + +E+D S  A   
Sbjct: 272 LASLMNKDGVLISEGQGFMTREFLKSLRKPFG-DFMEPKFEFAVKFNALELDDSDLAIFI 330
Query: 331 ALTLI 335
           A+ ++
Sbjct: 331 AVIIL 335

>pdb|3G9P|B Chain B, Gr Dna Binding Domain:sgk 16bp Complex-7 Length = 90

Iteration: 1
 Score = 57.4 bits (137), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 30/76 (39%), Positives = 36/76 (47%)
Query: 40  SQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXXX 99
           S +C VC D A+  HYGV TC  CK FFKR V+    Y+C     C +D           
Sbjct: 2   SHMCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACR 61
Query: 100 XXXCLQVGMVKEVVRT 115
              CLQ GM  E  +T
Sbjct: 62  YRKCLQAGMNLEARKT 77

>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 = 57.4 bits (137), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 27/100 (27%), Positives = 54/100 (54%)
Query: 235 SVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEK 294
           +V +I  FA ++PGF  L +EDQ  L ++ S E+ + R+A R   +   ++F N     +
Sbjct: 64  TVQLIVEFAKRLPGFDKLLREDQIALLKACSSEVMMFRMARRYDVQTDSILFVNNQPYSR 123
Query: 295 QQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
                +   + +  +L FC++++ M +D + +A L A+ +
Sbjct: 124 DSYNLAGMGETIEDLLHFCRTMYSMRVDNAEYALLTAIVI 163

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

Iteration: 1
 Score = 57.4 bits (137), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 32/116 (27%), Positives = 58/116 (50%), Gaps = 1/116 (0%)
Query: 220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRA 279
           A  ++   F  L   SV  I  FA ++PGF  L +EDQ  L +++++E+ +L  A R   
Sbjct: 55  ARQQRFAHFTELAIISVQEIVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETARRYNH 114
Query: 280 EDTKLIFCNGVVLEKQQCQRS-FGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
           E   + F       K    R+    +++N I EF +++  + +D + +A L A+ +
Sbjct: 115 ETESITFLKDFTYSKDDFHRAGLQVEFINPIFEFSRAMSSLGLDDAEYALLIAINI 170

>pdb|2C7A|A Chain A, Structure Of The Progesterone Receptor-Dna Complex Length = 78

Iteration: 1
 Score = 57.0 bits (136), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 28/71 (39%), Positives = 35/71 (49%)
Query: 39  PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXX 98
           P ++C +CGD A+  HYGV TC  CK FFKR ++    Y+C     C VD          
Sbjct: 1   PQKICLICGDEASGCHYGVLTCGSCKVFFKRAMEGQHNYLCAGRNDCIVDKIRRKNCPAC 60
Query: 99  XXXXCLQVGMV 109
               C Q GMV
Sbjct: 61  RLRKCCQAGMV 71

>pdb|1R4O|A Chain A, Crystallographic Analysis Of The Interaction Of The Glucocorticoid Receptor With Dna Length = 92

Iteration: 1
 Score = 57.0 bits (136), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 30/77 (38%), Positives = 37/77 (48%)
Query: 39  PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXX 98
           P++ C VC D A+  HYGV TC  CK FFKR V+    Y+C     C +D          
Sbjct: 3   PARPCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPAC 62
Query: 99  XXXXCLQVGMVKEVVRT 115
               CLQ GM  E  +T
Sbjct: 63  RYRKCLQAGMNLEARKT 79

>pdb|4HN5|A Chain A, Gr Dna Binding Domain - Tslp Ngre Complex Length = 117

Iteration: 1
 Score = 57.0 bits (136), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 31/78 (39%), Positives = 38/78 (48%)
Query: 38  SPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXX 97
           +P +LC VC D A+  HYGV TC  CK FFKR V+    Y+C     C +D         
Sbjct: 27  APPKLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPA 86
Query: 98  XXXXXCLQVGMVKEVVRT 115
                CLQ GM  E  +T
Sbjct: 87  CRYRKCLQAGMNLEARKT 104

>pdb|1R4R|B Chain B, Crystallographic Analysis Of The Interaction Of The Glucocorticoid Receptor With Dna Length = 92

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 30/77 (38%), Positives = 37/77 (48%)
Query: 39  PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXX 98
           P++ C VC D A+  HYGV TC  CK FFKR V+    Y+C     C +D          
Sbjct: 3   PARPCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPAC 62
Query: 99  XXXXCLQVGMVKEVVRT 115
               CLQ GM  E  +T
Sbjct: 63  RYRKCLQAGMNLEARKT 79

>pdb|1GLU|A Chain A, Crystallographic Analysis Of The Interaction Of The Glucocorticoid Receptor With Dna Length = 81

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 30/77 (38%), Positives = 37/77 (48%)
Query: 39  PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXX 98
           P++ C VC D A+  HYGV TC  CK FFKR V+    Y+C     C +D          
Sbjct: 3   PARPCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPAC 62
Query: 99  XXXXCLQVGMVKEVVRT 115
               CLQ GM  E  +T
Sbjct: 63  RYRKCLQAGMNLEARKT 79

>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 = 56.2 bits (134), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 32/116 (27%), Positives = 58/116 (50%), Gaps = 1/116 (0%)
Query: 220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRA 279
           A  ++   F  L   SV  I  FA ++PGF  L +EDQ  L +++++E+ +L  A R   
Sbjct: 59  ARQQRFAHFTELAIISVQEIVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETARRYNH 118
Query: 280 EDTKLIFCNGVVLEKQQCQRS-FGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
           E   + F       K    R+    +++N I EF +++  + +D + +A L A+ +
Sbjct: 119 ETECITFLKDFTYSKDDFHRAGLQVEFINPIFEFSRAMRRLGLDDAEYALLIAINI 174

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

Iteration: 1
 Score = 56.2 bits (134), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 32/116 (27%), Positives = 58/116 (50%), Gaps = 1/116 (0%)
Query: 220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRA 279
           A  ++   F  L   SV  I  FA ++PGF  L +EDQ  L +++++E+ +L  A R   
Sbjct: 55  ARQQRFAHFTELAIISVQEIVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETARRYNH 114
Query: 280 EDTKLIFCNGVVLEKQQCQRS-FGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
           E   + F       K    R+    +++N I EF +++  + +D + +A L A+ +
Sbjct: 115 ETECITFLKDFTYSKDDFHRAGLQVEFINPIFEFSRAMRRLGLDDAEYALLIAINI 170

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

Iteration: 1
 Score = 55.8 bits (133), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 32/116 (27%), Positives = 58/116 (50%), Gaps = 1/116 (0%)
Query: 220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRA 279
           A  ++   F  L   SV  I  FA ++PGF  L +EDQ  L +++++E+ +L  A R   
Sbjct: 52  ARQQRFAHFTELAIISVQEIVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETARRYNH 111
Query: 280 EDTKLIFCNGVVLEKQQCQRS-FGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
           E   + F       K    R+    +++N I EF +++  + +D + +A L A+ +
Sbjct: 112 ETECITFLKDFTYSKDDFHRAGLQVEFINPIFEFSRAMRRLGLDDAEYALLIAINI 167

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

Iteration: 1
 Score = 55.8 bits (133), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 32/116 (27%), Positives = 58/116 (50%), Gaps = 1/116 (0%)
Query: 220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRA 279
           A  ++   F  L   SV  I  FA ++PGF  L +EDQ  L +++++E+ +L  A R   
Sbjct: 49  ARQQRFAHFTELAIISVQEIVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETARRYNH 108
Query: 280 EDTKLIFCNGVVLEKQQCQRS-FGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
           E   + F       K    R+    +++N I EF +++  + +D + +A L A+ +
Sbjct: 109 ETECITFLKDFTYSKDDFHRAGLQVEFINPIFEFSRAMRRLGLDDAEYALLIAINI 164

>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 = 55.8 bits (133), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 28/75 (37%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 43  CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXXXXXX 102
           C VCGD A+  HYGV  CEGCKGFF+RT++   +Y    +++C +               
Sbjct: 10  CRVCGDKASGFHYGVHACEGCKGFFRRTIRMKLEYE-KCERSCKIQKKNRNKCQYCRFQK 68
Query: 103 CLQVGMVKEVVRTDS 117
           CL +GM    +R  S
Sbjct: 69  CLALGMSHNAIRFGS 83

>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 = 55.1 bits (131), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 31/109 (28%), Positives = 53/109 (48%)
Query: 227 QFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIF 286
           +F  L T  +  I  FA ++PGF+ L   DQ  L ++A L++ +LR+  R   E   + F
Sbjct: 75  KFSELATKCIIKIVEFAKRLPGFTGLTIADQITLLKAACLDILILRICTRYTPEQDTMTF 134
Query: 287 CNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            +G+ L + Q   +      + +  F   L  +E+D +    L A+ LI
Sbjct: 135 SDGLTLNRTQMHNAGFGPLTDLVFTFANQLLPLEMDDTETGLLSAICLI 183

>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 = 54.7 bits (130), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 29/109 (26%), Positives = 56/109 (51%)
Query: 226 QQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLI 285
           +Q   +   +V +I  FA  +PGFS + + DQ  L ++ S E+ +LR+A R  A    ++
Sbjct: 70  RQITEMTILTVQLIVEFAKGLPGFSKISQSDQITLLKACSSEVMMLRVARRYDAATDSVL 129
Query: 286 FCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
           F N     +   +++     +  +L FC+ ++ M +D   +A L A+ +
Sbjct: 130 FANNQAYTRDNYRKAGMAYVIEDLLHFCRCMYSMMMDNVHYALLTAIVI 178

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

Iteration: 1
 Score = 54.7 bits (130), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 31/109 (28%), Positives = 53/109 (48%)
Query: 227 QFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIF 286
           +F  L T  +  I  FA ++PGF+ L   DQ  L ++A L++ +LR+  R   E   + F
Sbjct: 73  KFSELATKCIIKIVEFAKRLPGFTGLTIADQITLLKAACLDILILRICTRYTPEQDTMTF 132
Query: 287 CNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            +G+ L + Q   +      + +  F   L  +E+D +    L A+ LI
Sbjct: 133 SDGLTLNRTQMHNAGFGPLTDLVFTFANQLLPLEMDDTETGLLSAICLI 181

>pdb|3G6T|A Chain A, Gr Gamma Dna-Binding Domain:fkbp5 16bp Complex-34 Length = 91

Iteration: 1
 Score = 54.3 bits (129), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 30/77 (38%), Positives = 37/77 (48%), Gaps = 1/77 (1%)
Query: 40  SQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQ-KGSKYVCLADKACPVDXXXXXXXXXX 98
           S +C VC D A+  HYGV TC  CK FFKR V+ +   Y+C     C +D          
Sbjct: 2   SHMCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGRQHNYLCAGRNDCIIDKIRRKNCPAC 61
Query: 99  XXXXCLQVGMVKEVVRT 115
               CLQ GM  E  +T
Sbjct: 62  RYRKCLQAGMNLEARKT 78

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 30/121 (24%), Positives = 57/121 (47%)
Query: 215 LEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLA 274
           ++P  +  E  ++F    T +V  +  FA +IPGF DL + DQ  L ++ + E+  +R A
Sbjct: 12  VDPHKSGHEIWEEFSXSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLXVRFA 71
Query: 275 YRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
               A++  + F +G              D LN+  EF + L+ +++     +   A+ L
Sbjct: 72  SLFDAKERTVTFLSGKKYSVDDLHSXGAGDLLNSXFEFSEKLNALQLSDEEXSLFTAVVL 131
Query: 335 I 335
           +
Sbjct: 132 V 132

>pdb|2GDA|A Chain A, Refined Solution Structure Of The Glucocorticoid Receptor Dna-Binding Domain Length = 72

Iteration: 1
 Score = 53.9 bits (128), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 28/67 (41%), Positives = 32/67 (47%)
Query: 42  LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXXXXX 101
           LC VC D A+  HYGV TC  CK FFKR V+    Y+C     C +D             
Sbjct: 1   LCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYR 60
Query: 102 XCLQVGM 108
            CLQ GM
Sbjct: 61  KCLQAGM 67

>pdb|1GDC|A Chain A, Refined Solution Structure Of The Glucocorticoid Receptor Dna-Binding Domain Length = 72

Iteration: 1
 Score = 53.9 bits (128), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 28/67 (41%), Positives = 32/67 (47%)
Query: 42  LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXXXXX 101
           LC VC D A+  HYGV TC  CK FFKR V+    Y+C     C +D             
Sbjct: 1   LCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYR 60
Query: 102 XCLQVGM 108
            CLQ GM
Sbjct: 61  KCLQAGM 67

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 32/116 (27%), Positives = 57/116 (49%), Gaps = 1/116 (0%)
Query: 220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRA 279
           A  ++   F  L   SV  I  FA ++PGF  L +EDQ  L +++++E+ +L  A R   
Sbjct: 49  ARQQRFAHFTELAIISVQEIVDFAKQVPGFLQLGREDQIALLKASTIEIXLLETARRYNH 108
Query: 280 EDTKLIFCNGVVLEKQQCQRS-FGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
           E   + F       K    R+    +++N I EF ++   + +D + +A L A+ +
Sbjct: 109 ETECITFLKDFTYSKDDFHRAGLQVEFINPIFEFSRAXRRLGLDDAEYALLIAINI 164

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 30/121 (24%), Positives = 57/121 (47%)
Query: 215 LEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLA 274
           ++P  +  E  ++F    T +V  +  FA +IPGF DL + DQ  L ++ + E+  +R A
Sbjct: 7   VDPHKSGHEIWEEFSXSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLXVRFA 66
Query: 275 YRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
               A++  + F +G              D LN+  EF + L+ +++     +   A+ L
Sbjct: 67  SLFDAKERTVTFLSGKKYSVDDLHSXGAGDLLNSXFEFSEKLNALQLSDEEXSLFTAVVL 126
Query: 335 I 335
           +
Sbjct: 127 V 127

>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 = 53.5 bits (127), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 31/109 (28%), Positives = 53/109 (48%)
Query: 227 QFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIF 286
           +F  L T  +  I  FA ++PGF+ L   DQ  L ++A L++ +LR+  R   E   + F
Sbjct: 73  KFSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMTF 132
Query: 287 CNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            +G+ L + Q   +      + +  F   L  +E+D +    L A+ LI
Sbjct: 133 SDGLTLNRTQMHNAGFGPLTDLVFAFAGQLLPLEMDDTETGLLSAICLI 181

>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 = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 31/109 (28%), Positives = 53/109 (48%)
Query: 227 QFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIF 286
           +F  L T  +  I  FA ++PGF+ L   DQ  L ++A L++ +LR+  R   E   + F
Sbjct: 48  KFSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMTF 107
Query: 287 CNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            +G+ L + Q   +      + +  F   L  +E+D +    L A+ LI
Sbjct: 108 SDGLTLNRTQMHNAGFGPLTDLVFAFAGQLLPLEMDDTETGLLSAICLI 156

>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 = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 31/109 (28%), Positives = 53/109 (48%)
Query: 227 QFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIF 286
           +F  L T  +  I  FA ++PGF+ L   DQ  L ++A L++ +LR+  R   E   + F
Sbjct: 47  KFSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMTF 106
Query: 287 CNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            +G+ L + Q   +      + +  F   L  +E+D +    L A+ LI
Sbjct: 107 SDGLTLNRTQMHNAGFGPLTDLVFAFAGQLLPLEMDDTETGLLSAICLI 155

>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 = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 31/109 (28%), Positives = 53/109 (48%)
Query: 227 QFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIF 286
           +F  L T  +  I  FA ++PGF+ L   DQ  L ++A L++ +LR+  R   E   + F
Sbjct: 52  KFSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMTF 111
Query: 287 CNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            +G+ L + Q   +      + +  F   L  +E+D +    L A+ LI
Sbjct: 112 SDGLTLNRTQMHNAGFGPLTDLVFAFAGQLLPLEMDDTETGLLSAICLI 160

>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 = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 25/71 (35%), Positives = 33/71 (46%)
Query: 39  PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXX 98
           P + C +CGD A+  HYG  TC  CK FFKR  +   KY+C +   C +D          
Sbjct: 6   PQKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSC 65
Query: 99  XXXXCLQVGMV 109
               C + GM 
Sbjct: 66  RLRKCYEAGMT 76

>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 = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 28/109 (25%), Positives = 56/109 (51%)
Query: 226 QQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLI 285
           +Q   +   +V +I  FA  +PGF+ + + DQ  L ++ S E+ +LR+A R  A    ++
Sbjct: 71  RQITEMTILTVQLIVEFAKGLPGFAKISQSDQITLLKACSSEVMMLRVARRYDAATDSVL 130
Query: 286 FCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
           F N     +   +++     +  +L FC+ ++ M +D   +A L A+ +
Sbjct: 131 FANNQAYTRDNYRKAGMAYVIEDLLHFCRCMYSMMMDNVHYALLTAIVI 179

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 33/128 (25%), Positives = 65/128 (50%), Gaps = 5/128 (3%)
Query: 212 PNPLEPPIAEPEKIQQ----FYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLE 267
           P P+ P     E  QQ    F  L   SV  I  FA ++PGF  L +EDQ  L +++++E
Sbjct: 56  PWPIAPDPQSREARQQRFAHFTELAIVSVQEIVDFAKQLPGFLQLSREDQIALLKTSAIE 115
Query: 268 LFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRS-FGDDWLNAILEFCQSLHLMEIDISAF 326
           + +L  + R       + F       ++   ++    +++N I EF ++++ ++++ + F
Sbjct: 116 VMLLETSRRYNPGSESITFLKDFSYNREDFAKAGLQVEFINPIFEFSRAMNELQLNDAEF 175
Query: 327 ACLCALTL 334
           A L A+++
Sbjct: 176 ALLIAISI 183

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 33/128 (25%), Positives = 65/128 (50%), Gaps = 5/128 (3%)
Query: 212 PNPLEPPIAEPEKIQQ----FYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLE 267
           P P+ P     E  QQ    F  L   SV  I  FA ++PGF  L +EDQ  L +++++E
Sbjct: 73  PWPMAPDPHSREARQQRFAHFTELAIVSVQEIVDFAKQLPGFLQLSREDQIALLKTSAIE 132
Query: 268 LFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRS-FGDDWLNAILEFCQSLHLMEIDISAF 326
           + +L  + R       + F       ++   ++    +++N I EF ++++ ++++ + F
Sbjct: 133 VMLLETSRRYNPGSESITFLKDFSYNREDFAKAGLQVEFINPIFEFSRAMNELQLNDAEF 192
Query: 327 ACLCALTL 334
           A L A+++
Sbjct: 193 ALLIAISI 200

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 33/128 (25%), Positives = 65/128 (50%), Gaps = 5/128 (3%)
Query: 212 PNPLEPPIAEPEKIQQ----FYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLE 267
           P P+ P     E  QQ    F  L   SV  I  FA ++PGF  L +EDQ  L +++++E
Sbjct: 32  PWPMAPDPHSREARQQRFAHFTELAIVSVQEIVDFAKQLPGFLQLSREDQIALLKTSAIE 91
Query: 268 LFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRS-FGDDWLNAILEFCQSLHLMEIDISAF 326
           + +L  + R       + F       ++   ++    +++N I EF ++++ ++++ + F
Sbjct: 92  VMLLETSRRYNPGSESITFLKDFSYNREDFAKAGLQVEFINPIFEFSRAMNELQLNDAEF 151
Query: 327 ACLCALTL 334
           A L A+++
Sbjct: 152 ALLIAISI 159

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 33/128 (25%), Positives = 65/128 (50%), Gaps = 5/128 (3%)
Query: 212 PNPLEPPIAEPEKIQQ----FYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLE 267
           P P+ P     E  QQ    F  L   SV  I  FA ++PGF  L +EDQ  L +++++E
Sbjct: 34  PWPIAPDPQSREARQQRFAHFTELAIVSVQEIVDFAKQLPGFLQLSREDQIALLKTSAIE 93
Query: 268 LFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRS-FGDDWLNAILEFCQSLHLMEIDISAF 326
           + +L  + R       + F       ++   ++    +++N I EF ++++ ++++ + F
Sbjct: 94  VMLLETSRRYNPGSESITFLKDFSYNREDFAKAGLQVEFINPIFEFSRAMNELQLNDAEF 153
Query: 327 ACLCALTL 334
           A L A+++
Sbjct: 154 ALLIAISI 161

>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 = 52.4 bits (124), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 27/66 (40%), Positives = 31/66 (46%)
Query: 43  CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDXXXXXXXXXXXXXX 102
           C VC D A+  HYGV TC  CK FFKR V+    Y+C     C +D              
Sbjct: 1   CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRK 60
Query: 103 CLQVGM 108
           CLQ GM
Sbjct: 61  CLQAGM 66

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 29/121 (23%), Positives = 57/121 (47%)
Query: 215 LEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLA 274
           ++P  +  E  ++F    T +V  +  FA +IPGF DL + DQ  L ++ + E+ ++R A
Sbjct: 7   VDPHKSGHEIWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFA 66
Query: 275 YRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
               A++  + F                 D LN++ EF + L+ +++     +   A+ L
Sbjct: 67  SLFDAKERTVTFLGSKKYSVDDLHSMGAGDLLNSMFEFSEKLNALQLSDEEMSLFTAVVL 126
Query: 335 I 335
           +
Sbjct: 127 V 127

>pdb|2H79|A Chain A, Crystal Structure Of Human Tr Alpha Bound T3 In Orthorhombic Space Group Length = 269

Iteration: 1
 Score = 52.0 bits (123), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 32/113 (28%), Positives = 56/113 (49%)
Query: 223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT 282
           E   +F  ++T ++  +  FA K+P FS+L  EDQ +L +   +E+  LR A R   E  
Sbjct: 72  EAFSEFTKIITPAITRVVDFAKKLPMFSELPXEDQIILLKGCCMEIMSLRAAVRYDPESD 131
Query: 283 KLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            L     + ++++Q +        +AI E  +SL    +D +  A L A+ L+
Sbjct: 132 TLTLSGEMAVKREQLKNGGLGVVSDAIFELGKSLSAFNLDDTEVALLQAVLLM 184

>pdb|3HZF|A Chain A, Structure Of Tr-alfa Bound To Selective Thyromimetic Gc-1 In C2 Space Group Length = 269

Iteration: 1
 Score = 52.0 bits (123), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 32/113 (28%), Positives = 56/113 (49%)
Query: 223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT 282
           E   +F  ++T ++  +  FA K+P FS+L  EDQ +L +   +E+  LR A R   E  
Sbjct: 72  EAFSEFTKIITPAITRVVDFAKKLPMFSELPXEDQIILLKGCCMEIMSLRAAVRYDPESD 131
Query: 283 KLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            L     + ++++Q +        +AI E  +SL    +D +  A L A+ L+
Sbjct: 132 TLTLSGEMAVKREQLKNGGLGVVSDAIFELGKSLSAFNLDDTEVALLQAVLLM 184

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 33/130 (25%), Positives = 64/130 (49%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L +SA L
Sbjct: 27  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLESAWL 85
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 86  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEE 145
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 146 FVCLKSIILL 155

>pdb|3JZB|A Chain A, Crystal Structure Of Tr-Alfa Bound To The Selective Thyromimetic Triac Length = 267

Iteration: 1
 Score = 51.6 bits (122), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 32/113 (28%), Positives = 56/113 (49%)
Query: 223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT 282
           E   +F  ++T ++  +  FA K+P FS+L  EDQ +L +   +E+  LR A R   E  
Sbjct: 70  EAFSEFTKIITPAITRVVDFAKKLPMFSELPXEDQIILLKGCCMEIMSLRAAVRYDPESD 129
Query: 283 KLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            L     + ++++Q +        +AI E  +SL    +D +  A L A+ L+
Sbjct: 130 TLTLSGEMAVKREQLKNGGLGVVSDAIFELGKSLSAFNLDDTEVALLQAVLLM 182

>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 = 51.6 bits (122), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 30/109 (27%), Positives = 52/109 (47%)
Query: 227 QFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIF 286
           +F  L T  +     FA ++PGF+ L   DQ  L ++A L++ +LR+  R   E   + F
Sbjct: 72  KFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTF 131
Query: 287 CNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            +G+ L + Q   +      + +  F   L  +E+D +    L A+ LI
Sbjct: 132 SDGLTLNRTQMHNAGFGPLTDLVFAFANQLLPLEMDDAETGLLSAICLI 180

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 33/130 (25%), Positives = 64/130 (49%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L +SA L
Sbjct: 23  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLESAWL 81
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 82  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEE 141
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 142 FVCLKSIILL 151

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

Iteration: 1
 Score = 51.2 bits (121), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 33/130 (25%), Positives = 64/130 (49%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L +SA L
Sbjct: 27  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLESAWL 85
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 86  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEE 145
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 146 FVCLKSIILL 155

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

Iteration: 1
 Score = 51.2 bits (121), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 33/130 (25%), Positives = 64/130 (49%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L +SA L
Sbjct: 23  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLESAWL 81
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 82  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEE 141
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 142 FVCLKSIILL 151

>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 = 51.2 bits (121), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 30/109 (27%), Positives = 52/109 (47%)
Query: 227 QFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIF 286
           +F  L T  +     FA ++PGF+ L   DQ  L ++A L++ +LR+  R   E   + F
Sbjct: 46  KFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTF 105
Query: 287 CNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            +G+ L + Q   +      + +  F   L  +E+D +    L A+ LI
Sbjct: 106 SDGLTLNRTQMHNAGFGPLTDLVFAFANQLLPLEMDDAETGLLSAICLI 154

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

Iteration: 1
 Score = 51.2 bits (121), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 30/109 (27%), Positives = 52/109 (47%)
Query: 227 QFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIF 286
           +F  L T  +     FA ++PGF+ L   DQ  L ++A L++ +LR+  R   E   + F
Sbjct: 46  KFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTF 105
Query: 287 CNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            +G+ L + Q   +      + +  F   L  +E+D +    L A+ LI
Sbjct: 106 SDGLTLNRTQMHNAGFGPLTDLVFAFANQLLPLEMDDAETGLLSAICLI 154

>pdb|3OS8|A Chain A, Estrogen Receptor Length = 258

Iteration: 1
 Score = 51.2 bits (121), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 64/130 (49%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL + DQ  L + A L
Sbjct: 31  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTRHDQVHLLECAWL 89
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 90  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEE 149
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 150 FVCLKSIILL 159

>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 = 51.2 bits (121), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 30/109 (27%), Positives = 52/109 (47%)
Query: 227 QFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIF 286
           +F  L T  +     FA ++PGF+ L   DQ  L ++A L++ +LR+  R   E   + F
Sbjct: 75  KFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTF 134
Query: 287 CNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            +G+ L + Q   +      + +  F   L  +E+D +    L A+ LI
Sbjct: 135 SDGLTLNRTQMHNAGFGPLTDLVFAFANQLLPLEMDDAETGLLSAICLI 183

>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 = 51.2 bits (121), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 29  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWL 87
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 88  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEE 147
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 148 FVCLKSIILL 157

>pdb|1NAV|A Chain A, Thyroid Receptor Alpha In Complex With An Agonist Selective For Thyroid Receptor Beta1 Length = 263

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 32/113 (28%), Positives = 56/113 (49%)
Query: 223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT 282
           E   +F  ++T ++  +  FA K+P FS+L  EDQ +L +   +E+  LR A R   E  
Sbjct: 68  EAFSEFTKIITPAITRVVDFAKKLPMFSELPCEDQIILLKGCCMEIMSLRAAVRYDPESD 127
Query: 283 KLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            L     + ++++Q +        +AI E  +SL    +D +  A L A+ L+
Sbjct: 128 TLTLSGEMAVKREQLKNGGLGVVSDAIFELGKSLSAFNLDDTEVALLQAVLLM 180

>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 = 50.4 bits (119), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/113 (24%), Positives = 52/113 (46%)
Query: 223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT 282
           E  + F    T +V  +  FA  IPGF DL + DQ  L ++ + E+ ++R A     +D 
Sbjct: 65  EIWEDFSMSFTPAVREVVEFAKHIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFNVKDQ 124
Query: 283 KLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            ++F +      Q+       D L+A+ +F + L+ + +         A+ L+
Sbjct: 125 TVMFLSRTTYSLQELGAMGMGDLLSAMFDFSEKLNSLALTEEELGLFTAVVLV 177

>pdb|2H77|A Chain A, Crystal Structure Of Human Tr Alpha Bound T3 In Monoclinic Space Group Length = 269

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 32/113 (28%), Positives = 56/113 (49%)
Query: 223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT 282
           E   +F  ++T ++  +  FA K+P FS+L  EDQ +L +   +E+  LR A R   E  
Sbjct: 72  EAFSEFTKIITPAITRVVDFAKKLPMFSELPCEDQIILLKGCCMEIMSLRAAVRYDPESD 131
Query: 283 KLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            L     + ++++Q +        +AI E  +SL    +D +  A L A+ L+
Sbjct: 132 TLTLSGEMAVKREQLKNGGLGVVSDAIFELGKSLSAFNLDDTEVALLQAVLLM 184

>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 = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 32  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWL 90
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 91  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEE 150
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 151 FVCLKSIILL 160

>pdb|3UU7|A Chain A, Crystal Structure Of Hera-Lbd (Y537s) In Complex With Bisphenol-A Length = 251

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 25  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWL 83
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 84  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEE 143
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 144 FVCLKSIILL 153

>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 = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 32  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWL 90
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 91  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEE 150
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 151 FVCLKSIILL 160

>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 = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 29  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWL 87
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 88  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEE 147
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 148 FVCLKSIILL 157

>pdb|3UU7|B Chain B, Crystal Structure Of Hera-Lbd (Y537s) In Complex With Bisphenol-A Length = 251

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 25  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWL 83
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 84  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEE 143
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 144 FVCLKSIILL 153

>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 = 49.7 bits (117), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 29  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWL 87
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 88  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEE 147
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 148 FVCLKSIILL 157

>pdb|2JFA|B Chain B, Estrogen Receptor Alpha Lbd In Complex With An Affinity- Selected Corepressor Peptide Length = 252

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 45  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWL 103
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 104 EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEE 163
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 164 FVCLKSIILL 173

>pdb|3OS8|C Chain C, Estrogen Receptor Length = 258

Iteration: 1
 Score = 49.7 bits (117), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 64/130 (49%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL + DQ  L + A L
Sbjct: 31  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTRHDQVHLLECAWL 89
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 90  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEE 149
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 150 FVCLKSIILL 159

>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 = 49.3 bits (116), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 33  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWL 91
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 92  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEE 151
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 152 FVCLKSIILL 161

>pdb|3UVV|A Chain A, Crystal Structure Of The Ligand Binding Domains Of The Thyroid Receptor:retinoid X Receptor Complexed With 3,3',5 Triiodo-L- Thyronine And 9-Cis Retinoic Acid Length = 265

Iteration: 1
 Score = 48.9 bits (115), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 31/113 (27%), Positives = 56/113 (49%)
Query: 223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT 282
           E   +F  ++T ++  +  FA K+P FS+L  EDQ +L +   +E+  LR A R   E  
Sbjct: 68  EAFSEFTKIITPAITRVVDFAKKLPMFSELPCEDQIILLKGCCMEIMSLRAAVRYDPESE 127
Query: 283 KLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            L     + ++++Q +        +AI +  +SL    +D +  A L A+ L+
Sbjct: 128 TLTLSGEMAVKREQLKNGGLGVVSDAIFDLGKSLSAFNLDDTEVALLQAVLLM 180

>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 = 48.9 bits (115), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 35/129 (27%), Positives = 59/129 (45%), Gaps = 1/129 (0%)
Query: 206 ELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSAS 265
           E  Y  P+P  P    P  +     L    + V   +A  IPGFS L   DQ  + QS  
Sbjct: 37  EKLYAMPDPAGPDGHLP-AVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVW 95
Query: 266 LELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISA 325
           +E+ VL +A R+     +L F   +VL+++  + +   +   A+L+  + L  + ++   
Sbjct: 96  MEVLVLGVAQRSLPLQDELAFAEDLVLDEEGARAAGLGELGAALLQLVRRLQALRLEREE 155
Query: 326 FACLCALTL 334
           +  L AL L
Sbjct: 156 YVLLKALAL 164

>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 = 48.9 bits (115), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 35/129 (27%), Positives = 59/129 (45%), Gaps = 1/129 (0%)
Query: 206 ELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSAS 265
           E  Y  P+P  P    P  +     L    + V   +A  IPGFS L   DQ  + QS  
Sbjct: 31  EKLYAMPDPAGPDGHLP-AVATLSDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVW 89
Query: 266 LELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISA 325
           +E+ VL +A R+     +L F   +VL+++  + +   +   A+L+  + L  + ++   
Sbjct: 90  MEVLVLGVAQRSLPLQDELAFAEDLVLDEEGARAAGLGELGAALLQLVRRLQALRLEREE 149
Query: 326 FACLCALTL 334
           +  L AL L
Sbjct: 150 YVLLKALAL 158

>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 = 48.5 bits (114), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 30  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWL 88
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 89  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEE 148
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 149 FVCLKSIILL 158

>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 = 48.5 bits (114), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 32  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWL 90
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 91  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEE 150
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 151 FVCLKSIILL 160

>pdb|2QZO|B Chain B, Crystal Structure Of The Estrogen Receptor Alpha Ligand Binding Domain Complexed With Way-169916 Length = 258

Iteration: 1
 Score = 48.1 bits (113), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 30  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWL 88
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 89  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEE 148
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 149 FVCLKSIILL 158

>pdb|1ERR|A Chain A, Human Estrogen Receptor Ligand-Binding Domain In Complex With Raloxifene Length = 253

Iteration: 1
 Score = 48.1 bits (113), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 26  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWL 84
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 85  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEE 144
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 145 FVCLKSIILL 154

>pdb|3UUC|A Chain A, Crystal Structure Of Hera-Lbd (Wt) In Complex With Bisphenol-C Length = 251

Iteration: 1
 Score = 48.1 bits (113), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 25  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWL 83
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 84  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEE 143
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 144 FVCLKSIILL 153

>pdb|3UUA|A Chain A, Crystal Structure Of Hera-Lbd (Y537s) In Complex With Bisphenol-Af Length = 251

Iteration: 1
 Score = 48.1 bits (113), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 25  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWL 83
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 84  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEE 143
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 144 FVCLKSIILL 153

>pdb|2BJ4|A Chain A, Estrogen Receptor Alpha Lbd In Complex With A Phage-Display Derived Peptide Antagonist Length = 252

Iteration: 1
 Score = 48.1 bits (113), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 45  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWL 103
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 104 EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEE 163
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 164 FVCLKSIILL 173

>pdb|3UUA|B Chain B, Crystal Structure Of Hera-Lbd (Y537s) In Complex With Bisphenol-Af Length = 251

Iteration: 1
 Score = 48.1 bits (113), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 25  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWL 83
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 84  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEE 143
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 144 FVCLKSIILL 153

>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 = 47.8 bits (112), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 35/129 (27%), Positives = 59/129 (45%), Gaps = 1/129 (0%)
Query: 206 ELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSAS 265
           E  Y  P+P  P    P  +     L    + V   +A  IPGFS L   DQ  + QS  
Sbjct: 31  EKLYAMPDPAGPDGHLP-AVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVW 89
Query: 266 LELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISA 325
           +E+ VL +A R+     +L F   +VL+++  + +   +   A+L+  + L  + ++   
Sbjct: 90  MEVLVLGVAQRSLPLQDELAFAEDLVLDEEGARAAGLGELGAALLQLVRRLQALRLEREE 149
Query: 326 FACLCALTL 334
           +  L AL L
Sbjct: 150 YVLLKALAL 158

>pdb|3K6P|A Chain A, Estrogen Related Receptor Alpha In Complex With An Ether Based Ligand Length = 248

Iteration: 1
 Score = 47.8 bits (112), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 35/129 (27%), Positives = 59/129 (45%), Gaps = 1/129 (0%)
Query: 206 ELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSAS 265
           E  Y  P+P  P    P  +     L    + V   +A  IPGFS L   DQ  + QS  
Sbjct: 32  EKLYAMPDPAGPDGHLP-AVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVW 90
Query: 266 LELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISA 325
           +E+ VL +A R+     +L F   +VL+++  + +   +   A+L+  + L  + ++   
Sbjct: 91  MEVLVLGVAQRSLPLQDELAFAEDLVLDEEGARAAGLGELGAALLQLVRRLQALRLEREE 150
Query: 326 FACLCALTL 334
           +  L AL L
Sbjct: 151 YVLLKALAL 159

>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 = 47.8 bits (112), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 33  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWL 91
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 92  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEE 151
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 152 FVCLKSIILL 161

>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 = 47.8 bits (112), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 30  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWL 88
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 89  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEE 148
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 149 FVCLKSIILL 158

>pdb|2IOK|A Chain A, Human Estrogen Receptor Alpha Ligand-binding Domain In Complex With Compound 1d Length = 254

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 26  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWL 84
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 85  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEE 144
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 145 FVCLKSIILL 154

>pdb|3DT3|A Chain A, Human Estrogen Receptor Alpha Lbd With Gw368 Length = 255

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 30  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWL 88
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 89  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEE 148
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 149 FVCLKSIILL 158

>pdb|1ERE|A Chain A, Human Estrogen Receptor Ligand-Binding Domain In Complex With 17beta-Estradiol Length = 253

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 26  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWL 84
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 85  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEE 144
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 145 FVCLKSIILL 154

>pdb|2IOG|A Chain A, Human Estrogen Receptor Alpha Ligand-Binding Domain In Complex With Compound 11f Length = 246

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 18  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWL 76
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 77  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEE 136
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 137 FVCLKSIILL 146

>pdb|1A52|A Chain A, Estrogen Receptor Alpha Ligand-Binding Domain Complexed To Estradiol Length = 258

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 30  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWL 88
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 89  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEE 148
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 149 FVCLKSIILL 158

>pdb|1X7E|A Chain A, Crystal Structure Of Estrogen Receptor Alpha Complexed With Way-244 Length = 245

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P   P +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 22  ILYSEYDP-TRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWL 80
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 81  EILMIGLVWRSMEHPVKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEE 140
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 141 FVCLKSIILL 150

>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 = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 20  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWL 78
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 79  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEE 138
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 139 FVCLKSIILL 148

>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 = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 30  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWL 88
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 89  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEE 148
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 149 FVCLKSIILL 158

>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 = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 26  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWL 84
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 85  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEE 144
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 145 FVCLKSIILL 154

>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 = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 29  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWL 87
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 88  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEE 147
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 148 FVCLKSIILL 157

>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 = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 30  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWL 88
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 89  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEE 148
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 149 FVCLKSIILL 158

>pdb|1QKU|A Chain A, Wild Type Estrogen Nuclear Receptor Ligand Binding Domain Complexed With Estradiol Length = 250

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 26  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWL 84
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 85  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEE 144
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 145 FVCLKSIILL 154

>pdb|1G50|A Chain A, Crystal Structure Of A Wild Type Her Alpha Lbd At 2.9 Angstrom Resolution Length = 247

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 23  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWL 81
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 82  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEE 141
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 142 FVCLKSIILL 151

>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 = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 29  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWL 87
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 88  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEE 147
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 148 FVCLKSIILL 157

>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 = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 22  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWL 80
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 81  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEE 140
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 141 FVCLKSIILL 150

>pdb|4DMA|A Chain A, Crystal Structure Of Era Lbd In Complex With Ru100132 Length = 247

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 63/130 (48%), Gaps = 2/130 (1%)
Query: 207 LFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 266
           + Y E +P  P  +E   +    +L    +  + ++A ++PGF DL   DQ  L + A L
Sbjct: 24  ILYSEYDPTRP-FSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWL 82
Query: 267 ELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISA 325
           E+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M +    
Sbjct: 83  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEE 142
Query: 326 FACLCALTLI 335
           F CL ++ L+
Sbjct: 143 FVCLKSIILL 152

>pdb|3L0L|A Chain A, Crystal Structure Of Orphan Nuclear Receptor Rorgamma In Com Natural Ligand Length = 248

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 28/105 (26%), Positives = 54/105 (51%), Gaps = 3/105 (2%)
Query: 232 LTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVV 291
           LT ++  +  FA ++ GF +LC+ DQ +L ++ ++E+ ++R+  R    D + +F  G  
Sbjct: 65  LTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMC-RAYNADNRTVFFEGKY 123
Query: 292 LEKQQCQRSFG-DDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
               +  R+ G  + +++I +F  SL  +       A   AL LI
Sbjct: 124 -GGMELFRALGCSELISSIFDFSHSLSALHFSEDEIALYTALVLI 167

>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 = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 61/110 (55%), Gaps = 14/110 (12%)
Query: 232 LTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVV 291
           +T ++  +  FA +I GF +LC+ DQ +L ++ SLE+  +R+    RA D++    N V 
Sbjct: 74  ITEAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSLEVVFIRMC---RAFDSQ---NNTVY 127
Query: 292 LEKQQCQ----RSFG-DDWLNAILEFCQSL---HLMEIDISAFACLCALT 333
            + +       +S G +D+++ + EF +SL   HL E +I+ F+    ++
Sbjct: 128 FDGKYASPDVFKSLGCEDFISFVFEFGKSLCSMHLTEDEIALFSAFVLMS 177

>pdb|3KYT|A Chain A, Crystal Structure Of Orphan Nuclear Receptor Rorgamma In Com Natural Ligand Length = 243

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 28/105 (26%), Positives = 54/105 (51%), Gaps = 3/105 (2%)
Query: 232 LTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVV 291
           LT ++  +  FA ++ GF +LC+ DQ +L ++ ++E+ ++R+  R    D + +F  G  
Sbjct: 60  LTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMC-RAYNADNRTVFFEGKY 118
Query: 292 LEKQQCQRSFG-DDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
               +  R+ G  + +++I +F  SL  +       A   AL LI
Sbjct: 119 -GGMELFRALGCSELISSIFDFSHSLSALHFSEDEIALYTALVLI 162

>pdb|3JZC|A Chain A, Crystal Structure Of Tr-Beta Bound To The Selective Thyromimetic Triac Length = 263

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 30/113 (26%), Positives = 51/113 (45%)
Query: 223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT 282
           E    F  ++T ++  +  FA K+P F +L  EDQ +L +   +E+  LR A R   E  
Sbjct: 69  EAFSHFTKIITPAITRVVDFAKKLPMFXELPXEDQIILLKGCCMEIMSLRAAVRYDPESE 128
Query: 283 KLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            L     + + + Q +        +AI +   SL    +D +  A L A+ L+
Sbjct: 129 TLTLNGEMAVTRGQLKNGGLGVVSDAIFDLGMSLSSFNLDDTEVALLQAVLLM 181

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 24/94 (25%), Positives = 46/94 (48%), Gaps = 1/94 (1%)
Query: 242 FADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRS- 300
           +A +IP FSDL  EDQ +L ++   EL +   ++R+ +    ++   G+ + +     + 
Sbjct: 61  WAKRIPHFSDLTLEDQVILLRAGWNELLIASFSHRSVSVQDGILLATGLHVHRSSAHSAG 120
Query: 301 FGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
            G  +   + E    +  M++D S   CL A+ L
Sbjct: 121 VGSIFDRVLTELVSKMKDMQMDKSELGCLRAIVL 154

>pdb|1N4H|A Chain A, Characterization Of Ligands For The Orphan Nuclear Receptor Rorbeta Length = 259

Iteration: 1
 Score = 44.7 bits (104), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 42/158 (26%), Positives = 70/158 (44%), Gaps = 5/158 (3%)
Query: 173 TSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLL 232
           T  ++ R   + I    + C+   E L Q A     Y E    +    E    QQ    +
Sbjct: 8   TMSEIDRIAQNIIKSHLETCQYTMEELHQLAWQTHTYEEIKAYQSKSREA-LWQQCAIQI 66
Query: 233 TTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVL 292
           T ++  +  FA +I GF +LC+ DQ LL +S  LE+ ++R+       +  ++F  G   
Sbjct: 67  THAIQYVVEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPLNNTVLF-EGKYG 125
Query: 293 EKQQCQRSFGDDWLNAILEFCQ---SLHLMEIDISAFA 327
             Q  +    DD +N   +F +   SL L E +I+ F+
Sbjct: 126 GMQMFKALGSDDLVNEAFDFAKNLCSLQLTEEEIALFS 163

>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 = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 29/99 (29%), Positives = 51/99 (51%), Gaps = 4/99 (4%)
Query: 232 LTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVV 291
           +T ++  +  FA +I GF +LC+ DQ LL +S  LE+ ++R+       +  ++F  G  
Sbjct: 66  ITHAIQYVVEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPLNNTVLF-EGKY 124
Query: 292 LEKQQCQRSFGDDWLNAILEFCQ---SLHLMEIDISAFA 327
              Q  +    DD +N   +F +   SL L E +I+ F+
Sbjct: 125 GGMQMFKALGSDDLVNEAFDFAKNLCSLQLTEEEIALFS 163

>pdb|2J4A|A Chain A, Human Thyroid Hormone Receptor Beta Ligand Binding Domain In Complex With Kb131084 Length = 253

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 30/113 (26%), Positives = 51/113 (45%)
Query: 223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT 282
           E    F  ++T ++  +  FA K+P F +L  EDQ +L +   +E+  LR A R   E  
Sbjct: 59  EAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESE 118
Query: 283 KLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            L     + + + Q +        +AI +   SL    +D +  A L A+ L+
Sbjct: 119 TLTLSGEMAVTRGQLKNGGLGVVSDAIFDLGMSLSSFNLDDTEVALLQAVLLM 171

>pdb|1NQ2|A Chain A, Two Rth Mutants With Impaired Hormone Binding Length = 264

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 30/113 (26%), Positives = 51/113 (45%)
Query: 223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT 282
           E    F  ++T ++  +  FA K+P F +L  EDQ +L +   +E+  LR A R   E  
Sbjct: 70  EAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRTAVRYEPESE 129
Query: 283 KLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            L     + + + Q +        +AI +   SL    +D +  A L A+ L+
Sbjct: 130 TLTLNGEMAVTRGQLKNGGLGVVSDAIFDLGMSLSSFNLDDTEVALLQAVLLM 182

>pdb|1XZX|X Chain X, Thyroxine-Thyroid Hormone Receptor Interactions Length = 281

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 30/113 (26%), Positives = 51/113 (45%)
Query: 223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT 282
           E    F  ++T ++  +  FA K+P F +L  EDQ +L +   +E+  LR A R   E  
Sbjct: 87  EAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESE 146
Query: 283 KLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            L     + + + Q +        +AI +   SL    +D +  A L A+ L+
Sbjct: 147 TLTLNGEMAVTRGQLKNGGLGVVSDAIFDLGMSLSSFNLDDTEVALLQAVLLM 199

>pdb|3GWS|X Chain X, Crystal Structure Of T3-Bound Thyroid Hormone Receptor Length = 259

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 30/113 (26%), Positives = 51/113 (45%)
Query: 223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT 282
           E    F  ++T ++  +  FA K+P F +L  EDQ +L +   +E+  LR A R   E  
Sbjct: 66  EAFSHFTKIITPAITRVVDFAKKLPMFXELPCEDQIILLKGCCMEIMSLRAAVRYDPESE 125
Query: 283 KLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            L     + + + Q +        +AI +   SL    +D +  A L A+ L+
Sbjct: 126 TLTLNGEMAVTRGQLKNGGLGVVSDAIFDLGMSLSSFNLDDTEVALLQAVLLM 178

>pdb|1NQ7|A Chain A, Characterization Of Ligands For The Orphan Nuclear Receptor Rorbeta Length = 244

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 29/99 (29%), Positives = 51/99 (51%), Gaps = 4/99 (4%)
Query: 232 LTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVV 291
           +T ++  +  FA +I GF +LC+ DQ LL +S  LE+ ++R+       +  ++F  G  
Sbjct: 59  ITHAIQYVVEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPLNNTVLF-EGKY 117
Query: 292 LEKQQCQRSFGDDWLNAILEFCQ---SLHLMEIDISAFA 327
              Q  +    DD +N   +F +   SL L E +I+ F+
Sbjct: 118 GGMQMFKALGSDDLVNEAFDFAKNLCSLQLTEEEIALFS 156

>pdb|3IMY|A Chain A, Structure Of Tr-Beta Bound To Selective Thyromimetic Gc-1 Length = 261

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 30/113 (26%), Positives = 51/113 (45%)
Query: 223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT 282
           E    F  ++T ++  +  FA K+P F +L  EDQ +L +   +E+  LR A R   E  
Sbjct: 67  EAFSHFTKIITPAITRVVDFAKKLPMFXELPCEDQIILLKGCCMEIMSLRAAVRYDPESE 126
Query: 283 KLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            L     + + + Q +        +AI +   SL    +D +  A L A+ L+
Sbjct: 127 TLTLNGEMAVTRGQLKNGGLGVVSDAIFDLGMSLSSFNLDDTEVALLQAVLLM 179

>pdb|1NAX|A Chain A, Thyroid Receptor Beta1 In Complex With A Beta-Selective Ligand Length = 252

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 30/113 (26%), Positives = 51/113 (45%)
Query: 223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT 282
           E    F  ++T ++  +  FA K+P F +L  EDQ +L +   +E+  LR A R   E  
Sbjct: 59  EAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESE 118
Query: 283 KLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            L     + + + Q +        +AI +   SL    +D +  A L A+ L+
Sbjct: 119 TLTLNGEMAVTRGQLKNGGLGVVSDAIFDLGMSLSSFNLDDTEVALLQAVLLM 171

>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 = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 30/113 (26%), Positives = 51/113 (45%)
Query: 223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT 282
           E    F  ++T ++  +  FA K+P F +L  EDQ +L +   +E+  LR A R   E  
Sbjct: 59  EAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESE 118
Query: 283 KLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            L     + + + Q +        +AI +   SL    +D +  A L A+ L+
Sbjct: 119 TLTLNGEMAVTRGQLKNGGLGVVSDAIFDLGMSLSSFNLDDTEVALLQAVLLM 171

>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 = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 30/113 (26%), Positives = 51/113 (45%)
Query: 223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT 282
           E    F  ++T ++  +  FA K+P F +L  EDQ +L +   +E+  LR A R   E  
Sbjct: 65  EAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESE 124
Query: 283 KLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            L     + + + Q +        +AI +   SL    +D +  A L A+ L+
Sbjct: 125 TLTLNGEMAVTRGQLKNGGLGVVSDAIFDLGMSLSSFNLDDTEVALLQAVLLM 177

>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 = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 30/113 (26%), Positives = 51/113 (45%)
Query: 223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT 282
           E    F  ++T ++  +  FA K+P F +L  EDQ +L +   +E+  LR A R   E  
Sbjct: 64  EAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESE 123
Query: 283 KLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            L     + + + Q +        +AI +   SL    +D +  A L A+ L+
Sbjct: 124 TLTLNGEMAVTRGQLKNGGLGVVSDAIFDLGMSLSSFNLDDTEVALLQAVLLM 176

>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 = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 30/113 (26%), Positives = 51/113 (45%)
Query: 223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT 282
           E    F  ++T ++  +  FA K+P F +L  EDQ +L +   +E+  LR A R   E  
Sbjct: 69  EAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESE 128
Query: 283 KLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            L     + + + Q +        +AI +   SL    +D +  A L A+ L+
Sbjct: 129 TLTLNGEMAVTRGQLKNGGLGVVSDAIFDLGMSLSSFNLDDTEVALLQAVLLM 181

>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 = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 30/113 (26%), Positives = 51/113 (45%)
Query: 223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT 282
           E    F  ++T ++  +  FA K+P F +L  EDQ +L +   +E+  LR A R   E  
Sbjct: 69  EAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESE 128
Query: 283 KLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            L     + + + Q +        +AI +   SL    +D +  A L A+ L+
Sbjct: 129 TLTLNGEMAVTRGQLKNGGLGVVSDAIFDLGMSLSSFNLDDTEVALLQAVLLM 181

>pdb|1BSX|A Chain A, Structure And Specificity Of Nuclear Receptor-Coactivator Interactions Length = 260

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 30/113 (26%), Positives = 51/113 (45%)
Query: 223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT 282
           E    F  ++T ++  +  FA K+P F +L  EDQ +L +   +E+  LR A R   E  
Sbjct: 66  EAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESE 125
Query: 283 KLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            L     + + + Q +        +AI +   SL    +D +  A L A+ L+
Sbjct: 126 TLTLNGEMAVTRGQLKNGGLGVVSDAIFDLGMSLSSFNLDDTEVALLQAVLLM 178

>pdb|3D57|A Chain A, Tr Variant D355r Length = 266

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 30/113 (26%), Positives = 50/113 (44%)
Query: 223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT 282
           E    F  ++T ++  +  FA K+P F +L  EDQ +L +   +E+  LR A R   E  
Sbjct: 73  EAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESE 132
Query: 283 KLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            L     + + + Q +        +AI     SL    +D +  A L A+ L+
Sbjct: 133 TLTLNGEMAVTRGQLKNGGLGVVSDAIFRLGMSLSSFNLDDTEVALLQAVLLM 185

>pdb|2PIN|A Chain A, Thyroid Receptor Beta In Complex With Inhibitor Length = 253

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 30/113 (26%), Positives = 50/113 (44%)
Query: 223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT 282
           E    F  ++T ++  +  FA K+P F +L  EDQ +L +   +E+  LR A R   E  
Sbjct: 59  EAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESE 118
Query: 283 KLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            L     + + + Q +        +AI     SL    +D +  A L A+ L+
Sbjct: 119 TLTLNGEMAVTRGQLKNGGLGVVSDAIFRLGMSLSSFNLDDTEVALLQAVLLM 171

>pdb|3P88|A Chain A, Fxr Bound To Isoquinolinecarboxylic Acid Length = 229

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 28/113 (24%), Positives = 54/113 (47%), Gaps = 3/113 (2%)
Query: 223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT 282
           E  +    + T  V V+  F  K+PGF  L  EDQ  L + +++E   LR A      + 
Sbjct: 39  ENFEILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSA---EIFNK 95
Query: 283 KLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
           KL   +  +LE++       D+++  +  F +S+  +++    +A L A+ ++
Sbjct: 96  KLPSGHSDLLEERIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVIL 148

>pdb|3GD2|A Chain A, Isoxazole Ligand Bound To Farnesoid X Receptor (Fxr) Length = 229

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 27/105 (25%), Positives = 52/105 (49%), Gaps = 3/105 (2%)
Query: 231 LLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGV 290
           + T  V V+  F  K+PGF  L  EDQ  L + +++E   LR A      + KL   +  
Sbjct: 47  MATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSA---EIFNKKLPSGHSD 103
Query: 291 VLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
           +LE++       D+++  +  F +S+  +++    +A L A+ ++
Sbjct: 104 LLEERIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVIL 148

>pdb|3HC6|A Chain A, Fxr With Src1 And Gsk088 Length = 232

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 27/105 (25%), Positives = 52/105 (49%), Gaps = 3/105 (2%)
Query: 231 LLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGV 290
           + T  V V+  F  K+PGF  L  EDQ  L + +++E   LR A      + KL   +  
Sbjct: 50  MATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSA---EIFNKKLPSGHSD 106
Query: 291 VLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
           +LE++       D+++  +  F +S+  +++    +A L A+ ++
Sbjct: 107 LLEERIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVIL 151

>pdb|3L1B|A Chain A, Complex Structure Of Fxr Ligand-Binding Domain With A Tetrahydroazepinoindole Compound Length = 233

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 27/105 (25%), Positives = 52/105 (49%), Gaps = 3/105 (2%)
Query: 231 LLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGV 290
           + T  V V+  F  K+PGF  L  EDQ  L + +++E   LR A      + KL   +  
Sbjct: 51  MATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSA---EIFNKKLPSGHSD 107
Query: 291 VLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
           +LE++       D+++  +  F +S+  +++    +A L A+ ++
Sbjct: 108 LLEERIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVIL 152

>pdb|3HC5|A Chain A, Fxr With Src1 And Gsk826 Length = 232

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 27/105 (25%), Positives = 52/105 (49%), Gaps = 3/105 (2%)
Query: 231 LLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGV 290
           + T  V V+  F  K+PGF  L  EDQ  L + +++E   LR A      + KL   +  
Sbjct: 50  MATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSA---EIFNKKLPSGHSD 106
Query: 291 VLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
           +LE++       D+++  +  F +S+  +++    +A L A+ ++
Sbjct: 107 LLEERIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVIL 151

>pdb|3BEJ|A Chain A, Structure Of Human Fxr In Complex With Mfa-1 And Co- Activator Peptide Length = 238

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 27/105 (25%), Positives = 52/105 (49%), Gaps = 3/105 (2%)
Query: 231 LLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGV 290
           + T  V V+  F  K+PGF  L  EDQ  L + +++E   LR A      + KL   +  
Sbjct: 56  MATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSA---EIFNKKLPSGHSD 112
Query: 291 VLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
           +LE++       D+++  +  F +S+  +++    +A L A+ ++
Sbjct: 113 LLEERIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVIL 157

>pdb|1OSH|A Chain A, A Chemical, Genetic, And Structural Analysis Of The Nuclear Bile Acid Receptor Fxr Length = 232

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 27/105 (25%), Positives = 52/105 (49%), Gaps = 3/105 (2%)
Query: 231 LLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGV 290
           + T  V V+  F  K+PGF  L  EDQ  L + +++E   LR A      + KL   +  
Sbjct: 50  MATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSA---EIFNKKLPSGHSD 106
Query: 291 VLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
           +LE++       D+++  +  F +S+  +++    +A L A+ ++
Sbjct: 107 LLEERIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVIL 151

>pdb|3FLI|A Chain A, Discovery Of Xl335, A Highly Potent, Selective And Orally- Active Agonist Of The Farnesoid X Receptor (Fxr) Length = 231

Iteration: 1
 Score = 42.0 bits (97), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 27/105 (25%), Positives = 52/105 (49%), Gaps = 3/105 (2%)
Query: 231 LLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGV 290
           + T  V V+  F  K+PGF  L  EDQ  L + +++E   LR A      + KL   +  
Sbjct: 49  MATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSA---EIFNKKLPSGHSD 105
Query: 291 VLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
           +LE++       D+++  +  F +S+  +++    +A L A+ ++
Sbjct: 106 LLEERIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVIL 150

>pdb|3DCT|A Chain A, Fxr With Src1 And Gw4064 Length = 235

Iteration: 1
 Score = 42.0 bits (97), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 27/105 (25%), Positives = 52/105 (49%), Gaps = 3/105 (2%)
Query: 231 LLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGV 290
           + T  V V+  F  K+PGF  L  EDQ  L + +++E   LR A      + KL   +  
Sbjct: 53  MATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSA---EIFNKKLPSGHSD 109
Query: 291 VLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
           +LE++       D+++  +  F +S+  +++    +A L A+ ++
Sbjct: 110 LLEERIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVIL 154

>pdb|3P89|A Chain A, Fxr Bound To A Quinolinecarboxylic Acid Length = 229

Iteration: 1
 Score = 42.0 bits (97), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 27/105 (25%), Positives = 52/105 (49%), Gaps = 3/105 (2%)
Query: 231 LLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGV 290
           + T  V V+  F  K+PGF  L  EDQ  L + +++E   LR A      + KL   +  
Sbjct: 47  MATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSA---EIFNKKLPSGHSD 103
Query: 291 VLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
           +LE++       D+++  +  F +S+  +++    +A L A+ ++
Sbjct: 104 LLEERIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVIL 148

>pdb|3RUT|A Chain A, Fxr With Src1 And Gsk359 Length = 229

Iteration: 1
 Score = 42.0 bits (97), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 27/105 (25%), Positives = 52/105 (49%), Gaps = 3/105 (2%)
Query: 231 LLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGV 290
           + T  V V+  F  K+PGF  L  EDQ  L + +++E   LR A      + KL   +  
Sbjct: 47  MATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSA---EIFNKKLPSGHSD 103
Query: 291 VLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
           +LE++       D+++  +  F +S+  +++    +A L A+ ++
Sbjct: 104 LLEERIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVIL 148

>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 = 41.6 bits (96), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 21/61 (34%), Positives = 36/61 (59%)
Query: 242 FADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSF 301
           +A KIPGF +L   DQ  L +S+ +E+ ++ L +R+     KLIF   +VL++ + +   
Sbjct: 56  WAKKIPGFVELSLFDQVRLLESSWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKSVE 115
Query: 302 G 302
           G
Sbjct: 116 G 116

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 22/94 (23%), Positives = 46/94 (48%), Gaps = 1/94 (1%)
Query: 242 FADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRS- 300
           +A +IP FS+L  +DQ +L ++   EL +   ++R+ A    ++   G+ + +     + 
Sbjct: 102 WAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAG 161
Query: 301 FGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
            G  +   + E    +  M++D +   CL A+ L
Sbjct: 162 VGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVL 195

>pdb|3FXV|A Chain A, Identification Of An N-Oxide Pyridine Gw4064 Analogue As A Potent Fxr Agonist Length = 233

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 27/105 (25%), Positives = 51/105 (48%), Gaps = 3/105 (2%)
Query: 231 LLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGV 290
           + T  V V+  F  K+PGF  L  EDQ  L + +++E   LR A      + KL   +  
Sbjct: 51  MATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSA---EIFNKKLPSGHSD 107
Query: 291 VLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
           +LE +       D+++  +  F +S+  +++    +A L A+ ++
Sbjct: 108 LLEARIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVIL 152

>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 = 41.2 bits (95), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 22/94 (23%), Positives = 46/94 (48%), Gaps = 1/94 (1%)
Query: 242 FADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRS- 300
           +A +IP FS+L  +DQ +L ++   EL +   ++R+ A    ++   G+ + +     + 
Sbjct: 64  WAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAG 123
Query: 301 FGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
            G  +   + E    +  M++D +   CL A+ L
Sbjct: 124 VGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVL 157

>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 = 41.2 bits (95), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 22/94 (23%), Positives = 46/94 (48%), Gaps = 1/94 (1%)
Query: 242 FADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRS- 300
           +A +IP FS+L  +DQ +L ++   EL +   ++R+ A    ++   G+ + +     + 
Sbjct: 62  WAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAG 121
Query: 301 FGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
            G  +   + E    +  M++D +   CL A+ L
Sbjct: 122 VGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVL 155

>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 = 41.2 bits (95), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 22/94 (23%), Positives = 46/94 (48%), Gaps = 1/94 (1%)
Query: 242 FADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRS- 300
           +A +IP FS+L  +DQ +L ++   EL +   ++R+ A    ++   G+ + +     + 
Sbjct: 60  WAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAG 119
Query: 301 FGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
            G  +   + E    +  M++D +   CL A+ L
Sbjct: 120 VGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVL 153

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	335
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	5e-73
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	2e-67
1cit_A	89	NGFI-B, protein (orphan nuclear receptor NGFI-B);	3e-50
1ovl_A	271	Orphan nuclear receptor NURR1 (MSe 414, 496, 511);	7e-50
2a66_A	113	Orphan nuclear receptor NR5A2; protein-DNA complex	5e-49
1lo1_A	98	Steroid hormone receptor ERR2; estrogen related re	5e-49
1dsz_A	86	RAR-alpha, retinoic acid receptor alpha; RAR, nucl	1e-47
2han_A	93	Protein ultraspiracle; transcription regulation, t	2e-47
1kb2_A	110	Vitamin D3 receptor; VDR, nuclear receptor, protei	1e-46
2han_B	119	Ecdysone receptor; transcription regulation, trans	4e-46
1dsz_B	85	RXR-alpha, retinoic acid receptor RXR-alpha; RAR,	5e-46
1ynw_B	99	Retinoic acid receptor RXR-alpha, retinoid X recep	1e-45
1hcq_A	84	Protein (estrogen receptor); protein-DNA complex,	3e-45
3g9m_A	90	Glucocorticoid receptor; glucocorticoid, DNA-bindi	4e-45
2ebl_A	89	COUP transcription factor 1; DNA-binding, metal-bi	4e-45
1r4i_A	105	Androgen receptor; AR, steroid receptor, protein-D	8e-45
3cbb_A	78	HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DN	1e-43
1a6y_A	94	Orphan nuclear receptor NR1D1; orphan receptor, DN	2e-43
2nll_B	103	Protein (thyroid hormone receptor); complex (trans	7e-43
1xdk_B	303	RAR-beta, retinoic acid receptor, beta; nuclear re	6e-41
1z5x_E	310	Ecdysone receptor ligand binding domain; ponastero	3e-40
1pdu_A	244	DHR38, nuclear hormone receptor HR38; nuclear rece	2e-37
1pdu_A	244	DHR38, nuclear hormone receptor HR38; nuclear rece	2e-14
2nxx_E	248	Ecdysone receptor (ECR, NRH1); hormone receptor, A	2e-36
2nxx_E	248	Ecdysone receptor (ECR, NRH1); hormone receptor, A	2e-12
1yje_A	264	Orphan nuclear receptor NR4A1; NGFI-B, NUR77, liga	4e-36
1fcy_A	236	RAR-gamma-1, retinoic acid receptor gamma-1; isoty	3e-35
1fcy_A	236	RAR-gamma-1, retinoic acid receptor gamma-1; isoty	8e-13
1lbd_A	282	RXR_LBD, retinoid X receptor; transcription factor	3e-35
3cqv_A	199	Nuclear receptor subfamily 1 group D member 2; rev	4e-35
3cqv_A	199	Nuclear receptor subfamily 1 group D member 2; rev	7e-13
2r40_D	266	Ecdysone receptor, 20-hydroxy-ecdysone receptor; n	2e-34
2r40_D	266	Ecdysone receptor, 20-hydroxy-ecdysone receptor; n	1e-14
2hc4_A	302	Vitamin D receptor; alpha helical sandwich, gene r	7e-34
3ilz_A	267	Thyroid hormone receptor, alpha isoform 1 variant;	3e-33
3ilz_A	267	Thyroid hormone receptor, alpha isoform 1 variant;	2e-10
3n00_A	245	REV-ERBA-alpha; reverba ncorid1, anti-parallel B-s	3e-33
3n00_A	245	REV-ERBA-alpha; reverba ncorid1, anti-parallel B-s	5e-12
3kmr_A	266	Retinoic acid receptor alpha; nuclear receptor tra	1e-32
3kmr_A	266	Retinoic acid receptor alpha; nuclear receptor tra	2e-12
3ipq_A	283	Oxysterols receptor LXR-alpha; LXR homodimer, LXR	3e-32
1osh_A	232	BIle acid receptor; nuclear receptor, ligand bindi	4e-32
1osh_A	232	BIle acid receptor; nuclear receptor, ligand bindi	7e-11
2e2r_A	244	Estrogen-related receptor gamma; ERR gamma, BPA, n	3e-31
2e2r_A	244	Estrogen-related receptor gamma; ERR gamma, BPA, n	2e-12
1xvp_B	246	Orphan nuclear receptor NR1I3; CAR, RXR, citco, SR	2e-30
1xvp_B	246	Orphan nuclear receptor NR1I3; CAR, RXR, citco, SR	1e-10
1xpc_A	248	Estrogen receptor; nuclear receptor, transcription	4e-30
3oll_A	240	Estrogen receptor beta; steroid binding, phosphory	1e-29
3k6p_A	248	Steroid hormone receptor ERR1; estrogen related re	1e-29
3k6p_A	248	Steroid hormone receptor ERR1; estrogen related re	3e-11
2ocf_A	298	Estrogen receptor; estrogen receptor, LBD, monobod	5e-29
2ocf_A	298	Estrogen receptor; estrogen receptor, LBD, monobod	9e-12
1nrl_A	316	Orphan nuclear receptor PXR; PXR, xenobiotic, SRC-	5e-29
1nrl_A	316	Orphan nuclear receptor PXR; PXR, xenobiotic, SRC-	5e-12
3b0t_A	254	Vitamin D3 receptor; nuclear receptor, transcripti	8e-29
3b0t_A	254	Vitamin D3 receptor; nuclear receptor, transcripti	3e-11
1n83_A	270	Nuclear receptor ROR-alpha; three-layered alpha he	2e-28
1n83_A	270	Nuclear receptor ROR-alpha; three-layered alpha he	3e-10
3l0l_A	248	Nuclear receptor ROR-gamma; nuclear receptor, rorg	2e-28
3l0l_A	248	Nuclear receptor ROR-gamma; nuclear receptor, rorg	3e-10
1nq7_A	244	Nuclear receptor ROR-beta; ligand-binding domain,	2e-28
1nq7_A	244	Nuclear receptor ROR-beta; ligand-binding domain,	3e-10
2o4j_A	292	Vitamin D3 receptor; nuclear receptor-ligand compl	2e-28
2o4j_A	292	Vitamin D3 receptor; nuclear receptor-ligand compl	5e-11
3u9q_A	269	Peroxisome proliferator-activated receptor gamma;	3e-28
3u9q_A	269	Peroxisome proliferator-activated receptor gamma;	3e-12
3plz_A	257	FTZ-F1 related protein; alpha helical sandwhich, f	2e-27
3plz_A	257	FTZ-F1 related protein; alpha helical sandwhich, f	9e-12
2p1t_A	240	Retinoic acid receptor RXR-alpha; protein-ligand c	2e-27
2p1t_A	240	Retinoic acid receptor RXR-alpha; protein-ligand c	2e-09
1yye_A	268	ER-beta, estrogen receptor beta; ER-beta, nuclear	2e-27
1yye_A	268	ER-beta, estrogen receptor beta; ER-beta, nuclear	2e-08
3vhv_A	260	Mineralocorticoid receptor; nuclear receptor, tran	3e-26
3vhv_A	260	Mineralocorticoid receptor; nuclear receptor, tran	3e-09
2p54_A	267	PPAR-alpha, peroxisome proliferator-activated rece	5e-26
2p54_A	267	PPAR-alpha, peroxisome proliferator-activated rece	9e-12
1l2j_A	271	Estrogen receptor beta; nuclear receptor, transcri	1e-25
1l2j_A	271	Estrogen receptor beta; nuclear receptor, transcri	5e-12
3vhu_A	294	Mineralocorticoid receptor; nuclear receptor, tran	1e-25
3vhu_A	294	Mineralocorticoid receptor; nuclear receptor, tran	5e-10
3mnp_A	261	Glucocorticoid receptor; protein-ligand complex, s	3e-25
3mnp_A	261	Glucocorticoid receptor; protein-ligand complex, s	1e-09
2nxx_A	235	Ultraspiracle (USP, NR2B4); hormone receptor, APO	3e-24
2nxx_A	235	Ultraspiracle (USP, NR2B4); hormone receptor, APO	2e-06
3tx7_B	352	Nuclear receptor subfamily 5 group A member 2; LRH	4e-24
3cjw_A	244	COUP transcription factor 2; COUP-TFII, nuclear re	8e-24
3cjw_A	244	COUP transcription factor 2; COUP-TFII, nuclear re	3e-08
1sqn_A	261	PR, progesterone receptor; nuclear receptor, stero	3e-23
1sqn_A	261	PR, progesterone receptor; nuclear receptor, stero	6e-09
1ymt_A	246	Steroidogenic factor 1; SF-1, ligand-binding domai	6e-23
1ymt_A	246	Steroidogenic factor 1; SF-1, ligand-binding domai	3e-09
1t7r_A	269	Androgen receptor; nuclear receptor, transcription	1e-22
1t7r_A	269	Androgen receptor; nuclear receptor, transcription	8e-08
3ltx_A	243	Estrogen receptor; constitutive, nuclear receptor,	7e-22
3ltx_A	243	Estrogen receptor; constitutive, nuclear receptor,	9e-07
3p0u_A	249	Nuclear receptor subfamily 2 group C member 2; lig	4e-21
3p0u_A	249	Nuclear receptor subfamily 2 group C member 2; lig	5e-07
2iz2_A	243	FTZ-F1 alpha, nuclear hormone receptor FTZ-F1; nuc	1e-20
2iz2_A	243	FTZ-F1 alpha, nuclear hormone receptor FTZ-F1; nuc	4e-06
3up3_A	243	Acedaf-12; ligand binding domain, nematode, steroi	2e-20
3up3_A	243	Acedaf-12; ligand binding domain, nematode, steroi	2e-08
1pzl_A	237	Hepatocyte nuclear factor 4-alpha; transcription;	1e-19
1pzl_A	237	Hepatocyte nuclear factor 4-alpha; transcription;	2e-05
1hg4_A	279	Ultraspiracle; nuclear hormone receptor, transcrip	8e-17
3gyt_A	244	Nuclear hormone receptor of the steroid/thyroid ho	3e-16
3gyt_A	244	Nuclear hormone receptor of the steroid/thyroid ho	2e-07
1g2n_A	264	Ultraspiracle protein; antiparallel alpha-helical	3e-15
3f5c_B	268	Nuclear receptor subfamily 0 group B member 1; tra	1e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-07

>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 =  232 bits (592), Expect = 5e-73
 Identities = 76/333 (22%), Positives = 130/333 (39%), Gaps = 53/333 (15%)

Query: 4   GRSSSSESPKLRHSAPLSSASSSPGCDTSRPTPPSPSQLCAVCGDIAACQHYGVRTCEGC 63
              +   S +        +         S         +CA+CGD ++ +HYGV +CEGC
Sbjct: 101 SPMNPVSSSEDIKPPLGLNGVLKVPAHPSGNMASFTKHICAICGDRSSGKHYGVYSCEGC 160

Query: 64  KGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLKGRRG 123
           KGFFKRTV+K   Y C  +K C +DKR+RNRCQ+CR+QKCL +GM +E V+ +  +G+  
Sbjct: 161 KGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRGKDR 220

Query: 124 RLPSKPKSPQESPPSPPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFAD 183
                  +   +   P   ++ A        E                            
Sbjct: 221 NENEVESTSSANEDMPVERILEAELAVEPKTET--------------------------- 253

Query: 184 KIPGFSDLCKEDQELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFA 243
                                    Y E N    P +  + +          +  +  +A
Sbjct: 254 -------------------------YVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWA 288

Query: 244 DKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD 303
            +IP FS+L  +DQ +L ++   EL +   ++R+ A    ++   G+ + +     +   
Sbjct: 289 KRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVG 348

Query: 304 DWLNAIL-EFCQSLHLMEIDISAFACLCALTLI 335
              + +L E    +  M++D +   CL A+ L 
Sbjct: 349 AIFDRVLTELVSKMRDMQMDKTELGCLRAIVLF 381

>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 =  216 bits (551), Expect = 2e-67
 Identities = 78/333 (23%), Positives = 127/333 (38%), Gaps = 16/333 (4%)

Query: 6   SSSSESPKLRHSAPLSSASSSPGCDTSRPTPPSPSQLCAVCGDIAACQHYGVRTCEGCKG 65
             S+   +       S  +         P+    +  C VCGD A+  HYGV  CEGCKG
Sbjct: 16  YQSAIKVEPASPPYYSEKTQLYNKPHEEPSNSLMAIECRVCGDKASGFHYGVHACEGCKG 75

Query: 66  FFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSL-KGRRGR 124
           FF+RT++    Y    D  C + K+ RN+CQ+CRFQKCL VGM    +R   + +  + +
Sbjct: 76  FFRRTIRLKLIYDR-CDLNCRIHKKSRNKCQYCRFQKCLAVGMSHNAIRFGRMPQAEKEK 134

Query: 125 LPSKPKSPQESPPSPPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADK 184
           L ++  S  +               +   L   + +        +       +     DK
Sbjct: 135 LLAEISSDIDQLNPES--------ADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDK 186

Query: 185 IPGFSDLCKEDQELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFAD 244
            P    +  +   L+     ++  +  P   +         Q        +V  I  +A 
Sbjct: 187 SPF---VIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAK 243

Query: 245 KIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVL--EKQQCQRSFG 302
            IPGF +L   DQ  L +    E+    LA     +D  LI      +  E  +  R   
Sbjct: 244 SIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLM-NKDGVLISEGQGFMTREFLKSLRKPF 302

Query: 303 DDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            D++    EF    + +E+D S  A   A+ ++
Sbjct: 303 GDFMEPKFEFAVKFNALELDDSDLAIFIAVIIL 335

>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 =  161 bits (409), Expect = 3e-50
 Identities = 79/87 (90%), Positives = 83/87 (95%)

Query: 43  CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
           CAVCGD A+CQHYGVRTCEGCKGFFKRTVQK +KY+CLA+K CPVDKRRRNRCQFCRFQK
Sbjct: 3   CAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQK 62

Query: 103 CLQVGMVKEVVRTDSLKGRRGRLPSKP 129
           CL VGMVKEVVRTDSLKGRRGRLPSKP
Sbjct: 63  CLAVGMVKEVVRTDSLKGRRGRLPSKP 89

>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 =  166 bits (422), Expect = 7e-50
 Identities = 109/229 (47%), Positives = 139/229 (60%), Gaps = 45/229 (19%)

Query: 108 MVKEVVRTDSLKGRRGRLPSKPKSPQE-SPPSPPVSLITALYREPNPLEPPIAEPEKIQQ 166
           MVKEVVRTDSLKGRRGRLPSKPKSPQE SPPSPPVSLI+AL R      P +   +  + 
Sbjct: 1   MVKEVVRTDSLKGRRGRLPSKPKSPQEPSPPSPPVSLISALVRAHVDSNPAMTSLDYSR- 59

Query: 167 FYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFYREPNPLEPPIAEPEKIQ 226
                                                     ++     +    + + IQ
Sbjct: 60  ------------------------------------------FQANPDYQMSGDDTQHIQ 77

Query: 227 QFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIF 286
           QFY LLT S+++IR +A+KIPGF+DL K DQ+LLF+SA LELFVLRLAYR+   + KLIF
Sbjct: 78  QFYDLLTGSMEIIRGWAEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIF 137

Query: 287 CNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
           CNGVVL + QC R FG +W+++I+EF  +L  M IDISAF+C+ AL ++
Sbjct: 138 CNGVVLHRLQCVRGFG-EWIDSIVEFSSNLQNMNIDISAFSCIAALAMV 185

>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 =  159 bits (403), Expect = 5e-49
 Identities = 47/104 (45%), Positives = 61/104 (58%)

Query: 34  PTPPSPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRN 93
                  +LC VCGD  +  HYG+ TCE CKGFFKRTVQ   +Y C+ ++ C +DK +R 
Sbjct: 3   FGDEDLEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQNCQIDKTQRK 62

Query: 94  RCQFCRFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPP 137
           RC +CRFQKCL VGM  E VR D ++G R +     K  +    
Sbjct: 63  RCPYCRFQKCLSVGMKLEAVRADRMRGGRNKFGPMYKRDRALKQ 106

>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 =  158 bits (401), Expect = 5e-49
 Identities = 49/95 (51%), Positives = 61/95 (64%)

Query: 39  PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFC 98
           P +LC VCGDIA+  HYGV +CE CK FFKRT+Q   +Y C A   C + KRRR  CQ C
Sbjct: 3   PKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQAC 62

Query: 99  RFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQ 133
           RF K L+VGM+KE VR D ++G R +   +  S  
Sbjct: 63  RFMKALKVGMLKEGVRLDRVRGGRQKYKRRLDSEN 97

>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 =  154 bits (391), Expect = 1e-47
 Identities = 45/86 (52%), Positives = 57/86 (66%)

Query: 37  PSPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQ 96
           P   + C VC D ++  HYGV  CEGCKGFF+R++QK   Y C  DK C ++K  RNRCQ
Sbjct: 1   PRIYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQ 60

Query: 97  FCRFQKCLQVGMVKEVVRTDSLKGRR 122
           +CR QKC +VGM KE VR D  K ++
Sbjct: 61  YCRLQKCFEVGMSKESVRNDRNKKKK 86

>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 =  154 bits (391), Expect = 2e-47
 Identities = 46/91 (50%), Positives = 61/91 (67%)

Query: 32  SRPTPPSPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRR 91
           S         LC++CGD A+ +HYGV +CEGCKGFFKRTV+K   Y C  ++ C +DKR+
Sbjct: 2   SNHPLSGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYACRENRNCIIDKRQ 61

Query: 92  RNRCQFCRFQKCLQVGMVKEVVRTDSLKGRR 122
           RNRCQ+CR+QKCL  GM +E V+ +     R
Sbjct: 62  RNRCQYCRYQKCLTCGMKREAVQEERQGIHR 92

>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 =  152 bits (386), Expect = 1e-46
 Identities = 37/106 (34%), Positives = 59/106 (55%)

Query: 38  SPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQF 97
           +  ++C VCGD A   H+   TCEGCKGFF+R++++ + + C  +  C + K  R  CQ 
Sbjct: 4   NVPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQA 63

Query: 98  CRFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVSL 143
           CR ++C+ +GM+KE + TD    R+  +  K K  +    S    L
Sbjct: 64  CRLKRCVDIGMMKEFILTDEEVQRKREMILKRKEEEALKDSLRPKL 109

>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 =  151 bits (384), Expect = 4e-46
 Identities = 44/107 (41%), Positives = 57/107 (53%)

Query: 34  PTPPSPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRN 93
             P    +LC VCGD A+  HY   TCEGCKGFF+R+V K + Y C   +AC +D   R 
Sbjct: 2   SAPRVQEELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRACEMDMYMRR 61

Query: 94  RCQFCRFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPP 140
           +CQ CR +KCL VGM  E V  ++    + R     K   +   SP 
Sbjct: 62  KCQECRLKKCLAVGMRPECVVPENQCAMKRREKKAQKEKDKMTTSPS 108

>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 =  150 bits (380), Expect = 5e-46
 Identities = 45/83 (54%), Positives = 62/83 (74%)

Query: 38  SPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQF 97
               +CA+CGD ++ +HYGV +CEGCKGFFKRTV+K   Y C  +K C +DKR+RNRCQ+
Sbjct: 3   FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQY 62

Query: 98  CRFQKCLQVGMVKEVVRTDSLKG 120
           CR+QKCL +GM +E V+ +  +G
Sbjct: 63  CRYQKCLAMGMKREAVQEERQRG 85

>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 =  149 bits (379), Expect = 1e-45
 Identities = 47/104 (45%), Positives = 67/104 (64%), Gaps = 7/104 (6%)

Query: 39  PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFC 98
              +CA+CGD ++ +HYGV +CEGCKGFFKRTV+K   Y C  +K C +DKR+RNRCQ+C
Sbjct: 2   TKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYC 61

Query: 99  RFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVS 142
           R+QKCL +GM +E V+ +       R   K ++  E   +   +
Sbjct: 62  RYQKCLAMGMKREAVQEE-------RQRGKDRNENEVESTSSAN 98

>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 =  148 bits (375), Expect = 3e-45
 Identities = 41/83 (49%), Positives = 54/83 (65%)

Query: 38  SPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQF 97
             ++ CAVC D A+  HYGV +CEGCK FFKR++Q  + Y+C A   C +DK RR  CQ 
Sbjct: 2   KETRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQA 61

Query: 98  CRFQKCLQVGMVKEVVRTDSLKG 120
           CR +KC +VGM+K  +R D   G
Sbjct: 62  CRLRKCYEVGMMKGGIRKDRRGG 84

>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 =  148 bits (375), Expect = 4e-45
 Identities = 37/88 (42%), Positives = 47/88 (53%)

Query: 40  SQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCR 99
           S +C VC D A+  HYGV TC  CK FFKR V+    Y+C     C +DK RR  C  CR
Sbjct: 2   SHMCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACR 61

Query: 100 FQKCLQVGMVKEVVRTDSLKGRRGRLPS 127
           ++KCLQ GM  E  +T        +  +
Sbjct: 62  YRKCLQAGMNLEARKTKKKIKGIQQATA 89

>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 =  148 bits (375), Expect = 4e-45
 Identities = 44/93 (47%), Positives = 61/93 (65%), Gaps = 7/93 (7%)

Query: 35  TPPSPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNR 94
           +  S    C VCGD ++ +HYG  TCEGCK FFKR+V++   Y C A++ CP+D+  RN+
Sbjct: 2   SSGSSGIECVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRANRNCPIDQHHRNQ 61

Query: 95  CQFCRFQKCLQVGMVKEVVRTDSLKGRRGRLPS 127
           CQ+CR +KCL+VGM +E V       +RG  PS
Sbjct: 62  CQYCRLKKCLKVGMRREAV-------QRGSGPS 87

>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 =  148 bits (374), Expect = 8e-45
 Identities = 34/101 (33%), Positives = 50/101 (49%), Gaps = 2/101 (1%)

Query: 38  SPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQF 97
            P + C +CGD A+  HYG  TC  CK FFKR  +   KY+C +   C +DK RR  C  
Sbjct: 5   PPQKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPS 64

Query: 98  CRFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPS 138
           CR +KC + GM     +   L   + +   + ++     P+
Sbjct: 65  CRLRKCYEAGMTLGARKLKKLGNLKLQ--EEGENSSAGSPT 103

>3cbb_A HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DNA binding domain, nuclear; zinc finger; 2.00A {Homo sapiens} Length = 78

 Score =  143 bits (363), Expect = 1e-43
 Identities = 38/75 (50%), Positives = 54/75 (72%)

Query: 42  LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQ 101
           LCA+CGD A  +HYG  +C+GCKGFF+R+V+K   Y C   + C VDK +RN+C++CR +
Sbjct: 2   LCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLK 61

Query: 102 KCLQVGMVKEVVRTD 116
           KC + GM KE V+ +
Sbjct: 62  KCFRAGMKKEAVQNE 76

>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 =  144 bits (364), Expect = 2e-43
 Identities = 45/97 (46%), Positives = 61/97 (62%), Gaps = 8/97 (8%)

Query: 35  TPPSPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYV-CLADKACPVDKRRRN 93
                  LC VCGD+A+  HYGV  CEGCKGFF+R++Q+  +Y  CL ++ C + +  RN
Sbjct: 2   KLNGMVLLCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRN 61

Query: 94  RCQFCRFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPK 130
           RCQ CRF+KCL VGM ++ V       R GR+P + K
Sbjct: 62  RCQQCRFKKCLSVGMSRDAV-------RFGRIPKREK 91

>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 =  142 bits (361), Expect = 7e-43
 Identities = 43/96 (44%), Positives = 59/96 (61%), Gaps = 2/96 (2%)

Query: 41  QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQK--GSKYVCLADKACPVDKRRRNRCQFC 98
           +LC VCGD A   HY   TCEGCKGFF+RT+QK     Y C  +  C +DK  RN+CQ C
Sbjct: 2   ELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQEC 61

Query: 99  RFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQE 134
           RF+KC+ VGM  ++V  DS +  + +L  + +  + 
Sbjct: 62  RFKKCIYVGMATDLVLDDSKRLAKRKLIEENREKRR 97

>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 =  144 bits (364), Expect = 6e-41
 Identities = 43/229 (18%), Positives = 79/229 (34%), Gaps = 47/229 (20%)

Query: 108 MVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVS-LITALYREPNPLEPPIAEPEKIQQ 166
           M KE VR D  + ++ + PSK +  +    +  +  L   + +      P + +  K   
Sbjct: 1   MSKESVRND--RNKKKKEPSKQECTESYEMTAELDDLTEKIRKAHQETFPSLCQLGKYTT 58

Query: 167 FYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFYREPNPLEPPIAEPEKIQ 226
                                                         +       +     
Sbjct: 59  --------------------------------------------NSSADHRVRLDLGLWD 74

Query: 227 QFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIF 286
           +F  L T  +  I  FA ++PGF+ L   DQ  L ++A L++ +LR+  R   E   + F
Sbjct: 75  KFSELATKCIIKIVEFAKRLPGFTGLTIADQITLLKAACLDILILRICTRYTPEQDTMTF 134

Query: 287 CNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
            +G+ L + Q   +      + +  F   L  +E+D +    L A+ LI
Sbjct: 135 SDGLTLNRTQMHNAGFGPLTDLVFTFANQLLPLEMDDTETGLLSAICLI 183

>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 =  142 bits (360), Expect = 3e-40
 Identities = 47/258 (18%), Positives = 90/258 (34%), Gaps = 47/258 (18%)

Query: 79  CLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPS 138
            + +  C V KR+  + Q  + +         + ++ +    R              P +
Sbjct: 17  VVPEFQCAV-KRKEKKAQKDKDKPNSTTSCSPDGIKQEIDPQRLDTDSQLLSVNGVKPIT 75

Query: 139 PP-VSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQE 197
           P    LI  L                             V      + P   D+      
Sbjct: 76  PEQEELIHRL-----------------------------VYFQNEYEHPSPEDI------ 100

Query: 198 LLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQ 257
                           P E  +AE E+ +    +   +V +I  F+ ++PGF  L +EDQ
Sbjct: 101 ---------KRIVNAAPEEENVAE-ERFRHITEITILTVQLIVEFSKRLPGFDKLIREDQ 150

Query: 258 ELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLH 317
             L ++ S E+ + R+A R  AE   ++F       ++    +   D +  +L FC+ + 
Sbjct: 151 IALLKACSSEVMMFRMARRYDAETDSILFATNQPYTRESYTVAGMGDTVEDLLRFCRHMC 210

Query: 318 LMEIDISAFACLCALTLI 335
            M++D + +A L A+ + 
Sbjct: 211 AMKVDNAEYALLTAIVIF 228

>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 =  133 bits (336), Expect = 2e-37
 Identities = 88/120 (73%), Positives = 102/120 (85%), Gaps = 1/120 (0%)

Query: 216 EPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAY 275
           E  ++E +K+QQFY LLT+SVDVI+ FA+KIPG+ DL  EDQELLFQSASLELFVLRLAY
Sbjct: 40  EQSMSEADKVQQFYQLLTSSVDVIKQFAEKIPGYFDLLPEDQELLFQSASLELFVLRLAY 99

Query: 276 RTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
           R R +DTKLIFCNG VL + QC RSFG +WLN I+EF +SLH +EIDISAFACLCALTLI
Sbjct: 100 RARIDDTKLIFCNGTVLHRTQCLRSFG-EWLNDIMEFSRSLHNLEIDISAFACLCALTLI 158

>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 = 70.9 bits (174), Expect = 2e-14
 Identities = 47/84 (55%), Positives = 57/84 (67%), Gaps = 13/84 (15%)

Query: 138 SPPVSLITALYR-----EPNP--------LEPPIAEPEKIQQFYSLLTTSVDVIRHFADK 184
              +SLITAL R      P+P         E  ++E +K+QQFY LLT+SVDVI+ FA+K
Sbjct: 10  HGAISLITALVRSHVDTTPDPSCLDYSHYEEQSMSEADKVQQFYQLLTSSVDVIKQFAEK 69

Query: 185 IPGFSDLCKEDQELLFQSASLELF 208
           IPG+ DL  EDQELLFQSASLELF
Sbjct: 70  IPGYFDLLPEDQELLFQSASLELF 93

>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 =  130 bits (329), Expect = 2e-36
 Identities = 29/142 (20%), Positives = 64/142 (45%)

Query: 194 EDQELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLC 253
             Q      +  ++      P++       + +    +   +V +I  FA ++PGF  L 
Sbjct: 23  YFQNEYEHPSEEDVKRIINQPMDGEDQCDVRFRHITEITILTVQLIVEFAKRLPGFDKLL 82

Query: 254 KEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFC 313
           +EDQ  L ++ S E+ + R+A R   +   ++F N     +     +   + +  +L FC
Sbjct: 83  REDQIALLKACSSEVMMFRMARRYDVQTDSILFVNNQPYSRDSYNLAGMGETIEDLLHFC 142

Query: 314 QSLHLMEIDISAFACLCALTLI 335
           ++++ M +D + +A L A+ + 
Sbjct: 143 RTMYSMRVDNAEYALLTAIVIF 164

>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 = 65.4 bits (160), Expect = 2e-12
 Identities = 15/58 (25%), Positives = 28/58 (48%)

Query: 151 PNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELF 208
             P++       + +    +   +V +I  FA ++PGF  L +EDQ  L ++ S E+ 
Sbjct: 41  NQPMDGEDQCDVRFRHITEITILTVQLIVEFAKRLPGFDKLLREDQIALLKACSSEVM 98

>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 =  130 bits (329), Expect = 4e-36
 Identities = 76/211 (36%), Positives = 106/211 (50%), Gaps = 45/211 (21%)

Query: 126 PSKPKSPQESPPSP-PVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADK 184
              P+     PP   P +L+T+L R         A  +       L  +           
Sbjct: 12  GLVPRGSHMQPPDASPTNLLTSLIR---------AHLDSGPNTAKLDYSK---------- 52

Query: 185 IPGFSDLCKEDQELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFAD 244
                                   ++E         +   +QQFY LL+ S+DVIR +A+
Sbjct: 53  ------------------------FQELVLPRFGKEDAGDVQQFYDLLSGSLDVIRKWAE 88

Query: 245 KIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDD 304
           KIPGF +L   DQ+LL +SA LELF+LRLAYR++  + KLIFC+G+VL + QC R FG D
Sbjct: 89  KIPGFIELSPGDQDLLLESAFLELFILRLAYRSKPGEGKLIFCSGLVLHRLQCARGFG-D 147

Query: 305 WLNAILEFCQSLHLMEIDISAFACLCALTLI 335
           W++ IL F +SLH + +D+ AFACL AL LI
Sbjct: 148 WIDNILAFSRSLHSLGVDVPAFACLSALVLI 178

>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 =  127 bits (320), Expect = 3e-35
 Identities = 35/145 (24%), Positives = 61/145 (42%)

Query: 191 LCKEDQELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFS 250
           + K  QE       L  +    +       +     +F  L T  +  I  FA ++PGF+
Sbjct: 12  VSKAHQETFPSLCQLGKYTTNSSADHRVQLDLGLWDKFSELATKCIIKIVEFAKRLPGFT 71

Query: 251 DLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAIL 310
            L   DQ  L ++A L++ +LR+  R   E   + F +G+ L + Q   +      + + 
Sbjct: 72  GLSIADQITLLKAACLDILMLRICTRYTPEQDTMTFSDGLTLNRTQMHNAGFGPLTDLVF 131

Query: 311 EFCQSLHLMEIDISAFACLCALTLI 335
            F   L  +E+D +    L A+ LI
Sbjct: 132 AFAGQLLPLEMDDTETGLLSAICLI 156

>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 = 66.2 bits (162), Expect = 8e-13
 Identities = 16/75 (21%), Positives = 29/75 (38%)

Query: 134 ESPPSPPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCK 193
                P +  +       +       +     +F  L T  +  I  FA ++PGF+ L  
Sbjct: 16  HQETFPSLCQLGKYTTNSSADHRVQLDLGLWDKFSELATKCIIKIVEFAKRLPGFTGLSI 75

Query: 194 EDQELLFQSASLELF 208
            DQ  L ++A L++ 
Sbjct: 76  ADQITLLKAACLDIL 90

>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 =  128 bits (323), Expect = 3e-35
 Identities = 32/245 (13%), Positives = 72/245 (29%), Gaps = 56/245 (22%)

Query: 92  RNRCQFCRFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVSLITALYREP 151
            +        +       +E V+ +  +G+         +   +   P   ++ A     
Sbjct: 7   HHHHSSGLVPR---GSHKREAVQEERQRGKDRNENEVESTSSANEDMPVERILEAELAVE 63

Query: 152 NPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFYRE 211
              E                                                     Y E
Sbjct: 64  PKTET----------------------------------------------------YVE 71

Query: 212 PNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVL 271
            N    P +  + +          +  +  +A +IP FS+L  +DQ +L ++   EL + 
Sbjct: 72  ANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIA 131

Query: 272 RLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAIL-EFCQSLHLMEIDISAFACLC 330
             ++R+ A    ++   G+ + +     +      + +L E    +  M++D +   CL 
Sbjct: 132 SFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLR 191

Query: 331 ALTLI 335
           A+ L 
Sbjct: 192 AIVLF 196

>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 =  125 bits (317), Expect = 4e-35
 Identities = 30/122 (24%), Positives = 59/122 (48%)

Query: 214 PLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRL 273
            ++P  +  E  ++F    T +V  +  FA +IPGF DL + DQ  L ++ + E+ ++R 
Sbjct: 11  YVDPHKSGHEIWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRF 70

Query: 274 AYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALT 333
           A    A++  + F +G              D LN++ EF + L+ +++     +   A+ 
Sbjct: 71  ASLFDAKERTVTFLSGKKYSVDDLHSMGAGDLLNSMFEFSEKLNALQLSDEEMSLFTAVV 130

Query: 334 LI 335
           L+
Sbjct: 131 LV 132

>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 = 65.5 bits (160), Expect = 7e-13
 Identities = 17/56 (30%), Positives = 30/56 (53%)

Query: 153 PLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELF 208
            ++P  +  E  ++F    T +V  +  FA +IPGF DL + DQ  L ++ + E+ 
Sbjct: 11  YVDPHKSGHEIWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVL 66

>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 =  125 bits (317), Expect = 2e-34
 Identities = 30/131 (22%), Positives = 60/131 (45%)

Query: 205 LELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSA 264
           L+   +     E         +Q   +   +V +I  FA  +PGF+ + + DQ  L ++ 
Sbjct: 50  LKRVTQTWQSDEDDEDSDMPFRQITEMTILTVQLIVEFAKGLPGFAKISQSDQITLLKAC 109

Query: 265 SLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDIS 324
           S E+ +LR+A R  A    ++F N     +   +++     +  +L FC+ ++ M +D  
Sbjct: 110 SSEVMMLRVARRYDAATDSVLFANNQAYTRDNYRKAGMAYVIEDLLHFCRCMYSMMMDNV 169

Query: 325 AFACLCALTLI 335
            +A L A+ + 
Sbjct: 170 HYALLTAIVIF 180

>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 = 72.1 bits (177), Expect = 1e-14
 Identities = 19/104 (18%), Positives = 35/104 (33%), Gaps = 15/104 (14%)

Query: 120 GRRGRLPSKPKSPQESPPSPPVSLITALYRE---------------PNPLEPPIAEPEKI 164
            + GR P K   P  +     ++ +                         E         
Sbjct: 11  QQMGRDPLKNVPPLTANQKSLIARLVWYQEGYEQPSEEDLKRVTQTWQSDEDDEDSDMPF 70

Query: 165 QQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELF 208
           +Q   +   +V +I  FA  +PGF+ + + DQ  L ++ S E+ 
Sbjct: 71  RQITEMTILTVQLIVEFAKGLPGFAKISQSDQITLLKACSSEVM 114

>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 =  125 bits (316), Expect = 7e-34
 Identities = 40/246 (16%), Positives = 72/246 (29%), Gaps = 57/246 (23%)

Query: 92  RNRCQFCRFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVSLITALYREP 151
            +   F RF+  ++ G V           R   L S   +  +S    P S+ T L    
Sbjct: 26  DSYSDFVRFRPPVREGPVTRSAS------RAASLHSLSDASSDSFNHSPESVDTKLNFSN 79

Query: 152 NPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFYRE 211
             +    +                                                    
Sbjct: 80  LLMMYQDSGSP------------------------------------------------- 90

Query: 212 PNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVL 271
            +  E   +    +     L++ S+  +  FA  IPGF DL  EDQ  L +S+++E+ +L
Sbjct: 91  DSSEEDQQSRLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIML 150

Query: 272 RLAYRTRAEDTKLIFCNGVV--LEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACL 329
           R       ED                  +     + L  +++F   L  +++       L
Sbjct: 151 RSNQSFSLEDMSWSCGGPDFKYCINDVTKAGHTLELLEPLVKFQVGLKKLKLHEEEHVLL 210

Query: 330 CALTLI 335
            A+ L+
Sbjct: 211 MAICLL 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 =  123 bits (309), Expect = 3e-33
 Identities = 34/148 (22%), Positives = 63/148 (42%), Gaps = 1/148 (0%)

Query: 188 FSDLCKEDQELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIP 247
            +      Q   F    +       +  +    + E   +F  ++T ++  +  FA K+P
Sbjct: 36  NAQGSHWKQRRKFLPDDI-GQSPIVSMPDGDKVDLEAFSEFTKIITPAITRVVDFAKKLP 94

Query: 248 GFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLN 307
            FS+L  EDQ +L +   +E+  LR A R   E   L     + ++++Q +        +
Sbjct: 95  MFSELPXEDQIILLKGCCMEIMSLRAAVRYDPESDTLTLSGEMAVKREQLKNGGLGVVSD 154

Query: 308 AILEFCQSLHLMEIDISAFACLCALTLI 335
           AI E  +SL    +D +  A L A+ L+
Sbjct: 155 AIFELGKSLSAFNLDDTEVALLQAVLLM 182

>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 = 59.5 bits (144), Expect = 2e-10
 Identities = 15/80 (18%), Positives = 32/80 (40%)

Query: 129 PKSPQESPPSPPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGF 188
            +          +          +  +    + E   +F  ++T ++  +  FA K+P F
Sbjct: 37  AQGSHWKQRRKFLPDDIGQSPIVSMPDGDKVDLEAFSEFTKIITPAITRVVDFAKKLPMF 96

Query: 189 SDLCKEDQELLFQSASLELF 208
           S+L  EDQ +L +   +E+ 
Sbjct: 97  SELPXEDQIILLKGCCMEIM 116

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

 Score =  122 bits (307), Expect = 3e-33
 Identities = 36/185 (19%), Positives = 64/185 (34%), Gaps = 14/185 (7%)

Query: 152 NPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFYRE 211
           +    P    E             DVI   A           +       + +       
Sbjct: 6   HHHHGPEPTVE-------------DVISQVARAHREIFTYAHDKLGSSPGNFNANHASGS 52

Query: 212 PNP-LEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFV 270
           P P         E  + F    T +V  +  FA  IPGF DL + DQ  L ++ + E+ +
Sbjct: 53  PYPHGRSGRTVQEIWEDFSMSFTPAVREVVEFAKHIPGFRDLSQHDQVTLLKAGTFEVLM 112

Query: 271 LRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLC 330
           +R A     +D  ++F +      Q+       D L+A+ +F + L+ + +         
Sbjct: 113 VRFASLFNVKDQTVMFLSRTTYSLQELGAMGMGDLLSAMFDFSEKLNSLALTEEELGLFT 172

Query: 331 ALTLI 335
           A+ L+
Sbjct: 173 AVVLV 177

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

 Score = 64.1 bits (156), Expect = 5e-12
 Identities = 20/81 (24%), Positives = 30/81 (37%), Gaps = 1/81 (1%)

Query: 129 PKSPQESPPSPPVSLITALYREPNP-LEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPG 187
             +  +   SP           P P         E  + F    T +V  +  FA  IPG
Sbjct: 31  TYAHDKLGSSPGNFNANHASGSPYPHGRSGRTVQEIWEDFSMSFTPAVREVVEFAKHIPG 90

Query: 188 FSDLCKEDQELLFQSASLELF 208
           F DL + DQ  L ++ + E+ 
Sbjct: 91  FRDLSQHDQVTLLKAGTFEVL 111

>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 =  121 bits (305), Expect = 1e-32
 Identities = 34/137 (24%), Positives = 60/137 (43%), Gaps = 1/137 (0%)

Query: 200 FQSASLELFYREPNPLEPPI-AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQE 258
           F +      Y   N  E  +  + +   +F  L T  +     FA ++PGF+ L   DQ 
Sbjct: 44  FPALCQLGKYTTNNSSEQRVSLDIDLWDKFSELSTKCIIKTVEFAKQLPGFTTLTIADQI 103

Query: 259 LLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHL 318
            L ++A L++ +LR+  R   E   + F +G+ L + Q   +      + +  F   L  
Sbjct: 104 TLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMHNAGFGPLTDLVFAFANQLLP 163

Query: 319 MEIDISAFACLCALTLI 335
           +E+D +    L A+ LI
Sbjct: 164 LEMDDAETGLLSAICLI 180

>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 = 65.1 bits (159), Expect = 2e-12
 Identities = 20/102 (19%), Positives = 36/102 (35%), Gaps = 19/102 (18%)

Query: 126 PSKPKSPQESPPSPPV--SLITALYR-----------------EPNPLEPPIAEPEKIQQ 166
              P+   ES    P    LI  + +                   +  +    + +   +
Sbjct: 13  GLVPRGSHESYTLTPEVGELIEKVRKAHQETFPALCQLGKYTTNNSSEQRVSLDIDLWDK 72

Query: 167 FYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELF 208
           F  L T  +     FA ++PGF+ L   DQ  L ++A L++ 
Sbjct: 73  FSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDIL 114

>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 =  120 bits (303), Expect = 3e-32
 Identities = 38/247 (15%), Positives = 82/247 (33%), Gaps = 48/247 (19%)

Query: 90  RRRNRCQFCRFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVSLITALYR 149
           + +++ Q     +               L+       +       SPP     L      
Sbjct: 2   KHQHQHQHQHQHQQ-------------PLQEEEQAHATSLPPRASSPPQILPQL------ 42

Query: 150 EPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFY 209
                        +       L  +             FSD  +               +
Sbjct: 43  -----------SPEQLGMIEKLVAA-----QQQCNRRSFSDRLRVTP------------W 74

Query: 210 REPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELF 269
                     A  ++   F  L   SV  I  FA ++PGF  L +EDQ  L +++++E+ 
Sbjct: 75  PMAPDPHSREARQQRFAHFTELAIVSVQEIVDFAKQLPGFLQLSREDQIALLKTSAIEVM 134

Query: 270 VLRLAYRTRAEDTKLIFCNGVVLEKQQCQRS-FGDDWLNAILEFCQSLHLMEIDISAFAC 328
           +L  + R       + F       ++   ++    +++N I EF ++++ ++++ + FA 
Sbjct: 135 LLETSRRYNPGSESITFLKDFSYNREDFAKAGLQVEFINPIFEFSRAMNELQLNDAEFAL 194

Query: 329 LCALTLI 335
           L A+++ 
Sbjct: 195 LIAISIF 201

>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 =  118 bits (299), Expect = 4e-32
 Identities = 35/152 (23%), Positives = 64/152 (42%), Gaps = 8/152 (5%)

Query: 189 SDLCKEDQELLFQSASLELFYREPNP-----LEPPIAEPEKIQQFYSLLTTSVDVIRHFA 243
            +L  + Q LL          R P       L+   +  E       + T  V V+  F 
Sbjct: 3   GELTPDQQTLLHFIMDSYNKQRMPQEITNKILKEEFSAEENFLILTEMATNHVQVLVEFT 62

Query: 244 DKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD 303
            K+PGF  L  EDQ  L + +++E   LR A      + KL   +  +LE++       D
Sbjct: 63  KKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEI---FNKKLPSGHSDLLEERIRNSGISD 119

Query: 304 DWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
           +++  +  F +S+  +++    +A L A+ ++
Sbjct: 120 EYITPMFSFYKSIGELKMTQEEYALLTAIVIL 151

>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 = 60.4 bits (147), Expect = 7e-11
 Identities = 16/56 (28%), Positives = 25/56 (44%)

Query: 153 PLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELF 208
            L+   +  E       + T  V V+  F  K+PGF  L  EDQ  L + +++E  
Sbjct: 33  ILKEEFSAEENFLILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAM 88

>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 =  117 bits (294), Expect = 3e-31
 Identities = 38/135 (28%), Positives = 68/135 (50%), Gaps = 1/135 (0%)

Query: 201 QSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELL 260
             A  E  Y  P+P  P  ++ + +     L    + VI  +A  IPGFS L   DQ  L
Sbjct: 27  LVAEPEKIYAMPDPTVPD-SDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSL 85

Query: 261 FQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLME 320
            QSA +E+ +L + YR+ + + +L++ +  ++++ Q + +   D  NAIL+  +    M+
Sbjct: 86  LQSAWMEILILGVVYRSLSFEDELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMK 145

Query: 321 IDISAFACLCALTLI 335
           ++   F  L A+ L 
Sbjct: 146 LEKEEFVTLKAIALA 160

>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 = 65.1 bits (159), Expect = 2e-12
 Identities = 25/92 (27%), Positives = 39/92 (42%), Gaps = 9/92 (9%)

Query: 126 PSKPKSPQESPP--SPPVSLITALYR-EPNPLEP------PIAEPEKIQQFYSLLTTSVD 176
             +  +PQ   P   P   +++ L   EP  +        P ++ + +     L    + 
Sbjct: 3   SPEFLNPQLVQPAKKPYNKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELV 62

Query: 177 VIRHFADKIPGFSDLCKEDQELLFQSASLELF 208
           VI  +A  IPGFS L   DQ  L QSA +E+ 
Sbjct: 63  VIIGWAKHIPGFSTLSLADQMSLLQSAWMEIL 94

>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 =  114 bits (288), Expect = 2e-30
 Identities = 26/142 (18%), Positives = 54/142 (38%), Gaps = 2/142 (1%)

Query: 194 EDQELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLC 253
            +Q + F+  +    + +P P   P      +  F  + T  V  +  F   +P F  L 
Sbjct: 27  FEQFVQFRPPAHLFIHHQPLPTLAP--VLPLVTHFADINTFMVLQVIKFTKDLPVFRSLP 84

Query: 254 KEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFC 313
            EDQ  L + A++E+  + L      +    +        +   +  F  ++L  +  F 
Sbjct: 85  IEDQISLLKGAAVEICHIVLNTTFCLQTQNFLCGPLRYTIEDGARVGFQVEFLELLFHFH 144

Query: 314 QSLHLMEIDISAFACLCALTLI 335
            +L  +++    +  L A+ L 
Sbjct: 145 GTLRKLQLQEPEYVLLAAMALF 166

>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 = 59.7 bits (145), Expect = 1e-10
 Identities = 20/80 (25%), Positives = 31/80 (38%), Gaps = 4/80 (5%)

Query: 129 PKSPQESPPSPPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGF 188
               Q     PP  L   ++ +P P   P      +  F  + T  V  +  F   +P F
Sbjct: 25  TMFEQFVQFRPPAHLF--IHHQPLPTLAP--VLPLVTHFADINTFMVLQVIKFTKDLPVF 80

Query: 189 SDLCKEDQELLFQSASLELF 208
             L  EDQ  L + A++E+ 
Sbjct: 81  RSLPIEDQISLLKGAAVEIC 100

>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 =  114 bits (286), Expect = 4e-30
 Identities = 33/136 (24%), Positives = 64/136 (47%), Gaps = 2/136 (1%)

Query: 201 QSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELL 260
             A   + Y E +P   P +E   +    +L    +  + ++A ++PGF DL   DQ  L
Sbjct: 14  LDAEPPILYSEYDP-TRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHL 72

Query: 261 FQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFG-DDWLNAILEFCQSLHLM 319
            + A LE+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M
Sbjct: 73  LECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMM 132

Query: 320 EIDISAFACLCALTLI 335
            +    F CL ++ L+
Sbjct: 133 NLQGEEFVCLKSIILL 148

>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 =  112 bits (282), Expect = 1e-29
 Identities = 28/118 (23%), Positives = 54/118 (45%), Gaps = 1/118 (0%)

Query: 218 PIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRT 277
           P  E   +     L    +  +  +A KIPGF +L   DQ  L +S  +E+ ++ L +R+
Sbjct: 28  PFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRS 87

Query: 278 RAEDTKLIFCNGVVLEKQQCQRSFG-DDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
                KLIF   +VL++ + +   G  +  + +L        +++    + C+ A+ L
Sbjct: 88  IDHPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMIL 145

>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 =  112 bits (282), Expect = 1e-29
 Identities = 33/127 (25%), Positives = 57/127 (44%), Gaps = 1/127 (0%)

Query: 209 YREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL 268
           Y  P+P  P       +     L    + V   +A  IPGFS L   DQ  + QS  +E+
Sbjct: 35  YAMPDPAGPD-GHLPAVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEV 93

Query: 269 FVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFAC 328
            VL +A R+     +L F   +VL+++  + +   +   A+L+  + L  + ++   +  
Sbjct: 94  LVLGVAQRSLPLQDELAFAEDLVLDEEGARAAGLGELGAALLQLVRRLQALRLEREEYVL 153

Query: 329 LCALTLI 335
           L AL L 
Sbjct: 154 LKALALA 160

>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 = 61.7 bits (150), Expect = 3e-11
 Identities = 21/84 (25%), Positives = 31/84 (36%), Gaps = 7/84 (8%)

Query: 132 PQESPPSPPVSLITALYR-EPNPLEP------PIAEPEKIQQFYSLLTTSVDVIRHFADK 184
            +     P  +L++ L   EP  L        P      +     L    + V   +A  
Sbjct: 11  LEVLFQGPVNALVSHLLVVEPEKLYAMPDPAGPDGHLPAVATLCDLFDREIVVTISWAKS 70

Query: 185 IPGFSDLCKEDQELLFQSASLELF 208
           IPGFS L   DQ  + QS  +E+ 
Sbjct: 71  IPGFSSLSLSDQMSVLQSVWMEVL 94

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

 Score =  112 bits (282), Expect = 5e-29
 Identities = 33/136 (24%), Positives = 64/136 (47%), Gaps = 2/136 (1%)

Query: 201 QSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELL 260
             A   + Y E +P   P +E   +    +L    +  + ++A ++PGF DL   DQ  L
Sbjct: 23  LDAEPPILYSEYDP-TRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHL 81

Query: 261 FQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFG-DDWLNAILEFCQSLHLM 319
            + A LE+ ++ L +R+     KL+F   ++L++ Q +   G  +  + +L       +M
Sbjct: 82  LECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMM 141

Query: 320 EIDISAFACLCALTLI 335
            +    F CL ++ L+
Sbjct: 142 NLQGEEFVCLKSIILL 157

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

 Score = 63.7 bits (155), Expect = 9e-12
 Identities = 30/145 (20%), Positives = 55/145 (37%), Gaps = 26/145 (17%)

Query: 127 SKPKSPQESPPSPPVSLITALYR-EPNPLEP------PIAEPEKIQQFYSLLTTSVDVIR 179
           SK  S   S  +    +++AL   EP  L        P +E   +    +L    +  + 
Sbjct: 4   SKKNSLALSLTAD--QMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMI 61

Query: 180 HFADKIPGFSDLCKEDQELLFQSASLELF-----YREPNPLEPPIAEPEKIQQFYSLLTT 234
           ++A ++PGF DL   DQ  L + A LE+      +R        +  P K+     L   
Sbjct: 62  NWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWR-------SMEHPGKL-----LFAP 109

Query: 235 SVDVIRHFADKIPGFSDLCKEDQEL 259
           ++ + R+    + G  ++       
Sbjct: 110 NLLLDRNQGKCVEGMVEIFDMLLAT 134

>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 =  112 bits (282), Expect = 5e-29
 Identities = 32/147 (21%), Positives = 52/147 (35%), Gaps = 1/147 (0%)

Query: 189 SDLCKEDQELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPG 248
            DLC     L  +     ++  +P            +     + T     I  FA  I  
Sbjct: 86  KDLCSLKVSLQLRGEDGSVWNYKPPADSGGKEIFSLLPHMADMSTYMFKGIISFAKVISY 145

Query: 249 FSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNA 308
           F DL  EDQ  L + A+ EL  LR      A +T    C  +    +     F    L  
Sbjct: 146 FRDLPIEDQISLLKGAAFELCQLRFNTVFNA-ETGTWECGRLSYCLEDTAGGFQQLLLEP 204

Query: 309 ILEFCQSLHLMEIDISAFACLCALTLI 335
           +L+F   L  +++    +  + A++L 
Sbjct: 205 MLKFHYMLKKLQLHEEEYVLMQAISLF 231

>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 = 64.9 bits (158), Expect = 5e-12
 Identities = 23/117 (19%), Positives = 34/117 (29%), Gaps = 8/117 (6%)

Query: 92  RNRCQFCRFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVSLITALYREP 151
                 C   + LQ    +E  +   ++     L    +   E             Y+ P
Sbjct: 58  GVLSSGCELPESLQAPSREEAAKWSQVRKDLCSLKVSLQLRGEDGSVW-------NYKPP 110

Query: 152 NPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELF 208
                       +     + T     I  FA  I  F DL  EDQ  L + A+ EL 
Sbjct: 111 ADSGGKEIF-SLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELC 166

>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 =  110 bits (277), Expect = 8e-29
 Identities = 24/127 (18%), Positives = 52/127 (40%), Gaps = 2/127 (1%)

Query: 211 EPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFV 270
               +   +++   +     L++ S+  +  FA  IPGF DL  EDQ +L +S+++E+ +
Sbjct: 44  GGGSVTLELSQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIM 103

Query: 271 LRLAYRTRAEDTKLIFCNGVVLEKQQCQRS--FGDDWLNAILEFCQSLHLMEIDISAFAC 328
           LR       +D      N     +           + +  +++F   L  + +       
Sbjct: 104 LRSNESFTMDDMSWTCGNQDYKYRVSDVTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVL 163

Query: 329 LCALTLI 335
           L A+ ++
Sbjct: 164 LMAICIV 170

>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 = 61.8 bits (150), Expect = 3e-11
 Identities = 20/83 (24%), Positives = 36/83 (43%), Gaps = 7/83 (8%)

Query: 126 PSKPKSPQESPPSPPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKI 185
           P+     Q  PP                +   +++   +     L++ S+  +  FA  I
Sbjct: 27  PTYSDFCQFRPPVRVND-------GGGSVTLELSQLSMLPHLADLVSYSIQKVIGFAKMI 79

Query: 186 PGFSDLCKEDQELLFQSASLELF 208
           PGF DL  EDQ +L +S+++E+ 
Sbjct: 80  PGFRDLTSEDQIVLLKSSAIEVI 102

>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 =  110 bits (276), Expect = 2e-28
 Identities = 29/136 (21%), Positives = 56/136 (41%), Gaps = 1/136 (0%)

Query: 200 FQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQEL 259
            Q  + + F +E              Q     +T ++  +  FA +I GF +LC+ DQ +
Sbjct: 42  LQQITWQTFLQEEIENYQNKQREVMWQLCAIKITEAIQYVVEFAKRIDGFMELCQNDQIV 101

Query: 260 LFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLM 319
           L ++ SLE+  +R+     +++  + F                 D+++ + EF +SL  M
Sbjct: 102 LLKAGSLEVVFIRMCRAFDSQNNTVYFDGKYASPDVFKSLGCE-DFISFVFEFGKSLCSM 160

Query: 320 EIDISAFACLCALTLI 335
            +     A   A  L+
Sbjct: 161 HLTEDEIALFSAFVLM 176

>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 = 58.7 bits (142), Expect = 3e-10
 Identities = 16/68 (23%), Positives = 32/68 (47%), Gaps = 1/68 (1%)

Query: 142 SLITALYREPNPLEPPIAEPEKI-QQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLF 200
            +    + +         + E + Q     +T ++  +  FA +I GF +LC+ DQ +L 
Sbjct: 44  QITWQTFLQEEIENYQNKQREVMWQLCAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLL 103

Query: 201 QSASLELF 208
           ++ SLE+ 
Sbjct: 104 KAGSLEVV 111

>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 =  109 bits (274), Expect = 2e-28
 Identities = 30/136 (22%), Positives = 60/136 (44%), Gaps = 1/136 (0%)

Query: 200 FQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQEL 259
                  +F RE        +  E  ++    LT ++  +  FA ++ GF +LC+ DQ +
Sbjct: 33  LLRQRSNIFSREEVTGYQRKSMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIV 92

Query: 260 LFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLM 319
           L ++ ++E+ ++R+  R    D + +F  G     +  +     + +++I +F  SL  +
Sbjct: 93  LLKAGAMEVVLVRMC-RAYNADNRTVFFEGKYGGMELFRALGCSELISSIFDFSHSLSAL 151

Query: 320 EIDISAFACLCALTLI 335
                  A   AL LI
Sbjct: 152 HFSEDEIALYTALVLI 167

>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 = 58.4 bits (141), Expect = 3e-10
 Identities = 15/60 (25%), Positives = 31/60 (51%)

Query: 149 REPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELF 208
           RE        +  E  ++    LT ++  +  FA ++ GF +LC+ DQ +L ++ ++E+ 
Sbjct: 43  REEVTGYQRKSMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVV 102

>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 =  109 bits (273), Expect = 2e-28
 Identities = 27/125 (21%), Positives = 52/125 (41%), Gaps = 1/125 (0%)

Query: 211 EPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFV 270
           E        +     QQ    +T ++  +  FA +I GF +LC+ DQ LL +S  LE+ +
Sbjct: 38  EEIKAYQSKSREALWQQCAIQITHAIQYVVEFAKRITGFMELCQNDQILLLKSGCLEVVL 97

Query: 271 LRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLC 330
           +R+       +  ++F       +         D +N   +F ++L  +++     A   
Sbjct: 98  VRMCRAFNPLNNTVLFEGKYGGMQMFKALGSD-DLVNEAFDFAKNLCSLQLTEEEIALFS 156

Query: 331 ALTLI 335
           +  LI
Sbjct: 157 SAVLI 161

>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 = 58.7 bits (142), Expect = 3e-10
 Identities = 18/59 (30%), Positives = 28/59 (47%)

Query: 150 EPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELF 208
           E        +     QQ    +T ++  +  FA +I GF +LC+ DQ LL +S  LE+ 
Sbjct: 38  EEIKAYQSKSREALWQQCAIQITHAIQYVVEFAKRITGFMELCQNDQILLLKSGCLEVV 96

>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 =  110 bits (276), Expect = 2e-28
 Identities = 22/127 (17%), Positives = 51/127 (40%), Gaps = 2/127 (1%)

Query: 211 EPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFV 270
               +   ++    +     L++ S+  +  FA  IPGF DL  +DQ +L +S+++E+ +
Sbjct: 47  STGSVTLDLSPLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIM 106

Query: 271 LRLAYRTRAEDTKLIFCNGVVL--EKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFAC 328
           LR       +D      +           +     + +  +++F   L  + +       
Sbjct: 107 LRSNQSFTMDDMSWDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVL 166

Query: 329 LCALTLI 335
           L A+ ++
Sbjct: 167 LMAICIV 173

>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 = 61.8 bits (150), Expect = 5e-11
 Identities = 20/83 (24%), Positives = 37/83 (44%), Gaps = 7/83 (8%)

Query: 126 PSKPKSPQESPPSPPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKI 185
           P+        PP        ++  + +PL         +     L++ S+  +  FA  I
Sbjct: 30  PTYADFRDFRPPVRMDGSTGSVTLDLSPLSM-------LPHLADLVSYSIQKVIGFAKMI 82

Query: 186 PGFSDLCKEDQELLFQSASLELF 208
           PGF DL  +DQ +L +S+++E+ 
Sbjct: 83  PGFRDLTSDDQIVLLKSSAIEVI 105

>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 =  109 bits (274), Expect = 3e-28
 Identities = 28/142 (19%), Positives = 51/142 (35%), Gaps = 3/142 (2%)

Query: 196 QELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKE 255
             L+     ++  +  P   +         Q        +V  I  +A  IPGF +L   
Sbjct: 46  NSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLN 105

Query: 256 DQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFG--DDWLNAILEFC 313
           DQ  L +    E+    LA     +D  LI      + ++  +       D++    EF 
Sbjct: 106 DQVTLLKYGVHEIIYTMLASLMN-KDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFA 164

Query: 314 QSLHLMEIDISAFACLCALTLI 335
              + +E+D S  A   A+ ++
Sbjct: 165 VKFNALELDDSDLAIFIAVIIL 186

>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 = 65.2 bits (159), Expect = 3e-12
 Identities = 23/116 (19%), Positives = 40/116 (34%), Gaps = 8/116 (6%)

Query: 101 QKCLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQESP------PSPPVSLITALYREPNPL 154
            + L   +    +++  L   + R     K+  +SP       S  +      ++   PL
Sbjct: 4   LRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPL 63

Query: 155 EPPIAEPEK--IQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELF 208
           +    E      Q        +V  I  +A  IPGF +L   DQ  L +    E+ 
Sbjct: 64  QEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEII 119

>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 =  107 bits (268), Expect = 2e-27
 Identities = 24/139 (17%), Positives = 48/139 (34%), Gaps = 5/139 (3%)

Query: 202 SASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLF 261
            A +  + ++         +         +   ++  I  +A     F +L  +DQ  L 
Sbjct: 35  QAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLL 94

Query: 262 QSASLELFVLRLAYR--TRAEDTKLIFCNGVVLEKQQCQRSFG---DDWLNAILEFCQSL 316
           Q+   EL +L   YR     ++  +    G  ++        G   ++ ++   E    L
Sbjct: 95  QNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQAGATLNNLMSHAQELVAKL 154

Query: 317 HLMEIDISAFACLCALTLI 335
             ++ D   F CL  L L 
Sbjct: 155 RSLQFDQREFVCLKFLVLF 173

>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 = 63.3 bits (154), Expect = 9e-12
 Identities = 27/167 (16%), Positives = 52/167 (31%), Gaps = 28/167 (16%)

Query: 121 RRGRLPSKPKSPQESPPSPPVSLITA-------------LYREPNPLEPPIAEPEKIQQF 167
           ++G        P+ S P   + L+                 ++         +       
Sbjct: 2   KKGHHHHHHLVPRGSIPHLILELLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLM 61

Query: 168 YSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELF-----YRE-PNPLEPPIAE 221
             +   ++  I  +A     F +L  +DQ  L Q+   EL      YR+  +  E  I  
Sbjct: 62  CKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSI-- 119

Query: 222 PEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL 268
                  + +    VD     +      ++L    QEL+ +  SL+ 
Sbjct: 120 -------FLVTGQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQF 159

>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 =  106 bits (267), Expect = 2e-27
 Identities = 27/140 (19%), Positives = 56/140 (40%), Gaps = 1/140 (0%)

Query: 197 ELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKED 256
           E           Y E N    P +  + +          +  +  +A +IP FS+L  +D
Sbjct: 15  EAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDD 74

Query: 257 QELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAIL-EFCQS 315
           Q +L ++   EL +   ++R+ A    ++   G+ + +     +      + +L E    
Sbjct: 75  QVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSK 134

Query: 316 LHLMEIDISAFACLCALTLI 335
           +  M++D +   CL A+ L 
Sbjct: 135 MRDMQMDKTELGCLRAIVLF 154

>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 = 56.7 bits (137), Expect = 2e-09
 Identities = 17/83 (20%), Positives = 32/83 (38%), Gaps = 9/83 (10%)

Query: 135 SPPSPPVSLITAL---------YREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKI 185
           +   P   ++ A          Y E N    P +  + +          +  +  +A +I
Sbjct: 5   NEDMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRI 64

Query: 186 PGFSDLCKEDQELLFQSASLELF 208
           P FS+L  +DQ +L ++   EL 
Sbjct: 65  PHFSELPLDDQVILLRAGWNELL 87

>1yye_A ER-beta, estrogen receptor beta; ER-beta, nuclear receptor, transcription factor, agonist; HET: 196; 2.03A {Homo sapiens} SCOP: a.123.1.1 PDB: 1yy4_A* Length = 268

 Score =  107 bits (268), Expect = 2e-27
 Identities = 28/119 (23%), Positives = 55/119 (46%), Gaps = 1/119 (0%)

Query: 218 PIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRT 277
           P  E   +     L    +  +  +A KIPGF +L   DQ  L +S  +E+ ++ L +R+
Sbjct: 26  PFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRS 85

Query: 278 RAEDTKLIFCNGVVLEKQQCQRSFG-DDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
                KLIF   +VL++ + +   G  +  + +L        +++    + C+ A+ L+
Sbjct: 86  IDHPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILL 144

>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 = 53.8 bits (129), Expect = 2e-08
 Identities = 19/77 (24%), Positives = 29/77 (37%), Gaps = 5/77 (6%)

Query: 136 PPSPPVSLITALYREPNPLEP----PIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDL 191
            P   V  +      P+ L      P  E   +     L    +  +  +A KIPGF +L
Sbjct: 2   SPEQLVLTLLE-AEPPHVLISRPSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVEL 60

Query: 192 CKEDQELLFQSASLELF 208
              DQ  L +S  +E+ 
Sbjct: 61  SLFDQVRLLESCWMEVL 77

>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 =  103 bits (259), Expect = 3e-26
 Identities = 23/137 (16%), Positives = 51/137 (37%), Gaps = 3/137 (2%)

Query: 201 QSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELL 260
           ++   E+ Y   +    P      +     L    +  +  +A  +PGF +L  EDQ  L
Sbjct: 19  ENIEPEIVYAGYDS-SKPDTAENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITL 77

Query: 261 FQSASLELFVLRLAYR--TRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHL 318
            Q + + L    L++R         L F   +V  +++  +S   +    + +       
Sbjct: 78  IQYSWMSLLSFALSWRSYKHTNSQFLYFAPDLVFNEEKMHQSAMYELCQGMHQISLQFVR 137

Query: 319 MEIDISAFACLCALTLI 335
           +++    +  +  L L+
Sbjct: 138 LQLTFEEYTIMKVLLLL 154

>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 = 56.1 bits (135), Expect = 3e-09
 Identities = 16/86 (18%), Positives = 30/86 (34%), Gaps = 6/86 (6%)

Query: 128 KPKSPQESPPSPPVSLITA-----LYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFA 182
              +   +    PV ++       +Y   +    P      +     L    +  +  +A
Sbjct: 2   SLSTISRALTPSPVMVLENIEPEIVYAGYDS-SKPDTAENLLSTLNRLAGKQMIQVVKWA 60

Query: 183 DKIPGFSDLCKEDQELLFQSASLELF 208
             +PGF +L  EDQ  L Q + + L 
Sbjct: 61  KVLPGFKNLPLEDQITLIQYSWMSLL 86

>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 =  103 bits (258), Expect = 5e-26
 Identities = 27/141 (19%), Positives = 53/141 (37%), Gaps = 8/141 (5%)

Query: 200 FQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIR---HFADKIPGFSDLCKED 256
              A   L  +          +  +++ F+    TSV+ +     FA  IPGF++L   D
Sbjct: 46  LCMAEKTLVAKLVAN--GIQNKEAEVRIFHCCQCTSVETVTELTEFAKAIPGFANLDLND 103

Query: 257 QELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQ--QCQRSFGDDWLNAILEFCQ 314
           Q  L +    E     L+     +   + + NG +  +     ++ F  D +    +F  
Sbjct: 104 QVTLLKYGVYEAIFAMLSSVMNKDGMLVAYGNGFITREFLKSLRKPFC-DIMEPKFDFAM 162

Query: 315 SLHLMEIDISAFACLCALTLI 335
             + +E+D S  +   A  + 
Sbjct: 163 KFNALELDDSDISLFVAAIIC 183

>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 = 63.4 bits (154), Expect = 9e-12
 Identities = 26/124 (20%), Positives = 44/124 (35%), Gaps = 11/124 (8%)

Query: 88  DKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVSLITAL 147
           D +   +  +  + K     M K   R   L G+    P       E+      +L    
Sbjct: 1   DLKSLAKRIYEAYLKNFN--MNKVKARVI-LSGKASNNPPFVIHDMETLCMAEKTL--VA 55

Query: 148 YREPNPLEPPIAEPEKIQQFYSLLTTSVDVIR---HFADKIPGFSDLCKEDQELLFQSAS 204
               N ++       +++ F+    TSV+ +     FA  IPGF++L   DQ  L +   
Sbjct: 56  KLVANGIQNK---EAEVRIFHCCQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGV 112

Query: 205 LELF 208
            E  
Sbjct: 113 YEAI 116

>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 =  102 bits (256), Expect = 1e-25
 Identities = 28/119 (23%), Positives = 55/119 (46%), Gaps = 1/119 (0%)

Query: 218 PIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRT 277
           P  E   +     L    +  +  +A KIPGF +L   DQ  L +S  +E+ ++ L +R+
Sbjct: 54  PFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRS 113

Query: 278 RAEDTKLIFCNGVVLEKQQCQRSFG-DDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
                KLIF   +VL++ + +   G  +  + +L        +++    + C+ A+ L+
Sbjct: 114 IDHPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILL 172

>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 = 64.2 bits (156), Expect = 5e-12
 Identities = 22/102 (21%), Positives = 35/102 (34%), Gaps = 7/102 (6%)

Query: 114 RTDSLKGRRGRLPSKPKSPQESPPS-PPVSLITALYR-EP-----NPLEPPIAEPEKIQQ 166
                    G +P      +    +  P  L+  L   EP     +    P  E   +  
Sbjct: 4   SHHHHHHSSGLVPRGSHMRELLLDALSPEQLVLTLLEAEPPHVLISRPSAPFTEASMMMS 63

Query: 167 FYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELF 208
              L    +  +  +A KIPGF +L   DQ  L +S  +E+ 
Sbjct: 64  LTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVL 105

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

 Score =  103 bits (257), Expect = 1e-25
 Identities = 23/137 (16%), Positives = 51/137 (37%), Gaps = 3/137 (2%)

Query: 201 QSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELL 260
           ++   E+ Y   +    P      +     L    +  +  +A  +PGF +L  EDQ  L
Sbjct: 53  ENIEPEIVYAGYDS-SKPDTAENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITL 111

Query: 261 FQSASLELFVLRLAYR--TRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHL 318
            Q + + L    L++R         L F   +V  +++  +S   +    + +       
Sbjct: 112 IQYSWMSLLSFALSWRSYKHTNSQFLYFAPDLVFNEEKMHQSAMYELCQGMHQISLQFVR 171

Query: 319 MEIDISAFACLCALTLI 335
           +++    +  +  L L+
Sbjct: 172 LQLTFEEYTIMKVLLLL 188

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

 Score = 58.4 bits (141), Expect = 5e-10
 Identities = 22/103 (21%), Positives = 36/103 (34%), Gaps = 15/103 (14%)

Query: 121 RRGRLPSKPKSPQESPPSPPVSLITALYREPNPL----EPPI-----------AEPEKIQ 165
            +G  P+K  S   +      ++  AL   P  +    EP I                + 
Sbjct: 18  FQGSAPAKEPSVNTALVPQLSTISRALTPSPVMVLENIEPEIVYAGYDSSKPDTAENLLS 77

Query: 166 QFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELF 208
               L    +  +  +A  +PGF +L  EDQ  L Q + + L 
Sbjct: 78  TLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQYSWMSLL 120

>3mnp_A Glucocorticoid receptor; protein-ligand complex, steroid nuclear receptor, mouse GR, hormone receptor; HET: DEX; 1.50A {Mus musculus} PDB: 3mno_A* 3mne_A* 1m2z_A* 3k22_A* 3cld_A* 3k23_A* 3e7c_A* 1nhz_A* 1p93_A* 3bqd_A* 3h52_A* 3gn8_A* 4e2j_A* Length = 261

 Score =  101 bits (253), Expect = 3e-25
 Identities = 27/128 (21%), Positives = 48/128 (37%), Gaps = 2/128 (1%)

Query: 210 REPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELF 269
                   P +    +     L    V     +A  IPGF +L  +DQ  L Q + + L 
Sbjct: 29  YAGYDSSVPDSAWRIMTTLNMLGGRQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLM 88

Query: 270 VLRLAYR--TRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFA 327
           V  L +R   +A    L F   +++ +Q+       D    +L     L  +++    + 
Sbjct: 89  VFALGWRSYRQASGNLLCFAPDLIINEQRMTLPCMYDQCKHMLFISTELQRLQVSYEEYL 148

Query: 328 CLCALTLI 335
           C+  L L+
Sbjct: 149 CMKTLLLL 156

>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 = 56.9 bits (137), Expect = 1e-09
 Identities = 20/81 (24%), Positives = 31/81 (38%), Gaps = 7/81 (8%)

Query: 135 SPPSPPVSLITALYR-EPNPL------EPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPG 187
           + P    +L++ L   EP  L        P +    +     L    V     +A  IPG
Sbjct: 8   ALPQLTPTLVSLLEVIEPEVLYAGYDSSVPDSAWRIMTTLNMLGGRQVIAAVKWAKAIPG 67

Query: 188 FSDLCKEDQELLFQSASLELF 208
           F +L  +DQ  L Q + + L 
Sbjct: 68  FRNLHLDDQMTLLQYSWMFLM 88

>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 = 97.9 bits (244), Expect = 3e-24
 Identities = 22/134 (16%), Positives = 48/134 (35%), Gaps = 1/134 (0%)

Query: 203 ASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQ 262
           A   +   +P            +          +  +  +A  +P F+ L   DQ  L +
Sbjct: 17  AEKRVECNDPLVALVVNENNTTVNNICQATHKQLFQLVQWAKLVPHFTSLPLTDQVQLLR 76

Query: 263 SASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAIL-EFCQSLHLMEI 321
           +   EL +   ++R+      ++   G+ + K         +  + +L E    +  M++
Sbjct: 77  AGWNELLIAAFSHRSMQAQDAIVLATGLTVNKSTAHAVGVGNIYDRVLSELVNKMKEMKM 136

Query: 322 DISAFACLCALTLI 335
           D +   CL A+ L 
Sbjct: 137 DKTELGCLRAIILY 150

>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 = 47.0 bits (112), Expect = 2e-06
 Identities = 12/79 (15%), Positives = 22/79 (27%), Gaps = 5/79 (6%)

Query: 135 SPPSPPVSLI-----TALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFS 189
                P+  I          +P            +          +  +  +A  +P F+
Sbjct: 5   LQADMPLERIIEAEKRVECNDPLVALVVNENNTTVNNICQATHKQLFQLVQWAKLVPHFT 64

Query: 190 DLCKEDQELLFQSASLELF 208
            L   DQ  L ++   EL 
Sbjct: 65  SLPLTDQVQLLRAGWNELL 83

>3tx7_B Nuclear receptor subfamily 5 group A member 2; LRH-1, beta-catenin, armadillo repeat, nuclear receptor LIGA binding domain, protein binding; HET: P6L; 2.76A {Homo sapiens} Length = 352

 Score =  100 bits (249), Expect = 4e-24
 Identities = 33/224 (14%), Positives = 67/224 (29%), Gaps = 25/224 (11%)

Query: 117 SLKGRRGRLPSKPKSPQESPPSPPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVD 176
           SL+G +       ++ +   P P  S   ++           + P  I      L     
Sbjct: 65  SLQGYQTYGHFPSRAIKSEYPDPYTSSPESIMGYSYMDSYQTSSPASIPHLILELLKC-- 122

Query: 177 VIRHFADKIPGFSDLCKEDQELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSV 236
                             + +     A +  + ++         +         +   ++
Sbjct: 123 ------------------EPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQTL 164

Query: 237 DVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYR--TRAEDTKLIFCNGVVLEK 294
             I  +A     F +L  +DQ  L Q+   EL +L   YR     ++  +    G  ++ 
Sbjct: 165 FSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDY 224

Query: 295 QQCQRSFG---DDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
                  G   ++ ++   E    L  ++ D   F CL  L L 
Sbjct: 225 SIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLF 268

>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 = 97.1 bits (242), Expect = 8e-24
 Identities = 30/129 (23%), Positives = 46/129 (35%), Gaps = 3/129 (2%)

Query: 209 YREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL 268
            R  +    P      I+    L    +     +A  IP F DL   DQ  L +    EL
Sbjct: 24  SRFGSQCMQP-NNIMGIENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSEL 82

Query: 269 FVLRLAYRT-RAEDTKLIFCNGVVLEKQQCQRSFGD-DWLNAILEFCQSLHLMEIDISAF 326
           FVL  A  +       L+   G+        R     D +    E  + L  + +D + +
Sbjct: 83  FVLNAAQCSMPLHVAPLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEY 142

Query: 327 ACLCALTLI 335
           +CL A+ L 
Sbjct: 143 SCLKAIVLF 151

>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 = 52.8 bits (127), Expect = 3e-08
 Identities = 21/83 (25%), Positives = 28/83 (33%), Gaps = 6/83 (7%)

Query: 131 SPQESPPSPPVSLITA-----LYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKI 185
           S   S  S  +SL+         R  +    P      I+    L    +     +A  I
Sbjct: 2   SNSHSYLSGYISLLLRAEPYPTSRFGSQCMQP-NNIMGIENICELAARMLFSAVEWARNI 60

Query: 186 PGFSDLCKEDQELLFQSASLELF 208
           P F DL   DQ  L +    ELF
Sbjct: 61  PFFPDLQITDQVALLRLTWSELF 83

>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 = 95.7 bits (238), Expect = 3e-23
 Identities = 26/137 (18%), Positives = 53/137 (38%), Gaps = 3/137 (2%)

Query: 201 QSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELL 260
            S   ++ Y   +  +P       +     L    +  +  ++  +PGF +L  +DQ  L
Sbjct: 20  MSIEPDVIYAGHDNTKPD-TSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITL 78

Query: 261 FQSASLELFVLRLAYR--TRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHL 318
            Q + + L V  L +R         L F   ++L +Q+ + S        + +  Q    
Sbjct: 79  IQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVK 138

Query: 319 MEIDISAFACLCALTLI 335
           +++    F C+  L L+
Sbjct: 139 LQVSQEEFLCMKVLLLL 155

>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 = 54.9 bits (132), Expect = 6e-09
 Identities = 19/85 (22%), Positives = 32/85 (37%), Gaps = 8/85 (9%)

Query: 131 SPQESPPSPPVSLITALYR-EPNPLEP------PIAEPEKIQQFYSLLTTSVDVIRHFAD 183
           SP +     P  LI  L   EP+ +        P      +     L    +  +  ++ 
Sbjct: 4   SPGQDIQLIP-PLINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSK 62

Query: 184 KIPGFSDLCKEDQELLFQSASLELF 208
            +PGF +L  +DQ  L Q + + L 
Sbjct: 63  SLPGFRNLHIDDQITLIQYSWMSLM 87

>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 = 94.5 bits (235), Expect = 6e-23
 Identities = 29/144 (20%), Positives = 47/144 (32%), Gaps = 5/144 (3%)

Query: 197 ELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKED 256
           E         +      P +    +P        +   +   I  +A +   F +L   D
Sbjct: 19  EPEEDQVRARIVGCLQEPAKSRSDQPAPFSLLCRMADQTFISIVDWARRCMVFKELEVAD 78

Query: 257 QELLFQSASLELFVLRLAYRTRAEDTK--LIFCNGVVLEKQQCQRSFG---DDWLNAILE 311
           Q  L Q++  EL VL   YR      +  ++   G  +E        G      +    E
Sbjct: 79  QMTLLQNSWSELLVLDHIYRQVQYGKEDSILLVTGQEVELSTVAVQAGSLLHSLVLRAQE 138

Query: 312 FCQSLHLMEIDISAFACLCALTLI 335
               LH +++D   F CL  L L 
Sbjct: 139 LVLQLHALQLDRQEFVCLKFLILF 162

>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 = 55.6 bits (134), Expect = 3e-09
 Identities = 13/72 (18%), Positives = 23/72 (31%)

Query: 137 PSPPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQ 196
           P         +     P +    +P        +   +   I  +A +   F +L   DQ
Sbjct: 20  PEEDQVRARIVGCLQEPAKSRSDQPAPFSLLCRMADQTFISIVDWARRCMVFKELEVADQ 79

Query: 197 ELLFQSASLELF 208
             L Q++  EL 
Sbjct: 80  MTLLQNSWSELL 91

>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 = 94.6 bits (235), Expect = 1e-22
 Identities = 24/132 (18%), Positives = 49/132 (37%), Gaps = 3/132 (2%)

Query: 206 ELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSAS 265
            +     +  +P  +    +     L    +  +  +A  +PGF +L  +DQ  + Q + 
Sbjct: 33  GVVCAGHDNNQPD-SFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSW 91

Query: 266 LELFVLRLAYRTRAEDTK--LIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDI 323
           + L V  + +R+        L F   +V  + +  +S        +    Q    ++I  
Sbjct: 92  MGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHKSRMYSQCVRMRHLSQEFGWLQITP 151

Query: 324 SAFACLCALTLI 335
             F C+ AL L 
Sbjct: 152 QEFLCMKALLLF 163

>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 = 51.8 bits (124), Expect = 8e-08
 Identities = 19/95 (20%), Positives = 32/95 (33%), Gaps = 6/95 (6%)

Query: 120 GRRGRLPSKPKSPQESPPSPPVSLITALYREPNPL------EPPIAEPEKIQQFYSLLTT 173
           G  G       S  E     P+ L      EP  +        P +    +     L   
Sbjct: 1   GSPGISGGGGGSHIEGYECQPIFLNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGER 60

Query: 174 SVDVIRHFADKIPGFSDLCKEDQELLFQSASLELF 208
            +  +  +A  +PGF +L  +DQ  + Q + + L 
Sbjct: 61  QLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLM 95

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

 Score = 91.7 bits (228), Expect = 7e-22
 Identities = 26/136 (19%), Positives = 52/136 (38%), Gaps = 2/136 (1%)

Query: 201 QSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELL 260
             A+L +     N  +PP  +   +     L    +  + ++A  +PG++DL   DQ  L
Sbjct: 15  NKAALPVLESHHNHGQPP-TKVHLLNSLVKLAERELVHLINWAKNVPGYTDLSLSDQVHL 73

Query: 261 FQSASLELFVLRLAYR-TRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLM 319
            +   +EL +L  A+R        L F   +VL++         +    +    + +   
Sbjct: 74  IECCWMELLLLNCAFRSIEHGGKSLAFAPDLVLDRSSWSTVEMTEIFEQVAAVSEQMMQN 133

Query: 320 EIDISAFACLCALTLI 335
            +       L A+ L+
Sbjct: 134 HLHKDELLLLQAMVLV 149

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

 Score = 48.2 bits (115), Expect = 9e-07
 Identities = 17/83 (20%), Positives = 32/83 (38%), Gaps = 6/83 (7%)

Query: 131 SPQESPPSPPVSLITA-----LYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKI 185
           S  +S     +  +       L    N  +PP  +   +     L    +  + ++A  +
Sbjct: 1   SNAKSQTVTILQALNKAALPVLESHHNHGQPP-TKVHLLNSLVKLAERELVHLINWAKNV 59

Query: 186 PGFSDLCKEDQELLFQSASLELF 208
           PG++DL   DQ  L +   +EL 
Sbjct: 60  PGYTDLSLSDQVHLIECCWMELL 82

>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 = 90.0 bits (223), Expect = 4e-21
 Identities = 33/150 (22%), Positives = 55/150 (36%), Gaps = 12/150 (8%)

Query: 194 EDQELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLC 253
           E +  L     +      P+P+   +      +    LL  S+    H+A  IP F  L 
Sbjct: 9   EVEGPLLSDTHVTFKLTMPSPMPEYLNVHYICESASRLLFLSM----HWARSIPAFQALG 64

Query: 254 KEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD--------DW 305
           ++    L ++   ELF L LA   +      I    V   +   Q             + 
Sbjct: 65  QDCNTSLVRACWNELFTLGLAQCAQVMSLSTILAAIVNHLQNSIQEDKLSGDRIKQVMEH 124

Query: 306 LNAILEFCQSLHLMEIDISAFACLCALTLI 335
           +  + EFC S+  ++ID   +A L A+ L 
Sbjct: 125 IWKLQEFCNSMAKLDIDGYEYAYLKAIVLF 154

>3p0u_A Nuclear receptor subfamily 2 group C member 2; ligand binding domain, orphan nuclear receptor, testicular R 4, signaling protein; 3.00A {Homo sapiens} Length = 249

 Score = 49.2 bits (117), Expect = 5e-07
 Identities = 26/150 (17%), Positives = 47/150 (31%), Gaps = 15/150 (10%)

Query: 124 RLPSKPKSPQESPPSPPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFAD 183
           R  S P    E P      +   L      +  P+ E   +       +  + +  H+A 
Sbjct: 1   RDQSTPIIEVEGPLLSDTHVTFKL-----TMPSPMPEYLNVHYICESASRLLFLSMHWAR 55

Query: 184 KIPGFSDLCKEDQELLFQSASLELF-----YREPNPLEPPIAEPEKIQQFYSLLTTSVDV 238
            IP F  L ++    L ++   ELF           +         +      L  S+  
Sbjct: 56  SIPAFQALGQDCNTSLVRACWNELFTLGLAQC-AQVMSLSTILAAIVN----HLQNSIQE 110

Query: 239 IRHFADKIPGFSDLCKEDQELLFQSASLEL 268
            +   D+I    +   + QE     A L++
Sbjct: 111 DKLSGDRIKQVMEHIWKLQEFCNSMAKLDI 140

>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 = 88.0 bits (218), Expect = 2e-20
 Identities = 16/147 (10%), Positives = 47/147 (31%), Gaps = 7/147 (4%)

Query: 196 QELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKE 255
             +      +     +       +   +      +++  ++      A ++P F+DL ++
Sbjct: 14  DLIQEAFKGMNDPMEQGRQATSFLKNEKSPADIMNIMDVTMRRFVKMAKRLPAFNDLSQD 73

Query: 256 DQELLFQSASLELFVLRLAYRTRAEDT-----KLIFCNGVVLEK-QQCQRSFGDDWLNAI 309
            +  L +   +E+  +R   R  +         L   + V +    Q       +     
Sbjct: 74  GKFALLKGGMIEMLTVRGVRRFDSSSGSWTTPTLGESSEVSINMFDQLNADVRSEQKMRF 133

Query: 310 LEFCQSLH-LMEIDISAFACLCALTLI 335
           L+F +  H  +  +    + +  + L 
Sbjct: 134 LQFFKIFHEDIRSNDLVISMIMLIVLF 160

>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 = 53.3 bits (128), Expect = 2e-08
 Identities = 7/61 (11%), Positives = 24/61 (39%)

Query: 148 YREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL 207
             +       +   +      +++  ++      A ++P F+DL ++ +  L +   +E+
Sbjct: 27  MEQGRQATSFLKNEKSPADIMNIMDVTMRRFVKMAKRLPAFNDLSQDGKFALLKGGMIEM 86

Query: 208 F 208
            
Sbjct: 87  L 87

>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 = 85.5 bits (212), Expect = 1e-19
 Identities = 21/121 (17%), Positives = 47/121 (38%), Gaps = 1/121 (0%)

Query: 216 EPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAY 275
           +    +   I      +   + V+  +A  IP F +L  +DQ  L ++ + E  +L    
Sbjct: 34  DIRAKKIASIADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATK 93

Query: 276 RTRAEDTKLIFCNGVVLEKQQCQRS-FGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
           R+      L+  N  ++ +   + +      +  + E       ++ID + +A L A+  
Sbjct: 94  RSMVFKDVLLLGNDYIVPRHCPELAEMSRVSIRILDELVLPFQELQIDDNEYAYLKAIIF 153

Query: 335 I 335
            
Sbjct: 154 F 154

>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 = 44.3 bits (105), Expect = 2e-05
 Identities = 15/87 (17%), Positives = 30/87 (34%), Gaps = 9/87 (10%)

Query: 131 SPQESPPSPPVSLITALYREPNPLEPPIAEPEK---------IQQFYSLLTTSVDVIRHF 181
           S  E    P ++ +         +  P++             I      +   + V+  +
Sbjct: 1   SSYELASLPSINALLQAEVLSRQITSPVSGINGDIRAKKIASIADVCESMKEQLLVLVEW 60

Query: 182 ADKIPGFSDLCKEDQELLFQSASLELF 208
           A  IP F +L  +DQ  L ++ + E  
Sbjct: 61  AKYIPAFCELPLDDQVALLRAHAGEHL 87

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

 Score = 78.5 bits (193), Expect = 8e-17
 Identities = 23/169 (13%), Positives = 52/169 (30%), Gaps = 29/169 (17%)

Query: 195 DQELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCK 254
             E      +L      P     P      +     ++   +  +  +A  +P F+ +  
Sbjct: 20  RAETQCGDRALTFLRVGPYSTVQP-DYKGAVSALCQVVNKQLFQMVEYARMMPHFAQVPL 78

Query: 255 EDQELLFQSASLELFVLRLAYR---------------------------TRAEDTKLIFC 287
           +DQ +L ++A +EL +  +A+                               +  +L   
Sbjct: 79  DDQVILLKAAWIELLIANVAWCSIVSLDDGGAGGGGGGLGHDGSFERRSPGLQPQQLFLN 138

Query: 288 NGVVLEKQQCQRSFGDDWLNAIL-EFCQSLHLMEIDISAFACLCALTLI 335
                 +    ++      + IL E    +  + +D    +CL A+ L 
Sbjct: 139 QSFSYHRNSAIKAGVSAIFDRILSELSVKMKRLNLDRRELSCLKAIILY 187

>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 = 76.2 bits (187), Expect = 3e-16
 Identities = 13/146 (8%), Positives = 42/146 (28%), Gaps = 6/146 (4%)

Query: 196 QELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKE 255
             +      +               +        +++  ++  +   A ++  F+++ + 
Sbjct: 14  DSIRDSFQCMNEPLDNDQQASTLAKKEHNPTDILNVMDITMRRLVKMAKRLGAFNEISEA 73

Query: 256 DQELLFQSASLELFVLRLAYR----TRAEDTKLIFCNGVVLEK-QQCQRSFGDDWLNAIL 310
            +  L +   +E+  +R             T +   + +      + +    D      L
Sbjct: 74  GKFSLLKGGMIEMLTIRGVTVFNADKGVWQTPVDGHSQISFNMFDKLRPDIKDTQKKGFL 133

Query: 311 EFCQSLH-LMEIDISAFACLCALTLI 335
            F   LH  +  +  A   +  + L 
Sbjct: 134 HFFNLLHSDVRKNDLAIDIIVLMVLF 159

>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 = 50.0 bits (119), Expect = 2e-07
 Identities = 12/129 (9%), Positives = 35/129 (27%), Gaps = 10/129 (7%)

Query: 142 SLITALYREPNPLEPP------IAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKED 195
           S+  +      PL+          +        +++  ++  +   A ++  F+++ +  
Sbjct: 15  SIRDSFQCMNEPLDNDQQASTLAKKEHNPTDILNVMDITMRRLVKMAKRLGAFNEISEAG 74

Query: 196 QELLFQSASLELFY----REPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSD 251
           +  L +   +E+         N  +     P       S              +  GF  
Sbjct: 75  KFSLLKGGMIEMLTIRGVTVFNADKGVWQTPVDGHSQISFNMFDKLRPDIKDTQKKGFLH 134

Query: 252 LCKEDQELL 260
                   +
Sbjct: 135 FFNLLHSDV 143

>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 = 73.3 bits (180), Expect = 3e-15
 Identities = 28/154 (18%), Positives = 55/154 (35%), Gaps = 20/154 (12%)

Query: 201 QSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELL 260
            S   +     P+   PP      +     +    +  +  +A  IP FS L  EDQ LL
Sbjct: 21  PSEEFQFLRVGPDSNVPP-KFRAPVSSLCQIGNKQIAALVVWARDIPHFSQLEMEDQILL 79

Query: 261 FQSASLELFVLRLAYR------------------TRAEDTKLIFCNGVVLEKQQCQRSFG 302
            + +  EL +  +A+R                  T +    +    G+ L +    ++  
Sbjct: 80  IKGSWNELLLFAIAWRSMEFLTEERDGVDGTGNRTTSPPQLMCLMPGMTLHRNSALQAGV 139

Query: 303 DDWLNAIL-EFCQSLHLMEIDISAFACLCALTLI 335
               + +L E    +  + +D + +  L A+ L+
Sbjct: 140 GQIFDRVLSELSLKMRTLRVDQAEYVALKAIILL 173

>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 = 60.2 bits (145), Expect = 1e-10
 Identities = 29/169 (17%), Positives = 44/169 (26%), Gaps = 35/169 (20%)

Query: 202 SASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVD---------VIRHFADKIPGFSDL 252
           SA       +  P  P       +Q+  +L    V              F   +P F  L
Sbjct: 17  SADQTPATPQEQPRAPWWDASPGVQRLITLKDPQVVCEAASAGLLKTLRFVKYLPCFQIL 76

Query: 253 CKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD--------- 303
             + Q +L +S    L +L LA      +   I       E    +R   +         
Sbjct: 77  PLDQQLVLVRSCWAPLLMLELAQDHLHFEMMEIPETNTTQEMLTTRRQETEGPEPAEPQA 136

Query: 304 -----------------DWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
                              + AI  F      + ID   +A L    L 
Sbjct: 137 TEQPQMVSAEAGHLLPAAAVQAIKSFFFKCWSLNIDTKEYAYLKGTVLF 185

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 52.2 bits (124), Expect = 2e-07
 Identities = 32/194 (16%), Positives = 63/194 (32%), Gaps = 57/194 (29%)

Query: 176 DVIRHFADKIPGFSDL-CKEDQELL---FQSASLELFYREPNPLEPP-------IAEPEK 224
           D++  F D      +  CK+ Q++         ++      + +          +++ E+
Sbjct: 20  DILSVFEDAF--VDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEE 77

Query: 225 I-QQF--------YSLLTTSVDVIRHFADKIP-GFSDLCKEDQELLFQSASL--ELFVLR 272
           + Q+F        Y  L + +        + P   + +  E ++ L+    +  +  V R
Sbjct: 78  MVQKFVEEVLRINYKFLMSPI----KTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSR 133

Query: 273 ----LAYRT---RAEDTKLIFCNGV------VL-------EKQQCQRSFGDDWLN----- 307
               L  R         K +  +GV       +        K QC+  F   WLN     
Sbjct: 134 LQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCN 193

Query: 308 ---AILEFCQSLHL 318
               +LE  Q L  
Sbjct: 194 SPETVLEMLQKLLY 207

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	335
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	100.0
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	100.0
1cit_A	89	NGFI-B, protein (orphan nuclear receptor NGFI-B);	100.0
2ebl_A	89	COUP transcription factor 1; DNA-binding, metal-bi	100.0
2han_A	93	Protein ultraspiracle; transcription regulation, t	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
1hcq_A	84	Protein (estrogen receptor); protein-DNA complex,	100.0
1lo1_A	98	Steroid hormone receptor ERR2; estrogen related re	100.0
1dsz_A	86	RAR-alpha, retinoic acid receptor alpha; RAR, nucl	100.0
1ynw_B	99	Retinoic acid receptor RXR-alpha, retinoid X recep	100.0
1a6y_A	94	Orphan nuclear receptor NR1D1; orphan receptor, DN	100.0
2a66_A	113	Orphan nuclear receptor NR5A2; protein-DNA complex	100.0
2han_B	119	Ecdysone receptor; transcription regulation, trans	100.0
1kb2_A	110	Vitamin D3 receptor; VDR, nuclear receptor, protei	100.0
4hn5_A	117	Glucocorticoid receptor; glucocorticoid receptor,	100.0
2nll_B	103	Protein (thyroid hormone receptor); complex (trans	100.0
1r4i_A	105	Androgen receptor; AR, steroid receptor, protein-D	100.0
3g9m_A	90	Glucocorticoid receptor; glucocorticoid, DNA-bindi	100.0
1lbd_A	282	RXR_LBD, retinoid X receptor; transcription factor	99.94
1ovl_A	271	Orphan nuclear receptor NURR1 (MSe 414, 496, 511);	99.94
3v3e_B	257	Nuclear receptor subfamily 4 group A member 1; orp	99.92
1xdk_B	303	RAR-beta, retinoic acid receptor, beta; nuclear re	99.91
2lze_A	87	A primordial catalytic fold generated by in vitro	99.9
1pdu_A	244	DHR38, nuclear hormone receptor HR38; nuclear rece	99.9
3cqv_A	199	Nuclear receptor subfamily 1 group D member 2; rev	99.89
1fcy_A	236	RAR-gamma-1, retinoic acid receptor gamma-1; isoty	99.88
3k6p_A	248	Steroid hormone receptor ERR1; estrogen related re	99.88
2nxx_E	248	Ecdysone receptor (ECR, NRH1); hormone receptor, A	99.88
2ocf_A	298	Estrogen receptor; estrogen receptor, LBD, monobod	99.88
1xpc_A	248	Estrogen receptor; nuclear receptor, transcription	99.88
1z5x_E	310	Ecdysone receptor ligand binding domain; ponastero	99.87
3oll_A	240	Estrogen receptor beta; steroid binding, phosphory	99.87
2e2r_A	244	Estrogen-related receptor gamma; ERR gamma, BPA, n	99.87
2r40_D	266	Ecdysone receptor, 20-hydroxy-ecdysone receptor; n	99.87
3kmr_A	266	Retinoic acid receptor alpha; nuclear receptor tra	99.87
1yye_A	268	ER-beta, estrogen receptor beta; ER-beta, nuclear	99.87
1nq7_A	244	Nuclear receptor ROR-beta; ligand-binding domain,	99.87
3n00_A	245	REV-ERBA-alpha; reverba ncorid1, anti-parallel B-s	99.87
3vhv_A	260	Mineralocorticoid receptor; nuclear receptor, tran	99.87
3ltx_A	243	Estrogen receptor; constitutive, nuclear receptor,	99.87
3l0l_A	248	Nuclear receptor ROR-gamma; nuclear receptor, rorg	99.86
3ilz_A	267	Thyroid hormone receptor, alpha isoform 1 variant;	99.86
1l2j_A	271	Estrogen receptor beta; nuclear receptor, transcri	99.86
3ipq_A	283	Oxysterols receptor LXR-alpha; LXR homodimer, LXR	99.86
1n83_A	270	Nuclear receptor ROR-alpha; three-layered alpha he	99.86
3b0t_A	254	Vitamin D3 receptor; nuclear receptor, transcripti	99.86
3vhu_A	294	Mineralocorticoid receptor; nuclear receptor, tran	99.86
1t7r_A	269	Androgen receptor; nuclear receptor, transcription	99.86
3vi8_A	273	Peroxisome proliferator-activated receptor alpha;	99.86
1g2n_A	264	Ultraspiracle protein; antiparallel alpha-helical	99.86
3mnp_A	261	Glucocorticoid receptor; protein-ligand complex, s	99.86
2o4j_A	292	Vitamin D3 receptor; nuclear receptor-ligand compl	99.85
1ymt_A	246	Steroidogenic factor 1; SF-1, ligand-binding domai	99.85
1sqn_A	261	PR, progesterone receptor; nuclear receptor, stero	99.85
2iz2_A	243	FTZ-F1 alpha, nuclear hormone receptor FTZ-F1; nuc	99.84
3plz_A	257	FTZ-F1 related protein; alpha helical sandwhich, f	99.84
1xvp_B	246	Orphan nuclear receptor NR1I3; CAR, RXR, citco, SR	99.84
2nxx_A	235	Ultraspiracle (USP, NR2B4); hormone receptor, APO	99.84
2hc4_A	302	Vitamin D receptor; alpha helical sandwich, gene r	99.84
1nrl_A	316	Orphan nuclear receptor PXR; PXR, xenobiotic, SRC-	99.83
3tx7_B	352	Nuclear receptor subfamily 5 group A member 2; LRH	99.83
2p1t_A	240	Retinoic acid receptor RXR-alpha; protein-ligand c	99.82
3up3_A	243	Acedaf-12; ligand binding domain, nematode, steroi	99.81
1hg4_A	279	Ultraspiracle; nuclear hormone receptor, transcrip	99.81
1osh_A	232	BIle acid receptor; nuclear receptor, ligand bindi	99.8
3u9q_A	269	Peroxisome proliferator-activated receptor gamma;	99.79
3cjw_A	244	COUP transcription factor 2; COUP-TFII, nuclear re	99.79
3f5c_B	268	Nuclear receptor subfamily 0 group B member 1; tra	99.79
1pzl_A	237	Hepatocyte nuclear factor 4-alpha; transcription;	99.78
3p0u_A	249	Nuclear receptor subfamily 2 group C member 2; lig	99.77
3gyt_A	244	Nuclear hormone receptor of the steroid/thyroid ho	99.73
2lze_A	87	A primordial catalytic fold generated by in vitro	92.76
1wfl_A	74	Zinc finger protein 216; ZF-AN1 domain, zinc bindi	90.31
1weu_A	91	Inhibitor of growth family, member 4; structural g	83.91
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	80.89

>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=1.1e-56  Score=412.82  Aligned_cols=245  Identities=30%  Similarity=0.618  Sum_probs=173.7

Q ss_pred             CCCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636          38 SPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS  117 (335)
Q Consensus        38 ~~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~  117 (335)
                      ...+.|.||||+|+|+||||.+|+|||+||||+|+++..|.|+++++|.|++..|++||+|||+||++|||++++||.+|
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            34567999999999999999999999999999999999999999999999999999999999999999999999999887


Q ss_pred             ccccCCCCCCCCCCCCCCCCCCCcchhhhhhcCCCCCCCCCCChhHHHHHHHhhcchhhhhhhcccCCCCCCCCCHHHHH
Q psy2636         118 LKGRRGRLPSKPKSPQESPPSPPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQE  197 (335)
Q Consensus       118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~i~~~~~~~p~~~~l~~~~~~  197 (335)
                      .+.++....    .. .......               ... ..+   .+......          ..+....+....  
T Consensus       215 ~~~k~r~~~----~~-~~~~~~~---------------~~~-~~~---~ll~a~~~----------~e~~~~~~~~~~--  258 (467)
T 3dzy_A          215 QRGKDRNEN----EV-ESTSSAN---------------EDM-PVE---RILEAELA----------VEPKTETYVEAN--  258 (467)
T ss_dssp             CCCCCCSCS----SC-TTSTTCS---------------CSS-CHH---HHHHHHHC------------------------
T ss_pred             ccccccccc----cc-ccccccC---------------CCC-chh---hhhhhhhh----------hcccchhhhhhc--
Confidence            543321100    00 0000000               000 001   11110000          000000000000  


Q ss_pred             HHHhhhhhccccCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhh
Q psy2636         198 LLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRT  277 (335)
Q Consensus       198 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~  277 (335)
                        .     .   ..+.      .....+..+.++....+..+|+|||+||+|.+|+.+||++|||++|+++++|+.|+++
T Consensus       259 --~-----~---~~~~------~~~~~~~~l~e~a~~~L~~vVeWAK~iP~F~~L~~~DQi~LLK~~w~elliL~~a~rs  322 (467)
T 3dzy_A          259 --M-----G---LNPS------SPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRS  322 (467)
T ss_dssp             --------------------------CCTTHHHHHHHHHHHHHHHHHHSTTSTTSCHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             --c-----c---CCCC------cccchHHHHHHHHHHHHHHHHHHHHhCcchhcCCHHHHHHHHHhHHHHHHHHHHHHHh
Confidence              0     0   0000      0000011234445567788999999999999999999999999999999999999999


Q ss_pred             ccCCCeEEeeCCeEeeHHhhhh-hhcHHHHHHHH-HHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         278 RAEDTKLIFCNGVVLEKQQCQR-SFGDDWLNAIL-EFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       278 ~~~~~~~~~~~g~~~~~~~~~~-~~~~~~~~~~~-~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ....+.+++++|..+..+.... +++ .+.+.++ +|+.+|++|+||++||+||+||+||
T Consensus       323 ~~~~~~~ll~~g~~i~~~~~~~~~~~-~~~~~il~~lv~~l~~L~ld~~E~~lLkAIvLf  381 (467)
T 3dzy_A          323 IAVKDGILLATGLHVHRNSAHSAGVG-AIFDRVLTELVSKMRDMQMDKTELGCLRAIVLF  381 (467)
T ss_dssp             SSSTTBCCCSSSCCCBTHHHHTTTCH-HHHHHHHHHTHHHHHHHTCCHHHHHHHHHHHHS
T ss_pred             ccCCCceEecCCceechhhhhhhcch-HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Confidence            8888888999999998876544 444 5555555 9999999999999999999999997

>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=3.4e-53  Score=385.85  Aligned_cols=282  Identities=27%  Similarity=0.457  Sum_probs=166.7

Q ss_pred             CCCCCCCCCcccccCCCCCccccCCccccccccceecccccCCeee-cCCCCCCcccccccccccchhhHHHHhcCceee
Q psy2636          33 RPTPPSPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYV-CLADKACPVDKRRRNRCQFCRFQKCLQVGMVKE  111 (335)
Q Consensus        33 ~~~~~~~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~-C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~  111 (335)
                      .++.......|.||||+|+|+||||.+|+|||+||||+|+++..|. |  +++|.|++..|++||+|||+||++|||+++
T Consensus        43 ~~~~~~~~~~C~vC~~~~~g~hygv~~C~~C~~FFrR~~~~~~~~~~c--~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~  120 (419)
T 3dzy_D           43 EPSNSLMAIECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLIYDRC--DLNCRIHKKSRNKCQYCRFQKCLAVGMSHN  120 (419)
T ss_dssp             -------CCCCSSSCSCCCSBCSSSBCCHHHHHHHHHHHTTTCCCCCC--CSCCCCCTTGGGTCHHHHHHHHHHTTCCGG
T ss_pred             CCCCCCCCCcCeECCCcCCCCccCcccchhhhHHHccchhcccccccc--cCCCCcccccCccchhhhHHHHhhcccchh
Confidence            3444456778999999999999999999999999999999999995 7  468999999999999999999999999999


Q ss_pred             eeeeccccccCCCCCCCCCCCCCCCCCCCcch----hhhhhcCCCCCCCCCCChhHHHHHHHhhcchhhhhhhcccCCCC
Q psy2636         112 VVRTDSLKGRRGRLPSKPKSPQESPPSPPVSL----ITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPG  187 (335)
Q Consensus       112 ~Vq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~i~~~~~~~p~  187 (335)
                      +||.+|.+...++..............+....    +..+..++...  ...........          +.......+.
T Consensus       121 ~vq~~R~~~~~k~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~a~~~~--~~~~~~~~~~~----------l~~~~~~~~p  188 (419)
T 3dzy_D          121 AIRFGRMPQAEKEKLLAEISSDIDQLNPESADLRALAKHLYDSYIKS--FPLTKAKARAI----------LTGKTTDKSP  188 (419)
T ss_dssp             GCCCSCCTTTTGGGSTTTTTSTTTTSCSTTHHHHHHHHHHHHHHHTT--CSSCHHHHHHH----------HHCCSSSCCC
T ss_pred             heecccccccccccccccccccccCCCCchhhHHHHHHHHHHhhhcc--CCccchhcccc----------ccCCCCCCCC
Confidence            99988754332211100000000000111000    00000000000  00000000000          0000000000


Q ss_pred             CCCCCHHHHHHHHhhhhhccccCCCCCCCCC--CChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhH
Q psy2636         188 FSDLCKEDQELLFQSASLELFYREPNPLEPP--IAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSAS  265 (335)
Q Consensus       188 ~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~  265 (335)
                      +..   .+...+... .....+....+....  ......+..+.......+..+|+|||+||+|.+|+.+||++|||++|
T Consensus       189 ~~~---~~~~~l~~a-e~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w  264 (419)
T 3dzy_D          189 FVI---YDMNSLMMG-EDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGV  264 (419)
T ss_dssp             EEE---CSHHHHHCC-C----------------CHHHHHHHHHHHHHHHHHHHHHHHHTTSTTTTTSCHHHHHHHHHHHH
T ss_pred             ccc---ccchhhhhc-ccccccccCCCcccccchhhhHHHHHHHHHHHHHHHHHHHHhccCCCcccCCHHHHHHHHHHHH
Confidence            000   000000000 000000000000000  00111222233334456778999999999999999999999999999


Q ss_pred             HHHHHHHHhhhhccCCCeEEeeCCeE-eeHHhhh---hhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         266 LELFVLRLAYRTRAEDTKLIFCNGVV-LEKQQCQ---RSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       266 ~~~~~l~~a~~~~~~~~~~~~~~g~~-~~~~~~~---~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      +|+++|+.|..+..  +.+++.+|.. +..+.+.   .+++ ++++.+++|+.+|++|+||++||+|||||+||
T Consensus       265 ~Ell~L~~a~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~-~l~~~i~~f~~~l~~L~ld~~E~alLkAivLf  335 (419)
T 3dzy_D          265 HEIIYTMLASLMNK--DGVLISEGQGFMTREFLKSLRKPFG-DFMEPKFEFAVKFNALELDDSDLAIFIAVIIL  335 (419)
T ss_dssp             HHHHHHHHGGGBCS--SEEEEGGGTEEEEHHHHHSSSGGGS-GGGHHHHHHHHHHHHTCCCHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHhcC--CCceeecCcccccHHHHHhhhhhHH-HHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHh
Confidence            99999999966543  4566666654 4555433   3455 78899999999999999999999999999997

>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=2.9e-41  Score=235.02  Aligned_cols=87  Identities=90%  Similarity=1.586  Sum_probs=82.9

Q ss_pred             cccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecccccc
Q psy2636          42 LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLKGR  121 (335)
Q Consensus        42 ~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~~~~  121 (335)
                      +|.||||+|+|+||||+||+|||+||||+|+.+..|.|..+++|.|++..|+.||+|||+|||+|||++++||.|+...+
T Consensus         2 ~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~~~~~~   81 (89)
T 1cit_A            2 RCAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTDSLKGR   81 (89)
T ss_dssp             CCSSSCCCCCEEETTEEECHHHHHHHHHHHHHTCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHTTCCGGGSCCGGGTTC
T ss_pred             CCeEeCCCCcceEeCccchhhhhhhceeeEEecceeeeccCCccccCCCCcccChhhhhHHHhHcCCCHHHeecccccCc
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999988888


Q ss_pred             CCCCCCC
Q psy2636         122 RGRLPSK  128 (335)
Q Consensus       122 ~~~~~~~  128 (335)
                      +++.|++
T Consensus        82 r~r~p~~   88 (89)
T 1cit_A           82 RGRLPSK   88 (89)
T ss_dssp             CSCCCCC
T ss_pred             cccCCCC
Confidence            8777654

>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=2.3e-40  Score=230.12  Aligned_cols=80  Identities=50%  Similarity=1.091  Sum_probs=76.0

Q ss_pred             CCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeeccc
Q psy2636          39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSL  118 (335)
Q Consensus        39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~  118 (335)
                      +..+|.||||+|+|+||||++|+|||+||||+|+.+..|.|+.+++|.|++..|+.||+|||+|||+|||++++||.++.
T Consensus         6 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~   85 (89)
T 2ebl_A            6 SGIECVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRANRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQRGSG   85 (89)
T ss_dssp             SSCBCTTTCSBCCSEETTEECCHHHHHHHHHHHTTTCCCCCSSCSCCCCCSSSSSCCSHHHHHHHHHHTCCHHHHSCSCC
T ss_pred             CCCCCcEeCCCCcceEeCchhhHHhhhhhheeeeeccceecccCccCCcCccCccccccchHHHhhhccCCHHHcccCCC
Confidence            34569999999999999999999999999999999999999999999999999999999999999999999999998764

>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=1.4e-40  Score=233.48  Aligned_cols=82  Identities=54%  Similarity=1.140  Sum_probs=75.5

Q ss_pred             CCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeeccc
Q psy2636          39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSL  118 (335)
Q Consensus        39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~  118 (335)
                      ...+|.||||+|+|+||||+||+|||+||||+|+.+..|.|+.+++|.|++..|+.||+|||+|||+|||++++||.++.
T Consensus         9 ~~~~C~VCgd~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~   88 (93)
T 2han_A            9 SKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYACRENRNCIIDKRQRNRCQYCRYQKCLTCGMKREAVQEERQ   88 (93)
T ss_dssp             -CCBCTTTCSBCCEEETTEEECHHHHHHHHHHHHHTCCCCCSSCSCCCCSTTTGGGCHHHHHHHHHHHTCCGGGSCCCC-
T ss_pred             CCCCCcEeCCCCcCeecCcchhHHHHHHHHhhhccccCcCcCCCCcCCcCCCCCccCccccHHHHhHhCCCHHHhhhccC
Confidence            34679999999999999999999999999999999999999999999999999999999999999999999999998865


Q ss_pred             cc
Q psy2636         119 KG  120 (335)
Q Consensus       119 ~~  120 (335)
                      ..
T Consensus        89 ~~   90 (93)
T 2han_A           89 GI   90 (93)
T ss_dssp             --
T ss_pred             cc
Confidence            43

>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=1.6e-40  Score=229.23  Aligned_cols=81  Identities=54%  Similarity=1.189  Sum_probs=76.7

Q ss_pred             CCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeeccc
Q psy2636          39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSL  118 (335)
Q Consensus        39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~  118 (335)
                      +..+|.||||+|+|+||||+||+|||+||||+|+.+..|.|+.+++|.|++..|+.||+|||+|||+|||++++||.++.
T Consensus         4 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~   83 (85)
T 1dsz_B            4 TKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQ   83 (85)
T ss_dssp             CCEECTTTCCEESSEETTEECCHHHHHHHHHHHHHTCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCCCC
T ss_pred             CCCCCCEeCCCCCceeeCccchHHHHHHHHHhhccccceeecccccccccccccccCcchhHHHHhHcCCCHHHhhcccC
Confidence            34579999999999999999999999999999999999999999999999999999999999999999999999998765


Q ss_pred             c
Q psy2636         119 K  119 (335)
Q Consensus       119 ~  119 (335)
                      +
T Consensus        84 ~   84 (85)
T 1dsz_B           84 R   84 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=2.2e-40  Score=224.97  Aligned_cols=76  Identities=50%  Similarity=1.173  Sum_probs=73.3

Q ss_pred             cccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636          42 LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS  117 (335)
Q Consensus        42 ~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~  117 (335)
                      +|.||||+|+|+||||+||+|||+||||+|+.+..|.|+.+++|.|++..|+.||+|||+|||+|||++++||.++
T Consensus         2 ~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R   77 (78)
T 3cbb_A            2 LCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNER   77 (78)
T ss_dssp             BCTTTSSBCCSEETTEECCHHHHHHHHHHHHTTCCCCCSSCSCCCCSTTTTTTCHHHHHHHHHHHTCCGGGCCCC-
T ss_pred             CCeEeCCCCCceEeCCcchhhhceeeeEEEecccCcccccccccCcCccccccChhhhhHHHhHcCCCHHHccccC
Confidence            5999999999999999999999999999999999999999999999999999999999999999999999999875

>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=3.4e-40  Score=227.00  Aligned_cols=80  Identities=50%  Similarity=1.058  Sum_probs=70.4

Q ss_pred             CCCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636          38 SPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS  117 (335)
Q Consensus        38 ~~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~  117 (335)
                      ++..+|.||||+|+|+||||+||+|||+||||+|+.+..|.|+.+++|.|++..|+.||+|||+|||+|||++++||.++
T Consensus         2 ~~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R   81 (84)
T 1hcq_A            2 KETRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRKDR   81 (84)
T ss_dssp             CCCCBCTTTCSBCCEEETTEEECHHHHHHHHHHHSSCCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHHTCCC-------
T ss_pred             CCCCcCcEECCCCCCeeeCccchHHhhhhhhhccccccccccccCccCCcCCcCcccChhhhhHHHhHcCCCHHHhcccC
Confidence            35578999999999999999999999999999999999999999999999999999999999999999999999999876

>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=2.2e-40  Score=234.54  Aligned_cols=87  Identities=55%  Similarity=1.071  Sum_probs=81.0

Q ss_pred             CCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeeccc
Q psy2636          39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSL  118 (335)
Q Consensus        39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~  118 (335)
                      +..+|.||||+|+|+||||+||+|||+||||+|+.+..|.|..+++|.|++..|+.||+|||+|||+|||++++||.++.
T Consensus         3 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~   82 (98)
T 1lo1_A            3 PKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKALKVGMLKEGVRLDRV   82 (98)
T ss_dssp             CCCEETTTTEECSEESSSSEECHHHHHHHHHHHHTTCCCCCSSCSCCCCCHHHHHHCHHHHHHHHHHHTCCGGGSCSSCC
T ss_pred             CCCCCcEeCCCCcCeeeCccchhhhhhhheeeecccCccccCccccccccccccccccchhHHHHhHcCCCHHHeecccc
Confidence            45679999999999999999999999999999999999999999999999999999999999999999999999999887


Q ss_pred             cccCCCC
Q psy2636         119 KGRRGRL  125 (335)
Q Consensus       119 ~~~~~~~  125 (335)
                      .+.+.+.
T Consensus        83 ~~~r~k~   89 (98)
T 1lo1_A           83 RGGRQKY   89 (98)
T ss_dssp             TTCCCCC
T ss_pred             cCccccc
Confidence            6665544

>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=4.9e-40  Score=227.60  Aligned_cols=81  Identities=54%  Similarity=1.071  Sum_probs=73.7

Q ss_pred             CCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecccc
Q psy2636          40 SQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLK  119 (335)
Q Consensus        40 ~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~~  119 (335)
                      ..+|.||||+|+|+||||+||+|||+||||+|+.+..|.|..+++|.|++..|+.||+|||+|||+|||++++||.++.+
T Consensus         4 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~   83 (86)
T 1dsz_A            4 YKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNK   83 (86)
T ss_dssp             --CCTTTCSCCCSEETTEECCHHHHHHHHHHHHTTCCCCCSSCSCCCCSTTTGGGCHHHHHHHHHHTTCCGGGSCCC---
T ss_pred             CCCCcEECCCccceeeCchhHHHHHHHHHHHhhcccceeeccCCccccCccccccchhhhHHHHHHhCCCHHHhhhcccc
Confidence            35699999999999999999999999999999999999999999999999999999999999999999999999988754


Q ss_pred             c
Q psy2636         120 G  120 (335)
Q Consensus       120 ~  120 (335)
                      .
T Consensus        84 ~   84 (86)
T 1dsz_A           84 K   84 (86)
T ss_dssp             -
T ss_pred             c
Confidence            3

>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=9.6e-40  Score=231.72  Aligned_cols=82  Identities=55%  Similarity=1.212  Sum_probs=72.1

Q ss_pred             CCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecccc
Q psy2636          40 SQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLK  119 (335)
Q Consensus        40 ~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~~  119 (335)
                      ..+|.||||+|+|+||||++|+|||+||||+|+.+..|.|+.+++|.|++..|+.||+|||+|||+|||++++||.++..
T Consensus         3 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~   82 (99)
T 1ynw_B            3 KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQR   82 (99)
T ss_dssp             --CBTTTBSCCCBCCTTSCBCSHHHHHHHHHHHTTCCCCCSSSSCCCCCSTTSSSCHHHHHHHHHHTTCCSTTCC-----
T ss_pred             CCCCceeCCCCcceeeCccchHHHHHHHHhhhccccccccCCCCcccccccCCccCccccHHHHhHcCCCHHHhhhcccc
Confidence            35799999999999999999999999999999999999999999999999999999999999999999999999988765


Q ss_pred             cc
Q psy2636         120 GR  121 (335)
Q Consensus       120 ~~  121 (335)
                      .+
T Consensus        83 ~~   84 (99)
T 1ynw_B           83 GK   84 (99)
T ss_dssp             --
T ss_pred             cc
Confidence            43

>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=2.6e-39  Score=227.53  Aligned_cols=82  Identities=50%  Similarity=1.074  Sum_probs=74.5

Q ss_pred             CCCcccccCCCCCccccCCccccccccceecccccCCee-ecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636          39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKY-VCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS  117 (335)
Q Consensus        39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y-~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~  117 (335)
                      +..+|.||||+|+|+||||+||+|||+||||+|+.+..| .|..+++|.|++..|+.||+|||+|||+|||++++||.++
T Consensus         6 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R   85 (94)
T 1a6y_A            6 MVLLCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGR   85 (94)
T ss_dssp             --CBCTTTSSBCCEEETTEEECHHHHHHHHHHHSSCCCCCCCSSTTCCCCCTTTTTSCHHHHHHHHTTTTCCSTTCCCCC
T ss_pred             CCCcCcEeCCCCcceEeCccchhhhhhehheeeecccceEEccCCCCCccCccccccccchhHHHhhHccCCHHHhccCc
Confidence            346799999999999999999999999999999999999 5999999999999999999999999999999999999876


Q ss_pred             ccc
Q psy2636         118 LKG  120 (335)
Q Consensus       118 ~~~  120 (335)
                      ...
T Consensus        86 ~~~   88 (94)
T 1a6y_A           86 IPK   88 (94)
T ss_dssp             ---
T ss_pred             CcC
Confidence            543

>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=3.3e-39  Score=234.04  Aligned_cols=84  Identities=55%  Similarity=1.167  Sum_probs=77.8

Q ss_pred             CCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeeccc
Q psy2636          39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSL  118 (335)
Q Consensus        39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~  118 (335)
                      +..+|.||||+|+|+||||+||+|||+||||+|..+..|.|..+++|.|++..|+.||+|||+|||+|||++++||.++.
T Consensus         8 ~~~~C~VCgd~a~G~HyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~R~~Cr~CR~~KCl~vGM~~~~vq~~R~   87 (113)
T 2a66_A            8 LEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRM   87 (113)
T ss_dssp             --CBCTTTCCBEEEEETTEEEEHHHHHHHHHHHHTTCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCTTCC
T ss_pred             CCCCCcEeCCCCcceeeCcccHHHHHHHHhhhhhccccccccccccCCcCCCccccccchhHHHHhHhCCCHHHhccccc
Confidence            44679999999999999999999999999999999999999999999999999999999999999999999999998876


Q ss_pred             cccC
Q psy2636         119 KGRR  122 (335)
Q Consensus       119 ~~~~  122 (335)
                      .+.+
T Consensus        88 ~~~r   91 (113)
T 2a66_A           88 RGGR   91 (113)
T ss_dssp             CSSC
T ss_pred             cCCC
Confidence            5444

>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=5.8e-39  Score=235.99  Aligned_cols=83  Identities=48%  Similarity=0.962  Sum_probs=77.8

Q ss_pred             CCCCCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeee
Q psy2636          36 PPSPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRT  115 (335)
Q Consensus        36 ~~~~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~  115 (335)
                      +.....+|.||||+|+|+||||++|+|||+||||+|..+..|.|+.+++|.|++..|+.||+|||+|||+|||++++||.
T Consensus         4 p~~~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~   83 (119)
T 2han_B            4 PRVQEELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECRLKKCLAVGMRPECVVP   83 (119)
T ss_dssp             -CCCSCBCTTTCSBCCEEETTEEECHHHHHHHHHHHHTTCCCCCSSCSCCCCSTTGGGTCHHHHHHHHHHTTCCGGGSSC
T ss_pred             CCCCCCcCeEeCCcCCcceECchhHHhhHHhhhhheEeccccccccccccccCccccccchhhHHHHHHHhCCCHHHccc
Confidence            33556789999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccc
Q psy2636         116 DSL  118 (335)
Q Consensus       116 ~~~  118 (335)
                      ++.
T Consensus        84 ~r~   86 (119)
T 2han_B           84 ENQ   86 (119)
T ss_dssp             SSH
T ss_pred             hhh
Confidence            764

>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=3.2e-39  Score=233.65  Aligned_cols=79  Identities=41%  Similarity=0.981  Sum_probs=75.1

Q ss_pred             CCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeeccc
Q psy2636          40 SQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSL  118 (335)
Q Consensus        40 ~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~  118 (335)
                      ..+|.||||+|+|+||||+||+|||+||||+|..+..|.|..+++|.|++..|+.||+|||+|||+|||++++|+.++.
T Consensus         6 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~   84 (110)
T 1kb2_A            6 PRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDEE   84 (110)
T ss_dssp             -CBCTTTCSBCCSEETTEECCHHHHHHHHHHHHTTCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCHHH
T ss_pred             CCCCcEeCCCCCceEeCchhHhhhhhhheeeeecccceeeCCCCCccCCcccceecccccHhhhhhcCCcHHhcccHHH
Confidence            4679999999999999999999999999999999999999999999999999999999999999999999999998754

>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=2.2e-38  Score=230.80  Aligned_cols=79  Identities=48%  Similarity=0.965  Sum_probs=70.8

Q ss_pred             CCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636          39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS  117 (335)
Q Consensus        39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~  117 (335)
                      +..+|.||||+|+|+||||.+|+|||+||||+|+.+..|.|+++++|.|++..|+.||+|||+|||+|||++++||.++
T Consensus        28 ~~~~C~VCgd~a~G~HyGv~sC~aCk~FFRRsv~~~~~y~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~avq~kR  106 (117)
T 4hn5_A           28 PPKLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEARKTKK  106 (117)
T ss_dssp             --CBCTTTCSBCCEEETTEEECHHHHHHHHHHHSSCCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHHTCCTTC-----
T ss_pred             CCCcCCcCCCcCcccccCCcccchhhhhhhcceecCCceecCCCCccccCcccccCCcccchHHHhHcCCCHHHhcccc
Confidence            3467999999999999999999999999999999999999999999999999999999999999999999999999865

>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=3.1e-38  Score=226.03  Aligned_cols=79  Identities=53%  Similarity=1.045  Sum_probs=74.7

Q ss_pred             CCcccccCCCCCccccCCccccccccceecccccCC--eeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636          40 SQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGS--KYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS  117 (335)
Q Consensus        40 ~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~--~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~  117 (335)
                      +++|.||||+|+|+||||+||+|||+||||+|..+.  .|.|..+++|.|++..|+.||+|||+|||+|||++++||.++
T Consensus         1 ~~~C~VCgd~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~~   80 (103)
T 2nll_B            1 DELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQECRFKKCIYVGMATDLVLDDS   80 (103)
T ss_dssp             CCBCTTTCSBCCSEETTEECCHHHHHHHHHHHHTTCGGGCCCSSCTTCCCSTTTTTSCHHHHHHHHHHTTCCGGGSCCHH
T ss_pred             CCCCeEeCCcCcCeecCcccHHHhhhhheecccccccchhhhhccCCcCcCccCccccchhhhHhhhHhCCCHHHhhhhh
Confidence            357999999999999999999999999999999876  899999999999999999999999999999999999999875


Q ss_pred             c
Q psy2636         118 L  118 (335)
Q Consensus       118 ~  118 (335)
                      .
T Consensus        81 ~   81 (103)
T 2nll_B           81 K   81 (103)
T ss_dssp             H
T ss_pred             h
Confidence            4

>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=5e-38  Score=225.08  Aligned_cols=80  Identities=40%  Similarity=0.899  Sum_probs=71.8

Q ss_pred             CCCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636          38 SPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS  117 (335)
Q Consensus        38 ~~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~  117 (335)
                      .+..+|.||||+|+|+||||++|+|||+||||+|..+..|.|+.+++|.|++..|+.||+|||+|||+|||++++++..+
T Consensus         5 ~~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~~k~~k   84 (105)
T 1r4i_A            5 PPQKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLGARKLKK   84 (105)
T ss_dssp             -CCCBCSSSCSBEEEEETTEEEEHHHHHHHHHHHTSCCCCCCSSSSCCCCCTTTTTTCHHHHHHHHHHHTCCSCC-----
T ss_pred             CCCCCCcEeCCCCCceEeCCcchhhhhhhhceeEEecCceeeccCCccccCccccccchhchHHHHHhhhcccchhhhcc
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999987654

>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=3.5e-38  Score=221.15  Aligned_cols=78  Identities=47%  Similarity=0.946  Sum_probs=75.1

Q ss_pred             CCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636          40 SQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS  117 (335)
Q Consensus        40 ~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~  117 (335)
                      ..+|.||||+|+|+||||.+|+|||+||||+|+.+..|.|..+++|.|++..|+.||+|||+|||+|||++++||.++
T Consensus         2 ~~~C~VCg~~a~g~hyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~avq~~r   79 (90)
T 3g9m_A            2 SHMCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEARKTKK   79 (90)
T ss_dssp             CCBCTTTCSBCCEEETTEEECHHHHHHHHHHHHSCCCCCCSSSSCCCCCTTGGGTCHHHHHHHHHHHTCCTTHHHHHC
T ss_pred             CCcCccCCCcCcccccCCccchhHhHHhhhhhhcCCceeCCCCCccccCcccccCCcchhhHHHHHcCCCHHHhcccc
Confidence            357999999999999999999999999999999999999999999999999999999999999999999999999875

>1lbd_A RXR_LBD, retinoid X receptor; transcription factor, nuclear receptor, structural proteomic europe, spine, structural genomics; 2.70A {Homo sapiens} SCOP: a.123.1.1 PDB: 1z5x_U* 2q60_A

Probab=99.94  E-value=5.9e-27  Score=203.47  Aligned_cols=111  Identities=20%  Similarity=0.413  Sum_probs=97.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh-hhc
Q psy2636         224 KIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR-SFG  302 (335)
Q Consensus       224 ~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~-~~~  302 (335)
                      .+..+.++....+..+|+|||+||+|.+|+.+||++|||++|+++++|+.||++....+.+++++|..+..+.... +.+
T Consensus        84 ~~~~~~~~a~~~l~~~vewaK~ip~F~~L~~~DQ~~LLk~~~~el~il~~a~rs~~~~~~~~~~~g~~~~~~~~~~~~~~  163 (282)
T 1lbd_A           84 PVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVG  163 (282)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHGGGGSSSEEECTTSCEEEHHHHHHTTTH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCcChhcCCHHHHHHHHHHHHHHHHHHHHHHhcccCCCceEecCCcccccchhhhcccH
Confidence            4566777788889999999999999999999999999999999999999999998877888999999998876543 444


Q ss_pred             HHHHH-HHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         303 DDWLN-AILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       303 ~~~~~-~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                       .+.+ .+.+++.+|++|+||.+||+|||||+||
T Consensus       164 -~~~~~~~~~~~~~l~~L~ld~~E~~lLkaivL~  196 (282)
T 1lbd_A          164 -AIFDRVLTELVSKMRDMQMDKTELGCLRAIVLF  196 (282)
T ss_dssp             -HHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHS
T ss_pred             -HHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHc
Confidence             4444 4568999999999999999999999997

>1ovl_A Orphan nuclear receptor NURR1 (MSe 414, 496, 511); NUUR1, LBD, transcription; 2.20A {Homo sapiens} SCOP: a.123.1.1

Probab=99.94  E-value=1.4e-26  Score=199.93  Aligned_cols=115  Identities=59%  Similarity=1.065  Sum_probs=106.1

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR  299 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~  299 (335)
                      .+.+.+..++++.+..+..+|+|||++|+|.+|+.+||++|||++|+++++|+.|+++....+.+++++|..++.+....
T Consensus        71 ~~~~~~~~~~~~~~~~l~~~v~waK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~~l~~~~g~~~~~~~~~~  150 (271)
T 1ovl_A           71 DDTQHIQQFYDLLTGSMEIIRGWAEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIFCNGVVLHRLQCVR  150 (271)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHSBTTTTEEECTTSBEEEHHHHTT
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHcCCCcccCChHHHHHHHHHhHHHHHHHHHHHHhcCCCCeEEeeCCeeecHHHHHh
Confidence            34567888999999999999999999999999999999999999999999999999999888899999999998877666


Q ss_pred             hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 ~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      +++ ++++.+++++.+|++|++|.+||+|||||+||
T Consensus       151 ~~~-~~~~~l~~~~~~l~~L~ld~~E~~lLkAivL~  185 (271)
T 1ovl_A          151 GFG-EWIDSIVEFSSNLQNMNIDISAFSCIAALAMV  185 (271)
T ss_dssp             TTT-THHHHHHHHHHHHHTTCCCHHHHHHHHHHHHS
T ss_pred             hHH-HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Confidence            666 78889999999999999999999999999987

>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=99.92  E-value=7.9e-25  Score=186.60  Aligned_cols=116  Identities=55%  Similarity=1.034  Sum_probs=109.8

Q ss_pred             CChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhh
Q psy2636         219 IAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQ  298 (335)
Q Consensus       219 ~~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~  298 (335)
                      ..+.+.++.|+++++..|+.+|+|||++|||.+|+.+||++|||++|+|+++|+.|+++....+.+++.+|..+.+....
T Consensus        48 ~~~~~~~~~~~~l~~~~i~~iV~wAK~iP~F~~L~~~DQi~LLk~~w~ElllL~~a~~~~~~~~~l~~~~~~~~~~~~~~  127 (257)
T 3v3e_B           48 KEDAGDVQQFYDLLSGSLEVIRKWAEKIPGFAELSPADQDLLLESAFLELFILRLAYRSKPGEGKLIFCSGLVLHRLQCA  127 (257)
T ss_dssp             CCCHHHHHHHHHHHHHTHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHSBGGGTEEECTTSBEEEHHHHH
T ss_pred             CCcHHHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhccCCCCeeEeCCCccccHHHHH
Confidence            45677899999999999999999999999999999999999999999999999999999988889999999999988877


Q ss_pred             hhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         299 RSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       299 ~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      .+++ ++++.+++|+.+|++|++|++||+|||||+||
T Consensus       128 ~~~~-~~~~~l~~~~~~l~~L~ld~~E~a~LkAivLf  163 (257)
T 3v3e_B          128 RGFG-DWIDSILAFSRSLHSLLVDVPAFACLSALVLI  163 (257)
T ss_dssp             HHHT-THHHHHHHHHHHHHHTTCCHHHHHHHHHHHHS
T ss_pred             hhhH-HHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHh
Confidence            7888 88999999999999999999999999999997

>1xdk_B RAR-beta, retinoic acid receptor, beta; nuclear receptor, coactivator, ligand, hormone/growth factor receptor complex; HET: REA; 2.90A {Mus musculus} SCOP: a.123.1.1

Probab=99.91  E-value=4.2e-24  Score=186.89  Aligned_cols=114  Identities=29%  Similarity=0.517  Sum_probs=104.7

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh-
Q psy2636         221 EPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR-  299 (335)
Q Consensus       221 ~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~-  299 (335)
                      +.+.|..++++....+..+|+|||+||+|.+|+.+||++|||++|+++++|+.|+++....+.+++++|..+.++.+.. 
T Consensus        69 ~~~~~~~~~~~~~~~l~~~VewaK~iP~F~~L~~~DQi~LLk~~~~el~lL~~a~~s~~~~~~l~~~~g~~~~~~~~~~~  148 (303)
T 1xdk_B           69 DLGLWDKFSELATKCIIKIVEFAKRLPGFTGLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMHNA  148 (303)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHTSTTTSSSCHHHHHHHHHHHHHHHHHHHHHTTEETTTTEEECTTCBEEEHHHHHHT
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHcCcccccCCHHHHHHHHHhhHHHHHHHHHHHHhcccCCeEEecCCceecHHHHhhc
Confidence            4567888999999999999999999999999999999999999999999999999999888899999999998876643 


Q ss_pred             hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 ~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      +++ ++++.+++|+.+|++|+||.+||+|||||+||
T Consensus       149 g~~-~~~~~i~~~~~~l~~L~ld~~E~~lLkAivL~  183 (303)
T 1xdk_B          149 GFG-PLTDLVFTFANQLLPLEMDDTETGLLSAICLI  183 (303)
T ss_dssp             TTG-GGHHHHHHHHHHHGGGCCCHHHHHHHHHHHHS
T ss_pred             CcH-HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHh
Confidence            455 67888999999999999999999999999987

>2lze_A A primordial catalytic fold generated by in vitro evolution; ligase, de novo protein; NMR {Synthetic construct}

Probab=99.90  E-value=4.3e-25  Score=151.52  Aligned_cols=64  Identities=22%  Similarity=0.301  Sum_probs=55.8

Q ss_pred             CCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeee
Q psy2636          49 IAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVR  114 (335)
Q Consensus        49 ~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq  114 (335)
                      ++.|.||+++ |.+|++||||++ ++..|+|+.+++|.|++..|++||+|||||||+|||+...+.
T Consensus        13 p~~g~h~c~v-Cgd~asfFRRt~-~~~~y~C~~~~~C~i~~~~R~~C~~CR~qKCl~VgM~~~~~~   76 (87)
T 2lze_A           13 PRGGKHICAI-CGNNAEDYKHTD-MDLTYTDRDYKNCESYHKCSDLCQYCRYQKDLAIHHQHHHGG   76 (87)
T ss_dssp             CSCCSSSCSS-SSSSSSSCTTTT-TSCTTTSCCCCCCCCSSCCSSSCSGGGTSCCHHHHCSSCCCC
T ss_pred             CCCCCEEccC-CCCccceECccc-CCCeeEcCCCCccccCCCccCcCCcccChhhccCcCEeccCc
Confidence            4557777776 777999999995 678899999999999999999999999999999999877553

>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=99.90  E-value=4.3e-23  Score=174.75  Aligned_cols=116  Identities=75%  Similarity=1.232  Sum_probs=107.5

Q ss_pred             CChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhh
Q psy2636         219 IAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQ  298 (335)
Q Consensus       219 ~~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~  298 (335)
                      ..+.+.|..++++.+..++.+|+|||++|+|.+|+.+||++|||++|+++++|+.||++....+.+++++|..+.++...
T Consensus        43 ~~~~~~~~~~~~~~~~~l~~~VewAK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~rs~~~~~~l~~~~g~~~~~~~~~  122 (244)
T 1pdu_A           43 MSEADKVQQFYQLLTSSVDVIKQFAEKIPGYFDLLPEDQELLFQSASLELFVLRLAYRARIDDTKLIFCNGTVLHRTQCL  122 (244)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHCCSSCSEEECTTSBEEEHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCceEeeCCeeecHHHHH
Confidence            46778899999999999999999999999999999999999999999999999999999887788999999999987765


Q ss_pred             hhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         299 RSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       299 ~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      .+++ ++++.+++++.+|++|++|++||+|||||+||
T Consensus       123 ~~~~-~~~~~l~~~~~~l~~L~ld~~E~~lLkAIvLf  158 (244)
T 1pdu_A          123 RSFG-EWLNDIMEFSRSLHNLEIDISAFACLCALTLI  158 (244)
T ss_dssp             HHHT-THHHHHHHHHHHHHHHCCCHHHHHHHHHHHHS
T ss_pred             hHHH-HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            5666 78888999999999999999999999999987

>3cqv_A Nuclear receptor subfamily 1 group D member 2; reverb beta, heme, NR1D2, DNA-binding, metal-binding, nucleus, repressor, transcription; HET: HEM; 1.90A {Homo sapiens} PDB: 2v7c_A 2v0v_A

Probab=99.89  E-value=1.1e-22  Score=167.47  Aligned_cols=116  Identities=26%  Similarity=0.464  Sum_probs=105.7

Q ss_pred             CChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhh
Q psy2636         219 IAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQ  298 (335)
Q Consensus       219 ~~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~  298 (335)
                      ....+.|..+.+..+..+..+|+|||++|+|.+|+.+||++|||++|+++++++.|+++....+.+++++|..+..+...
T Consensus        16 ~~~~~~~~~~~~~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~e~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~   95 (199)
T 3cqv_A           16 KSGHEIWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLFDAKERTVTFLSGKKYSVDDLH   95 (199)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHHHHHHHTSGGGGGSCHHHHHHHHHHHHHHHHHHHTGGGEETTTTEEECTTSCEEEHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHHhcCCChhhCCHHHHHHHHHHhHHHHHHHHHHHHhCCCCCeEEecCCCeecHHHHH
Confidence            45677888899999999999999999999999999999999999999999999999988888889999999999887654


Q ss_pred             h-hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         299 R-SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       299 ~-~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      . +++ ++++.+++++.+|++|++|.+||+|||||+||
T Consensus        96 ~~~~~-~~~~~i~~~~~~~~~L~ld~~E~~lLkaivL~  132 (199)
T 3cqv_A           96 SMGAG-DLLNSMFEFSEKLNALQLSDEEMSLFTAVVLV  132 (199)
T ss_dssp             HTTCC-HHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHH
T ss_pred             hcCcH-HHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHh
Confidence            3 455 78889999999999999999999999999986

>1fcy_A RAR-gamma-1, retinoic acid receptor gamma-1; isotype selectivity, retinoid ligand complexes, drug design, antiparallel alpha-helical sandwich fold; HET: 564 LMU; 1.30A {Homo sapiens} SCOP: a.123.1.1 PDB: 1fcz_A* 1fcx_A* 1fd0_A* 1exa_A* 1exx_A* 1dkf_B*

Probab=99.88  E-value=5e-22  Score=167.88  Aligned_cols=114  Identities=29%  Similarity=0.509  Sum_probs=104.6

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh-
Q psy2636         221 EPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR-  299 (335)
Q Consensus       221 ~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~-  299 (335)
                      +.+.+..+.++....+..+|+|||++|+|.+|+.+||++|||++|+++++|+.|+++....+.+++++|..+.++.... 
T Consensus        42 ~~~~~~~~~~~~~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~l~~a~~~~~~~~~l~~~~g~~~~~~~~~~~  121 (236)
T 1fcy_A           42 DLGLWDKFSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMTFSDGLTLNRTQMHNA  121 (236)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETTTTEEECTTCBEEEHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhccCCCeEEeCCCceecHHHHHHc
Confidence            4677888999999999999999999999999999999999999999999999999999888899999999998876543 


Q ss_pred             hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 ~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      +++ ++.+.+++++.+|++|++|++||+|||||+||
T Consensus       122 g~~-~~~~~i~~~~~~l~~L~ld~~E~~lLkaivL~  156 (236)
T 1fcy_A          122 GFG-PLTDLVFAFAGQLLPLEMDDTETGLLSAICLI  156 (236)
T ss_dssp             TTG-GGHHHHHHHHHHHGGGCCCHHHHHHHHHHHHS
T ss_pred             CcH-HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhc
Confidence            455 67888999999999999999999999999986

>3k6p_A Steroid hormone receptor ERR1; estrogen related receptor alpha, DNA-binding, isopeptide BON binding, nucleus, phosphoprotein, transcription; HET: 5FB; 2.00A {Homo sapiens} SCOP: a.123.1.1 PDB: 1xb7_A 2pjl_A* 3d24_A

Probab=99.88  E-value=6e-22  Score=168.43  Aligned_cols=114  Identities=26%  Similarity=0.439  Sum_probs=103.5

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhh-h
Q psy2636         221 EPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQ-R  299 (335)
Q Consensus       221 ~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~-~  299 (335)
                      ....+..++++....+..+|+|||+||+|.+|+.+||++|||++|+++++|+.||++...++.+++++|..+.++... .
T Consensus        46 ~~~~~~~l~e~a~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~lL~~a~~s~~~~~~l~~~~g~~~~~~~~~~~  125 (248)
T 3k6p_A           46 HLPAVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQDELAFAEDLVLDEEGARAA  125 (248)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCEEEETTEEECHHHHHHT
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHhcCcccccCCHHHHHHHHHHHHHHHHHHHHHHHccCCCCeEEeCCCcccChhhhhhc
Confidence            445678889999999999999999999999999999999999999999999999999887788999999999886543 3


Q ss_pred             hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 ~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      +++ ++++.+.+++.+|++|++|.+||+|||||+||
T Consensus       126 ~~~-~~~~~l~~~~~~l~~L~ld~~E~~lLkAivL~  160 (248)
T 3k6p_A          126 GLG-ELGAALLQLVRRLQALRLEREEYVLLKALALA  160 (248)
T ss_dssp             TTT-THHHHHHHHHHHHHTTTCCHHHHHHHHHHHHH
T ss_pred             cHH-HHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHh
Confidence            455 77899999999999999999999999999986

>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=99.88  E-value=8.7e-22  Score=167.49  Aligned_cols=113  Identities=25%  Similarity=0.526  Sum_probs=102.5

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh-h
Q psy2636         222 PEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR-S  300 (335)
Q Consensus       222 ~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~-~  300 (335)
                      ...+..+.++....++.+|+|||++|+|.+|+.+||++|||++|+++++|+.|+++....+.+++++|..+.++.... +
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            455677888888999999999999999999999999999999999999999999998888899999999998776543 4


Q ss_pred             hcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         301 FGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       301 ~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ++ ++++.+++++.+|++|++|.+||+|||||+||
T Consensus       131 ~~-~~~~~i~~~~~~l~~L~ld~~E~~lLkAivL~  164 (248)
T 2nxx_E          131 MG-ETIEDLLHFCRTMYSMRVDNAEYALLTAIVIF  164 (248)
T ss_dssp             CH-HHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHT
T ss_pred             hH-HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHc
Confidence            55 78899999999999999999999999999987

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

Probab=99.88  E-value=1.4e-21  Score=169.88  Aligned_cols=115  Identities=23%  Similarity=0.466  Sum_probs=104.3

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhh--
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQC--  297 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~--  297 (335)
                      .....+..+.++....+..+|+|||+||+|.+|+.+||++|||++|+++++|+.||++....+.+++++|..+.++..  
T Consensus        41 ~~~~~~~~l~e~a~~~L~~~VewAK~lP~F~~L~~~DQi~LLk~~w~el~lL~~a~rs~~~~~~l~~~~g~~~~~~~~~~  120 (298)
T 2ocf_A           41 SEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKC  120 (298)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTSTTEEEEETTEEEEHHHHTT
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHhCcchhcCCHHHHHHHHHHhhHHHHHHHHHHHhcccCCceeecCCceechhhhhh
Confidence            455677888999999999999999999999999999999999999999999999999998888999999999988753  


Q ss_pred             hhhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         298 QRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       298 ~~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ..++. ++++.+++++.+|++|+||.+||+|||||+||
T Consensus       121 ~~g~~-~~~~~l~~~~~~l~~L~ld~~Ey~lLkAIvLf  157 (298)
T 2ocf_A          121 VEGMV-EIFDMLLATSSRFRMMNLQGEEFVCLKSIILL  157 (298)
T ss_dssp             STTHH-HHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             hhhHH-HHHHHHHHHHHhHhhhCcCHHHHHHHHHHHHc
Confidence            23555 77888899999999999999999999999986

>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=99.88  E-value=9.7e-22  Score=167.37  Aligned_cols=114  Identities=24%  Similarity=0.466  Sum_probs=102.5

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhh--h
Q psy2636         221 EPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQC--Q  298 (335)
Q Consensus       221 ~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~--~  298 (335)
                      ....+..+.+...+.+..+|+|||++|+|.+|+.+||++|||++|+++++|+.||++....+.+++++|..++.+..  .
T Consensus        33 ~~~~~~~l~~~a~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~~l~~~~g~~~~~~~~~~~  112 (248)
T 1xpc_A           33 EASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCV  112 (248)
T ss_dssp             TSCHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTSTTEEEEETTEEEEHHHHTTS
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHcCCccccCCHHHHHHHHHHHhHHHHHHHHHHHhccccCceeecCCceeCccchhhh
Confidence            34567788888899999999999999999999999999999999999999999999998888999999999887653  2


Q ss_pred             hhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         299 RSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       299 ~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      .+++ ++++.+++++.+|++|++|.+||+|||||+||
T Consensus       113 ~~~~-~~~~~l~~~~~~l~~L~ld~~E~~lLkAivL~  148 (248)
T 1xpc_A          113 EGMV-EIFDMLLATSSRFRMMNLQGEEFVCLKSIILL  148 (248)
T ss_dssp             TTHH-HHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             ccHH-HHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHc
Confidence            3454 77888999999999999999999999999986

>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=99.87  E-value=1.2e-21  Score=171.17  Aligned_cols=115  Identities=26%  Similarity=0.541  Sum_probs=104.0

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR  299 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~  299 (335)
                      .....+..+.++....+..+|+|||+||+|.+|+.+||++|||++|+++++|+.|+++....+.+++++|..+..+....
T Consensus       113 ~~~~~~~~l~el~~~~l~~~VewAK~lP~F~~L~~~DQi~LLk~~w~el~lL~~a~rs~~~~~~l~~~~g~~~~~~~~~~  192 (310)
T 1z5x_E          113 VAEERFRHITEITILTVQLIVEFSKRLPGFDKLIREDQIALLKACSSEVMMFRMARRYDAETDSILFATNQPYTRESYTV  192 (310)
T ss_dssp             SSHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEETTTTEEECTTSCEECHHHHHH
T ss_pred             chhhHHHHHHHHHHHHHHHHHHHHHcCcchhhCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCeEEeCCCccccHHHHHh
Confidence            34566778888888999999999999999999999999999999999999999999998888899999999988776433


Q ss_pred             -hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 -SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 -~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                       +++ ++++.+++|+.+|++|+||.+||+|||||+||
T Consensus       193 ~g~~-~~~~~i~~~~~~l~~L~ld~~E~alLkAIvLf  228 (310)
T 1z5x_E          193 AGMG-DTVEDLLRFCRHMCAMKVDNAEYALLTAIVIF  228 (310)
T ss_dssp             TTTH-HHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHT
T ss_pred             cchh-HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHc
Confidence             555 78899999999999999999999999999987

>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=99.87  E-value=1e-21  Score=166.52  Aligned_cols=115  Identities=23%  Similarity=0.421  Sum_probs=104.7

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhh-
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQ-  298 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~-  298 (335)
                      .....+..++++....+..+|+|||++|+|.+|+.+||++|||++|+++++|+.||++....+.+++++|..+.++... 
T Consensus        30 ~~~~~~~~~~~~a~~~l~~~vewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~~l~~~~g~~~~~~~~~~  109 (240)
T 3oll_A           30 TEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKC  109 (240)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTSTTEEEEETBEEEEGGGGGG
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHccCCCCeeEecCCcccchhhHHH
Confidence            4667788899999999999999999999999999999999999999999999999999988889999999999876543 


Q ss_pred             -hhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         299 -RSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       299 -~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                       .+++ ++++.+++++.+|++|++|.+||+|||||+||
T Consensus       110 ~~~~~-~~~~~l~~~~~~l~~L~ld~~E~~lLkAivL~  146 (240)
T 3oll_A          110 VEGIL-EIFDMLLATTSRFRELKLQHKEYLCVKAMILL  146 (240)
T ss_dssp             STTHH-HHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HhhHH-HHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHc
Confidence             3455 77888999999999999999999999999985

>2e2r_A Estrogen-related receptor gamma; ERR gamma, BPA, nuclear receptor, transcription; HET: 2OH; 1.60A {Homo sapiens} SCOP: a.123.1.1 PDB: 2zas_A* 2zbs_A 2zkc_A* 2p7g_A* 1vjb_A* 1tfc_A 2p7a_A* 2p7z_A* 2gpu_A* 1kv6_A 2gp7_A 2gpp_A* 2gpo_A* 2gpv_A* 1s9q_A* 1s9p_A* 2ewp_A*

Probab=99.87  E-value=1.5e-21  Score=165.65  Aligned_cols=115  Identities=28%  Similarity=0.480  Sum_probs=103.8

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhh-
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQ-  298 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~-  298 (335)
                      .....+..+.++....+..+|+|||++|+|.+|+.+||++|||++|+++++|+.||++...++.+++++|..++.+... 
T Consensus        45 ~~~~~~~~~~~~~~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~a~rs~~~~~~~~~~~~~~~~~~~~~~  124 (244)
T 2e2r_A           45 SDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDELVYADDYIMDEDQSKL  124 (244)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTSSSCEEEETTEEECHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHhHHHHHHHHHHHHhcccCCeEEecCCEeecHHHhhh
Confidence            4556778889999999999999999999999999999999999999999999999999888888999999988876543 


Q ss_pred             hhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         299 RSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       299 ~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      .+++ ++++.+++++.+|++|++|.+||+|||||+||
T Consensus       125 ~~~~-~~~~~l~~~~~~l~~L~ld~~E~~lLkAivL~  160 (244)
T 2e2r_A          125 AGLL-DLNNAILQLVKKYKSMKLEKEEFVTLKAIALA  160 (244)
T ss_dssp             TTCH-HHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             ccHH-HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            3444 77888999999999999999999999999986

>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=99.87  E-value=8.5e-22  Score=169.14  Aligned_cols=112  Identities=25%  Similarity=0.478  Sum_probs=102.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh-hh
Q psy2636         223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR-SF  301 (335)
Q Consensus       223 ~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~-~~  301 (335)
                      ..+..++++....+..+|+|||++|+|.+|+.+||++|||++|+++++|+.|+++....+.+++++|..+.++.... ++
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            35778889999999999999999999999999999999999999999999999998888899999999998876543 55


Q ss_pred             cHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         302 GDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       302 ~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      + ++++.+++++.+|++|++|++||+|||||+||
T Consensus       148 ~-~~~~~l~~~~~~l~~L~ld~~E~~lLkAivL~  180 (266)
T 2r40_D          148 A-YVIEDLLHFCRCMYSMMMDNVHYALLTAIVIF  180 (266)
T ss_dssp             H-HHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHT
T ss_pred             H-HHHHHHHHHHHHHhcccCCHHHHHHHhhheee
Confidence            5 78899999999999999999999999999987

>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=99.87  E-value=9.8e-22  Score=168.55  Aligned_cols=115  Identities=28%  Similarity=0.497  Sum_probs=105.5

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR  299 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~  299 (335)
                      .+.+.|..+++.....+..+|+|||+||+|.+|+.+||++|||++|+++++|+.|+++....+.+++++|..+.++....
T Consensus        65 ~~~~~~~~~~e~~~~~l~~~VewaK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~~s~~~~~~l~~~~g~~~~~~~~~~  144 (266)
T 3kmr_A           65 LDIDLWDKFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMHN  144 (266)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETTTTEEECTTSBEEEHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHcCcChhhCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCeEEecCCcccchHHHhh
Confidence            35677889999999999999999999999999999999999999999999999999999888899999999998877653


Q ss_pred             -hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 -SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 -~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                       +++ .+.+.+++|+.+|++|++|++||+|||||+||
T Consensus       145 ~g~~-~~~~~i~~~~~~l~~L~ld~~E~~lLkAIvL~  180 (266)
T 3kmr_A          145 AGFG-PLTDLVFAFANQLLPLEMDDAETGLLSAICLI  180 (266)
T ss_dssp             HTTG-GGHHHHHHHHHHHGGGCCCHHHHHHHHHHHHS
T ss_pred             cchH-HHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHh
Confidence             455 67888899999999999999999999999986

>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=99.87  E-value=1.3e-21  Score=168.15  Aligned_cols=115  Identities=23%  Similarity=0.421  Sum_probs=103.7

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhh-
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQ-  298 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~-  298 (335)
                      .....+..+.++....+..+|+|||+||+|.+|+.+||++|||++|+++++|+.||++....+.+++++|..++.+... 
T Consensus        28 ~~~~~~~~l~e~a~~~l~~~VewAK~lp~F~~L~~~DQi~LLk~~w~el~lL~~a~rs~~~~~~l~~~~g~~~~~~~~~~  107 (268)
T 1yye_A           28 TEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKC  107 (268)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTSTTEEEEETTEEEEGGGGGG
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHhcCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCceEecCCcccChhhHhh
Confidence            3456678889999999999999999999999999999999999999999999999999988889999999998876532 


Q ss_pred             -hhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         299 -RSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       299 -~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                       .+++ ++++.+++++.+|++|++|.+||+|||||+||
T Consensus       108 ~~~~~-~~~~~l~~~~~~l~~L~ld~~E~~lLkAIvLf  144 (268)
T 1yye_A          108 VEGIL-EIFDMLLATTSRFRELKLQHKEYLCVKAMILL  144 (268)
T ss_dssp             STTHH-HHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             hccHH-HHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHc
Confidence             3555 77888999999999999999999999999986

>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=99.87  E-value=1.2e-21  Score=166.34  Aligned_cols=114  Identities=25%  Similarity=0.417  Sum_probs=103.1

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR  299 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~  299 (335)
                      ...+.|..+.+..+..+..+|+|||++|+|.+|+.+||++|||++|+++++|+.|+++....+.+++ +|..+..+....
T Consensus        47 ~~~~~~~~~~~~~~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~l~~a~~~~~~~~~~~~-~g~~~~~~~~~~  125 (244)
T 1nq7_A           47 SREALWQQCAIQITHAIQYVVEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPLNNTVLF-EGKYGGMQMFKA  125 (244)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHTSCHHHHHHHHHHHHHHHHHHHHGGGEETTTTEEEE-TTEEEEGGGGGG
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcCCCCEEeE-CCEEecHHHHhh
Confidence            4566788888899999999999999999999999999999999999999999999999888888999 999888776543


Q ss_pred             -hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 -SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 -~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                       +++ ++++.+++++.+|++|++|++||+|||||+||
T Consensus       126 ~~~~-~~~~~i~~~~~~l~~L~ld~~E~~lLkAivL~  161 (244)
T 1nq7_A          126 LGSD-DLVNEAFDFAKNLCSLQLTEEEIALFSSAVLI  161 (244)
T ss_dssp             GSCH-HHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHS
T ss_pred             cChH-HHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHc
Confidence             344 78899999999999999999999999999987

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

Probab=99.87  E-value=5.6e-22  Score=167.89  Aligned_cols=115  Identities=25%  Similarity=0.461  Sum_probs=91.1

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR  299 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~  299 (335)
                      +..+.|..+...++..+..+|+|||+||+|.+|+.+||++|||++|+++++|+.|+++....+.+++++|..+..+....
T Consensus        62 s~~~~~~~~~~~~~~~l~~~VewAK~lP~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~l~~~~g~~~~~~~~~~  141 (245)
T 3n00_A           62 TVQEIWEDFSMSFTPAVREVVEFAKHIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFNVKDQTVMFLSRTTYSLQELGA  141 (245)
T ss_dssp             -CCHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTCCSCC--------------CCGG
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEecCCCeecHHHHhh
Confidence            44578888999999999999999999999999999999999999999999999999877777889999999988766543


Q ss_pred             -hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 -SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 -~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                       +++ ++.+.+++|+.+|++|++|.+||+|||||+||
T Consensus       142 ~~~~-~~~~~i~~~~~~l~~L~ld~~E~~lLkAIvL~  177 (245)
T 3n00_A          142 MGMG-DLLSAMFDFSEKLNSLALTEEELGLFTAVVLV  177 (245)
T ss_dssp             GTTH-HHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHH
T ss_pred             ccHH-HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence             444 88999999999999999999999999999986

>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=99.87  E-value=2.1e-21  Score=166.05  Aligned_cols=116  Identities=16%  Similarity=0.307  Sum_probs=103.7

Q ss_pred             CChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccC--CCeEEeeCCeEeeHHh
Q psy2636         219 IAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAE--DTKLIFCNGVVLEKQQ  296 (335)
Q Consensus       219 ~~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~--~~~~~~~~g~~~~~~~  296 (335)
                      ......+..++++....+..+|+|||++|+|.+|+.+||++|||++|+++++|+.||++...  .+.+++++|..+..+.
T Consensus        36 ~~~~~~~~~l~e~a~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~rs~~~~~~~~l~~~~g~~~~~~~  115 (260)
T 3vhv_A           36 DTAENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQYSWMSLLSFALSWRSYKHTNSQFLYFAPDLVFNEEK  115 (260)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECHHH
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHHhChHHhcCCHHHHHHHHHHhHHHHHHHHHHHHhhccCCCCeEEecCCccccHHH
Confidence            35667788999999999999999999999999999999999999999999999999997653  3579999999998876


Q ss_pred             hhh-hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         297 CQR-SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       297 ~~~-~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ... +++ ++++.+.+++.+|++|++|.+||+|||||+||
T Consensus       116 ~~~~~~~-~~~~~l~~~~~~l~~L~ld~~E~~lLkAIvLf  154 (260)
T 3vhv_A          116 MHQSAMY-ELCQGMHQISLQFVRLQLTFEEYTIMKVLLLL  154 (260)
T ss_dssp             HHHTTCH-HHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHT
T ss_pred             hhcccHH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence            543 444 78889999999999999999999999999987

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

Probab=99.87  E-value=2.4e-21  Score=164.28  Aligned_cols=115  Identities=18%  Similarity=0.361  Sum_probs=103.2

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCC-CeEEeeCCeEeeHHhhh
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAED-TKLIFCNGVVLEKQQCQ  298 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~-~~~~~~~g~~~~~~~~~  298 (335)
                      .....+..++++....+..+|+|||+||+|.+|+.+||++|||++|+++++|+.||++...+ +.+++++|..+.++...
T Consensus        33 ~~~~~~~~~~~~a~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~~~l~~~~g~~~~~~~~~  112 (243)
T 3ltx_A           33 TKVHLLNSLVKLAERELVHLINWAKNVPGYTDLSLSDQVHLIECCWMELLLLNCAFRSIEHGGKSLAFAPDLVLDRSSWS  112 (243)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTTTTSEEEEETTEEEEHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHcCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCCeEEecCCcccchhhhc
Confidence            46677888999999999999999999999999999999999999999999999999987654 46999999999887654


Q ss_pred             h-hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         299 R-SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       299 ~-~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      . +++ ++.+.+++++.+|++|++|.+||+|||||+||
T Consensus       113 ~~~~~-~~~~~i~~~~~~l~~L~ld~~E~~lLkaivL~  149 (243)
T 3ltx_A          113 TVEMT-EIFEQVAAVSEQMMQNHLHKDELLLLQAMVLV  149 (243)
T ss_dssp             HTTCH-HHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             ccCHH-HHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHh
Confidence            3 444 78888999999999999999999999999986

>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=99.86  E-value=2.6e-21  Score=164.38  Aligned_cols=115  Identities=23%  Similarity=0.404  Sum_probs=101.6

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR  299 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~  299 (335)
                      ...+.|..+++..+..+..+|+|||++|+|.+|+.+||++|||++|+++++|+.|+++...++.+.+ +|.++..+....
T Consensus        53 ~~~~~~~~~~~~~~~~l~~~VewaK~iP~F~~L~~~DQi~LLk~~~~el~lL~~a~~~~~~~~~~~~-~g~~~~~~~~~~  131 (248)
T 3l0l_A           53 SMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNRTVFF-EGKYGGMELFRA  131 (248)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHGGGGEETTTTEEEE-TTEEECGGGGGG
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcCCCCEEEe-CCCcccHHHHhh
Confidence            4567788899999999999999999999999999999999999999999999999998888888888 777776554433


Q ss_pred             hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 ~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ....++++.+++++.+|++|++|.+||+|||||+||
T Consensus       132 ~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkAivLf  167 (248)
T 3l0l_A          132 LGCSELISSIFDFSHSLSALHFSEDEIALYTALVLI  167 (248)
T ss_dssp             GSCHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHS
T ss_pred             ccHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            223488999999999999999999999999999987

>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=99.86  E-value=1.6e-21  Score=167.47  Aligned_cols=115  Identities=29%  Similarity=0.464  Sum_probs=106.0

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR  299 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~  299 (335)
                      .+.+.|..+.+..+..+..+|+|||+||+|.+|+.+||++|||++|+++++|+.|+++....+.+++++|..+.++....
T Consensus        67 ~~~~~~~~~~~~~~~~l~~~VewaK~lP~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~l~~~~g~~~~~~~~~~  146 (267)
T 3ilz_A           67 VDLEAFSEFTKIITPAITRVVDFAKKLPMFSELPXEDQIILLKGCCMEIMSLRAAVRYDPESDTLTLSGEMAVKREQLKN  146 (267)
T ss_dssp             BCHHHHHHHHHHHHHHHHHHHHHHHTSHHHHTSCHHHHHHHHHHHHHHHHHHHHHTTCBTTTTBEEETTTEEECHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHhcCcchhhCCHhHHHHHHHHHHHHHHHHHHHHHhcCCCCEEEecCCeeecHHHHhc
Confidence            45678899999999999999999999999999999999999999999999999999999888899999999998877643


Q ss_pred             -hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 -SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 -~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                       +.+ .+.+.+++|+.+|++|++|.+||+|||||+||
T Consensus       147 ~~~~-~~~~~i~~~~~~l~~L~ld~~E~~lLkAivL~  182 (267)
T 3ilz_A          147 GGLG-VVSDAIFELGKSLSAFNLDDTEVALLQAVLLM  182 (267)
T ss_dssp             TTTT-HHHHHHHHHHHHHGGGCCCHHHHHHHHHHHHS
T ss_pred             cCHH-HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhc
Confidence             445 78889999999999999999999999999987

>1l2j_A Estrogen receptor beta; nuclear receptor, transcription factor, antagonist transcription receptor; HET: ETC; 2.95A {Homo sapiens} SCOP: a.123.1.1

Probab=99.86  E-value=8.5e-22  Score=169.51  Aligned_cols=115  Identities=23%  Similarity=0.421  Sum_probs=103.3

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhh-
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQ-  298 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~-  298 (335)
                      .+...+..+.++....+..+|+|||+||+|.+|+.+||++|||++|+++++|+.||++....+.+++++|..+..+... 
T Consensus        56 ~~~~~~~~l~~~a~~~l~~~VewAK~lP~F~~L~~~DQi~LLk~~w~el~iL~~a~rs~~~~~~l~~~~g~~~~~~~~~~  135 (271)
T 1l2j_A           56 TEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKC  135 (271)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHTTHHHHHHHHHHHHTSSSTTEECSSSSCCEETGGGGG
T ss_pred             cchhHHHHHHHHHHHHHHHHHHHHHhCcccccCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCeeeecCCccccchhhhh
Confidence            3455678889999999999999999999999999999999999999999999999999988889999999988876432 


Q ss_pred             -hhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         299 -RSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       299 -~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                       .+++ ++++.+++++.+|++|++|.+||+|||||+||
T Consensus       136 ~~g~~-~~~~~l~~~~~~l~~L~ld~~E~~lLkAIvLf  172 (271)
T 1l2j_A          136 VEGIL-EIFDMLLATTSRFRELKLQHKEYLCVKAMILL  172 (271)
T ss_dssp             STTHH-HHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             hccHH-HHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHc
Confidence             3555 77888999999999999999999999999986

>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=99.86  E-value=1.7e-21  Score=168.72  Aligned_cols=116  Identities=24%  Similarity=0.497  Sum_probs=106.3

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhh-
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQ-  298 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~-  298 (335)
                      .....+..+.++....+..+|+|||+||+|.+|+.+||++|||++|+++++|+.|+++....+.+.+++|..+.++... 
T Consensus        85 ~~~~~~~~l~e~~~~~l~~~VewaK~lP~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~~~~~g~~~~~~~~~~  164 (283)
T 3ipq_A           85 ARQQRFAHFTELAIVSVQEIVDFAKQLPGFLQLSREDQIALLKTSAIEVMLLETSRRYNPGSESITFLKDFSYNREDFAK  164 (283)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETTTTEEEETTTEEECHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhcCcChhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEeCCCceecHHHHHH
Confidence            3466788899999999999999999999999999999999999999999999999999888889999999999887653 


Q ss_pred             hhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         299 RSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       299 ~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      .+++.++++.+++++.+|++|+||.+||+|||||+||
T Consensus       165 ~g~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkAIvL~  201 (283)
T 3ipq_A          165 AGLQVEFINPIFEFSRAMNELQLNDAEFALLIAISIF  201 (283)
T ss_dssp             TTCCHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHT
T ss_pred             cCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            4666688999999999999999999999999999987

>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=99.86  E-value=4.7e-21  Score=164.65  Aligned_cols=114  Identities=24%  Similarity=0.429  Sum_probs=100.5

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR  299 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~  299 (335)
                      ...+.|..+++..+..+..+|+|||++|+|.+|+.+||++|||++|+++++|+.|+++....+.+.+ +|.++..+....
T Consensus        62 ~~~~~~~~~~~~~~~~l~~~VewaK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~~~~~~~~~~l~-~g~~~~~~~~~~  140 (270)
T 1n83_A           62 QREVMWQLCAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQNNTVYF-DGKYASPDVFKS  140 (270)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHSTTTTTSCHHHHHHHHHHHHHHHHHHHGGGGEETTTTEEEE-TTEEECGGGGGG
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHcCCChhhcCHHHHHHHHHHhHHHHHHHHHHHHhcCCCCeEEe-CCccccHHHHHh
Confidence            3456788888999999999999999999999999999999999999999999999998887777877 677776554433


Q ss_pred             -hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 -SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 -~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                       +.+ ++++.+++++.+|++|++|++||+|||||+||
T Consensus       141 ~~~~-~~~~~i~~~~~~l~~L~ld~~E~~lLkAivLf  176 (270)
T 1n83_A          141 LGCE-DFISFVFEFGKSLCSMHLTEDEIALFSAFVLM  176 (270)
T ss_dssp             GSCH-HHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHS
T ss_pred             cCHH-HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence             344 78999999999999999999999999999987

>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=99.86  E-value=1.7e-21  Score=166.52  Aligned_cols=113  Identities=21%  Similarity=0.371  Sum_probs=101.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeC-CeEeeHHhhhh-h
Q psy2636         223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCN-GVVLEKQQCQR-S  300 (335)
Q Consensus       223 ~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~-g~~~~~~~~~~-~  300 (335)
                      +.+..++++....+..+|+|||++|+|.+|+.+||++|||++|+++++|+.|+++....+.+++++ |..+..++... +
T Consensus        56 ~~~~~~~~~~~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~  135 (254)
T 3b0t_A           56 SMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVSDVTKAG  135 (254)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHGGGTEETTTTEEECSSGGGEECHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhCCCCcccCCHHHHHHHHHHhhHHHHHHHHHHHhccCCCeEEecCCCeeeeHHHHHHcC
Confidence            347788899999999999999999999999999999999999999999999999888888899986 66677665433 6


Q ss_pred             hcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         301 FGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       301 ~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ++.++++.+++++.+|++|++|++||+|||||+||
T Consensus       136 ~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkAivL~  170 (254)
T 3b0t_A          136 HSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIV  170 (254)
T ss_dssp             CCHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHS
T ss_pred             CcHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Confidence            66688999999999999999999999999999987

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

Probab=99.86  E-value=4.6e-21  Score=166.18  Aligned_cols=116  Identities=16%  Similarity=0.307  Sum_probs=103.5

Q ss_pred             CChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccC--CCeEEeeCCeEeeHHh
Q psy2636         219 IAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAE--DTKLIFCNGVVLEKQQ  296 (335)
Q Consensus       219 ~~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~--~~~~~~~~g~~~~~~~  296 (335)
                      ......+..++++....+..+|+|||+||+|.+|+.+||++|||++|+++++|+.||++...  .+.+++++|..+..+.
T Consensus        70 ~~~~~~~~~l~e~a~~~l~~~VewAK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~rS~~~~~~~~l~~~~g~~~~~~~  149 (294)
T 3vhu_A           70 DTAENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQYSWMSLLSFALSWRSYKHTNSQFLYFAPDLVFNEEK  149 (294)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHTCTTTTSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECHHH
T ss_pred             CChHHHHHHHHHHHHHHHHHHHHHHHhCcchhhCCHHHHHHHHHHhHHHHHHHHHHHHhhhcCCCCeEEeCCCccccHHH
Confidence            35667788999999999999999999999999999999999999999999999999997653  3579999999998776


Q ss_pred             hhh-hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         297 CQR-SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       297 ~~~-~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ... +++ ++++.+.+++.+|++|++|.+||+|||||+||
T Consensus       150 ~~~~~~~-~~~~~l~~~~~~l~~L~ld~~EyalLkAIvLf  188 (294)
T 3vhu_A          150 MHQSAMY-ELCQGMHQISLQFVRLQLTFEEYTIMKVLLLL  188 (294)
T ss_dssp             HHHTTCH-HHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHT
T ss_pred             hhcccHH-HHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHh
Confidence            543 444 78889999999999999999999999999997

>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=99.86  E-value=6.7e-21  Score=163.84  Aligned_cols=116  Identities=20%  Similarity=0.316  Sum_probs=101.5

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccC--CCeEEeeCCeEeeHHhh
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAE--DTKLIFCNGVVLEKQQC  297 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~--~~~~~~~~g~~~~~~~~  297 (335)
                      .....+..+.+.....+..+|+|||++|+|.+|+.+||++|||++|+++++|+.||++...  +..+++++|.+++.+..
T Consensus        46 ~~~~~~~~l~e~a~~~l~~~VewAK~ip~F~~L~~~DQv~LLk~~w~el~iL~~a~rs~~~~~~~~l~~~~g~~~~~~~~  125 (269)
T 1t7r_A           46 SFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRM  125 (269)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECHHHH
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHhCccHhhCCHHHHHHHHHHhHHHHHHHHHHHHhcccCCCCeEEeCCCceecHHhh
Confidence            4556678888899999999999999999999999999999999999999999999997653  33688999999988765


Q ss_pred             hhhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         298 QRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       298 ~~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ......++++.+++++.+|++|++|.+||+|||||+||
T Consensus       126 ~~~~~~~~~~~i~~~~~~l~~L~ld~~E~~lLkAIvLf  163 (269)
T 1t7r_A          126 HKSRMYSQCVRMRHLSQEFGWLQITPQEFLCMKALLLF  163 (269)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHT
T ss_pred             hhhhHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHc
Confidence            44333367788899999999999999999999999997

>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=99.86  E-value=2.3e-21  Score=166.47  Aligned_cols=115  Identities=21%  Similarity=0.317  Sum_probs=95.8

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHh-h-
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQ-C-  297 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~-~-  297 (335)
                      .+...|..+....+..|+.+|+|||++|+|.+|+.+||++|||++|+++++++.|++++.++..+.+.++....... . 
T Consensus        73 ~~~~~~~~~~~~~~~~v~~iVewAK~iPgF~~L~~~DQi~LLk~~w~ElllL~~a~~~~~~~~~~~~~~~~~~~~~~~~~  152 (273)
T 3vi8_A           73 AEVRIFHCCQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGMLVAYGNGFITREFLKSL  152 (273)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHGGGSTTTTTSCHHHHHHHHHHHHHHHHHHHHGGGEETTEEEETTTTEEEEHHHHHHS
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHccCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeeeeCCCccchHHHHHh
Confidence            34456788888899999999999999999999999999999999999999999999988766555555444333221 1 


Q ss_pred             hhhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         298 QRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       298 ~~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ..+++ ++++.+++|+.+|++|++|.+||+|||||+||
T Consensus       153 ~~~~~-~~~~~l~~~~~~~~~L~ld~~E~alLkAivLf  189 (273)
T 3vi8_A          153 RKPFC-DIMEPKFDFAMKFNALELDDSDISLFVAAIIC  189 (273)
T ss_dssp             CTTTH-HHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHS
T ss_pred             hhhHH-HHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHh
Confidence            12344 88899999999999999999999999999987

>1g2n_A Ultraspiracle protein; antiparallel alpha-helical sandwich, structural proteomics in europe, spine, structural genomics, gene regulation; HET: EPH; 1.65A {Heliothis virescens} SCOP: a.123.1.1 PDB: 2r40_A* 1r20_A* 1r1k_A* 3ixp_A*

Probab=99.86  E-value=1.1e-20  Score=162.27  Aligned_cols=112  Identities=21%  Similarity=0.387  Sum_probs=98.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccC----CCe--------------E
Q psy2636         223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAE----DTK--------------L  284 (335)
Q Consensus       223 ~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~----~~~--------------~  284 (335)
                      ..+..++++....+..+|+|||++|+|.+|+.+||++|||++|+++++|+.||++...    .+.              +
T Consensus        42 ~~~~~l~~~~~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~w~el~lL~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~l  121 (264)
T 1g2n_A           42 APVSSLCQIGNKQIAALVVWARDIPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLTEERDGVDGTGNRTTSPPQLM  121 (264)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHGGGSCCC----------CCCCCCEE
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHcCCChhcCCHHHHHHHHHHhhHHHHHHHHHHHccccccccccccccccccccccccce
Confidence            5678888999999999999999999999999999999999999999999999998866    555              9


Q ss_pred             EeeCCeEeeHHhhhh-hhcHHHH-HHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         285 IFCNGVVLEKQQCQR-SFGDDWL-NAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       285 ~~~~g~~~~~~~~~~-~~~~~~~-~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ++++|..++++.... +++ ++. +.+.+++.+|++|++|.+||+|||||+||
T Consensus       122 ~~~~g~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~L~ld~~E~~lLkAivL~  173 (264)
T 1g2n_A          122 CLMPGMTLHRNSALQAGVG-QIFDRVLSELSLKMRTLRVDQAEYVALKAIILL  173 (264)
T ss_dssp             EEETTEEEEHHHHHHHTCH-HHHHHHHHHTHHHHHHTTCCHHHHHHHHHHHHS
T ss_pred             eecCCcccCchhhhhccHH-HHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHh
Confidence            999999999876543 455 455 67789999999999999999999999997

>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=99.86  E-value=5.4e-21  Score=163.48  Aligned_cols=115  Identities=22%  Similarity=0.343  Sum_probs=102.1

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccC--CCeEEeeCCeEeeHHhh
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAE--DTKLIFCNGVVLEKQQC  297 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~--~~~~~~~~g~~~~~~~~  297 (335)
                      .....+..+.++..+.+..+|+|||++|+|.+|+.+||++|||++|+++++|+.||++...  ++.+++++|..+..+..
T Consensus        39 ~~~~~~~~l~~~a~~~l~~~VewaK~iP~F~~L~~~DQ~~LLk~~~~el~iL~~a~rs~~~~~~~~l~~~~g~~~~~~~~  118 (261)
T 3mnp_A           39 SAWRIMTTLNMLGGRQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMVFALGWRSYRQASGNLLCFAPDLIINEQRM  118 (261)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHhCcChhcCCHHHHHHHHHHHHHHHHHHHHHHHcccCCCCCEEEecCCcccchhhh
Confidence            4566778889999999999999999999999999999999999999999999999998753  33589999999988765


Q ss_pred             hh-hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         298 QR-SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       298 ~~-~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      .. +++ ++++.+++++.+|++|++|.+||+|||||+||
T Consensus       119 ~~~~~~-~~~~~l~~~~~~l~~L~ld~~E~~lLkAIvL~  156 (261)
T 3mnp_A          119 TLPCMY-DQCKHMLFISTELQRLQVSYEEYLCMKTLLLL  156 (261)
T ss_dssp             TSTTTH-HHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHT
T ss_pred             hhhhHH-HHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHc
Confidence            43 444 77888999999999999999999999999987

>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=99.85  E-value=2.6e-21  Score=168.17  Aligned_cols=115  Identities=19%  Similarity=0.342  Sum_probs=103.3

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeC-CeEeeHHhhhh
Q psy2636         221 EPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCN-GVVLEKQQCQR  299 (335)
Q Consensus       221 ~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~-g~~~~~~~~~~  299 (335)
                      +.+.|..+.+.....+..+|+|||+||+|.+|+.+||++|||++|+++++|+.|+++...++.+++++ |..+.+++...
T Consensus        57 ~~~~~~~l~~~~~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~  136 (292)
T 2o4j_A           57 PLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMSWDCGSQDYKYDVTDVSK  136 (292)
T ss_dssp             CCTTHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHGGGTEETTTTEEECSSGGGEECHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHcCcchhhccHHHHHHHHHHhHHHHHHHHHHHHhcCCCCeEEecCCCeEEcHHHHHh
Confidence            34567888889999999999999999999999999999999999999999999999888888899984 87787766543


Q ss_pred             -hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 -SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 -~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                       +++.++++.+++|+.+|++|+||++||+|||||+||
T Consensus       137 ~g~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkAIvLf  173 (292)
T 2o4j_A          137 AGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIV  173 (292)
T ss_dssp             TTCCHHHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHS
T ss_pred             cCCcHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence             666688999999999999999999999999999997

>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=99.85  E-value=4e-21  Score=163.37  Aligned_cols=111  Identities=23%  Similarity=0.292  Sum_probs=98.1

Q ss_pred             HHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccC--CCeEEeeCCeEeeHHhhhh--h
Q psy2636         225 IQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAE--DTKLIFCNGVVLEKQQCQR--S  300 (335)
Q Consensus       225 ~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~--~~~~~~~~g~~~~~~~~~~--~  300 (335)
                      +..+.++....+..+|+|||++|+|.+|+.+||++|||++|+++++|+.||++...  .+.+++++|..+..+....  +
T Consensus        47 ~~~l~~~a~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~rs~~~~~~~~~~~~~g~~~~~~~~~~~~~  126 (246)
T 1ymt_A           47 FSLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNSWSELLVLDHIYRQVQYGKEDSILLVTGQEVELSTVAVQAG  126 (246)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCTTEEECTTSCEEEHHHHHHHCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHhChhHHhCCHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCeeEecCCCccchhhhhhhcc
Confidence            56678888889999999999999999999999999999999999999999998764  6789999999998765432  2


Q ss_pred             hc-HHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         301 FG-DDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       301 ~~-~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      .+ .++++.+.+++.+|++|++|.+||+|||||+||
T Consensus       127 ~~~~~~~~~~~~~~~~~~~L~ld~~E~~lLkAivL~  162 (246)
T 1ymt_A          127 SLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILF  162 (246)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHT
T ss_pred             hhHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHhc
Confidence            22 367888999999999999999999999999987

>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=99.85  E-value=5.5e-21  Score=163.64  Aligned_cols=115  Identities=21%  Similarity=0.370  Sum_probs=100.9

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCC--CeEEeeCCeEeeHHhh
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAED--TKLIFCNGVVLEKQQC  297 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~--~~~~~~~g~~~~~~~~  297 (335)
                      .....+..++++....+..+|+|||++|+|.+|+.+||++|||++|+++++|+.||++....  +.+++++|..++.+..
T Consensus        38 ~~~~~~~~l~e~a~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~~~~l~~~~~~~~~~~~~  117 (261)
T 1sqn_A           38 TSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRM  117 (261)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECGGGC
T ss_pred             chhhHHHHHHHHHHHHHHHHHHHHHhCccHhhCCHHHHHHHHHhhHHHHHHHHHHHHhhhcCCCCeEEeCCCcccchHhh
Confidence            45566788899999999999999999999999999999999999999999999999987543  3588999998887654


Q ss_pred             hh-hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         298 QR-SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       298 ~~-~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      .. +++ ++++.+++++.+|++|++|.+||+|||||+||
T Consensus       118 ~~~~~~-~~~~~i~~~~~~l~~L~ld~~E~~lLkAIvLf  155 (261)
T 1sqn_A          118 KESSFY-SLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLL  155 (261)
T ss_dssp             CSHHHH-HHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHT
T ss_pred             hhhhHH-HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHc
Confidence            32 444 67788999999999999999999999999997

>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=99.84  E-value=6.6e-21  Score=162.67  Aligned_cols=114  Identities=19%  Similarity=0.278  Sum_probs=100.5

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccC--CCeEEeeCCeEeeHHhhhh
Q psy2636         222 PEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAE--DTKLIFCNGVVLEKQQCQR  299 (335)
Q Consensus       222 ~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~--~~~~~~~~g~~~~~~~~~~  299 (335)
                      ...+..++++....+..+|+|||+||+|.+|+.+||++|||++|+++++|+.||++...  .+.+++++|..+..+.+..
T Consensus        55 ~~~~~~l~~~a~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~lL~~a~rs~~~~~~~~l~~~~g~~~~~~~~~~  134 (257)
T 3plz_A           55 LSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIAS  134 (257)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCBTTEEECTTSCEEEHHHHHT
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHcCcChhcCCHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCeEEecCCCccChHHHhh
Confidence            44577788888899999999999999999999999999999999999999999998753  4789999999998876542


Q ss_pred             --hhc-HHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 --SFG-DDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 --~~~-~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                        +.. .++++.+.+++.+|++|++|.+||+|||||+||
T Consensus       135 ~~g~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkAivL~  173 (257)
T 3plz_A          135 QAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLF  173 (257)
T ss_dssp             TSCHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHS
T ss_pred             hcCCcHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence              221 477888999999999999999999999999987

>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=99.84  E-value=1.3e-20  Score=160.27  Aligned_cols=115  Identities=19%  Similarity=0.318  Sum_probs=100.8

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhh-h
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQC-Q  298 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~-~  298 (335)
                      .....+..++++....+..+|+|||++|+|.+|+.+||++|||++|+++++|+.|+++....+.+ +.++..+..+.. .
T Consensus        51 ~~~~~~~~~~e~~~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~l~~a~~~~~~~~~~-~~~~~~~~~~~~~~  129 (246)
T 1xvp_B           51 PVLPLVTHFADINTFMVLQVIKFTKDLPVFRSLPIEDQISLLKGAAVEICHIVLNTTFCLQTQNF-LCGPLRYTIEDGAR  129 (246)
T ss_dssp             CSHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHSCHHHHHHHHHHHHHHHHHHHHGGGEETTTTEE-ECSSCEECHHHHHH
T ss_pred             hHhHHHHHHHHHHHHHHHHHHHHHHcCcchhhCCHHHHHHHHHhhHHHHHHHHHHHHhccccCeE-eeCCeeecHHHHHH
Confidence            45677889999999999999999999999999999999999999999999999999988776665 556666666543 3


Q ss_pred             hhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         299 RSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       299 ~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      .+++.++.+.+++|+.+|++|++|++||+|||||+||
T Consensus       130 ~~~~~~~~~~i~~~~~~l~~L~ld~~E~~lLkAivL~  166 (246)
T 1xvp_B          130 VGFQVEFLELLFHFHGTLRKLQLQEPEYVLLAAMALF  166 (246)
T ss_dssp             HTCCHHHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHS
T ss_pred             ccccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHc
Confidence            4666688899999999999999999999999999987

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

Probab=99.84  E-value=5.5e-21  Score=161.44  Aligned_cols=113  Identities=18%  Similarity=0.349  Sum_probs=97.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhh-hhh
Q psy2636         223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQ-RSF  301 (335)
Q Consensus       223 ~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~-~~~  301 (335)
                      ..+..+.++....+..+|+|||++|+|.+|+.+||++|||++|+++++|+.||++....+.+++++|..+.++... .+.
T Consensus        37 ~~~~~~~~~~~~~l~~~vewaK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~a~rs~~~~~~~~~~~g~~~~~~~~~~~~~  116 (235)
T 2nxx_A           37 TTVNNICQATHKQLFQLVQWAKLVPHFTSLPLTDQVQLLRAGWNELLIAAFSHRSMQAQDAIVLATGLTVNKSTAHAVGV  116 (235)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHHSTTSTTSCHHHHHHHHHHHHHHHHHHHHHHTTSSSSSSEECSSSCEECSSSCSSSSC
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHhHHHHHHHHHHHhcccCCCceEecCCcccccchhhhhch
Confidence            3567778888899999999999999999999999999999999999999999999887778999999999876543 244


Q ss_pred             cHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         302 GDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       302 ~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      +..+.+.+.+++.+|++|++|.+||+|||||+||
T Consensus       117 ~~~~~~~~~~~~~~l~~L~ld~~E~~lLkaivL~  150 (235)
T 2nxx_A          117 GNIYDRVLSELVNKMKEMKMDKTELGCLRAIILY  150 (235)
T ss_dssp             SSSHHHHHHHTHHHHHHHTCCHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            4223344568999999999999999999999987

>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=99.84  E-value=2.9e-20  Score=162.15  Aligned_cols=115  Identities=23%  Similarity=0.327  Sum_probs=99.9

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeC-CeEeeHHhhh-
Q psy2636         221 EPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCN-GVVLEKQQCQ-  298 (335)
Q Consensus       221 ~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~-g~~~~~~~~~-  298 (335)
                      ....|..++++....+..+|+|||+||+|.+|+.+||++|||++|+++++|+.|+++...++.+.+++ |..+..+... 
T Consensus       100 ~~~~~~~l~e~~~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~  179 (302)
T 2hc4_A          100 RLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLRSNQSFSLEDMSWSCGGPDFKYCINDVTK  179 (302)
T ss_dssp             CCTTHHHHHHHHHHHHHHHHHHHTTSTTTTTSCHHHHHHHHHHHHHHHHHHHGGGTEETTTTEEECSSSTTEECHHHHHT
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCeEEecCCCeeecHHHHHH
Confidence            34567888999999999999999999999999999999999999999999999988777777788875 4556555443 


Q ss_pred             hhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         299 RSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       299 ~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      .++..++++.+++|+.+|++|+||.+||+|||||+||
T Consensus       180 ~g~~~~~~~~l~~~~~~l~~L~ld~~E~alLkAIvLf  216 (302)
T 2hc4_A          180 AGHTLELLEPLVKFQVGLKKLKLHEEEHVLLMAICLL  216 (302)
T ss_dssp             TTCCHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHT
T ss_pred             ccCcHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Confidence            3554688999999999999999999999999999997

>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=99.83  E-value=4.7e-21  Score=167.48  Aligned_cols=113  Identities=23%  Similarity=0.244  Sum_probs=99.7

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhhhh
Q psy2636         222 PEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSF  301 (335)
Q Consensus       222 ~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~~~  301 (335)
                      .+.+..+++.....+..+|+|||+||+|.+|+.+||++|||++|+++++|+.|+++....+.+++++ ..+..+....++
T Consensus       119 ~~~~~~l~e~~~~~L~~~VewAK~lP~F~~L~~~DQi~LLk~~w~el~lL~~a~~~~~~~~~~l~~~-~~~~~~~~~~g~  197 (316)
T 1nrl_A          119 FSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECGR-LSYCLEDTAGGF  197 (316)
T ss_dssp             GTTHHHHHHHHHHHHHHHHHHHHHCHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTEETTTTEEEETT-EEEEECCCSSCH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCcchhhcCHHHHHHHHHHHHHHHHHHHHHHHhhcCCCeEEECC-EeecHHHHhccc
Confidence            4567888999999999999999999999999999999999999999999999999988777888754 666655443355


Q ss_pred             cHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         302 GDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       302 ~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      +.++++.+++|+.+|++|+||++||+|||||+||
T Consensus       198 ~~~~~~~i~~~~~~l~~L~ld~~E~alLkAIvLf  231 (316)
T 1nrl_A          198 QQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLF  231 (316)
T ss_dssp             HHHTTSHHHHHHHHHHHTCCCHHHHHHHHHHHHT
T ss_pred             cHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHh
Confidence            5578889999999999999999999999999997

>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=99.83  E-value=1.1e-20  Score=167.20  Aligned_cols=114  Identities=19%  Similarity=0.278  Sum_probs=90.1

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccC--CCeEEeeCCeEeeHHhhhh
Q psy2636         222 PEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAE--DTKLIFCNGVVLEKQQCQR  299 (335)
Q Consensus       222 ~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~--~~~~~~~~g~~~~~~~~~~  299 (335)
                      ...+..+.++..+.+..+|+|||+||+|.+|+.+||++|||++|+++++|+.||++...  .+.+++++|..+..+.+..
T Consensus       150 ~~~~~~l~e~a~~~L~~~VewAK~iP~F~~L~~~DQi~LLk~~w~ElllL~~a~rs~~~~~~~~ll~~~G~~i~~~~~~~  229 (352)
T 3tx7_B          150 LSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIAS  229 (352)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHTCCC----------CHHHHHHHHHHHHHHHHHHHHHHTCCSSCCBCTTCCBCCHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHcChhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEecCCCcccHHHHHH
Confidence            45677888888999999999999999999999999999999999999999999998754  3678899999998776532


Q ss_pred             --hhc-HHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 --SFG-DDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 --~~~-~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                        +.. .++++.+.+++.+|++|+||.+||+|||||+||
T Consensus       230 ~~g~~~~~l~~~l~~l~~~l~~L~ld~~EyalLkAIvLf  268 (352)
T 3tx7_B          230 QAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLF  268 (352)
T ss_dssp             TSCHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHS
T ss_pred             hccccHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence              221 377888999999999999999999999999997

>2p1t_A Retinoic acid receptor RXR-alpha; protein-ligand complex, hormone receptor; HET: 3TN; 1.80A {Homo sapiens} SCOP: a.123.1.1 PDB: 1mvc_A* 1mzn_A* 1mv9_A* 2p1u_A* 2p1v_A* 2zxz_A* 2zy0_A* 3fug_A* 3nsp_A 3nsq_A* 3r29_A 3r2a_A* 3r5m_A* 3e94_A* 3kwy_A* 1fby_A* 3uvv_B* 3fc6_A* 1rdt_A* 3fal_A* ...

Probab=99.82  E-value=7.6e-20  Score=155.05  Aligned_cols=111  Identities=20%  Similarity=0.413  Sum_probs=96.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh-hhc
Q psy2636         224 KIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR-SFG  302 (335)
Q Consensus       224 ~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~-~~~  302 (335)
                      .+..+.+++...+..+|+|||++|+|.+|+.+||++|||++|.++++++.|+++....+.+++++|..++.+.... +.+
T Consensus        42 ~~~~l~~~~~~~l~~~vewak~ip~F~~L~~~DQ~~LLk~~w~e~~il~~a~rs~~~~~~~~~~~g~~~~~~~~~~~~~~  121 (240)
T 2p1t_A           42 PVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVG  121 (240)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTSSSEEECTTSCEEEHHHHHTTTCH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCcChhcCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCcccccchhhhhchH
Confidence            4566777888889999999999999999999999999999999999999999988877788899999998876543 444


Q ss_pred             HHHHH-HHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         303 DDWLN-AILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       303 ~~~~~-~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                       .+.+ .+.+++.+|++|++|.+||++||||+||
T Consensus       122 -~~~~~~~~~~~~~l~~L~ld~~E~~~Lkai~l~  154 (240)
T 2p1t_A          122 -AIFDRVLTELVSKMRDMQMDKTELGCLRAIVLF  154 (240)
T ss_dssp             -HHHHHHHHHTHHHHHHTTCCHHHHHHHHHHHHS
T ss_pred             -HHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHh
Confidence             4444 4568999999999999999999999987

>3up3_A Acedaf-12; ligand binding domain, nematode, steroid binding protein- transcription complex; HET: XCA; 1.25A {Ancylostoma ceylanicum} PDB: 3up0_A*

Probab=99.81  E-value=2.8e-20  Score=157.14  Aligned_cols=109  Identities=12%  Similarity=0.253  Sum_probs=93.5

Q ss_pred             HHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEE---eeCCeEeeHHhhh---hh
Q psy2636         227 QFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLI---FCNGVVLEKQQCQ---RS  300 (335)
Q Consensus       227 ~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~---~~~g~~~~~~~~~---~~  300 (335)
                      .+.++.+..++.+|+|||++|+|.+|+.+||++|||++|+++++|+.|+++....+.+.   +.+|..+..+...   .+
T Consensus        45 ~l~~l~~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w~Ell~L~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g  124 (243)
T 3up3_A           45 DIMNIMDVTMRRFVKMAKRLPAFNDLSQDGKFALLKGGMIEMLTVRGVRRFDSSSGSWTTPTLGESSEVSINMFDQLNAD  124 (243)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHEETTTTEECCTTSCTTCCEEGGGGGGSCTT
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcccCCeeeecccCCCccccHHHHhhhccc
Confidence            45677788899999999999999999999999999999999999999999988888763   4577777655433   35


Q ss_pred             hcHHHHHHHHHHHHHhhc-CCCCHHHHHHHHHHHcC
Q psy2636         301 FGDDWLNAILEFCQSLHL-MEIDISAFACLCALTLI  335 (335)
Q Consensus       301 ~~~~~~~~~~~~~~~l~~-l~l~~~E~~ll~ai~l~  335 (335)
                      ++..+++.+.+++.+|++ |++|.+||+|||||+||
T Consensus       125 ~~~~~~~~l~~~~~~~~~~L~ld~~E~alLkAivLf  160 (243)
T 3up3_A          125 VRSEQKMRFLQFFKIFHEDIRSNDLVISMIMLIVLF  160 (243)
T ss_dssp             THHHHHHHHHHHHHTSCHHHHTCHHHHHHHHHHHHS
T ss_pred             ccHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhc
Confidence            553367889999999997 99999999999999987

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

Probab=99.81  E-value=1.4e-19  Score=156.77  Aligned_cols=113  Identities=15%  Similarity=0.282  Sum_probs=86.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCe--------EEeeCCe----
Q psy2636         223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTK--------LIFCNGV----  290 (335)
Q Consensus       223 ~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~--------~~~~~g~----  290 (335)
                      ..+..+.++....+..+|+|||++|+|.+|+.+||++|||++|+++++|+.||++....+.        ++++||.    
T Consensus        47 ~~~~~l~~~~~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~rs~~~~~~~~~~~~~~~~~~dGs~~~~  126 (279)
T 1hg4_A           47 GAVSALCQVVNKQLFQMVEYARMMPHFAQVPLDDQVILLKAAWIELLIANVAWCSIVSLDDGGAGGGGGGLGHDGSFERR  126 (279)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTTC---------------------
T ss_pred             hhHHHHHHHHHHHHHHHHHHHhcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhccCcccccccccccccCcccccc
Confidence            3577888889999999999999999999999999999999999999999999998764332        4555554    


Q ss_pred             ---------------EeeHHhhh-hhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         291 ---------------VLEKQQCQ-RSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       291 ---------------~~~~~~~~-~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                                     .+.++... .+++..+.+.+.+++.+|++|++|.+||+|||||+||
T Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~ld~~E~~lLkAivL~  187 (279)
T 1hg4_A          127 SPGLQPQQLFLNQSFSYHRNSAIKAGVSAIFDRILSELSVKMKRLNLDRRELSCLKAIILY  187 (279)
T ss_dssp             ----CCCEEESSSSCEEEHHHHHHHTCHHHHHHHHHHTHHHHHHHTCCHHHHHHHHHHHHS
T ss_pred             ccccccceeeecCCcccchhhHhhcchHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHc
Confidence                           33333322 2445333444568999999999999999999999987

>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=99.80  E-value=9.9e-20  Score=153.49  Aligned_cols=111  Identities=23%  Similarity=0.393  Sum_probs=91.3

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhh-h
Q psy2636         221 EPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQ-R  299 (335)
Q Consensus       221 ~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~-~  299 (335)
                      +.+.+..+.++....+..+|+|||++|+|.+|+.+||++|||++|+++++|+.|+++.....    .+|..+..+... .
T Consensus        40 ~~~~~~~~~~~~~~~l~~~vewaK~lp~F~~L~~~DQ~~LLk~~~~e~~~l~~a~~~~~~~~----~~~~~~~~~~~~~~  115 (232)
T 1osh_A           40 AEENFLILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLP----SGHSDLLEERIRNS  115 (232)
T ss_dssp             --CHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHTSC----HHHHHHHHHHHHTS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcCCchhhCCHHHHHHHHHHhHHHHHHHHHHHHhCCccC----CCCceecHHHHHHc
Confidence            34567888899999999999999999999999999999999999999999999998754321    233444443332 2


Q ss_pred             hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 ~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ++..++++.+++++.+|++|++|.+||+|||||+||
T Consensus       116 ~~~~~~~~~i~~~~~~l~~L~ld~~E~~lLkaivL~  151 (232)
T 1osh_A          116 GISDEYITPMFSFYKSIGELKMTQEEYALLTAIVIL  151 (232)
T ss_dssp             SCCTTTHHHHHHHHHHHHTTCCCHHHHHHHHHHHHT
T ss_pred             CCcHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence            455578899999999999999999999999999986

>3u9q_A Peroxisome proliferator-activated receptor gamma; nuclear receptor, adipogenesis, RXRA, nucleus, transcription; HET: DKA; 1.52A {Homo sapiens} SCOP: a.123.1.1 PDB: 1i7i_A* 3ty0_A* 1zeo_A* 2p4y_A* 3et3_A* 3et0_A* 2hwq_A* 2ath_A* 2f4b_A* 2g0g_A* 2g0h_A* 2gtk_A* 2fvj_A* 2hwr_A* 2prg_A* 2q8s_A* 3fej_A* 3g9e_A* 3gbk_A* 3ia6_A* ...

Probab=99.79  E-value=6.5e-19  Score=151.03  Aligned_cols=103  Identities=24%  Similarity=0.405  Sum_probs=86.4

Q ss_pred             HHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeE-eeHHhhh---hhhcHHH
Q psy2636         230 SLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVV-LEKQQCQ---RSFGDDW  305 (335)
Q Consensus       230 ~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~-~~~~~~~---~~~~~~~  305 (335)
                      ......++.+|+|||++|+|.+|+.+||++|||++|+++++|+.|+++..  +.+++++|.. +..+...   .+++ ++
T Consensus        80 ~~~~~~v~~~VewAK~iP~F~~L~~~DQi~LLk~~~~el~lL~~a~~~~~--~~~~~~~g~~~~~~~~~~~~~~~~~-~~  156 (269)
T 3u9q_A           80 FRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNK--DGVLISEGQGFMTREFLKSLRKPFG-DF  156 (269)
T ss_dssp             HHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEET--TEEEETTTTEEEEHHHHHHSCTTGG-GS
T ss_pred             HHHHHHHHHHHHHHcCCCChhhcCHHHHHHHHHHhhHHHHHHHHHHhcCC--CCeEEeCCCccccHHHHHHhhhhHH-HH
Confidence            33445577899999999999999999999999999999999999987654  4677777765 5655433   3444 67


Q ss_pred             HHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         306 LNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       306 ~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ++.+.+|+.+|++|++|++||+|||||+||
T Consensus       157 ~~~l~~~~~~l~~L~ld~~E~alLkAIvLf  186 (269)
T 3u9q_A          157 MEPKFEFAVKFNALELDDSDLAIFIAVIIL  186 (269)
T ss_dssp             SHHHHHHHHHHHTTCCCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhhcCCHHHHHHHHHHHHh
Confidence            888899999999999999999999999987

>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=99.79  E-value=4.3e-19  Score=150.66  Aligned_cols=109  Identities=25%  Similarity=0.328  Sum_probs=82.1

Q ss_pred             HHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCC-CeEEeeCCeEeeHHhh--hhhhc
Q psy2636         226 QQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAED-TKLIFCNGVVLEKQQC--QRSFG  302 (335)
Q Consensus       226 ~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~-~~~~~~~g~~~~~~~~--~~~~~  302 (335)
                      ..+.++....+..+|+|||++|+|.+|+.+||++|||++|+++++|+.|+++...+ +.+.+++|........  ...+.
T Consensus        40 ~~l~e~a~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~~~~l~~~g~~~~~~~~~~~~~~~  119 (244)
T 3cjw_A           40 ENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHVAPLLAAAGLHASPMSADRVVAFM  119 (244)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHSSSGGGSCHHHHHHHHHHHHHHHHHHHHHHHTCCCSCCC-----------------CCCS
T ss_pred             HHHHHHHHHHHHHHHhHHHhCCChhcCCHHHHHHHHHHHHHHHHHHHHHHHhccccccccccccccccCccchhhhHHHH
Confidence            44667778889999999999999999999999999999999999999999988644 3466777765422111  12333


Q ss_pred             HHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         303 DDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       303 ~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                       +.++.+.+++.+|++|++|.+||+|||||+||
T Consensus       120 -~~~~~~~~~~~~~~~L~ld~~E~~lLkaivL~  151 (244)
T 3cjw_A          120 -DHIRIFQEQVEKLKALHVDSAEYSCLKAIVLF  151 (244)
T ss_dssp             -HHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHS
T ss_pred             -HHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHh
Confidence             45677889999999999999999999999987

>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=99.79  E-value=1.9e-19  Score=154.24  Aligned_cols=111  Identities=19%  Similarity=0.159  Sum_probs=85.3

Q ss_pred             HHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeE----EeeCCeEeeHHh----
Q psy2636         225 IQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKL----IFCNGVVLEKQQ----  296 (335)
Q Consensus       225 ~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~----~~~~g~~~~~~~----  296 (335)
                      .+.++++....+..+|+|||++|+|.+|+.+||++|||++|+++++|+.|+++...+...    .+.+|.......    
T Consensus        49 ~~~l~e~a~~~L~~~V~wAK~iP~F~~L~~~DQv~LLk~~w~ElllL~~A~rs~~~~~~~~~~~~~~~~il~~~~~~~~~  128 (268)
T 3f5c_B           49 PQVVCEAASAGLLKTLRFVKYLPCFQILPLDQQLVLVRSCWAPLLMLELAQDHLHFEMMEIPETNTTQEMLTTRRQETEG  128 (268)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTCHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTTCCCCCCCC-------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHccCCCcccCCHHHHHHHHHHHhHHHHHHHHHHHhccccccccchhhhhhhhhccccccccc
Confidence            466778888999999999999999999999999999999999999999999988654421    111222221111    


Q ss_pred             ------------------hhhhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         297 ------------------CQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       297 ------------------~~~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                                        ...+...++++.+++|+.+|++|+||.+||+|||||+||
T Consensus       129 ~~~~~p~~~~~~~~~~~~~~~~~~~~~i~~l~~~~~~l~~L~ld~~E~~lLkAivL~  185 (268)
T 3f5c_B          129 PEPAEPQATEQPQMVSAEAGHLLPAAAVQAIKSFFFKCWSLNIDTKEYAYLKGTVLF  185 (268)
T ss_dssp             --------------------CCCCSSHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHS
T ss_pred             ccccccccccccccccchhccccHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHh
Confidence                              011223467889999999999999999999999999987

>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=99.78  E-value=4.4e-19  Score=150.17  Aligned_cols=110  Identities=20%  Similarity=0.263  Sum_probs=95.2

Q ss_pred             HHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh-hhcH
Q psy2636         225 IQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR-SFGD  303 (335)
Q Consensus       225 ~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~-~~~~  303 (335)
                      +..+..++...+..+|+|||+||+|.+|+.+||++|||++|+++++|+.|+++....+.+++++|..++.+.... +.. 
T Consensus        43 ~~~~~~~~~~~l~~~v~wak~~p~F~~L~~~DQ~~LLk~~~~~~~~L~~a~~s~~~~~~~~~~~g~~~~~~~~~~~~~~-  121 (237)
T 1pzl_A           43 IADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVLLLGNDYIVPRHCPELAEMS-  121 (237)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTCHHHHTSCHHHHHHHHHHSHHHHHHHHHHHHHTTSSSEEECTTSCEEESSCGGGGGGH-
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCceeecCCcccCccchhhhhhH-
Confidence            566777788889999999999999999999999999999999999999999998877889999999887654332 333 


Q ss_pred             HHHHHH-HHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         304 DWLNAI-LEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       304 ~~~~~~-~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      .+...+ .+++.+|++|++|.+||++|+||+||
T Consensus       122 ~~~~~~~~~l~~~l~~L~ld~~E~~~L~ai~l~  154 (237)
T 1pzl_A          122 RVSIRILDELVLPFQELQIDDNEYAYLKAIIFF  154 (237)
T ss_dssp             HHHHHHHHHTHHHHHHHTCCHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHh
Confidence            445554 48999999999999999999999987

>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=99.77  E-value=1.1e-18  Score=148.35  Aligned_cols=110  Identities=22%  Similarity=0.299  Sum_probs=84.9

Q ss_pred             HHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCC-CeEEeeCCeEe----eHHhhh-h
Q psy2636         226 QQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAED-TKLIFCNGVVL----EKQQCQ-R  299 (335)
Q Consensus       226 ~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~-~~~~~~~g~~~----~~~~~~-~  299 (335)
                      ..++++..+.+..+|+|||++|+|.+|+.+||++|||++|+++++|+.|+++...+ +.+.+++|.+.    ..+... .
T Consensus        37 ~~~~e~a~~~L~~~VewaK~iP~F~~L~~~DQ~~LLk~~w~el~~L~~a~~s~~~~~~~~l~~~~~~~~~~~~~~~~~~~  116 (249)
T 3p0u_A           37 HYICESASRLLFLSMHWARSIPAFQALGQDCNTSLVRACWNELFTLGLAQCAQVMSLSTILAAIVNHLQNSIQEDKLSGD  116 (249)
T ss_dssp             SCHHHHHHHHHHHHHHHHHTCTTTGGGCHHHHHHHHHTTHHHHHHHHHHHTTTSCCCCCCCCC-CC---CC---------
T ss_pred             HHHHHHHHHHHHHHHHHHHcCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHcccCCcchhhcccccccccccccccchhh
Confidence            34667778889999999999999999999999999999999999999999987643 44555555442    112111 1


Q ss_pred             hhc--HHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 SFG--DDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 ~~~--~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ..+  .+.++.+.+++.+|++|++|.+||+|||||+||
T Consensus       117 ~~~~~~~~i~~l~~~~~~l~~L~ld~~E~~lLkAivL~  154 (249)
T 3p0u_A          117 RIKQVMEHIWKLQEFCNSMAKLDIDGYEYAYLKAIVLF  154 (249)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHT
T ss_pred             hhhhHHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHh
Confidence            111  256677889999999999999999999999987

>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=99.73  E-value=6.8e-18  Score=141.92  Aligned_cols=106  Identities=8%  Similarity=0.123  Sum_probs=83.4

Q ss_pred             HHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeE--eeHHh---hhhh-
Q psy2636         227 QFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVV--LEKQQ---CQRS-  300 (335)
Q Consensus       227 ~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~--~~~~~---~~~~-  300 (335)
                      .+.++.+..++.+|+|||++|||.+|+.+||++|||++|+|+++|+.|++++.+.+.+.+++|..  +....   +..+ 
T Consensus        45 ~i~~l~~~~l~~iVefAK~iPgF~~L~~~DQi~LLK~~~~ElliLr~a~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~  124 (244)
T 3gyt_A           45 DILNVMDITMRRLVKMAKRLGAFNEISEAGKFSLLKGGMIEMLTIRGVTVFNADKGVWQTPVDGHSQISFNMFDKLRPDI  124 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCGGGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETTTTEECCTTSTTCCEEGGGGGGSCTTT
T ss_pred             HHHHHHHHHHHHHHHHHccCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcccCCeEeecCCcccchhHHHHHHhhhcc
Confidence            45567778899999999999999999999999999999999999999999988888898887632  22211   1111 


Q ss_pred             ---hcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         301 ---FGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       301 ---~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                         ....+++.+++|..+|+.   ++.||+||+||+||
T Consensus       125 ~~~~~~~~~~~~~~f~~~l~~---~~~E~alLkAivLf  159 (244)
T 3gyt_A          125 KDTQKKGFLHFFNLLHSDVRK---NDLAIDIIVLMVLF  159 (244)
T ss_dssp             HHHHHHHHHHHHHHSCHHHHT---CHHHHHHHHHHHHS
T ss_pred             hhhHHHHHHHHHHHHHHHHHH---hHHHHHHHHHHHHH
Confidence               112456667777777776   45699999999997

>2lze_A A primordial catalytic fold generated by in vitro evolution; ligase, de novo protein; NMR {Synthetic construct}

Probab=92.76  E-value=0.096  Score=35.59  Aligned_cols=19  Identities=26%  Similarity=0.565  Sum_probs=15.6

Q ss_pred             CCCCcccccCCCCCccccC
Q psy2636          38 SPSQLCAVCGDIAACQHYG   56 (335)
Q Consensus        38 ~~~~~C~VCgd~a~g~HyG   56 (335)
                      .....|.||||.|+||+.-
T Consensus        15 ~g~h~c~vCgd~asfFRRt   33 (87)
T 2lze_A           15 GGKHICAICGNNAEDYKHT   33 (87)
T ss_dssp             CCSSSCSSSSSSSSSCTTT
T ss_pred             CCCEEccCCCCccceECcc
Confidence            3457799999999998764

>1wfl_A Zinc finger protein 216; ZF-AN1 domain, zinc binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.80.1.1

Probab=90.31  E-value=0.59  Score=30.32  Aligned_cols=24  Identities=21%  Similarity=0.592  Sum_probs=17.3

Q ss_pred             CCcccccCCCCCccccCCccccccccce
Q psy2636          40 SQLCAVCGDIAACQHYGVRTCEGCKGFF   67 (335)
Q Consensus        40 ~~~C~VCgd~a~g~HyGv~sC~gCk~FF   67 (335)
                      ..-|..|+.+..-.   ...|+ |.++|
T Consensus        25 ~nRC~~CrKkvgL~---gf~Cr-Cg~~F   48 (74)
T 1wfl_A           25 KNRCFMCRKKVGLT---GFDCR-CGNLF   48 (74)
T ss_dssp             TTBCSSSCCBCGGG---CEECT-TSCEE
T ss_pred             CCcChhhCCccccc---CeecC-CCCEe
Confidence            34699999885322   26799 99888

>1weu_A Inhibitor of growth family, member 4; structural genomics, PHD domain, ING1-like protein, DNA binding protein, NPPSFA; NMR {Mus musculus} SCOP: g.50.1.2

Probab=83.91  E-value=4.4  Score=27.63  Aligned_cols=22  Identities=18%  Similarity=0.723  Sum_probs=16.9

Q ss_pred             CCCcccccCCCCCccccCCccccc--cc
Q psy2636          39 PSQLCAVCGDIAACQHYGVRTCEG--CK   64 (335)
Q Consensus        39 ~~~~C~VCgd~a~g~HyGv~sC~g--Ck   64 (335)
                      ....| ||++...|   -.+.|++  |.
T Consensus        35 e~~yC-iC~~~~~g---~MI~CD~~dC~   58 (91)
T 1weu_A           35 EPTYC-LCHQVSYG---EMIGCDNPDCS   58 (91)
T ss_dssp             CCBCS-TTCCBCCS---CCCCCSCSSCS
T ss_pred             CCcEE-ECCCCCCC---CEeEecCCCCC
Confidence            44569 99998766   3778999  86

>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens}

Probab=80.89  E-value=1.5  Score=28.38  Aligned_cols=54  Identities=15%  Similarity=0.354  Sum_probs=34.6

Q ss_pred             CCCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHH
Q psy2636          38 SPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK  102 (335)
Q Consensus        38 ~~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~K  102 (335)
                      .....|.||++..+.--=..+.|.+|..-|--.        |..-..   .....-.|+.|+.++
T Consensus        14 ~~~~~C~vC~~~~s~~~~~ll~CD~C~~~~H~~--------Cl~~~~---vP~g~W~C~~C~~~~   67 (71)
T 2ku3_A           14 DEDAVCSICMDGESQNSNVILFCDMCNLAVHQE--------CYGVPY---IPEGQWLCRHCLQSR   67 (71)
T ss_dssp             CSSCSCSSSCCCCCCSSSCEEECSSSCCEEEHH--------HHTCSS---CCSSCCCCHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCCCccccc--------cCCCCc---CCCCCcCCccCcCcC
Confidence            445679999987644444678899997666444        432211   233567899998764

---

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	335
d1cita_	89	g.39.1.2 (A:) Orphan nuclear receptor NGFI-B DNA-b	5e-33
d1pdua_	230	a.123.1.1 (A:) Nuclear hormone receptor HR38 {Frui	2e-32
d1pdua_	230	a.123.1.1 (A:) Nuclear hormone receptor HR38 {Frui	1e-14
d1ovla_	236	a.123.1.1 (A:) Orphan nuclear receptor NURR1 {Huma	2e-31
d1ovla_	236	a.123.1.1 (A:) Orphan nuclear receptor NURR1 {Huma	1e-14
d1kb2a_	89	g.39.1.2 (A:) Vitamin D3 receptor, VDR, DNA-bindin	9e-31
d1dszb_	84	g.39.1.2 (B:) Retinoid X receptor (RXR-alpha) DNA-	6e-30
d2qw4a1	233	a.123.1.1 (A:32-264) Orphan nuclear receptor NR4A1	9e-30
d2qw4a1	233	a.123.1.1 (A:32-264) Orphan nuclear receptor NR4A1	2e-13
d1lo1a_	90	g.39.1.2 (A:) Steroid hormone receptor Err2 DNA-bi	2e-29
d2hanb1	83	g.39.1.2 (B:5-87) Ecdysone receptor DNA-binding do	3e-28
d1fcya_	236	a.123.1.1 (A:) Retinoic acid receptor gamma (RAR-g	9e-27
d1fcya_	236	a.123.1.1 (A:) Retinoic acid receptor gamma (RAR-g	2e-08
d1dsza_	75	g.39.1.2 (A:) Retinoic acid receptor DNA-binding d	2e-26
d1a6ya_	78	g.39.1.2 (A:) Orphan nuclear receptor reverb DNA-b	4e-26
d1r4ia_	74	g.39.1.2 (A:) Androgen receptor {Rat (Rattus norve	7e-26
d1hcqa_	74	g.39.1.2 (A:) Estrogen receptor DNA-binding domain	1e-25
d1lata_	71	g.39.1.2 (A:) Glucocorticoid receptor DNA-binding	2e-24
d1n46a_	251	a.123.1.1 (A:) Thyroid hormone receptor beta (TR-b	3e-24
d1n46a_	251	a.123.1.1 (A:) Thyroid hormone receptor beta (TR-b	1e-08
d2r40d1	243	a.123.1.1 (D:287-529) Ecdysone receptor {Noctuid m	4e-24
d2r40d1	243	a.123.1.1 (D:287-529) Ecdysone receptor {Noctuid m	1e-07
d1pq9a_	239	a.123.1.1 (A:) Oxysterols receptor LXR-beta {Human	1e-22
d1pq9a_	239	a.123.1.1 (A:) Oxysterols receptor LXR-beta {Human	9e-08
d2nllb_	103	g.39.1.2 (B:) Thyroid hormone receptor (TR-beta) D	2e-22
d1osha_	231	a.123.1.1 (A:) Bile acid receptor FXR {Human (Homo	3e-22
d1osha_	231	a.123.1.1 (A:) Bile acid receptor FXR {Human (Homo	2e-09
d1xnxa_	232	a.123.1.1 (A:) Orphan nuclear receptor NR1I3 (CAR)	2e-21
d1xnxa_	232	a.123.1.1 (A:) Orphan nuclear receptor NR1I3 (CAR)	6e-08
d2b50b1	265	a.123.1.1 (B:211-475) Peroxisome proliferator-acti	2e-21
d2b50b1	265	a.123.1.1 (B:211-475) Peroxisome proliferator-acti	1e-07
d1n83a_	251	a.123.1.1 (A:) Orphan nuclear receptor ROR-alpha {	3e-21
d1n83a_	251	a.123.1.1 (A:) Orphan nuclear receptor ROR-alpha {	7e-08
d1nrla_	292	a.123.1.1 (A:) Pregnane x receptor, PXR {Human (Ho	2e-20
d1nrla_	292	a.123.1.1 (A:) Pregnane x receptor, PXR {Human (Ho	9e-08
d3d24a1	227	a.123.1.1 (A:194-420) Steroid hormone receptor ERR	3e-20
d3d24a1	227	a.123.1.1 (A:194-420) Steroid hormone receptor ERR	4e-05
d1nq7a_	244	a.123.1.1 (A:) Orphan nuclear receptor ROR-beta {R	5e-20
d1nq7a_	244	a.123.1.1 (A:) Orphan nuclear receptor ROR-beta {R	3e-06
d2e2ra1	223	a.123.1.1 (A:234-456) Orphan nuclear receptor ERR3	1e-19
d2e2ra1	223	a.123.1.1 (A:234-456) Orphan nuclear receptor ERR3	2e-04
d1xvpb_	246	a.123.1.1 (B:) Orphan nuclear receptor NR1I3 (CAR)	3e-19
d1xvpb_	246	a.123.1.1 (B:) Orphan nuclear receptor NR1I3 (CAR)	4e-07
d2p54a1	267	a.123.1.1 (A:202-468) Peroxisome proliferator acti	4e-19
d2p54a1	267	a.123.1.1 (A:202-468) Peroxisome proliferator acti	6e-06
d2fvja1	271	a.123.1.1 (A:207-477) Peroxisome proliferator acti	2e-18
d2fvja1	271	a.123.1.1 (A:207-477) Peroxisome proliferator acti	9e-06
d1ie9a_	255	a.123.1.1 (A:) Vitamin D nuclear receptor {Human (	2e-18
d1ie9a_	255	a.123.1.1 (A:) Vitamin D nuclear receptor {Human (	3e-06
d1xpca_	245	a.123.1.1 (A:) Estrogen receptor alpha {Human (Hom	3e-18
d1xpca_	245	a.123.1.1 (A:) Estrogen receptor alpha {Human (Hom	2e-05
d2j7ya1	236	a.123.1.1 (A:217-452) Estrogen receptor beta {Rat	4e-18
d2j7ya1	236	a.123.1.1 (A:217-452) Estrogen receptor beta {Rat	0.001
d1pk5a_	242	a.123.1.1 (A:) Orphan nuclear receptor NR5a2 (LRH-	4e-17
d1pk5a_	242	a.123.1.1 (A:) Orphan nuclear receptor NR5a2 (LRH-	7e-05
d1pzla_	233	a.123.1.1 (A:) Hepatocyte nuclear factor 4-alpha {	1e-16
d1pzla_	233	a.123.1.1 (A:) Hepatocyte nuclear factor 4-alpha {	8e-04
d2p1ta1	230	a.123.1.1 (A:229-458) Retinoid-X receptor alpha (R	6e-16
d1g2na_	256	a.123.1.1 (A:) Ultraspiracle protein, usp {Helioth	1e-14
d1hg4a_	265	a.123.1.1 (A:) Ultraspiracle protein, usp {Drosoph	2e-14
d1nhza_	247	a.123.1.1 (A:) Glucocorticoid receptor {Human (Hom	6e-14
d1sqna_	251	a.123.1.1 (A:) Progesterone receptor {Human (Homo	9e-14
d1t7ra_	250	a.123.1.1 (A:) Androgen receptor {Chimpanzee (Pan	2e-12

>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 =  115 bits (289), Expect = 5e-33
 Identities = 79/87 (90%), Positives = 83/87 (95%)

Query: 43  CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
           CAVCGD A+CQHYGVRTCEGCKGFFKRTVQK +KY+CLA+K CPVDKRRRNRCQFCRFQK
Sbjct: 3   CAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQK 62

Query: 103 CLQVGMVKEVVRTDSLKGRRGRLPSKP 129
           CL VGMVKEVVRTDSLKGRRGRLPSKP
Sbjct: 63  CLAVGMVKEVVRTDSLKGRRGRLPSKP 89

>d1pdua_ a.123.1.1 (A:) Nuclear hormone receptor HR38 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 230

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Nuclear hormone receptor HR38
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score =  118 bits (297), Expect = 2e-32
 Identities = 88/120 (73%), Positives = 102/120 (85%), Gaps = 1/120 (0%)

Query: 216 EPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAY 275
           E  ++E +K+QQFY LLT+SVDVI+ FA+KIPG+ DL  EDQELLFQSASLELFVLRLAY
Sbjct: 29  EQSMSEADKVQQFYQLLTSSVDVIKQFAEKIPGYFDLLPEDQELLFQSASLELFVLRLAY 88

Query: 276 RTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
           R R +DTKLIFCNG VL + QC RSFG +WLN I+EF +SLH +EIDISAFACLCALTLI
Sbjct: 89  RARIDDTKLIFCNGTVLHRTQCLRSFG-EWLNDIMEFSRSLHNLEIDISAFACLCALTLI 147

>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 = 70.0 bits (171), Expect = 1e-14
 Identities = 55/205 (26%), Positives = 83/205 (40%), Gaps = 26/205 (12%)

Query: 141 VSLITALYR-----EPNP--------LEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPG 187
           +SLITAL R      P+P         E  ++E +K+QQFY LLT+SVDVI+ FA+KIPG
Sbjct: 2   ISLITALVRSHVDTTPDPSCLDYSHYEEQSMSEADKVQQFYQLLTSSVDVIKQFAEKIPG 61

Query: 188 FSDLCKEDQELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIP 247
           + DL  EDQELLFQSASLELF            +  K+      +      +R F + + 
Sbjct: 62  YFDLLPEDQELLFQSASLELFVLRLAYRARI--DDTKLIFCNGTVLHRTQCLRSFGEWLN 119

Query: 248 GFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLN 307
              +  +    L    +      L             +      L + +         + 
Sbjct: 120 DIMEFSRSLHNLEIDIS--AFACLCAL---------TLITERHGLREPKKVEQLQMKIIG 168

Query: 308 AILEFCQSLHLMEIDISAFACLCAL 332
           ++ +        +     F+ L   
Sbjct: 169 SLRDHVTYNAEAQKKQHYFSRLLGK 193

>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 =  116 bits (291), Expect = 2e-31
 Identities = 68/127 (53%), Positives = 94/127 (74%), Gaps = 1/127 (0%)

Query: 209 YREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL 268
           ++     +    + + IQQFY LLT S+++IR +A+KIPGF+DL K DQ+LLF+SA LEL
Sbjct: 25  FQANPDYQMSGDDTQHIQQFYDLLTGSMEIIRGWAEKIPGFADLPKADQDLLFESAFLEL 84

Query: 269 FVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFAC 328
           FVLRLAYR+   + KLIFCNGVVL + QC R FG +W+++I+EF  +L  M IDISAF+C
Sbjct: 85  FVLRLAYRSNPVEGKLIFCNGVVLHRLQCVRGFG-EWIDSIVEFSSNLQNMNIDISAFSC 143

Query: 329 LCALTLI 335
           + AL ++
Sbjct: 144 IAALAMV 150

>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 = 70.0 bits (171), Expect = 1e-14
 Identities = 44/193 (22%), Positives = 75/193 (38%), Gaps = 29/193 (15%)

Query: 148 YREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL 207
           ++     +    + + IQQFY LLT S+++IR +A+KIPGF+DL K DQ+LLF+SA LEL
Sbjct: 25  FQANPDYQMSGDDTQHIQQFYDLLTGSMEIIRGWAEKIPGFADLPKADQDLLFESAFLEL 84

Query: 208 ----FYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQS 263
                    NP+E               L     V+ H    + GF +      E     
Sbjct: 85  FVLRLAYRSNPVEGK-------------LIFCNGVVLHRLQCVRGFGEWIDSIVEFSSNL 131

Query: 264 ASLEL----FVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLM 319
            ++ +    F    A          +      L++ +      +  +N + +     +  
Sbjct: 132 QNMNIDISAFSCIAAL--------AMVTERHGLKEPKRVEELQNKIVNCLKDHVTFNNGG 183

Query: 320 EIDISAFACLCAL 332
               +  + L   
Sbjct: 184 LNRPNYLSKLLGK 196

>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 =  109 bits (274), Expect = 9e-31
 Identities = 34/88 (38%), Positives = 54/88 (61%)

Query: 41  QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRF 100
           ++C VCGD A   H+   TCEGCKGFF+R++++ + + C  +  C + K  R  CQ CR 
Sbjct: 1   RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRL 60

Query: 101 QKCLQVGMVKEVVRTDSLKGRRGRLPSK 128
           ++C+ +GM+KE + TD    R+  +  K
Sbjct: 61  KRCVDIGMMKEFILTDEEVQRKREMILK 88

>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 =  107 bits (268), Expect = 6e-30
 Identities = 44/78 (56%), Positives = 60/78 (76%)

Query: 39  PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFC 98
              +CA+CGD ++ +HYGV +CEGCKGFFKRTV+K   Y C  +K C +DKR+RNRCQ+C
Sbjct: 4   TKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYC 63

Query: 99  RFQKCLQVGMVKEVVRTD 116
           R+QKCL +GM +E V+ +
Sbjct: 64  RYQKCLAMGMKREAVQEE 81

>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 =  111 bits (279), Expect = 9e-30
 Identities = 63/124 (50%), Positives = 90/124 (72%), Gaps = 1/124 (0%)

Query: 209 YREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL 268
           ++E         +   +QQFY LL+ S++VIR +A+KIPGF++L   DQ+LL +SA LEL
Sbjct: 25  FQELVLPHFGKEDAGDVQQFYDLLSGSLEVIRKWAEKIPGFAELSPADQDLLLESAFLEL 84

Query: 269 FVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFAC 328
           F+LRLAYR++  + KLIFC+G+VL + QC R FG DW+++IL F +SLH + +D+ AFAC
Sbjct: 85  FILRLAYRSKPGEGKLIFCSGLVLHRLQCARGFG-DWIDSILAFSRSLHSLLVDVPAFAC 143

Query: 329 LCAL 332
           L AL
Sbjct: 144 LSAL 147

>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 = 66.6 bits (162), Expect = 2e-13
 Identities = 28/61 (45%), Positives = 41/61 (67%)

Query: 148 YREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL 207
           ++E         +   +QQFY LL+ S++VIR +A+KIPGF++L   DQ+LL +SA LEL
Sbjct: 25  FQELVLPHFGKEDAGDVQQFYDLLSGSLEVIRKWAEKIPGFAELSPADQDLLLESAFLEL 84

Query: 208 F 208
           F
Sbjct: 85  F 85

>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 =  106 bits (265), Expect = 2e-29
 Identities = 48/84 (57%), Positives = 58/84 (69%)

Query: 39  PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFC 98
           P +LC VCGDIA+  HYGV +CE CK FFKRT+Q   +Y C A   C + KRRR  CQ C
Sbjct: 3   PKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQAC 62

Query: 99  RFQKCLQVGMVKEVVRTDSLKGRR 122
           RF K L+VGM+KE VR D ++G R
Sbjct: 63  RFMKALKVGMLKEGVRLDRVRGGR 86

>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 =  103 bits (257), Expect = 3e-28
 Identities = 39/82 (47%), Positives = 51/82 (62%)

Query: 41  QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRF 100
           +LC VCGD A+  HY   TCEGCKGFF+R+V K + Y C   +AC +D   R +CQ CR 
Sbjct: 1   ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECRL 60

Query: 101 QKCLQVGMVKEVVRTDSLKGRR 122
           +KCL VGM  E V  ++    +
Sbjct: 61  KKCLAVGMRPECVVPENQCAMK 82

>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 =  103 bits (258), Expect = 9e-27
 Identities = 35/145 (24%), Positives = 61/145 (42%)

Query: 191 LCKEDQELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFS 250
           + K  QE       L  +    +       +     +F  L T  +  I  FA ++PGF+
Sbjct: 12  VSKAHQETFPSLCQLGKYTTNSSADHRVQLDLGLWDKFSELATKCIIKIVEFAKRLPGFT 71

Query: 251 DLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAIL 310
            L   DQ  L ++A L++ +LR+  R   E   + F +G+ L + Q   +      + + 
Sbjct: 72  GLSIADQITLLKAACLDILMLRICTRYTPEQDTMTFSDGLTLNRTQMHNAGFGPLTDLVF 131

Query: 311 EFCQSLHLMEIDISAFACLCALTLI 335
            F   L  +E+D +    L A+ LI
Sbjct: 132 AFAGQLLPLEMDDTETGLLSAICLI 156

>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 = 52.3 bits (125), Expect = 2e-08
 Identities = 15/60 (25%), Positives = 26/60 (43%)

Query: 149 REPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELF 208
              +       +     +F  L T  +  I  FA ++PGF+ L   DQ  L ++A L++ 
Sbjct: 31  TNSSADHRVQLDLGLWDKFSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDIL 90

>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 = 97.8 bits (243), Expect = 2e-26
 Identities = 43/74 (58%), Positives = 52/74 (70%)

Query: 43  CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
           C VC D ++  HYGV  CEGCKGFF+R++QK   Y C  DK C ++K  RNRCQ+CR QK
Sbjct: 2   CFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQK 61

Query: 103 CLQVGMVKEVVRTD 116
           C +VGM KE VR D
Sbjct: 62  CFEVGMSKESVRND 75

>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 = 97.4 bits (242), Expect = 4e-26
 Identities = 41/76 (53%), Positives = 55/76 (72%), Gaps = 1/76 (1%)

Query: 42  LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKY-VCLADKACPVDKRRRNRCQFCRF 100
           LC VCGD+A+  HYGV  CEGCKGFF+R++Q+  +Y  CL ++ C + +  RNRCQ CRF
Sbjct: 2   LCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRF 61

Query: 101 QKCLQVGMVKEVVRTD 116
           +KCL VGM ++ VR  
Sbjct: 62  KKCLSVGMSRDAVRFG 77

>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 = 96.3 bits (239), Expect = 7e-26
 Identities = 32/73 (43%), Positives = 41/73 (56%)

Query: 39  PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFC 98
           P + C +CGD A+  HYG  TC  CK FFKR  +   KY+C +   C +DK RR  C  C
Sbjct: 1   PQKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSC 60

Query: 99  RFQKCLQVGMVKE 111
           R +KC + GM   
Sbjct: 61  RLRKCYEAGMTLG 73

>d1hcqa_ g.39.1.2 (A:) Estrogen receptor DNA-binding domain {Human and chicken (Homo sapiens) and (Gallus gallus) [TaxId: 9606]} Length = 74

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Estrogen receptor DNA-binding domain
species: Human and chicken (Homo sapiens) and (Gallus gallus) [TaxId: 9606]

 Score = 95.6 bits (237), Expect = 1e-25
 Identities = 38/72 (52%), Positives = 50/72 (69%)

Query: 39  PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFC 98
            ++ CAVC D A+  HYGV +CEGCK FFKR++Q  + Y+C A   C +DK RR  CQ C
Sbjct: 3   ETRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQAC 62

Query: 99  RFQKCLQVGMVK 110
           R +KC +VGM+K
Sbjct: 63  RLRKCYEVGMMK 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 = 92.4 bits (229), Expect = 2e-24
 Identities = 37/69 (53%), Positives = 44/69 (63%)

Query: 43  CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102
           C VC D A+  HYGV TCEGCK FFKR V+    Y+C  +  C +DK RR  C  CR++K
Sbjct: 3   CLVCSDEASGCHYGVLTCEGCKAFFKRAVEGQHNYLCKYEGKCIIDKIRRKNCPACRYRK 62

Query: 103 CLQVGMVKE 111
           CLQ GM  E
Sbjct: 63  CLQAGMNLE 71

>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 = 97.4 bits (242), Expect = 3e-24
 Identities = 34/148 (22%), Positives = 59/148 (39%), Gaps = 1/148 (0%)

Query: 188 FSDLCKEDQELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIP 247
            +      Q+  F    +       N  E    + E    F  ++T ++  +  FA K+P
Sbjct: 23  NAQGSHWKQKRKFLPEDIG-QAPIVNAPEGGKVDLEAFSHFTKIITPAITRVVDFAKKLP 81

Query: 248 GFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLN 307
            F +L  EDQ +L +   +E+  LR A R   E   L     + + + Q +        +
Sbjct: 82  MFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLNGEMAVTRGQLKNGGLGVVSD 141

Query: 308 AILEFCQSLHLMEIDISAFACLCALTLI 335
           AI +   SL    +D +  A L A+ L+
Sbjct: 142 AIFDLGMSLSSFNLDDTEVALLQAVLLM 169

>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 = 52.7 bits (126), Expect = 1e-08
 Identities = 18/76 (23%), Positives = 32/76 (42%), Gaps = 3/76 (3%)

Query: 133 QESPPSPPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLC 192
           Q+    P       +   P   E    + E    F  ++T ++  +  FA K+P F +L 
Sbjct: 31  QKRKFLPEDIGQAPIVNAP---EGGKVDLEAFSHFTKIITPAITRVVDFAKKLPMFCELP 87

Query: 193 KEDQELLFQSASLELF 208
            EDQ +L +   +E+ 
Sbjct: 88  CEDQIILLKGCCMEIM 103

>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 = 96.6 bits (240), Expect = 4e-24
 Identities = 32/157 (20%), Positives = 68/157 (43%), Gaps = 12/157 (7%)

Query: 191 LCKEDQELL---------FQSASLELF--YREPNPLEPPIAEPE-KIQQFYSLLTTSVDV 238
           L    + L+         ++  S E      +    +    + +   +Q   +   +V +
Sbjct: 4   LTANQKSLIARLVWYQEGYEQPSEEDLKRVTQTWQSDEDDEDSDMPFRQITEMTILTVQL 63

Query: 239 IRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQ 298
           I  FA  +PGF+ + + DQ  L ++ S E+ +LR+A R  A    ++F N     +   +
Sbjct: 64  IVEFAKGLPGFAKISQSDQITLLKACSSEVMMLRVARRYDAATDSVLFANNQAYTRDNYR 123

Query: 299 RSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
           ++     +  +L FC+ ++ M +D   +A L A+ + 
Sbjct: 124 KAGMAYVIEDLLHFCRCMYSMMMDNVHYALLTAIVIF 160

>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 = 49.2 bits (117), Expect = 1e-07
 Identities = 17/77 (22%), Positives = 31/77 (40%)

Query: 133 QESPPSPPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLC 192
           QE    P    +  + +     E         +Q   +   +V +I  FA  +PGF+ + 
Sbjct: 19  QEGYEQPSEEDLKRVTQTWQSDEDDEDSDMPFRQITEMTILTVQLIVEFAKGLPGFAKIS 78

Query: 193 KEDQELLFQSASLELFY 209
           + DQ  L ++ S E+  
Sbjct: 79  QSDQITLLKACSSEVMM 95

>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 = 92.4 bits (229), Expect = 1e-22
 Identities = 32/128 (25%), Positives = 60/128 (46%), Gaps = 1/128 (0%)

Query: 209 YREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL 268
           +      +   A  ++   F  L   SV  I  FA ++PGF  L +EDQ  L +++++E+
Sbjct: 33  WPLGADPQSRDARQQRFAHFTELAIISVQEIVDFAKQVPGFLQLGREDQIALLKASTIEI 92

Query: 269 FVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRS-FGDDWLNAILEFCQSLHLMEIDISAFA 327
            +L  A R   E   + F       K    R+    +++N I EF +++  + +D + +A
Sbjct: 93  MLLETARRYNHETECITFLKDFTYSKDDFHRAGLQVEFINPIFEFSRAMRRLGLDDAEYA 152

Query: 328 CLCALTLI 335
            L A+ + 
Sbjct: 153 LLIAINIF 160

>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 = 50.0 bits (119), Expect = 9e-08
 Identities = 18/73 (24%), Positives = 31/73 (42%)

Query: 136 PPSPPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKED 195
             S         +      +   A  ++   F  L   SV  I  FA ++PGF  L +ED
Sbjct: 21  KRSFSDQPKVTPWPLGADPQSRDARQQRFAHFTELAIISVQEIVDFAKQVPGFLQLGRED 80

Query: 196 QELLFQSASLELF 208
           Q  L +++++E+ 
Sbjct: 81  QIALLKASTIEIM 93

>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 = 88.3 bits (218), Expect = 2e-22
 Identities = 42/98 (42%), Positives = 58/98 (59%), Gaps = 2/98 (2%)

Query: 41  QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYV--CLADKACPVDKRRRNRCQFC 98
           +LC VCGD A   HY   TCEGCKGFF+RT+QK       C  +  C +DK  RN+CQ C
Sbjct: 2   ELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQEC 61

Query: 99  RFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQESP 136
           RF+KC+ VGM  ++V  DS +  + +L  + +  +   
Sbjct: 62  RFKKCIYVGMATDLVLDDSKRLAKRKLIEENREKRRRE 99

>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 = 91.2 bits (226), Expect = 3e-22
 Identities = 35/152 (23%), Positives = 64/152 (42%), Gaps = 8/152 (5%)

Query: 189 SDLCKEDQELLFQSASLELFYREPN-----PLEPPIAEPEKIQQFYSLLTTSVDVIRHFA 243
            +L  + Q LL          R P       L+   +  E       + T  V V+  F 
Sbjct: 3   GELTPDQQTLLHFIMDSYNKQRMPQEITNKILKEEFSAEENFLILTEMATNHVQVLVEFT 62

Query: 244 DKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD 303
            K+PGF  L  EDQ  L + +++E   LR A      + KL   +  +LE++       D
Sbjct: 63  KKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIF---NKKLPSGHSDLLEERIRNSGISD 119

Query: 304 DWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
           +++  +  F +S+  +++    +A L A+ ++
Sbjct: 120 EYITPMFSFYKSIGELKMTQEEYALLTAIVIL 151

>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 = 55.0 bits (132), Expect = 2e-09
 Identities = 19/116 (16%), Positives = 36/116 (31%), Gaps = 11/116 (9%)

Query: 153 PLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFYREP 212
            L+   +  E       + T  V V+  F  K+PGF  L  EDQ  L + +++E  +   
Sbjct: 33  ILKEEFSAEENFLILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRS 92

Query: 213 NPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL 268
             +               L +   D++           +              L++
Sbjct: 93  AEIFNKK-----------LPSGHSDLLEERIRNSGISDEYITPMFSFYKSIGELKM 137

>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 = 89.3 bits (221), Expect = 2e-21
 Identities = 25/122 (20%), Positives = 45/122 (36%)

Query: 214 PLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRL 273
           P +P       +  F  + T  V  I  F   +P F  L  EDQ  L + A++E+  + L
Sbjct: 44  PFQPRGPVLPLLTHFADINTFMVQQIIKFTKDLPLFRSLTMEDQISLLKGAAVEILHISL 103

Query: 274 AYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALT 333
                 +             +      F  ++L +IL F ++L  + +    +  + A  
Sbjct: 104 NTTFCLQTENFFCGPLCYKMEDAVHAGFQYEFLESILHFHKNLKGLHLQEPEYVLMAATA 163

Query: 334 LI 335
           L 
Sbjct: 164 LF 165

>d1xnxa_ a.123.1.1 (A:) Orphan nuclear receptor NR1I3 (CAR) {Mouse (Mus musculus) [TaxId: 10090]} Length = 232

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NR1I3 (CAR)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 50.4 bits (120), Expect = 6e-08
 Identities = 16/56 (28%), Positives = 24/56 (42%)

Query: 153 PLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELF 208
           P +P       +  F  + T  V  I  F   +P F  L  EDQ  L + A++E+ 
Sbjct: 44  PFQPRGPVLPLLTHFADINTFMVQQIIKFTKDLPLFRSLTMEDQISLLKGAAVEIL 99

>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 = 89.6 bits (222), Expect = 2e-21
 Identities = 35/140 (25%), Positives = 53/140 (37%), Gaps = 5/140 (3%)

Query: 200 FQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRH---FADKIPGFSDLCKED 256
              A   L +++     PP  E   +  FY    T+V+ +R    FA  IP FS L   D
Sbjct: 45  LWQAEKGLVWKQLVNGLPPYKEIS-VHVFYRCQCTTVETVRELTEFAKSIPSFSSLFLND 103

Query: 257 QELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVL-EKQQCQRSFGDDWLNAILEFCQS 315
           Q  L +    E     LA     +   +   +G V  E  +  R    D +    EF   
Sbjct: 104 QVTLLKYGVHEAIFAMLASIVNKDGLLVANGSGFVTREFLRSLRKPFSDIIEPKFEFAVK 163

Query: 316 LHLMEIDISAFACLCALTLI 335
            + +E+D S  A   A  ++
Sbjct: 164 FNALELDDSDLALFIAAIIL 183

>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 = 50.0 bits (119), Expect = 1e-07
 Identities = 29/130 (22%), Positives = 46/130 (35%), Gaps = 11/130 (8%)

Query: 145 TALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRH---FADKIPGFSDLCKEDQELLFQ 201
             ++++     PP  E   +  FY    T+V+ +R    FA  IP FS L   DQ  L +
Sbjct: 51  GLVWKQLVNGLPPYKEIS-VHVFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLK 109

Query: 202 SASLELF-------YREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCK 254
               E           +   L    +     +   SL     D+I    +    F+ L  
Sbjct: 110 YGVHEAIFAMLASIVNKDGLLVANGSGFVTREFLRSLRKPFSDIIEPKFEFAVKFNALEL 169

Query: 255 EDQELLFQSA 264
           +D +L    A
Sbjct: 170 DDSDLALFIA 179

>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 = 88.6 bits (219), Expect = 3e-21
 Identities = 29/136 (21%), Positives = 60/136 (44%), Gaps = 1/136 (0%)

Query: 200 FQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQEL 259
            Q  + + F +E              Q     +T ++  +  FA +I GF +LC+ DQ +
Sbjct: 35  LQQITWQTFLQEEIENYQNKQREVMWQLCAIKITEAIQYVVEFAKRIDGFMELCQNDQIV 94

Query: 260 LFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLM 319
           L ++ SLE+  +R+     +++   ++ +G        +    +D+++ + EF +SL  M
Sbjct: 95  LLKAGSLEVVFIRMCRAFDSQN-NTVYFDGKYASPDVFKSLGCEDFISFVFEFGKSLCSM 153

Query: 320 EIDISAFACLCALTLI 335
            +     A   A  L+
Sbjct: 154 HLTEDEIALFSAFVLM 169

>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 = 50.5 bits (120), Expect = 7e-08
 Identities = 16/68 (23%), Positives = 32/68 (47%), Gaps = 1/68 (1%)

Query: 142 SLITALYREPNPLEPPIAEPEKI-QQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLF 200
            +    + +         + E + Q     +T ++  +  FA +I GF +LC+ DQ +L 
Sbjct: 37  QITWQTFLQEEIENYQNKQREVMWQLCAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLL 96

Query: 201 QSASLELF 208
           ++ SLE+ 
Sbjct: 97  KAGSLEVV 104

>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 = 87.5 bits (216), Expect = 2e-20
 Identities = 39/188 (20%), Positives = 62/188 (32%), Gaps = 10/188 (5%)

Query: 148 YREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL 207
           +R P  L      PE +Q            +R          DLC     L  +     +
Sbjct: 31  FRLPGVLSSGCELPESLQAPSREEAAKWSQVRK---------DLCSLKVSLQLRGEDGSV 81

Query: 208 FYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLE 267
           +  +P            +     + T     I  FA  I  F DL  EDQ  L + A+ E
Sbjct: 82  WNYKPPADSGGKEIFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFE 141

Query: 268 LFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFA 327
           L  LR      A +T    C  +    +     F    L  +L+F   L  +++    + 
Sbjct: 142 LCQLRFNTVFNA-ETGTWECGRLSYCLEDTAGGFQQLLLEPMLKFHYMLKKLQLHEEEYV 200

Query: 328 CLCALTLI 335
            + A++L 
Sbjct: 201 LMQAISLF 208

>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 = 50.5 bits (120), Expect = 9e-08
 Identities = 27/120 (22%), Positives = 38/120 (31%), Gaps = 8/120 (6%)

Query: 95  CQFCRFQKCLQVGMVKEVVRTDSLKGRRGRLPSKPKSPQESPPSPPVSLITALYREPNPL 154
             F  F+    +    E    +SL+       +K    ++   S  VSL           
Sbjct: 26  SHFKNFRLPGVLSSGCE--LPESLQAPSREEAAKWSQVRKDLCSLKVSLQLRGEDGSVWN 83

Query: 155 EPPIAEPEKI------QQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELF 208
             P A+               + T     I  FA  I  F DL  EDQ  L + A+ EL 
Sbjct: 84  YKPPADSGGKEIFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELC 143

>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 = 85.9 bits (212), Expect = 3e-20
 Identities = 34/130 (26%), Positives = 58/130 (44%), Gaps = 1/130 (0%)

Query: 206 ELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSAS 265
           E  Y  P+P   P      +     L    + V   +A  IPGFS L   DQ  + QS  
Sbjct: 14  EKLYAMPDP-AGPDGHLPAVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVW 72

Query: 266 LELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISA 325
           +E+ VL +A R+     +L F   +VL+++  + +   +   A+L+  + L  + ++   
Sbjct: 73  MEVLVLGVAQRSLPLQDELAFAEDLVLDEEGARAAGLGELGAALLQLVRRLQALRLEREE 132

Query: 326 FACLCALTLI 335
           +  L AL L 
Sbjct: 133 YVLLKALALA 142

>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 = 42.0 bits (98), Expect = 4e-05
 Identities = 27/124 (21%), Positives = 42/124 (33%), Gaps = 7/124 (5%)

Query: 147 LYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLE 206
           LY  P+P   P      +     L    + V   +A  IPGFS L   DQ  + QS  +E
Sbjct: 16  LYAMPDP-AGPDGHLPAVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWME 74

Query: 207 LF------YREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELL 260
           +          P   E   AE   + +  +      ++       +     L  E +E +
Sbjct: 75  VLVLGVAQRSLPLQDELAFAEDLVLDEEGARAAGLGELGAALLQLVRRLQALRLEREEYV 134

Query: 261 FQSA 264
              A
Sbjct: 135 LLKA 138

>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 = 85.6 bits (211), Expect = 5e-20
 Identities = 34/146 (23%), Positives = 61/146 (41%), Gaps = 2/146 (1%)

Query: 190 DLCKEDQELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGF 249
           + C+   E L Q A     Y E    +    E    QQ    +T ++  +  FA +I GF
Sbjct: 18  ETCQYTMEELHQLAWQTHTYEEIKAYQSKSRE-ALWQQCAIQITHAIQYVVEFAKRITGF 76

Query: 250 SDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAI 309
            +LC+ DQ LL +S  LE+ ++R+       +  ++F       +         D +N  
Sbjct: 77  MELCQNDQILLLKSGCLEVVLVRMCRAFNPLNNTVLFEGKYGGMQMFKALGSD-DLVNEA 135

Query: 310 LEFCQSLHLMEIDISAFACLCALTLI 335
            +F ++L  +++     A   +  LI
Sbjct: 136 FDFAKNLCSLQLTEEEIALFSSAVLI 161

>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 = 45.5 bits (107), Expect = 3e-06
 Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 1/70 (1%)

Query: 140 PVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELL 199
            ++  T  Y E    +    E    QQ    +T ++  +  FA +I GF +LC+ DQ LL
Sbjct: 29  QLAWQTHTYEEIKAYQSKSRE-ALWQQCAIQITHAIQYVVEFAKRITGFMELCQNDQILL 87

Query: 200 FQSASLELFY 209
            +S  LE+  
Sbjct: 88  LKSGCLEVVL 97

>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 = 83.9 bits (207), Expect = 1e-19
 Identities = 36/127 (28%), Positives = 66/127 (51%), Gaps = 1/127 (0%)

Query: 209 YREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL 268
           Y  P+P  P  ++ + +     L    + VI  +A  IPGFS L   DQ  L QSA +E+
Sbjct: 17  YAMPDPTVPD-SDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEI 75

Query: 269 FVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFAC 328
            +L + YR+ + + +L++ +  ++++ Q + +   D  NAIL+  +    M+++   F  
Sbjct: 76  LILGVVYRSLSFEDELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVT 135

Query: 329 LCALTLI 335
           L A+ L 
Sbjct: 136 LKAIALA 142

>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 = 40.0 bits (93), Expect = 2e-04
 Identities = 29/124 (23%), Positives = 49/124 (39%), Gaps = 7/124 (5%)

Query: 147 LYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLE 206
           +Y  P+P  P  ++ + +     L    + VI  +A  IPGFS L   DQ  L QSA +E
Sbjct: 16  IYAMPDPTVPD-SDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWME 74

Query: 207 LF------YREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELL 260
           +              E   A+   + +  S L   +D+       +  +  +  E +E +
Sbjct: 75  ILILGVVYRSLSFEDELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFV 134

Query: 261 FQSA 264
              A
Sbjct: 135 TLKA 138

>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 = 83.2 bits (205), Expect = 3e-19
 Identities = 23/122 (18%), Positives = 45/122 (36%)

Query: 214 PLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRL 273
           PL         +  F  + T  V  +  F   +P F  L  EDQ  L + A++E+  + L
Sbjct: 45  PLPTLAPVLPLVTHFADINTFMVLQVIKFTKDLPVFRSLPIEDQISLLKGAAVEICHIVL 104

Query: 274 AYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALT 333
                 +    +        +   +  F  ++L  +  F  +L  +++    +  L A+ 
Sbjct: 105 NTTFCLQTQNFLCGPLRYTIEDGARVGFQVEFLELLFHFHGTLRKLQLQEPEYVLLAAMA 164

Query: 334 LI 335
           L 
Sbjct: 165 LF 166

>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 = 48.1 bits (114), Expect = 4e-07
 Identities = 19/116 (16%), Positives = 36/116 (31%), Gaps = 8/116 (6%)

Query: 153 PLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFYREP 212
           PL         +  F  + T  V  +  F   +P F  L  EDQ  L + A++E+ +   
Sbjct: 45  PLPTLAPVLPLVTHFADINTFMVLQVIKFTKDLPVFRSLPIEDQISLLKGAAVEICHIVL 104

Query: 213 NPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL 268
           N       +        + L   +        ++    +  +           L+L
Sbjct: 105 NTTFCLQTQ--------NFLCGPLRYTIEDGARVGFQVEFLELLFHFHGTLRKLQL 152

>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 = 83.1 bits (205), Expect = 4e-19
 Identities = 28/126 (22%), Positives = 51/126 (40%), Gaps = 5/126 (3%)

Query: 215 LEPPIAEPE-KIQQFYSLLTTSVDVIRH---FADKIPGFSDLCKEDQELLFQSASLELFV 270
           +   I   E +++ F+    TSV+ +     FA  IPGF++L   DQ  L +    E   
Sbjct: 58  VANGIQNKEAEVRIFHCCQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIF 117

Query: 271 LRLAYRTRAEDTKLIFCNGVVL-EKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACL 329
             L+     +   + + NG +  E  +  R    D +    +F    + +E+D S  +  
Sbjct: 118 AMLSSVMNKDGMLVAYGNGFITREFLKSLRKPFCDIMEPKFDFAMKFNALELDDSDISLF 177

Query: 330 CALTLI 335
            A  + 
Sbjct: 178 VAAIIC 183

>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 = 44.6 bits (105), Expect = 6e-06
 Identities = 26/122 (21%), Positives = 44/122 (36%), Gaps = 11/122 (9%)

Query: 154 LEPPIAEPE-KIQQFYSLLTTSVDVIRH---FADKIPGFSDLCKEDQELLFQSASLELF- 208
           +   I   E +++ F+    TSV+ +     FA  IPGF++L   DQ  L +    E   
Sbjct: 58  VANGIQNKEAEVRIFHCCQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIF 117

Query: 209 ------YREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQ 262
                   +   L          +   SL     D++    D    F+ L  +D ++   
Sbjct: 118 AMLSSVMNKDGMLVAYGNGFITREFLKSLRKPFCDIMEPKFDFAMKFNALELDDSDISLF 177

Query: 263 SA 264
            A
Sbjct: 178 VA 179

>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 = 81.6 bits (201), Expect = 2e-18
 Identities = 30/140 (21%), Positives = 55/140 (39%), Gaps = 5/140 (3%)

Query: 200 FQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRH---FADKIPGFSDLCKED 256
                 ++ ++   PL+    E   I+ F      SV+ ++    +A  IPGF +L   D
Sbjct: 49  LMMGEDKIKFKHITPLQEQSKEVA-IRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLND 107

Query: 257 QELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVL-EKQQCQRSFGDDWLNAILEFCQS 315
           Q  L +    E+    LA     +   +    G +  E  +  R    D++    EF   
Sbjct: 108 QVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVK 167

Query: 316 LHLMEIDISAFACLCALTLI 335
            + +E+D S  A   A+ ++
Sbjct: 168 FNALELDDSDLAIFIAVIIL 187

>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 = 44.2 bits (104), Expect = 9e-06
 Identities = 31/147 (21%), Positives = 52/147 (35%), Gaps = 15/147 (10%)

Query: 149 REPNPLEPPIAEPEKIQQFYSLLTTSVDVIRH---FADKIPGFSDLCKEDQELLFQSASL 205
           +   PL+    E   I+ F      SV+ ++    +A  IPGF +L   DQ  L +    
Sbjct: 59  KHITPLQEQSKEVA-IRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVH 117

Query: 206 EL----FYREPNPLEPPIAEPEKI---QQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQE 258
           E+         N     I+E +     +   SL     D +    +    F+ L  +D +
Sbjct: 118 EIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSD 177

Query: 259 LLFQSASLELFVLRLAYRTRAEDTKLI 285
           L    A     ++    R    + K I
Sbjct: 178 L----AIFIAVIILSGDRPGLLNVKPI 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 = 81.3 bits (200), Expect = 2e-18
 Identities = 25/127 (19%), Positives = 53/127 (41%), Gaps = 2/127 (1%)

Query: 211 EPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFV 270
               +   +++   +     L++ S+  +  FA  IPGF DL  EDQ +L +S+++E+ +
Sbjct: 45  GGGSVTLELSQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIM 104

Query: 271 LRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFG--DDWLNAILEFCQSLHLMEIDISAFAC 328
           LR       +D      N     +       G   + +  +++F   L  + +       
Sbjct: 105 LRSNESFTMDDMSWTCGNQDYKYRVSDVTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVL 164

Query: 329 LCALTLI 335
           L A+ ++
Sbjct: 165 LMAICIV 171

>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 = 45.5 bits (107), Expect = 3e-06
 Identities = 16/60 (26%), Positives = 31/60 (51%)

Query: 150 EPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFY 209
               +   +++   +     L++ S+  +  FA  IPGF DL  EDQ +L +S+++E+  
Sbjct: 45  GGGSVTLELSQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIM 104

>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 = 80.5 bits (198), Expect = 3e-18
 Identities = 29/119 (24%), Positives = 58/119 (48%), Gaps = 1/119 (0%)

Query: 218 PIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRT 277
           P +E   +    +L    +  + ++A ++PGF DL   DQ  L + A LE+ ++ L +R+
Sbjct: 30  PFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRS 89

Query: 278 RAEDTKLIFCNGVVLEKQQCQRSFG-DDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
                KL+F   ++L++ Q +   G  +  + +L       +M +    F CL ++ L+
Sbjct: 90  MEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILL 148

>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 = 43.1 bits (101), Expect = 2e-05
 Identities = 20/78 (25%), Positives = 34/78 (43%), Gaps = 7/78 (8%)

Query: 139 PPVSLITALYR-EPNPLEP------PIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDL 191
               +++AL   EP  L        P +E   +    +L    +  + ++A ++PGF DL
Sbjct: 5   TADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDL 64

Query: 192 CKEDQELLFQSASLELFY 209
              DQ  L + A LE+  
Sbjct: 65  TLHDQVHLLECAWLEILM 82

>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 = 80.1 bits (197), Expect = 4e-18
 Identities = 29/131 (22%), Positives = 58/131 (44%), Gaps = 4/131 (3%)

Query: 206 ELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSAS 265
            +    P+    P  E   +     L    +  +  +A KIPGF +L   DQ  L +S  
Sbjct: 18  NVLVSRPSM---PFTEASMMMSLTKLADKELVHMIGWAKKIPGFVELSLLDQVRLLESCW 74

Query: 266 LELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFG-DDWLNAILEFCQSLHLMEIDIS 324
           +E+ ++ L +R+     KLIF   +VL++ + +   G  +  + +L        +++   
Sbjct: 75  MEVLMVGLMWRSIDHPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHK 134

Query: 325 AFACLCALTLI 335
            + C+ A+ L+
Sbjct: 135 EYLCVKAMILL 145

>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 = 37.8 bits (87), Expect = 0.001
 Identities = 22/170 (12%), Positives = 48/170 (28%), Gaps = 19/170 (11%)

Query: 157 PIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFY----REP 212
           P  E   +     L    +  +  +A KIPGF +L   DQ  L +S  +E+         
Sbjct: 27  PFTEASMMMSLTKLADKELVHMIGWAKKIPGFVELSLLDQVRLLESCWMEVLMVGLMWRS 86

Query: 213 NPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL---- 268
                 +           +    + + R     + G  ++         +   L+L    
Sbjct: 87  IDHPGKL-----------IFAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKE 135

Query: 269 FVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHL 318
           ++   A          +       E  +      +   +A++       +
Sbjct: 136 YLCVKAMILLNSSMYPLASANQEAESSRKLTHLLNAVTDALVWVIAKSGI 185

>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 = 77.4 bits (190), Expect = 4e-17
 Identities = 27/148 (18%), Positives = 50/148 (33%), Gaps = 7/148 (4%)

Query: 192 CKEDQELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSD 251
           C+ D+  +       L   + N       +         +   ++  I  +A     F +
Sbjct: 13  CEPDEPQVQAKIMAYLQQEQSNRNRQE--KLSAFGLLCKMADQTLFSIVEWARSSIFFRE 70

Query: 252 LCKEDQELLFQSASLELFVLRLAYRT--RAEDTKLIFCNGVVLEKQQCQRSFG---DDWL 306
           L  +DQ  L Q+   EL +L   YR     ++  +    G  ++            ++ L
Sbjct: 71  LKVDDQMKLLQNCWSELLILDHIYRQVAHGKEGTIFLVTGEHVDYSTIISHTEVAFNNLL 130

Query: 307 NAILEFCQSLHLMEIDISAFACLCALTL 334
           +   E    L  ++ D   F CL  L L
Sbjct: 131 SLAQELVVRLRSLQFDQREFVCLKFLVL 158

>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 = 41.2 bits (96), Expect = 7e-05
 Identities = 15/75 (20%), Positives = 27/75 (36%), Gaps = 3/75 (4%)

Query: 136 PPSPPV--SLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCK 193
           P  P V   ++  L +E +       +         +   ++  I  +A     F +L  
Sbjct: 15  PDEPQVQAKIMAYLQQEQSNRNRQ-EKLSAFGLLCKMADQTLFSIVEWARSSIFFRELKV 73

Query: 194 EDQELLFQSASLELF 208
           +DQ  L Q+   EL 
Sbjct: 74  DDQMKLLQNCWSELL 88

>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 = 75.5 bits (185), Expect = 1e-16
 Identities = 26/143 (18%), Positives = 53/143 (37%), Gaps = 4/143 (2%)

Query: 197 ELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSL---LTTSVDVIRHFADKIPGFSDLC 253
             L Q+  L      P          +KI     +   +   + V+  +A  IP F +L 
Sbjct: 8   NALLQAEVLSRQITSPVSGINGDIRAKKIASIADVCESMKEQLLVLVEWAKYIPAFCELP 67

Query: 254 KEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRS-FGDDWLNAILEF 312
            +DQ  L ++ + E  +L    R+      L+  N  ++ +   + +      +  + E 
Sbjct: 68  LDDQVALLRAHAGEHLLLGATKRSMVFKDVLLLGNDYIVPRHCPELAEMSRVSIRILDEL 127

Query: 313 CQSLHLMEIDISAFACLCALTLI 335
                 ++ID + +A L A+   
Sbjct: 128 VLPFQELQIDDNEYAYLKAIIFF 150

>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 = 38.1 bits (88), Expect = 8e-04
 Identities = 16/84 (19%), Positives = 33/84 (39%), Gaps = 11/84 (13%)

Query: 125 LPSKPKSPQESPPSPPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADK 184
           L ++  S Q + P   ++         +     IA    + +    +   + V+  +A  
Sbjct: 11  LQAEVLSRQITSPVSGIN--------GDIRAKKIASIADVCE---SMKEQLLVLVEWAKY 59

Query: 185 IPGFSDLCKEDQELLFQSASLELF 208
           IP F +L  +DQ  L ++ + E  
Sbjct: 60  IPAFCELPLDDQVALLRAHAGEHL 83

>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 = 73.6 bits (180), Expect = 6e-16
 Identities = 26/128 (20%), Positives = 55/128 (42%), Gaps = 1/128 (0%)

Query: 209 YREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL 268
           Y E N    P +  + +          +  +  +A +IP FS+L  +DQ +L ++   EL
Sbjct: 21  YVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNEL 80

Query: 269 FVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRS-FGDDWLNAILEFCQSLHLMEIDISAFA 327
            +   ++R+ A    ++   G+ + +     +  G  +   + E    +  M++D +   
Sbjct: 81  LIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELG 140

Query: 328 CLCALTLI 335
           CL A+ L 
Sbjct: 141 CLRAIVLF 148

>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 = 70.5 bits (172), Expect = 1e-14
 Identities = 30/158 (18%), Positives = 54/158 (34%), Gaps = 20/158 (12%)

Query: 197 ELLFQSASLELFYREPNPLEP-PIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKE 255
           E L    S E  +    P    P      +     +    +  +  +A  IP FS L  E
Sbjct: 15  ESLVADPSEEFQFLRVGPDSNVPPKFRAPVSSLCQIGNKQIAALVVWARDIPHFSQLEME 74

Query: 256 DQELLFQSASLELFVLRLAYRT------------------RAEDTKLIFCNGVVLEKQQ- 296
           DQ LL + +  EL +  +A+R+                   +    +    G+ L +   
Sbjct: 75  DQILLIKGSWNELLLFAIAWRSMEFLTEERDGVDGTGNRTTSPPQLMCLMPGMTLHRNSA 134

Query: 297 CQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334
            Q   G  +   + E    +  + +D + +  L A+ L
Sbjct: 135 LQAGVGQIFDRVLSELSLKMRTLRVDQAEYVALKAIIL 172

>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 = 69.8 bits (170), Expect = 2e-14
 Identities = 21/167 (12%), Positives = 52/167 (31%), Gaps = 29/167 (17%)

Query: 197 ELLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKED 256
           E      +L      P     P      +     ++   +  +  +A  +P F+ +  +D
Sbjct: 14  ETQCGDRALTFLRVGPYSTVQP-DYKGAVSALCQVVNKQLFQMVEYARMMPHFAQVPLDD 72

Query: 257 QELLFQSASLELFVLRLAYRT---------------------------RAEDTKLIFCNG 289
           Q +L ++A +EL +  +A+ +                             +  +L     
Sbjct: 73  QVILLKAAWIELLIANVAWCSIVSLDDGGAGGGGGGLGHDGSFERRSPGLQPQQLFLNQS 132

Query: 290 VVLEKQQCQRS-FGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335
               +    ++     +   + E    +  + +D    +CL A+ L 
Sbjct: 133 FSYHRNSAIKAGVSAIFDRILSELSVKMKRLNLDRRELSCLKAIILY 179

>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 = 68.2 bits (166), Expect = 6e-14
 Identities = 28/133 (21%), Positives = 51/133 (38%), Gaps = 8/133 (6%)

Query: 211 EPNPLE--PPIAEPEKIQQFYSLLTTSVD----VIRHFADKIPGFSDLCKEDQELLFQSA 264
           EP  L      + P+   +  + L             +A  IPGF +L  +DQ  L Q +
Sbjct: 11  EPEVLYAGYDSSVPDSTWRIMTTLNMLGGRQVIAAVKWAKAIPGFRNLHLDDQMTLLQYS 70

Query: 265 SLELFVLRLAYRTRA--EDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEID 322
            + L    L +R+        L F   +++ +Q+       D    +L     LH +++ 
Sbjct: 71  WMSLMAFALGWRSYRQSSANLLCFAPDLIINEQRMTLPDMYDQCKHMLYVSSELHRLQVS 130

Query: 323 ISAFACLCALTLI 335
              + C+  L L+
Sbjct: 131 YEEYLCMKTLLLL 143

>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 = 67.8 bits (165), Expect = 9e-14
 Identities = 26/133 (19%), Positives = 54/133 (40%), Gaps = 8/133 (6%)

Query: 211 EPNPLE--PPIAEPEKIQQFYSLLTTSVD----VIRHFADKIPGFSDLCKEDQELLFQSA 264
           EP+ +       +P+      + L    +     +  ++  +PGF +L  +DQ  L Q +
Sbjct: 14  EPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYS 73

Query: 265 SLELFVLRLAYRT--RAEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEID 322
            + L V  L +R+        L F   ++L +Q+ + S        + +  Q    +++ 
Sbjct: 74  WMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVS 133

Query: 323 ISAFACLCALTLI 335
              F C+  L L+
Sbjct: 134 QEEFLCMKVLLLL 146

>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 = 64.0 bits (155), Expect = 2e-12
 Identities = 27/133 (20%), Positives = 50/133 (37%), Gaps = 8/133 (6%)

Query: 211 EPNPLE--PPIAEPEKIQQFYSLLTTSVD----VIRHFADKIPGFSDLCKEDQELLFQSA 264
           EP  +       +P+      S L    +     +  +A  +PGF +L  +DQ  + Q +
Sbjct: 13  EPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYS 72

Query: 265 SLELFVLRLAYRTRAEDTK--LIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEID 322
            + L V  + +R+        L F   +V  + +  +S        +    Q    ++I 
Sbjct: 73  WMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHKSRMYSQCVRMRHLSQEFGWLQIT 132

Query: 323 ISAFACLCALTLI 335
              F C+ AL L 
Sbjct: 133 PQEFLCMKALLLF 145

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	335
d1lo1a_	90	Steroid hormone receptor Err2 DNA-binding domain {	100.0
d1dszb_	84	Retinoid X receptor (RXR-alpha) DNA-binding domain	100.0
d2hanb1	83	Ecdysone receptor DNA-binding domain {Fruit fly (D	100.0
d1dsza_	75	Retinoic acid receptor DNA-binding domain {Human (	100.0
d1r4ia_	74	Androgen receptor {Rat (Rattus norvegicus) [TaxId:	100.0
d1cita_	89	Orphan nuclear receptor NGFI-B DNA-binding domain	100.0
d1a6ya_	78	Orphan nuclear receptor reverb DNA-binding domain	100.0
d1kb2a_	89	Vitamin D3 receptor, VDR, DNA-binding domain {Huma	100.0
d1lata_	71	Glucocorticoid receptor DNA-binding domain {Rat (R	100.0
d2nllb_	103	Thyroid hormone receptor (TR-beta) DNA-binding dom	100.0
d1hcqa_	74	Estrogen receptor DNA-binding domain {Human and ch	100.0
d1ovla_	236	Orphan nuclear receptor NURR1 {Human (Homo sapiens	99.92
d2qw4a1	233	Orphan nuclear receptor NR4A1 {Human (Homo sapiens	99.92
d1pdua_	230	Nuclear hormone receptor HR38 {Fruit fly (Drosophi	99.92
d1n46a_	251	Thyroid hormone receptor beta (TR-beta) {Human (Ho	99.9
d2r40d1	243	Ecdysone receptor {Noctuid moth (Heliothis viresce	99.9
d1fcya_	236	Retinoic acid receptor gamma (RAR-gamma) {Human (H	99.89
d1xnxa_	232	Orphan nuclear receptor NR1I3 (CAR) {Mouse (Mus mu	99.89
d1pq9a_	239	Oxysterols receptor LXR-beta {Human (Homo sapiens)	99.89
d2e2ra1	223	Orphan nuclear receptor ERR3 {Human (Homo sapiens)	99.87
d1xvpb_	246	Orphan nuclear receptor NR1I3 (CAR) {Human (Homo s	99.87
d1xpca_	245	Estrogen receptor alpha {Human (Homo sapiens) [Tax	99.87
d3d24a1	227	Steroid hormone receptor ERR1 {Human (Homo sapiens	99.86
d1n83a_	251	Orphan nuclear receptor ROR-alpha {Human (Homo sap	99.86
d1ie9a_	255	Vitamin D nuclear receptor {Human (Homo sapiens) [	99.86
d2j7ya1	236	Estrogen receptor beta {Rat (Rattus norvegicus) [T	99.86
d1nq7a_	244	Orphan nuclear receptor ROR-beta {Rat (Rattus norv	99.85
d1t7ra_	250	Androgen receptor {Chimpanzee (Pan troglodytes) [T	99.84
d1nhza_	247	Glucocorticoid receptor {Human (Homo sapiens) [Tax	99.84
d1sqna_	251	Progesterone receptor {Human (Homo sapiens) [TaxId	99.84
d2p1ta1	230	Retinoid-X receptor alpha (RXR-alpha) {Human (Homo	99.83
d1g2na_	256	Ultraspiracle protein, usp {Heliothis virescens [T	99.83
d1osha_	231	Bile acid receptor FXR {Human (Homo sapiens) [TaxI	99.83
d1pzla_	233	Hepatocyte nuclear factor 4-alpha {Human (Homo sap	99.83
d1pk5a_	242	Orphan nuclear receptor NR5a2 (LRH-1) {Mouse (Mus	99.82
d1hg4a_	265	Ultraspiracle protein, usp {Drosophila melanogaste	99.82
d2p54a1	267	Peroxisome proliferator activated receptor alpha,	99.82
d1nrla_	292	Pregnane x receptor, PXR {Human (Homo sapiens) [Ta	99.81
d2fvja1	271	Peroxisome proliferator activated receptor gamma,	99.79
d2b50b1	265	Peroxisome proliferator-activated receptor delta,	99.79
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	90.95
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	84.81
d2qw4a1	233	Orphan nuclear receptor NR4A1 {Human (Homo sapiens	80.19

>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=9.9e-40  Score=225.11  Aligned_cols=85  Identities=56%  Similarity=1.082  Sum_probs=79.9

Q ss_pred             CCCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636          38 SPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS  117 (335)
Q Consensus        38 ~~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~  117 (335)
                      .|.++|.||||+++|+||||++|+|||+||||+|..+..|.|..+++|.|++..|+.||+|||+|||+|||++++||.++
T Consensus         2 ~P~~~C~VCg~~~~~~hyG~~sC~aC~~FFRR~v~~~~~~~c~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~r   81 (90)
T d1lo1a_           2 IPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKALKVGMLKEGVRLDR   81 (90)
T ss_dssp             CCCCEETTTTEECSEESSSSEECHHHHHHHHHHHHTTCCCCCSSCSCCCCCHHHHHHCHHHHHHHHHHHTCCGGGSCSSC
T ss_pred             CCCCcCCcCCCcCCceEcCeeechhhHHHHHHHHhcCCccchhcCCCCccCCCCccccchhhHHHHHHcCCCHHHhcccc
Confidence            46688999999999999999999999999999999999999999999999999999999999999999999999999887


Q ss_pred             ccccC
Q psy2636         118 LKGRR  122 (335)
Q Consensus       118 ~~~~~  122 (335)
                      +...+
T Consensus        82 ~~~~r   86 (90)
T d1lo1a_          82 VRGGR   86 (90)
T ss_dssp             CTTCC
T ss_pred             ccccc
Confidence            65444

>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=1.5e-39  Score=221.12  Aligned_cols=80  Identities=55%  Similarity=1.193  Sum_probs=76.2

Q ss_pred             CCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeeccc
Q psy2636          39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSL  118 (335)
Q Consensus        39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~  118 (335)
                      +.++|.||||+|+|+||||++|+|||+||||+|..+..|.|..+++|.+++..|+.||+|||+|||+|||++++||.+++
T Consensus         4 ~~~~C~VC~~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~c~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~Rd   83 (84)
T d1dszb_           4 TKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQ   83 (84)
T ss_dssp             CCEECTTTCCEESSEETTEECCHHHHHHHHHHHHHTCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCCCC
T ss_pred             CCCcCccCCCcCCccCCCHHHHHHhHHHHHHHHhcCCCeeccCCCCcccCCCCCccCCCCccHHHHHcCCChHHcccccC
Confidence            45679999999999999999999999999999999999999999999999999999999999999999999999998754

>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=2.9e-39  Score=219.60  Aligned_cols=79  Identities=49%  Similarity=0.975  Sum_probs=75.7

Q ss_pred             CcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecccc
Q psy2636          41 QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLK  119 (335)
Q Consensus        41 ~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~~  119 (335)
                      ++|.||||+++|+||||+||+|||+||||+|..+..|.|..+++|.+++..|+.||+|||+|||++||++++||.++..
T Consensus         1 e~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~c~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~   79 (83)
T d2hanb1           1 ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECRLKKCLAVGMRPECVVPENQC   79 (83)
T ss_dssp             CBCTTTCSBCCEEETTEEECHHHHHHHHHHHHTTCCCCCSSCSCCCCSTTGGGTCHHHHHHHHHHTTCCGGGSSCSSHH
T ss_pred             CcCccCCCcCCccCcCHHhHhHhHHHHHHHHhcCCceeecCCCCcccCCcccccCccchHHHHHHcCCCHHHccccchh
Confidence            5799999999999999999999999999999999999999999999999999999999999999999999999987653

>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=8.2e-39  Score=213.25  Aligned_cols=75  Identities=57%  Similarity=1.163  Sum_probs=72.9

Q ss_pred             cccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeec
Q psy2636          42 LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTD  116 (335)
Q Consensus        42 ~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~  116 (335)
                      ||.|||++++|+||||.+|+|||+||||+|..+..|.|..+++|.+++..|..||+|||+|||+|||++++||.|
T Consensus         1 PC~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~c~~~~~c~~~~~~r~~Cr~CR~~KCl~~GM~~~~vq~d   75 (75)
T d1dsza_           1 PCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRND   75 (75)
T ss_dssp             CCTTTCSCCCSEETTEECCHHHHHHHHHHHHTTCCCCCSSCSCCCCSTTTGGGCHHHHHHHHHHTTCCGGGSCCC
T ss_pred             CCccCCCcCCccCcCHHHhhhhHHHHHHHHhcCCceecccCCccccCCccccccchhHHHHHHHhCCCHHHccCC
Confidence            699999999999999999999999999999999999999999999999999999999999999999999999864

>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=8.4e-39  Score=212.33  Aligned_cols=74  Identities=43%  Similarity=0.970  Sum_probs=71.1

Q ss_pred             CCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeee
Q psy2636          39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEV  112 (335)
Q Consensus        39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~  112 (335)
                      |.++|.||||+|+|+||||+||+|||+||||+|..+..|.|..+++|.|++..|+.||+|||+|||+|||+.+|
T Consensus         1 P~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~c~~~~~C~~~~~~r~~C~~CR~~KCl~vGM~~~A   74 (74)
T d1r4ia_           1 PQKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLGA   74 (74)
T ss_dssp             CCCBCSSSCSBEEEEETTEEEEHHHHHHHHHHHTSCCCCCCSSSSCCCCCTTTTTTCHHHHHHHHHHHTCCSCC
T ss_pred             CCCcCccCCCcCCccCCCHHhhHHHHHHHHHHHhcccceeeecCCCcccCCCCcccchhhhHHHHHHcCCcCCC
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999875

>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=100.00  E-value=2.1e-38  Score=218.59  Aligned_cols=86  Identities=90%  Similarity=1.592  Sum_probs=80.7

Q ss_pred             cccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecccccc
Q psy2636          42 LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLKGR  121 (335)
Q Consensus        42 ~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~~~~  121 (335)
                      +|+|||++|+|+||||.+|+|||+||||+|..+..|.|..+++|.+++..|+.||+|||+|||+|||++++||.++...+
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            69999999999999999999999999999999999999999999999999999999999999999999999999887776


Q ss_pred             CCCCCC
Q psy2636         122 RGRLPS  127 (335)
Q Consensus       122 ~~~~~~  127 (335)
                      +.+.|.
T Consensus        82 r~~~p~   87 (89)
T d1cita_          82 RGRLPS   87 (89)
T ss_dssp             CSCCCC
T ss_pred             cCCCCC
Confidence            665554

>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=2e-38  Score=213.10  Aligned_cols=77  Identities=53%  Similarity=1.155  Sum_probs=72.2

Q ss_pred             CcccccCCCCCccccCCccccccccceecccccCCeee-cCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636          41 QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYV-CLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS  117 (335)
Q Consensus        41 ~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~-C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~  117 (335)
                      .+|.|||++|+|+||||++|+|||+||||++..+..|. |..+++|.|++..|..||+|||+|||++||++++||.+|
T Consensus         1 ~iC~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~~~~~~~~c~~~~~~r~~Cr~CR~~KCl~~GM~~~~vq~~R   78 (78)
T d1a6ya_           1 LLCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGR   78 (78)
T ss_dssp             CBCTTTSSBCCEEETTEEECHHHHHHHHHHHSSCCCCCCCSSTTCCCCCTTTTTSCHHHHHHHHTTTTCCSTTCCCCC
T ss_pred             CCCeeCCCcCCcccCcchhhhhchhhhhhhhccCCceeeeccCCCcccCCCCCccchhhHHHHHHHhCCCHHHhcCCC
Confidence            36999999999999999999999999999999999997 566889999999999999999999999999999998753

>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=1.3e-38  Score=219.32  Aligned_cols=79  Identities=41%  Similarity=0.972  Sum_probs=75.4

Q ss_pred             CcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecccc
Q psy2636          41 QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLK  119 (335)
Q Consensus        41 ~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~~  119 (335)
                      ++|.|||++|+|+||||++|+|||+||||+|..+..|.|..+++|.|++..|+.||+|||+|||+|||++++||.++..
T Consensus         1 r~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~c~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~   79 (89)
T d1kb2a_           1 RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDEEV   79 (89)
T ss_dssp             CBCTTTCSBCCSEETTEECCHHHHHHHHHHHHTTCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCHHHH
T ss_pred             CCCeeCCCcCCccCCCHHHHHHHHHHHHHHHhcCCCeecCCCCccCCCCcCCccCchhhHHHHHHcCCCHhhccccchh
Confidence            4799999999999999999999999999999999999999999999999999999999999999999999999987643

>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=1.9e-37  Score=204.37  Aligned_cols=71  Identities=52%  Similarity=1.044  Sum_probs=68.7

Q ss_pred             CcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceee
Q psy2636          41 QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKE  111 (335)
Q Consensus        41 ~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~  111 (335)
                      ++|.|||++|+|+||||+||+|||+||||+|..+..|.|..+++|.+++..|+.||+|||+|||+|||++|
T Consensus         1 k~C~VC~~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~c~~~~~C~~~~~~r~~Cr~CR~~KCl~~GM~~e   71 (71)
T d1lata_           1 RPCLVCSDEASGCHYGVLTCEGCKAFFKRAVEGQHNYLCKYEGKCIIDKIRRKNCPACRYRKCLQAGMNLE   71 (71)
T ss_dssp             CBCTTTCSBCCEEETTEEECHHHHHHHHHHHHSCCCCCCSSCSCCCCSTTTTTTCHHHHHHHHHHTTCCCC
T ss_pred             CcCeeCCCcCCceEcCHhhHHHHHHHHHHHHhcCcceeeecCcccccccCccccCCccchhHHhHccCCCC
Confidence            47999999999999999999999999999999999999999999999999999999999999999999975

>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=1e-37  Score=221.92  Aligned_cols=79  Identities=52%  Similarity=1.001  Sum_probs=72.7

Q ss_pred             CCcccccCCCCCccccCCccccccccceecccccCCee--ecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636          40 SQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKY--VCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS  117 (335)
Q Consensus        40 ~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y--~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~  117 (335)
                      +++|.||||+|+|+||||+||+|||+||||+|..+..|  .|..+++|.|++..|+.||+|||+|||+|||++++||.++
T Consensus         1 ~~~C~VCg~~a~g~HfGv~sC~aCkaFFRR~v~~~~~~~~~c~~~~~c~~~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r   80 (103)
T d2nllb_           1 DELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQECRFKKCIYVGMATDLVLDDS   80 (103)
T ss_dssp             CCBCTTTCSBCCSEETTEECCHHHHHHHHHHHHTTCGGGCCCSSCTTCCCSTTTTTSCHHHHHHHHHHTTCCGGGSCCHH
T ss_pred             CCcCccCCCcCCcccCchhhhHHHHHHhHHHhhccccceeecccCCCCcCCCCccCCCccccchhHHHhhccHHhhhccc
Confidence            46899999999999999999999999999999987655  5677899999999999999999999999999999999875


Q ss_pred             c
Q psy2636         118 L  118 (335)
Q Consensus       118 ~  118 (335)
                      .
T Consensus        81 ~   81 (103)
T d2nllb_          81 K   81 (103)
T ss_dssp             H
T ss_pred             c
Confidence            4

>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=100.00  E-value=3.3e-37  Score=204.59  Aligned_cols=73  Identities=52%  Similarity=1.122  Sum_probs=69.9

Q ss_pred             CCCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCcee
Q psy2636          38 SPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVK  110 (335)
Q Consensus        38 ~~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~  110 (335)
                      .+.++|.|||++|+|+||||++|+|||+||||+|..+..|.|+.+++|.|++..|+.||+|||+|||+|||++
T Consensus         2 ~~~~~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~k   74 (74)
T d1hcqa_           2 KETRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMK   74 (74)
T ss_dssp             CCCCBCTTTCSBCCEEETTEEECHHHHHHHHHHHSSCCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHHTCCC
T ss_pred             CCCCCCccCCCcCCceEcCeeehHHHHHHHHHHHHcccccccccCCCCccCCCccccchHhhHHHHHHcCCcC
Confidence            4567899999999999999999999999999999999999999999999999999999999999999999974

>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=99.92  E-value=2.8e-25  Score=184.95  Aligned_cols=116  Identities=59%  Similarity=1.043  Sum_probs=108.9

Q ss_pred             CChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhh
Q psy2636         219 IAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQ  298 (335)
Q Consensus       219 ~~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~  298 (335)
                      ..+.+.|++|++.++..|+.+|+|||++|||.+|+.+||++|||++|+|+++|+.|+++...++.+++.+|.++.+.+..
T Consensus        35 ~~~~~~~~~f~~~~~~~i~~iv~fAK~iPgF~~L~~~DQi~LLk~~~~ElllL~~a~~~~~~~~~l~~~~~~~~~~~~~~  114 (236)
T d1ovla_          35 GDDTQHIQQFYDLLTGSMEIIRGWAEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIFCNGVVLHRLQCV  114 (236)
T ss_dssp             --CHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHSBTTTTEEECTTSBEEEHHHHT
T ss_pred             CCchhHHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEecCCceechHhhc
Confidence            45677889999999999999999999999999999999999999999999999999999988889999999999998887


Q ss_pred             hhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         299 RSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       299 ~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      .+++ ++++.+++|+.+|++|++|++||+|||||+||
T Consensus       115 ~~~~-~~~~~i~~~~~~l~~L~ld~~E~alLkAI~L~  150 (236)
T d1ovla_         115 RGFG-EWIDSIVEFSSNLQNMNIDISAFSCIAALAMV  150 (236)
T ss_dssp             TTTT-THHHHHHHHHHHHHTTCCCHHHHHHHHHHHHS
T ss_pred             ccHH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence            8888 88999999999999999999999999999986

>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=99.92  E-value=9e-25  Score=181.88  Aligned_cols=118  Identities=54%  Similarity=1.001  Sum_probs=111.0

Q ss_pred             CCCChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHh
Q psy2636         217 PPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQ  296 (335)
Q Consensus       217 ~~~~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~  296 (335)
                      ....+.+.+++|++.++..|+.+|+|||++|||.+|+.+||++|||++|+++++++.|+++.+.++.+++.+|..+..+.
T Consensus        33 ~~~~~~~~~~~~~~~~~~~i~~iv~wAK~iPgF~~L~~~DQi~LLk~~~~el~lL~~a~~~~~~~~~l~~~~~~~~~~~~  112 (233)
T d2qw4a1          33 FGKEDAGDVQQFYDLLSGSLEVIRKWAEKIPGFAELSPADQDLLLESAFLELFILRLAYRSKPGEGKLIFCSGLVLHRLQ  112 (233)
T ss_dssp             CSCCCHHHHHHHHHHHHHHHHHHHHHHHTSTTTTTSCHHHHHHHHHHHHHHHHHHHHHHHSBGGGTEEECTTSCEEEHHH
T ss_pred             CCCCchHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhCCCCCCceeecCCeeecHHh
Confidence            33456788999999999999999999999999999999999999999999999999999999888999999999999988


Q ss_pred             hhhhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         297 CQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       297 ~~~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ...+++ ++++.+++|+.+|++|++|++||+|||||+||
T Consensus       113 ~~~~~~-~~~~~i~~~~~~l~~L~ld~~E~alLkAivL~  150 (233)
T d2qw4a1         113 CARGFG-DWIDSILAFSRSLHSLLVDVPAFACLSALVLI  150 (233)
T ss_dssp             HHHHHT-THHHHHHHHHHHHHHHTCCHHHHHHHHHHHHS
T ss_pred             hhhhhH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhc
Confidence            888888 88999999999999999999999999999986

>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=99.92  E-value=1.1e-24  Score=180.90  Aligned_cols=116  Identities=75%  Similarity=1.232  Sum_probs=110.1

Q ss_pred             CChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhh
Q psy2636         219 IAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQ  298 (335)
Q Consensus       219 ~~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~  298 (335)
                      ..+.+.+++|++.++..|+.+|+|||++|||.+|+.+||++|||++|+|+++|+.|+++....+.+++.+|..+.+++..
T Consensus        32 ~~~~~~~~~~~~~~~~~i~~ivefAK~iPgF~~L~~~DQi~LLk~~~~El~~L~~a~~~~~~~~~l~~~~g~~~~~~~~~  111 (230)
T d1pdua_          32 MSEADKVQQFYQLLTSSVDVIKQFAEKIPGYFDLLPEDQELLFQSASLELFVLRLAYRARIDDTKLIFCNGTVLHRTQCL  111 (230)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHCCSSCSEEECTTSBEEEHHHHH
T ss_pred             CChHHHHHHHHHHHHHHHHHHHHHHHcCCChhcCCHHHHHHHHHHHHHHHHHHHHHHhccCCCCeEEecCCccccHHHHH
Confidence            46778899999999999999999999999999999999999999999999999999999999899999999999998877


Q ss_pred             hhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         299 RSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       299 ~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      .+++ ++++.+++|+.+|++|++|.+||+||+||+||
T Consensus       112 ~~~~-~~~~~i~~~~~~~~~L~ld~~E~alL~AivL~  147 (230)
T d1pdua_         112 RSFG-EWLNDIMEFSRSLHNLEIDISAFACLCALTLI  147 (230)
T ss_dssp             HHHT-THHHHHHHHHHHHHHHCCCHHHHHHHHHHHHS
T ss_pred             HhHH-HHHHHHHHHHHHHHHcCCCHHHHHHHhhheee
Confidence            7888 88999999999999999999999999999987

>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=99.90  E-value=2.2e-23  Score=175.03  Aligned_cols=116  Identities=26%  Similarity=0.365  Sum_probs=107.9

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR  299 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~  299 (335)
                      ...+.|.++++.++..|+.+|+|||++|||.+|+.+||++|||++|+++++|+.|+++...++.+.+.+|.++.++.+..
T Consensus        54 ~~~~~~~~~~~~~~~~i~~vV~fAK~iPgF~~L~~~DQi~LLk~~~~El~lL~~a~~~~~~~~~~~~~~~~~~~~~~~~~  133 (251)
T d1n46a_          54 VDLEAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLNGEMAVTRGQLKN  133 (251)
T ss_dssp             CCHHHHHHHHTTHHHHHHHHHHHHHTCTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTCBTTTTBEEETTTEEECHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEeCCCccccHHHHhh
Confidence            45677899999999999999999999999999999999999999999999999999999888899999999999988766


Q ss_pred             hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 ~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      +...++.+.+++|+.+|++|+||++||+||+||+||
T Consensus       134 ~~~~~~~~~i~~f~~~l~~L~ld~~E~alL~AivL~  169 (251)
T d1n46a_         134 GGLGVVSDAIFDLGMSLSSFNLDDTEVALLQAVLLM  169 (251)
T ss_dssp             TTTTTHHHHHHHHHHHHGGGTCCHHHHHHHHHHHHT
T ss_pred             cccHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence            544488999999999999999999999999999987

>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=99.90  E-value=3.8e-23  Score=173.07  Aligned_cols=114  Identities=25%  Similarity=0.437  Sum_probs=105.6

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhhhh
Q psy2636         222 PEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSF  301 (335)
Q Consensus       222 ~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~~~  301 (335)
                      ...+.++.++.+..|+.+|+|||++|+|.+|+.+||++|||++|+++++++.|+++....+.+++++|..+..+......
T Consensus        47 ~~~~~~~~~~~~~~i~~iV~faK~lP~F~~L~~~DQi~LLk~~~~El~lL~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~  126 (243)
T d2r40d1          47 DMPFRQITEMTILTVQLIVEFAKGLPGFAKISQSDQITLLKACSSEVMMLRVARRYDAATDSVLFANNQAYTRDNYRKAG  126 (243)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEETTTTEEECTTSCEECHHHHHHTT
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHcCcChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCeEEecCCeeecHHHHhhcc
Confidence            34678888989999999999999999999999999999999999999999999999998899999999999988876644


Q ss_pred             cHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         302 GDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       302 ~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ..++++.+++|+.+|++|++|++||+||+||+||
T Consensus       127 ~~~~~~~l~~f~~~l~~L~ld~~E~alL~AivL~  160 (243)
T d2r40d1         127 MAYVIEDLLHFCRCMYSMMMDNVHYALLTAIVIF  160 (243)
T ss_dssp             CHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHT
T ss_pred             cHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHhc
Confidence            4489999999999999999999999999999987

>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=99.89  E-value=5.6e-23  Score=171.35  Aligned_cols=116  Identities=27%  Similarity=0.431  Sum_probs=107.8

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR  299 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~  299 (335)
                      .+...|.++++.++..++.+|+|||++|||.+|+.+||++|||++|+++++|+.|+++..+.+.+.+.+|..+.++....
T Consensus        41 ~~~~~~~~~~~~~~~~i~~iV~faK~ip~F~~L~~~DQi~LLk~~~~el~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~  120 (236)
T d1fcya_          41 LDLGLWDKFSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMTFSDGLTLNRTQMHN  120 (236)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETTTTEEECTTCBEEEHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcccCCeeeccCCceecHHHHhh
Confidence            45667889999999999999999999999999999999999999999999999999999988999999999999988776


Q ss_pred             hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 ~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ....++.+.+.+|+.+|++|++|++||+||+||+||
T Consensus       121 ~~~~~l~~~~~~~~~~l~~L~ld~~E~alL~Ai~L~  156 (236)
T d1fcya_         121 AGFGPLTDLVFAFAGQLLPLEMDDTETGLLSAICLI  156 (236)
T ss_dssp             HTTGGGHHHHHHHHHHHGGGCCCHHHHHHHHHHHHS
T ss_pred             cccHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhhc
Confidence            444488999999999999999999999999999986

>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=99.89  E-value=3.9e-23  Score=171.57  Aligned_cols=116  Identities=20%  Similarity=0.290  Sum_probs=106.1

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR  299 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~  299 (335)
                      ...+.+.+++++.+..|+.+|+|||++|||.+|+.+||++|||++|+++++|+.|+++....+.+.+.+|.+...+....
T Consensus        50 ~~~~~~~~~~~~~~~~i~~iV~faK~lP~F~~L~~eDQi~LLk~~~~El~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~  129 (232)
T d1xnxa_          50 PVLPLLTHFADINTFMVQQIIKFTKDLPLFRSLTMEDQISLLKGAAVEILHISLNTTFCLQTENFFCGPLCYKMEDAVHA  129 (232)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHTSCHHHHHHHHHHHHHHHHHHHHGGGEETTTTEEEETTEEECHHHHHHT
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCceeeCCcccchHHHHhc
Confidence            34567888999999999999999999999999999999999999999999999999999888888888877776666667


Q ss_pred             hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 ~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      +++.++++.+++|+.+|++|+||++||+||+||+||
T Consensus       130 ~~~~~~~~~i~~f~~~l~~L~ld~~E~alLkAivLf  165 (232)
T d1xnxa_         130 GFQYEFLESILHFHKNLKGLHLQEPEYVLMAATALF  165 (232)
T ss_dssp             TCCHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHT
T ss_pred             cccHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHh
Confidence            777789999999999999999999999999999987

>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=99.89  E-value=1.2e-22  Score=169.64  Aligned_cols=115  Identities=27%  Similarity=0.504  Sum_probs=105.9

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh-
Q psy2636         221 EPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR-  299 (335)
Q Consensus       221 ~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~-  299 (335)
                      ....+.++.+..+..|+.+|+|||++|+|.+|+.+||++|||++|+++++++.|+++....+.+.+.+|..+....... 
T Consensus        45 ~~~~~~~~~~~~~~~i~~iVefAK~lP~F~~L~~~DQi~LLk~~~~el~ll~~a~~~~~~~~~~~~~~~~~~~~~~~~~~  124 (239)
T d1pq9a_          45 RQQRFAHFTELAIISVQEIVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETARRYNHETECITFLKDFTYSKDDFHRA  124 (239)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTSTTSTTSCHHHHHHHHHHHHHHHHHHHHHHTEETTTTEEEEETTEEECHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHhHhhhcCcCHHhcCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEeecCCCcccHHHHhhh
Confidence            3456778889999999999999999999999999999999999999999999999999888999999999998877654 


Q ss_pred             hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 ~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      +++.++++.+++|+.+|++|++|++||+|||||+||
T Consensus       125 ~~~~~~~~~i~~~~~~l~~L~ld~~E~alLkAivL~  160 (239)
T d1pq9a_         125 GLQVEFINPIFEFSRAMRRLGLDDAEYALLIAINIF  160 (239)
T ss_dssp             TCCHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHT
T ss_pred             hhhHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence            566789999999999999999999999999999987

>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=99.87  E-value=6.5e-22  Score=163.40  Aligned_cols=116  Identities=28%  Similarity=0.441  Sum_probs=106.6

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR  299 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~  299 (335)
                      .....+..++++..+.+..+|+|||++|+|.+|+.+||++|||++|+++++++.|+++...++.+++.+|.++..+....
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            45667788889999999999999999999999999999999999999999999999999888889999999999887665


Q ss_pred             hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 ~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ....++.+.+.+++.+|++|++|.+||++||||+||
T Consensus       107 ~~~~~~~~~i~~~~~~l~~L~ld~~E~~lLkaivL~  142 (223)
T d2e2ra1         107 AGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALA  142 (223)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence            555689999999999999999999999999999985

>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=99.87  E-value=3.3e-22  Score=167.69  Aligned_cols=115  Identities=18%  Similarity=0.256  Sum_probs=103.2

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhhh
Q psy2636         221 EPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRS  300 (335)
Q Consensus       221 ~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~~  300 (335)
                      ....|.+++++.+..|+.+|+|||++|||.+|+.+||++|||++|+++++++.++++..+++.+.+.++.+...+....+
T Consensus        52 ~~~~~~~~~~~~~~~i~~iV~waK~lP~F~~L~~~DQi~LLk~~~~El~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  131 (246)
T d1xvpb_          52 VLPLVTHFADINTFMVLQVIKFTKDLPVFRSLPIEDQISLLKGAAVEICHIVLNTTFCLQTQNFLCGPLRYTIEDGARVG  131 (246)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHSCHHHHHHHHHHHHHHHHHHHHGGGEETTTTEEECSSCEECHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHhcccCCeeecCCCccchHHHhccc
Confidence            45668889999999999999999999999999999999999999999999999999988888888777666655555556


Q ss_pred             hcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         301 FGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       301 ~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      +..++++.+++|+.+|++|++|++||+|||||+||
T Consensus       132 ~~~~~~~~~~~f~~~l~~L~ld~~E~alLkAivL~  166 (246)
T d1xvpb_         132 FQVEFLELLFHFHGTLRKLQLQEPEYVLLAAMALF  166 (246)
T ss_dssp             CCHHHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHS
T ss_pred             cchHHHHHHHHHHHHHHHhCCCHHHHHHHhhhhhc
Confidence            66689999999999999999999999999999997

>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=99.87  E-value=1.2e-21  Score=164.13  Aligned_cols=115  Identities=23%  Similarity=0.467  Sum_probs=103.5

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR  299 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~  299 (335)
                      .+...+..++++....+..+|+|||++|+|.+|+.+||++|||++|+++++|+.||++....+.+.+.+|..++......
T Consensus        32 ~~~~~~~~l~~la~~~l~~~V~waK~ip~F~~L~~~DQi~LLk~~~~el~iL~~a~~s~~~~~~l~~~~~~~~~~~~~~~  111 (245)
T d1xpca_          32 SEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKC  111 (245)
T ss_dssp             TTSCHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTSTTEEEEETTEEEEHHHHTT
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHhCccHHhcCHHHHHHHHHHHHHHHHHHHHHHHhhccCCceeecCCcccchhHHhh
Confidence            34455777888888999999999999999999999999999999999999999999999888899999999999877653


Q ss_pred             --hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 --SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 --~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                        +++ ++.+.+.+++.+|++|++|.+||++||||+||
T Consensus       112 ~~~~~-~~~~~~~~~~~~~~~L~ld~~E~~lLkaI~L~  148 (245)
T d1xpca_         112 VEGMV-EIFDMLLATSSRFRMMNLQGEEFVCLKSIILL  148 (245)
T ss_dssp             STTHH-HHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             hccHH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence              444 78899999999999999999999999999985

>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=99.86  E-value=8.1e-22  Score=163.43  Aligned_cols=112  Identities=26%  Similarity=0.402  Sum_probs=102.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhhhhcH
Q psy2636         224 KIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD  303 (335)
Q Consensus       224 ~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~~~~~  303 (335)
                      .+..+++...+.+..+|+|||++|+|.+|+.+||++|||++|+++++|+.|+++...++.+.+++|.+++.+........
T Consensus        31 ~~~~l~~~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~~  110 (227)
T d3d24a1          31 AVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQDELAFAEDLVLDEEGARAAGLG  110 (227)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHSTTTTTSCHHHHHHHHHHHHHHHHHHHHHHHHTTSSSEEEEETTEEEEHHHHHHTTCT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCcchhcCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCeeeecCCcccchhhhccccHH
Confidence            46677788889999999999999999999999999999999999999999999998888999999999998776554444


Q ss_pred             HHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         304 DWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       304 ~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ++.+.+.+++.+|++|++|.+||++||||+||
T Consensus       111 ~~~~~l~~~~~~~~~L~ld~~E~~lLkaivLf  142 (227)
T d3d24a1         111 ELGAALLQLVRRLQALRLEREEYVLLKALALA  142 (227)
T ss_dssp             THHHHHHHHHHHHHTTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence            88999999999999999999999999999986

>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=99.86  E-value=1.9e-21  Score=163.50  Aligned_cols=115  Identities=23%  Similarity=0.403  Sum_probs=103.2

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR  299 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~  299 (335)
                      .....|+.+...++..|+.+|+|||++|||.+|+.+||++|||++|+++++++.|+++...+. +++.+|.++..+....
T Consensus        55 ~~~~~~~~~~~~~~~~i~~vV~faK~iPgF~~L~~~DQi~LLk~~~~el~ll~~a~~~~~~~~-~~~~~~~~~~~~~~~~  133 (251)
T d1n83a_          55 QREVMWQLCAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQNN-TVYFDGKYASPDVFKS  133 (251)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHSTTTTTSCHHHHHHHHHHHHHHHHHHHGGGGEETTTT-EEEETTEEECGGGGGG
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHcCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHhCCCCC-EEecCCeeecHHHHhh
Confidence            355678889999999999999999999999999999999999999999999999998887655 5566899988887766


Q ss_pred             hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 ~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      +...++++.+++|+.+|++|++|++||+||+||+||
T Consensus       134 ~~~~~~~~~~~~~~~~~~~L~ld~~E~alL~AivL~  169 (251)
T d1n83a_         134 LGCEDFISFVFEFGKSLCSMHLTEDEIALFSAFVLM  169 (251)
T ss_dssp             GSCHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHS
T ss_pred             ccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence            555689999999999999999999999999999986

>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=99.86  E-value=1e-21  Score=165.42  Aligned_cols=112  Identities=21%  Similarity=0.358  Sum_probs=99.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeH-Hh-hhhhh
Q psy2636         224 KIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEK-QQ-CQRSF  301 (335)
Q Consensus       224 ~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~-~~-~~~~~  301 (335)
                      .+.+++++.+..|+.+|+|||++|||.+|+.+||++|||++|+++++++.|+++..+++.+.+.+|..... .+ ...++
T Consensus        58 ~~~~~~~l~~~~i~~iVefAK~iPgF~~L~~~DQi~LLK~~~~El~ll~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  137 (255)
T d1ie9a_          58 MLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVSDVTKAGH  137 (255)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHGGGTEETTTTEEECSSGGGEECHHHHHTTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCcccccCCHHHHHHHHHHHHHHHHHHHHHHheeCCCCeEEeCCCCeeecHHHHHhccc
Confidence            56788999999999999999999999999999999999999999999999999998888888888765543 22 23355


Q ss_pred             cHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         302 GDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       302 ~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ..++++.+++|+.+|++|+||++||+|||||+||
T Consensus       138 ~~~~~~~i~~f~~~l~~L~ld~~E~~lLkAiiL~  171 (255)
T d1ie9a_         138 SLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIV  171 (255)
T ss_dssp             CHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHS
T ss_pred             hHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHhc
Confidence            5689999999999999999999999999999986

>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=99.86  E-value=3.2e-21  Score=161.01  Aligned_cols=115  Identities=23%  Similarity=0.411  Sum_probs=103.9

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR  299 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~  299 (335)
                      .+.+.+..+.++..+.+..+|+|||++|+|.+|+.+||++|||++|+++++|+.||++....+.+++.+|.....+....
T Consensus        29 ~~~~~~~~l~~~a~~~l~~~V~waK~lp~F~~L~~~DQi~LLk~~~~el~~L~~a~~s~~~~~~~~~~~~~~~~~~~~~~  108 (236)
T d2j7ya1          29 TEASMMMSLTKLADKELVHMIGWAKKIPGFVELSLLDQVRLLESCWMEVLMVGLMWRSIDHPGKLIFAPDLVLDRDEGKC  108 (236)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTSTTEEEEETTEEEEGGGGGG
T ss_pred             ChHHHHHHHHHHHHHHHHHHHHHHHcCchHHHhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcEEecCCcccCHHHHHH
Confidence            45566677788888999999999999999999999999999999999999999999999988899999999998776543


Q ss_pred             --hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 --SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 --~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                        +.+ ++++.+++++.+|++|+||.+||++||||+||
T Consensus       109 ~~~~~-~~~~~i~~~~~~l~~L~ld~~E~~lLkaIvLf  145 (236)
T d2j7ya1         109 VEGIL-EIFDMLLATTSRFRELKLQHKEYLCVKAMILL  145 (236)
T ss_dssp             STTHH-HHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHT
T ss_pred             HhhHH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence              344 88899999999999999999999999999987

>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=99.85  E-value=2.5e-21  Score=162.21  Aligned_cols=115  Identities=25%  Similarity=0.413  Sum_probs=103.5

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR  299 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~  299 (335)
                      ...+.|..++..++..|+.+|+|||++|||.+|+.+||++|||++|+++++++.|+++...++.+++ +|.++..+....
T Consensus        47 ~~~~~~~~~~~~~~~~i~~vV~faK~lP~F~~L~~~DQi~LLk~~~~el~~l~~a~~~~~~~~~~~~-~~~~~~~~~~~~  125 (244)
T d1nq7a_          47 SREALWQQCAIQITHAIQYVVEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPLNNTVLF-EGKYGGMQMFKA  125 (244)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHTSCHHHHHHHHHHHHHHHHHHHHGGGEETTTTEEEE-TTEEEEGGGGGG
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHccCCCCeEee-CCccccHHHHhh
Confidence            4566788899999999999999999999999999999999999999999999999999888777777 666777776666


Q ss_pred             hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 ~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ....++++.+++|+.+|++|++|++||+||+||+||
T Consensus       126 ~~~~~~~~~~~~~~~~~~~L~l~~~E~all~AivL~  161 (244)
T d1nq7a_         126 LGSDDLVNEAFDFAKNLCSLQLTEEEIALFSSAVLI  161 (244)
T ss_dssp             GSCHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHS
T ss_pred             cccHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            555589999999999999999999999999999986

>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=99.84  E-value=1.7e-20  Score=157.58  Aligned_cols=116  Identities=20%  Similarity=0.316  Sum_probs=101.2

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhcc--CCCeEEeeCCeEeeHHhh
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRA--EDTKLIFCNGVVLEKQQC  297 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~--~~~~~~~~~g~~~~~~~~  297 (335)
                      .....+..+.++..+.+..+|+|||++|+|.+|+.+||++|||++|+++++|+.||++..  +...+.+.++...+....
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            455566778888889999999999999999999999999999999999999999999875  444688888888887665


Q ss_pred             hhhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         298 QRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       298 ~~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ......++...+.+++.+|++|+||++||+|||||+||
T Consensus       108 ~~~~~~~~~~~~~~~~~~~~~L~ld~~E~~lLkaIvL~  145 (250)
T d1t7ra_         108 HKSRMYSQCVRMRHLSQEFGWLQITPQEFLCMKALLLF  145 (250)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHT
T ss_pred             hhchhHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhc
Confidence            55544577888899999999999999999999999987

>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=99.84  E-value=2.1e-20  Score=156.72  Aligned_cols=116  Identities=22%  Similarity=0.329  Sum_probs=101.3

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhcc--CCCeEEeeCCeEeeHHhh
Q psy2636         220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRA--EDTKLIFCNGVVLEKQQC  297 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~--~~~~~~~~~g~~~~~~~~  297 (335)
                      .+...+..+..+..+.+..+|+|||++|+|.+|+.+||++|||++|+++++|+.||++..  .+..+.+.+|........
T Consensus        26 ~~~~~~~~l~~la~r~L~~~IewaK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~s~~~~~~~~~~~~~~~~~~~~~~  105 (247)
T d1nhza_          26 STWRIMTTLNMLGGRQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMSLMAFALGWRSYRQSSANLLCFAPDLIINEQRM  105 (247)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECTTGG
T ss_pred             ChHHHHHHHHHHHHHHHHHHHHHHHhcccHhhcCHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCeEeccccceecHHhh
Confidence            455566778888889999999999999999999999999999999999999999999753  445688888888877666


Q ss_pred             hhhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         298 QRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       298 ~~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      .......+.+.+.+++.+|++|+||++||+|||||+||
T Consensus       106 ~~~~~~~~~~~~~~~~~~l~~L~l~~~E~~lLkaIvLf  143 (247)
T d1nhza_         106 TLPDMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLL  143 (247)
T ss_dssp             GSTTHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHT
T ss_pred             ccccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence            55555578889999999999999999999999999987

>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=99.84  E-value=1.8e-20  Score=157.32  Aligned_cols=117  Identities=20%  Similarity=0.322  Sum_probs=101.4

Q ss_pred             CChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhcc--CCCeEEeeCCeEeeHHh
Q psy2636         219 IAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRA--EDTKLIFCNGVVLEKQQ  296 (335)
Q Consensus       219 ~~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~--~~~~~~~~~g~~~~~~~  296 (335)
                      ..+...+..+.++..+.+..+|||||++|+|.+|+.+||++|||++|+++++|+.||++..  .++.+.+.+|.......
T Consensus        28 ~~~~~~~~~l~~la~r~L~~~VewaK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~rs~~~~~~~~l~~~~~~~~~~~~  107 (251)
T d1sqna_          28 DTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQR  107 (251)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECGGG
T ss_pred             CCchHHHHHHHHHHHHHHHHHHHHHHhccchhhcCHHHHHHHHHHHHHHHHHHHHHHHhhhccCcceeeccCCceecHHh
Confidence            3556677888888899999999999999999999999999999999999999999999875  44568888888887765


Q ss_pred             hhhhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         297 CQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       297 ~~~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      .......++++.+.+++.+|++|+||++||+|||||+||
T Consensus       108 ~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~~lLkAIiL~  146 (251)
T d1sqna_         108 MKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLL  146 (251)
T ss_dssp             CCSHHHHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHT
T ss_pred             hccccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence            444333477888899999999999999999999999986

>d2p1ta1 a.123.1.1 (A:229-458) Retinoid-X receptor alpha (RXR-alpha) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Retinoid-X receptor alpha (RXR-alpha)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=1.4e-20  Score=156.37  Aligned_cols=114  Identities=19%  Similarity=0.389  Sum_probs=100.5

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh-h
Q psy2636         222 PEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR-S  300 (335)
Q Consensus       222 ~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~-~  300 (335)
                      ...+..++++..+.+..+|+|||++|+|..|+.+||++|||++|+++++|+.||++....+.+.+.+|.++..+.... +
T Consensus        34 ~~~~~~l~~~a~~~l~~~v~wak~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~  113 (230)
T d2p1ta1          34 NDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAG  113 (230)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTSSSEEECTTSCEEEHHHHHTTT
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHcCCccccCCHHHHHHHHHHHHHHHHHHHHHHHhhcCCCeEEecCCeeecHhHHHhcc
Confidence            344667788888889999999999999999999999999999999999999999999888899999999999877654 4


Q ss_pred             hcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         301 FGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       301 ~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ++..+.+.+.+++.+|++|++|.+||+|||||+||
T Consensus       114 ~~~~~~~~~~~~~~~~~~L~ld~~E~~lLkaivL~  148 (230)
T d2p1ta1         114 VGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLF  148 (230)
T ss_dssp             CHHHHHHHHHHTHHHHHHTTCCHHHHHHHHHHHHS
T ss_pred             chHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence            55444556678999999999999999999999987

>d1g2na_ a.123.1.1 (A:) Ultraspiracle protein, usp {Heliothis virescens [TaxId: 7102]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Ultraspiracle protein, usp
species: Heliothis virescens [TaxId: 7102]

Probab=99.83  E-value=1.9e-20  Score=157.90  Aligned_cols=113  Identities=20%  Similarity=0.366  Sum_probs=96.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccC------------------CCeE
Q psy2636         223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAE------------------DTKL  284 (335)
Q Consensus       223 ~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~------------------~~~~  284 (335)
                      ..+..++++..+.+..+|+|||++|+|.+|+.+||++|||++|.++++|+.||++...                  .+.+
T Consensus        42 ~~~~~lc~~~~~~L~~~VewAK~lP~F~~L~~~DQi~LLk~~w~el~iL~~a~rs~~~~~~~~~~~~~~~~~~~~~~~~~  121 (256)
T d1g2na_          42 APVSSLCQIGNKQIAALVVWARDIPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLTEERDGVDGTGNRTTSPPQLM  121 (256)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHGGGSCCC----------CCCCCCEE
T ss_pred             cHHHHHHHHHHHHHHHHHHHHhcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccCcchhh
Confidence            3466778888899999999999999999999999999999999999999999997532                  2357


Q ss_pred             EeeCCeEeeHHhhhh-hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         285 IFCNGVVLEKQQCQR-SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       285 ~~~~g~~~~~~~~~~-~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      .+.+|..++++.... +++..+.+.+.+++.+|++|+||.+||+|||||+||
T Consensus       122 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~L~ld~~E~~~LkaIvLf  173 (256)
T d1g2na_         122 CLMPGMTLHRNSALQAGVGQIFDRVLSELSLKMRTLRVDQAEYVALKAIILL  173 (256)
T ss_dssp             EEETTEEEEHHHHHHHTCHHHHHHHHHHTHHHHHHTTCCHHHHHHHHHHHHS
T ss_pred             ccCCCcccCHHHHHhcchHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence            788888888876543 566445566779999999999999999999999997

>d1osha_ a.123.1.1 (A:) Bile acid receptor FXR {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Bile acid receptor FXR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=4.8e-21  Score=158.92  Aligned_cols=111  Identities=23%  Similarity=0.379  Sum_probs=91.6

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhh-hh
Q psy2636         221 EPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQC-QR  299 (335)
Q Consensus       221 ~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~-~~  299 (335)
                      ..+.+..++++.+..++.+|+|||++|||.+|+.+||++|||++|+++++++.|++++...    +.+|..+..+.. ..
T Consensus        40 ~~~~~~~l~~~~~~~i~~iVe~AK~iP~F~~L~~~DQi~LLk~~~~El~~L~~~~~~~~~~----~~~~~~~~~~~~~~~  115 (231)
T d1osha_          40 AEENFLILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKL----PSGHSDLLEERIRNS  115 (231)
T ss_dssp             --CHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHTS----CHHHHHHHHHHHHTS
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhcCccc----cCCCccccHHHHHhc
Confidence            3456778899999999999999999999999999999999999999999999998875431    223333333333 23


Q ss_pred             hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 ~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      +++.++++.+.+|+.+|++|++|++||+|||||+||
T Consensus       116 ~~~~~~~~~i~~~~~~l~~L~ld~~E~~lLkAivL~  151 (231)
T d1osha_         116 GISDEYITPMFSFYKSIGELKMTQEEYALLTAIVIL  151 (231)
T ss_dssp             SCCTTTHHHHHHHHHHHHTTCCCHHHHHHHHHHHHT
T ss_pred             cchHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence            555678999999999999999999999999999987

>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=99.83  E-value=6.5e-21  Score=158.62  Aligned_cols=112  Identities=19%  Similarity=0.268  Sum_probs=98.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh-hhc
Q psy2636         224 KIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR-SFG  302 (335)
Q Consensus       224 ~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~-~~~  302 (335)
                      .+..+++...+.+..+|+|||++|+|.+|+.+||++|||++|.++++|+.||++...++.+++.+|..+..+.... ...
T Consensus        38 ~~~~l~~~a~~~l~~~vewaK~ip~F~~L~~~DQ~~LLk~~~~el~lL~~a~~s~~~~~~~~l~~~~~~~~~~~~~~~~~  117 (233)
T d1pzla_          38 SIADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVLLLGNDYIVPRHCPELAEMS  117 (233)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHTTCHHHHTSCHHHHHHHHHHSHHHHHHHHHHHHHTTSSSEEECTTSCEEESSCGGGGGGH
T ss_pred             cHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCceeecCCccccchhhhhhhhH
Confidence            3556777788889999999999999999999999999999999999999999999988899999999887765433 334


Q ss_pred             HHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         303 DDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       303 ~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ....+.+.+++.+|++|++|.+||++||||+||
T Consensus       118 ~~~~~~l~~~~~~~~~L~ld~~E~~lLkaiiL~  150 (233)
T d1pzla_         118 RVSIRILDELVLPFQELQIDDNEYAYLKAIIFF  150 (233)
T ss_dssp             HHHHHHHHHTHHHHHHHTCCHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhc
Confidence            456677889999999999999999999999997

>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=99.82  E-value=4.1e-20  Score=154.71  Aligned_cols=111  Identities=23%  Similarity=0.324  Sum_probs=96.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhcc--CCCeEEeeCCeEeeHHhhhh--
Q psy2636         224 KIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRA--EDTKLIFCNGVVLEKQQCQR--  299 (335)
Q Consensus       224 ~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~--~~~~~~~~~g~~~~~~~~~~--  299 (335)
                      .+..+.+.....+..+|+|||++|+|.+|+.+||++|||++|+++++|+.||++..  ..+.+.+.+|..++......  
T Consensus        43 ~~~~l~~~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~iL~~a~~s~~~~~~~~~~~~~g~~~~~~~~~~~~  122 (242)
T d1pk5a_          43 AFGLLCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVAHGKEGTIFLVTGEHVDYSTIISHT  122 (242)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCSSEEECTTSCEEEHHHHHHTS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCCHhhcCHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCeeEecCCCcccchHHhhhc
Confidence            35566777788899999999999999999999999999999999999999999864  44579999999988655432  


Q ss_pred             --hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         300 --SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       300 --~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                        +++ .+.+.+.+++.+|++|++|.+||++||||+||
T Consensus       123 ~~~~~-~~~~~~~~l~~~l~~L~ld~~E~~lLkai~Lf  159 (242)
T d1pk5a_         123 EVAFN-NLLSLAQELVVRLRSLQFDQREFVCLKFLVLF  159 (242)
T ss_dssp             CHHHH-HHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHS
T ss_pred             ccchH-HHHHHHHHHHHHHHHhCCCHHHHHHHHHHHhc
Confidence              333 67888899999999999999999999999987

>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=99.82  E-value=5.5e-20  Score=156.17  Aligned_cols=115  Identities=15%  Similarity=0.300  Sum_probs=98.0

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCC-------------------
Q psy2636         221 EPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAED-------------------  281 (335)
Q Consensus       221 ~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~-------------------  281 (335)
                      ....+..++++....+..+|+|||++|+|.+|+.+||++|||++|.++++|+.||++....                   
T Consensus        37 ~~~~~~~l~~~~~~~L~~~VewaK~lP~F~~L~~~DQ~~LLk~~~~el~iL~~a~~s~~~~~~~~~~~~~~~~~~~~~~~  116 (265)
T d1hg4a_          37 YKGAVSALCQVVNKQLFQMVEYARMMPHFAQVPLDDQVILLKAAWIELLIANVAWCSIVSLDDGGAGGGGGGLGHDGSFE  116 (265)
T ss_dssp             GHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTTC-------------------
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHcCCchhcCCHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccccchhhh
Confidence            3456778888889999999999999999999999999999999999999999999876432                   


Q ss_pred             --------CeEEeeCCeEeeHHhhhh-hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         282 --------TKLIFCNGVVLEKQQCQR-SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       282 --------~~~~~~~g~~~~~~~~~~-~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                              +.+.+.+|..++.+.... +++..+.+.+.+++.+|++|+||.+||+|||||+||
T Consensus       117 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~L~ld~~E~~lLkaivLf  179 (265)
T d1hg4a_         117 RRSPGLQPQQLFLNQSFSYHRNSAIKAGVSAIFDRILSELSVKMKRLNLDRRELSCLKAIILY  179 (265)
T ss_dssp             ------CCCEEESSSSCEEEHHHHHHHTCHHHHHHHHHHTHHHHHHHTCCHHHHHHHHHHHHS
T ss_pred             ccCcccCcceeeccCCcccchHHHHHhccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence                    246677777777766544 555566777889999999999999999999999997

>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=99.82  E-value=1.5e-20  Score=158.38  Aligned_cols=110  Identities=20%  Similarity=0.315  Sum_probs=89.4

Q ss_pred             HHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhh--hhhhc
Q psy2636         225 IQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQC--QRSFG  302 (335)
Q Consensus       225 ~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~--~~~~~  302 (335)
                      +..........|+.+|+|||++|||.+|+.+||++|||++|+++++++.|+++..+++.+.+.+|........  ..+++
T Consensus        72 ~~~~~~~~~~~i~~iVewAK~iPgF~~L~~~DQi~LLK~~~~Ellil~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (267)
T d2p54a1          72 FHCCQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGMLVAYGNGFITREFLKSLRKPFC  151 (267)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHGGGEETTEEEETTTTEEEEHHHHHHSCTTGG
T ss_pred             HHHHHHHHHHHHHHHHHHHhhCcChhhCCHHHHHHHHHHHHHHHHHHHHHHhccCCCCEEEeCCCccchHHHHHhcchHH
Confidence            3444455667789999999999999999999999999999999999999999887655555555544433221  22444


Q ss_pred             HHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         303 DDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       303 ~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                       ++++.+++|+.+|++|+||++||+||+||+||
T Consensus       152 -~~~~~~~~~~~~~~~L~ld~~E~alLkAIvLf  183 (267)
T d2p54a1         152 -DIMEPKFDFAMKFNALELDDSDISLFVAAIIC  183 (267)
T ss_dssp             -GTSHHHHHHHHHHHTTCCCHHHHHHHHHHHHS
T ss_pred             -HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence             77889999999999999999999999999987

>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=99.81  E-value=1.4e-20  Score=161.72  Aligned_cols=113  Identities=24%  Similarity=0.284  Sum_probs=97.9

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhhhh
Q psy2636         222 PEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSF  301 (335)
Q Consensus       222 ~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~~~  301 (335)
                      ...+.++.+..+..|+.+|+|||++|+|.+|+.+||++|||++|+++++|+.|+++..++..+. .++..+..+....+.
T Consensus        96 ~~~l~~~~~~~~~~i~~iV~fAK~iP~F~~L~~~DQi~LLk~~~~el~~l~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~  174 (292)
T d1nrla_          96 FSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWE-CGRLSYCLEDTAGGF  174 (292)
T ss_dssp             GTTHHHHHHHHHHHHHHHHHHHHHCHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTEETTTTEEE-ETTEEEEECCCSSCH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCcCHhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeee-CCCccccHHHhhhhh
Confidence            3457788888999999999999999999999999999999999999999999999887766554 456666655555555


Q ss_pred             cHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         302 GDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       302 ~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ..++.+.+++|+.+|++|+||++||+|||||+||
T Consensus       175 ~~~~~~~~~~~~~~l~~L~ld~~E~~lLkAi~L~  208 (292)
T d1nrla_         175 QQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLF  208 (292)
T ss_dssp             HHHTTSHHHHHHHHHHHTCCCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence            5578899999999999999999999999999987

>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=99.79  E-value=7.6e-20  Score=154.62  Aligned_cols=111  Identities=23%  Similarity=0.372  Sum_probs=92.1

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeE-eeHHhhh--
Q psy2636         222 PEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVV-LEKQQCQ--  298 (335)
Q Consensus       222 ~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~-~~~~~~~--  298 (335)
                      ...++.+....+..|+.+|+|||++|+|.+|+.+||++|||++|+++++++.|++++.+  ...+.+|.. +......  
T Consensus        73 ~~~~~~~~~~~~~~i~~vVefAK~iP~F~~L~~~DQi~LLK~~~~ElllL~~a~~~~~~--~~~~~~g~~~~~~~~~~~~  150 (271)
T d2fvja1          73 IRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKD--GVLISEGQGFMTREFLKSL  150 (271)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEETT--EEEETTTTEEEEHHHHHTS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhCcChhhCCHHHHHHHHHHHHHHHHHHHHHHHcCCC--CCeeeCCCccchHHHHHHh
Confidence            34667778888899999999999999999999999999999999999999999987644  344555544 3333222  


Q ss_pred             -hhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         299 -RSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       299 -~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                       ..++ ++++.+.+|+.+|+.|++|++||+|||||+||
T Consensus       151 ~~~~~-~~~~~i~~f~~~~~~L~ld~~E~alLkAIvLf  187 (271)
T d2fvja1         151 RKPFG-DFMEPKFEFAVKFNALELDDSDLAIFIAVIIL  187 (271)
T ss_dssp             CTTGG-GSSHHHHHHHHHHHTTCCCHHHHHHHHHHHHT
T ss_pred             hhhHH-HHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence             2334 67889999999999999999999999999987

>d2b50b1 a.123.1.1 (B:211-475) Peroxisome proliferator-activated receptor delta, PPAR-DELTA {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Peroxisome proliferator-activated receptor delta, PPAR-DELTA
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=3.4e-19  Score=149.93  Aligned_cols=110  Identities=24%  Similarity=0.285  Sum_probs=91.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh---h
Q psy2636         224 KIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR---S  300 (335)
Q Consensus       224 ~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~---~  300 (335)
                      .+..........|+.+|+|||++|+|.+|+.+||++|||++|+++++++.|+++..  +.+.+.+|..+.......   .
T Consensus        71 ~f~~~~~~~~~~I~~iVefAK~iPgF~~L~~~DQi~LLK~~~~Ellil~~a~~~~~--d~~~~~~g~~~~~~~~~~~~~~  148 (265)
T d2b50b1          71 VFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNK--DGLLVANGSGFVTREFLRSLRK  148 (265)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTSHHHHTSCHHHHHHHHHHHHHHHHHHHHGGGEET--TEEEETTTTEEEEHHHHHTSCH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCcChhhCCHHHHHHHHHHHHHHHHHHHHHHHhCC--CCceEeCCcccccHHHHHHhhh
Confidence            34455566677888999999999999999999999999999999999999998764  457777877666544322   2


Q ss_pred             hcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636         301 FGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI  335 (335)
Q Consensus       301 ~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~  335 (335)
                      ...++.+.+++|+.+|+.|++|++||+||+||+||
T Consensus       149 ~~~~~~~~~~~f~~~~~~L~ld~~E~alLkAiiL~  183 (265)
T d2b50b1         149 PFSDIIEPKFEFAVKFNALELDDSDLALFIAAIIL  183 (265)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHS
T ss_pred             hHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHhhc
Confidence            22478889999999999999999999999999986

>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=90.95  E-value=0.099  Score=31.76  Aligned_cols=51  Identities=20%  Similarity=0.600  Sum_probs=32.4

Q ss_pred             CcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhh
Q psy2636          41 QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRF  100 (335)
Q Consensus        41 ~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~  100 (335)
                      ..|.||++....-++ .+.|++|..+|-..        |..-..=.+.......|..|+-
T Consensus         7 ~~C~~C~~~~~~~~~-~I~Cd~C~~w~H~~--------C~~~~~~~~~~~~~w~C~~C~~   57 (64)
T d1we9a_           7 GQCGACGESYAADEF-WICCDLCEMWFHGK--------CVKITPARAEHIKQYKCPSCSN   57 (64)
T ss_dssp             CCCSSSCCCCCSSSC-EEECSSSCCEEETT--------TTTCCTTGGGGCSSCCCHHHHT
T ss_pred             CcCcCcCCCCCCCCC-EEEcCCCCccCCcc--------cCCcChHHCCCCCeEECcCCcC
Confidence            359999987544332 46899999998776        4332222222233568999973

>d1weva_ g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 22
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=84.81  E-value=0.15  Score=33.14  Aligned_cols=31  Identities=16%  Similarity=0.583  Sum_probs=22.0

Q ss_pred             CCCCcccccCCCCCccccCCcccccccccee
Q psy2636          38 SPSQLCAVCGDIAACQHYGVRTCEGCKGFFK   68 (335)
Q Consensus        38 ~~~~~C~VCgd~a~g~HyGv~sC~gCk~FFR   68 (335)
                      .....|.||+.....-+--++.|.+|...|-
T Consensus        14 ~~~~~C~iC~~~~~~~~~~~v~Cd~C~~~~H   44 (88)
T d1weva_          14 EMGLACVVCRQMTVASGNQLVECQECHNLYH   44 (88)
T ss_dssp             HHCCSCSSSCCCCCCTTCCEEECSSSCCEEE
T ss_pred             cCcCCccCCCCccCCCCCeEEEcCCCCCccc
Confidence            3345699999765555555788999987663

>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=80.19  E-value=1.2  Score=34.51  Aligned_cols=46  Identities=52%  Similarity=0.915  Sum_probs=40.2

Q ss_pred             ChhHHHHHHHhhcchhhhhhhcccCCCCCCCCCHHHHHHHHhhhhh
Q psy2636         160 EPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL  205 (335)
Q Consensus       160 ~~~~~~~~~~~l~~~~~~i~~~~~~~p~~~~l~~~~~~~l~~~~~~  205 (335)
                      ..+..++++..++.....+..|++.+|.|.+|..+|+..|++.+..
T Consensus        37 ~~~~~~~~~~~~~~~i~~iv~wAK~iPgF~~L~~~DQi~LLk~~~~   82 (233)
T d2qw4a1          37 DAGDVQQFYDLLSGSLEVIRKWAEKIPGFAELSPADQDLLLESAFL   82 (233)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHTSTTTTTSCHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHH
Confidence            4567788999988888889999999999999999999999987753