Psyllid ID: psy11505

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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--
Protein Sequence
NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLRFWSTVHKDGKVLMNKLFVEMLEAYLR
Secondary Structure (PSIPRED)
cccEEcccccccccccccccccHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHcccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccEEEEcccccccHHHHHHHcHHHHHHHHHHccccccccccHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHHccccccHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHccccccEEEEccccEEEcccccccHHHHHHHHHHHHHHccccHHHHHHcEEccccccccccEEccEEccHHHHHHHHHHHHcccccccHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
nieytcpasndceiNKRRRKACQACRFQKCLRKGmlkegvrldrvrggrqkyrrnpdllsqqwppnksipsleENKMLEALLLcepemltvrsetpqsdptlqtinsLSDLYDRELVCIIGWakqipgftdlsLNDQMRLLQSTWAEILTLTIAYRslphcagkirfasdlvlderqarecgFSEIYQQVKhsgsldgikeeelprrlclvcgdvasgfhyGVASCEACKAFFKRTIQVYSGyrqtgacgtlvlansdvkldefssLKKFRNSILSSLGDCIYVLRFWSTVHKDGKVLMNKLFVEMLEAYLR
Flexible Loop (DISEMBL)
nieytcpasndceinkrRRKACQACRfqkclrkgmlkegvrldrvrggrqkyrrnpdllsqqwppnksipSLEENKMLEALLLCEPEMLTvrsetpqsdptlqTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLRFWSTVHKDGKVLMNKLFVEMLEAYLR
Low Complexity Region (SEG)
NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLRFWSTVHKDGKVLMNKLFVEMLEAYLR
Disordered region (IsUnstruct)
************EINKRRRKACQACRFQKCLRKGMLKEGVRLDR*********************************LEALLLCEP*****************TINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLRFWSTVHKDGKVLMNKLFVEMLEAY**
Disordered Region (DISOPRED)
NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE*****************************************ALLLC*******************TINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFH****************IQVYSGYRQTGACGTLVL***********SLKKFRNSILSSLGDCIYVLRFWSTVHKDGKVLMNKLFVEMLEAY**
Disordered Region (DISEMBL)
NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEENKMLEALLLCEPEMLTVR********TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLRFWSTVHKDGKVLMNKLFVEMLEAYLR
Disordered Region (DISPRO)
**EYTCPASNDCEINKRRRKACQACRFQKCLRKG***********************************PSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLRFWSTVHKDGKVLMNKLFVEMLEAYL*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLRFWSTVHKDGKVLMNKLFVEMLEAYLR
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	312	2.2.26 [Sep-21-2011]
O95718	508	Steroid hormone receptor	yes	N/A	0.923	0.566	0.416	5e-53
Q6QMY5	422	Steroid hormone receptor	no	N/A	0.583	0.431	0.532	7e-53
P62510	458	Estrogen-related receptor	yes	N/A	0.926	0.631	0.393	2e-52
P62509	458	Estrogen-related receptor	yes	N/A	0.926	0.631	0.393	2e-52
P62508	458	Estrogen-related receptor	no	N/A	0.926	0.631	0.393	2e-52
Q5QJV7	422	Steroid hormone receptor	no	N/A	0.583	0.431	0.527	2e-52
O08580	422	Steroid hormone receptor	no	N/A	0.583	0.431	0.527	2e-52
Q5RAM2	435	Estrogen-related receptor	no	N/A	0.926	0.664	0.393	3e-52
P11475	433	Steroid hormone receptor	no	N/A	0.926	0.667	0.396	3e-52
P11474	423	Steroid hormone receptor	no	N/A	0.586	0.432	0.527	7e-52

>sp|O95718|ERR2_HUMAN Steroid hormone receptor ERR2 OS=Homo sapiens GN=ESRRB PE=1 SV=2

 Score =  208 bits (529), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 133/319 (41%), Positives = 174/319 (54%), Gaps = 31/319 (9%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRR------ 54
           NIEY+CPA+N+CEI KRRRK+CQACRF KCL+ GMLKEGVRLDRVRGGRQKY+R      
Sbjct: 134 NIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRLDSES 193

Query: 55  NPDLLSQQWPPNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDR 114
           +P L  Q  PP K        K++  LL+ EP+ L         +  ++ + +L DL DR
Sbjct: 194 SPYLSLQISPPAKK----PLTKIVSYLLVAEPDKLYAMPPPGMPEGDIKALTTLCDLADR 249

Query: 115 ELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLD 174
           ELV IIGWAK IPGF+ LSL DQM LLQS W EIL L I YRSLP+   K+ +A D ++D
Sbjct: 250 ELVVIIGWAKHIPGFSSLSLGDQMSLLQSAWMEILILGIVYRSLPY-DDKLVYAEDYIMD 308

Query: 175 ERQARECGFSEIY----QQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACK 230
           E  +R  G  E+Y    Q V+    L  +++EE      L   +  S +   + + +  +
Sbjct: 309 EEHSRLAGLLELYRAILQLVRRYKKLK-VEKEEFVTLKALALANSDSMYIEDLEAVQKLQ 367

Query: 231 AFFKRTIQVYSGYRQTGACGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLRFWST 290
                 +Q Y                S    + + + K      L        V  F+S 
Sbjct: 368 DLLHEALQDYE--------------LSQRHEEPWRTGKLLLTLPLLRQTAAKAVQHFYS- 412

Query: 291 VHKDGKVLMNKLFVEMLEA 309
           V   GKV M+KLF+EMLEA
Sbjct: 413 VKLQGKVPMHKLFLEMLEA 431

Nuclear receptor, may regulate ESR1 transcriptional activity.
Homo sapiens (taxid: 9606)

>sp|Q6QMY5|ERR1_CANFA Steroid hormone receptor ERR1 OS=Canis familiaris GN=ESRRA PE=2 SV=1

 Score =  207 bits (528), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 106/199 (53%), Positives = 130/199 (65%), Gaps = 17/199 (8%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
           +IEY+CPASN+CEI KRRRKACQACRF KCLR GMLKEGVRLDRVRGGRQKY+R P++  
Sbjct: 110 SIEYSCPASNECEITKRRRKACQACRFTKCLRVGMLKEGVRLDRVRGGRQKYKRRPEVDP 169

Query: 61  QQWP-------------PNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINS 107
             +P             P K+ P    N ++  LL+ EPE L    +    D  L  + +
Sbjct: 170 LPFPGSFPAGPLAVAGGPRKTAPV---NALVSHLLVVEPEKLYAMPDPAGPDGHLPAVAT 226

Query: 108 LSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRF 167
           L DL+DRE+V  I WAK IPGF+ LSL+DQM +LQS W E+L L +A RSLP    ++ F
Sbjct: 227 LCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLP-LQDELAF 285

Query: 168 ASDLVLDERQARECGFSEI 186
           A DLVLDE  AR  G  E+
Sbjct: 286 AEDLVLDEEGARAAGLGEL 304

Binds to an ERR-alpha response element (ERRE) containing a single consensus half-site, 5'-TNAAGGTCA-3'. Can bind to the medium-chain acyl coenzyme A dehydrogenase (MCAD) response element NRRE-1 and may act as an important regulator of MCAD promoter. May function as a modulator of the estrogen signaling pathway in the uterus.

Canis familiaris (taxid: 9615)

>sp|P62510|ERR3_RAT Estrogen-related receptor gamma OS=Rattus norvegicus GN=Esrrg PE=2 SV=1

 Score =  206 bits (524), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 125/318 (39%), Positives = 177/318 (55%), Gaps = 29/318 (9%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
           NIEY+CPA+N+CEI KRRRK+CQACRF KCL+ GMLKEGVRLDRVRGGRQKY+R  D  +
Sbjct: 159 NIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRIDAEN 218

Query: 61  QQW-PPNKSIPSLEE-NKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVC 118
             +  P    P+ +  NK++  LL+ EPE +    +    D  ++ + +L DL DRELV 
Sbjct: 219 SPYLNPQLVQPAKKPYNKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVV 278

Query: 119 IIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQA 178
           IIGWAK IPGF+ LSL DQM LLQS W EIL L + YRSL     ++ +A D ++DE Q+
Sbjct: 279 IIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSF-EDELVYADDYIMDEDQS 337

Query: 179 RECGF----SEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFK 234
           +  G     + I Q VK   S+  +++EE      +   +  S     V + +  +    
Sbjct: 338 KLAGLLDLNNAILQLVKKYKSMK-LEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLH 396

Query: 235 RTIQVYSGYRQTGA---CGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLRFWSTV 291
             +Q Y   +        G +++    ++     +++ F N                  +
Sbjct: 397 EALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYN------------------I 438

Query: 292 HKDGKVLMNKLFVEMLEA 309
             +GKV M+KLF+EMLEA
Sbjct: 439 KLEGKVPMHKLFLEMLEA 456

Orphan receptor that acts as transcription activator in the absence of bound ligand. Binds specifically to an estrogen response element and activates reporter genes controlled by estrogen response elements.

Rattus norvegicus (taxid: 10116)

>sp|P62509|ERR3_MOUSE Estrogen-related receptor gamma OS=Mus musculus GN=Esrrg PE=1 SV=1

 Score =  206 bits (524), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 125/318 (39%), Positives = 177/318 (55%), Gaps = 29/318 (9%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
           NIEY+CPA+N+CEI KRRRK+CQACRF KCL+ GMLKEGVRLDRVRGGRQKY+R  D  +
Sbjct: 159 NIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRIDAEN 218

Query: 61  QQW-PPNKSIPSLEE-NKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVC 118
             +  P    P+ +  NK++  LL+ EPE +    +    D  ++ + +L DL DRELV 
Sbjct: 219 SPYLNPQLVQPAKKPYNKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVV 278

Query: 119 IIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQA 178
           IIGWAK IPGF+ LSL DQM LLQS W EIL L + YRSL     ++ +A D ++DE Q+
Sbjct: 279 IIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSF-EDELVYADDYIMDEDQS 337

Query: 179 RECGF----SEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFK 234
           +  G     + I Q VK   S+  +++EE      +   +  S     V + +  +    
Sbjct: 338 KLAGLLDLNNAILQLVKKYKSMK-LEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLH 396

Query: 235 RTIQVYSGYRQTGA---CGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLRFWSTV 291
             +Q Y   +        G +++    ++     +++ F N                  +
Sbjct: 397 EALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYN------------------I 438

Query: 292 HKDGKVLMNKLFVEMLEA 309
             +GKV M+KLF+EMLEA
Sbjct: 439 KLEGKVPMHKLFLEMLEA 456

Orphan receptor that acts as transcription activator in the absence of bound ligand. Binds specifically to an estrogen response element and activates reporter genes controlled by estrogen response elements.

Mus musculus (taxid: 10090)

>sp|P62508|ERR3_HUMAN Estrogen-related receptor gamma OS=Homo sapiens GN=ESRRG PE=1 SV=1

 Score =  206 bits (524), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 125/318 (39%), Positives = 177/318 (55%), Gaps = 29/318 (9%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
           NIEY+CPA+N+CEI KRRRK+CQACRF KCL+ GMLKEGVRLDRVRGGRQKY+R  D  +
Sbjct: 159 NIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRIDAEN 218

Query: 61  QQW-PPNKSIPSLEE-NKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVC 118
             +  P    P+ +  NK++  LL+ EPE +    +    D  ++ + +L DL DRELV 
Sbjct: 219 SPYLNPQLVQPAKKPYNKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVV 278

Query: 119 IIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQA 178
           IIGWAK IPGF+ LSL DQM LLQS W EIL L + YRSL     ++ +A D ++DE Q+
Sbjct: 279 IIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSF-EDELVYADDYIMDEDQS 337

Query: 179 RECGF----SEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFK 234
           +  G     + I Q VK   S+  +++EE      +   +  S     V + +  +    
Sbjct: 338 KLAGLLDLNNAILQLVKKYKSMK-LEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLH 396

Query: 235 RTIQVYSGYRQTGA---CGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLRFWSTV 291
             +Q Y   +        G +++    ++     +++ F N                  +
Sbjct: 397 EALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYN------------------I 438

Query: 292 HKDGKVLMNKLFVEMLEA 309
             +GKV M+KLF+EMLEA
Sbjct: 439 KLEGKVPMHKLFLEMLEA 456

Orphan receptor that acts as transcription activator in the absence of bound ligand. Binds specifically to an estrogen response element and activates reporter genes controlled by estrogen response elements.

Homo sapiens (taxid: 9606)

>sp|Q5QJV7|ERR1_RAT Steroid hormone receptor ERR1 OS=Rattus norvegicus GN=Esrra PE=2 SV=2

 Score =  206 bits (524), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 105/199 (52%), Positives = 130/199 (65%), Gaps = 17/199 (8%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL-- 58
           +IEY+CPASN+CEI KRRRKACQACRF KCLR GMLKEGVRLDRVRGGRQKY+R P++  
Sbjct: 110 SIEYSCPASNECEITKRRRKACQACRFTKCLRVGMLKEGVRLDRVRGGRQKYKRRPEVDP 169

Query: 59  -----------LSQQWPPNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINS 107
                      L+    P K+ P    N ++  LL+ EPE L    +    D  L  + +
Sbjct: 170 LPFPGPFPAGPLAVAGGPRKTAPV---NALVSHLLVVEPEKLYAMPDPASPDGHLPAVAT 226

Query: 108 LSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRF 167
           L DL+DRE+V  I WAK IPGF+ LSL+DQM +LQS W E+L L +A RSLP    ++ F
Sbjct: 227 LCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLP-LQDELAF 285

Query: 168 ASDLVLDERQARECGFSEI 186
           A DLVLDE  AR  G  ++
Sbjct: 286 AEDLVLDEEGARAAGLGDL 304

Binds to an ERR-alpha response element (ERRE) containing a single consensus half-site, 5'-TNAAGGTCA-3'. Can bind to the medium-chain acyl coenzyme A dehydrogenase (MCAD) response element NRRE-1 and may act as an important regulator of MCAD promoter. Binds to the C1 region of the lactoferrin gene promoter. Requires dimerization and the coactivator, PGC-1A, for full activity. The ERRalpha/PGC1alpha complex is a regulator of energy metabolism.

Rattus norvegicus (taxid: 10116)

>sp|O08580|ERR1_MOUSE Steroid hormone receptor ERR1 OS=Mus musculus GN=Esrra PE=1 SV=4

 Score =  206 bits (524), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 105/199 (52%), Positives = 130/199 (65%), Gaps = 17/199 (8%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL-- 58
           +IEY+CPASN+CEI KRRRKACQACRF KCLR GMLKEGVRLDRVRGGRQKY+R P++  
Sbjct: 110 SIEYSCPASNECEITKRRRKACQACRFTKCLRVGMLKEGVRLDRVRGGRQKYKRRPEVDP 169

Query: 59  -----------LSQQWPPNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINS 107
                      L+    P K+ P    N ++  LL+ EPE L    +    D  L  + +
Sbjct: 170 LPFPGPFPAGPLAVAGGPRKTAPV---NALVSHLLVVEPEKLYAMPDPASPDGHLPAVAT 226

Query: 108 LSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRF 167
           L DL+DRE+V  I WAK IPGF+ LSL+DQM +LQS W E+L L +A RSLP    ++ F
Sbjct: 227 LCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLP-LQDELAF 285

Query: 168 ASDLVLDERQARECGFSEI 186
           A DLVLDE  AR  G  ++
Sbjct: 286 AEDLVLDEEGARAAGLGDL 304

Binds to an ERR-alpha response element (ERRE) containing a single consensus half-site, 5'-TNAAGGTCA-3'. Can bind to the medium-chain acyl coenzyme A dehydrogenase (MCAD) response element NRRE-1 and may act as an important regulator of MCAD promoter. Binds to the C1 region of the lactoferrin gene promoter. Requires dimerization and the coactivator, PGC-1A, for full activity. The ERRalpha/PGC1alpha complex is a regulator of energy metabolism.

Mus musculus (taxid: 10090)

>sp|Q5RAM2|ERR3_PONAB Estrogen-related receptor gamma OS=Pongo abelii GN=ESRRG PE=2 SV=1

 Score =  205 bits (522), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 125/318 (39%), Positives = 176/318 (55%), Gaps = 29/318 (9%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
           NIEY+CPA+N+CEI KRRRK+CQACRF KCL+ GMLKEGVRLDRVRGGRQKY+R  D  +
Sbjct: 136 NIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRIDAEN 195

Query: 61  QQW-PPNKSIPSLEE-NKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVC 118
             +  P    P+ +  NK++  LL+ EPE +    +    D  ++ + +L DL DRELV 
Sbjct: 196 SPYLNPQLVQPAKKPYNKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVV 255

Query: 119 IIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQA 178
           IIGWAK IPGF+ LSL DQM LLQS W EIL L + YRSL     ++ +A D ++DE Q+
Sbjct: 256 IIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSF-EDELVYADDYIMDEDQS 314

Query: 179 RECGF----SEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFK 234
           +  G     + I Q VK   S+  +++EE      +   +  S     V + +  +    
Sbjct: 315 KLAGLLDLNNAILQLVKKYKSMK-LEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLH 373

Query: 235 RTIQVYSGYRQTGA---CGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLRFWSTV 291
             +Q Y   +        G +++    ++     +++ F N                  +
Sbjct: 374 EALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYN------------------I 415

Query: 292 HKDGKVLMNKLFVEMLEA 309
             +GKV M+KLF EMLEA
Sbjct: 416 KLEGKVPMHKLFSEMLEA 433

Orphan receptor that acts as transcription activator in the absence of bound ligand. Binds specifically to an estrogen response element and activates reporter genes controlled by estrogen response elements.

Pongo abelii (taxid: 9601)

>sp|P11475|ERR2_RAT Steroid hormone receptor ERR2 OS=Rattus norvegicus GN=Esrrb PE=2 SV=1

 Score =  205 bits (522), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 126/318 (39%), Positives = 174/318 (54%), Gaps = 29/318 (9%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRR-----N 55
           NIEY+CPA+N+CEI KRRRK+CQACRF KCL+ GMLKEGVRLDRVRGGRQKY+R     N
Sbjct: 134 NIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRLDSEN 193

Query: 56  PDLLSQQWPPNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRE 115
              LS Q  P    P     K++  LL+ EP+ L         +  ++ + +L DL DRE
Sbjct: 194 SPYLSLQISPPAKKPL---TKIVSYLLVAEPDKLYAMPPDDVPEGDIKALTTLCDLADRE 250

Query: 116 LVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDE 175
           LV +I WAK IPGF++L+L DQM LLQS W EIL L I YRSLP+   K+ +A D ++DE
Sbjct: 251 LVFLISWAKHIPGFSNLTLGDQMSLLQSAWMEILILGIVYRSLPY-DDKLAYAEDYIMDE 309

Query: 176 RQARECGFSEIY----QQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKA 231
             +R  G  E+Y    Q V+    L  +++EE      L   +  S +   + + +  + 
Sbjct: 310 EHSRLVGLLELYRAILQLVRRYKKLK-VEKEEFVMLKALALANSDSMYIENLEAVQKLQD 368

Query: 232 FFKRTIQVYSGYRQTGACGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLRFWSTV 291
                +Q Y   ++                +E     K   ++          ++ + +V
Sbjct: 369 LLHEALQDYELSQRH---------------EEPRRAGKLLLTLPLLRQTAAKAVQHFYSV 413

Query: 292 HKDGKVLMNKLFVEMLEA 309
              GKV M+KLF+EMLEA
Sbjct: 414 KLQGKVPMHKLFLEMLEA 431

Nuclear receptor, may regulate ESR1 transcriptional activity.

Rattus norvegicus (taxid: 10116)

>sp|P11474|ERR1_HUMAN Steroid hormone receptor ERR1 OS=Homo sapiens GN=ESRRA PE=1 SV=3

 Score =  204 bits (519), Expect = 7e-52,   Method: Compositional matrix adjust.
 Identities = 105/199 (52%), Positives = 130/199 (65%), Gaps = 16/199 (8%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL-- 58
           +IEY+CPASN+CEI KRRRKACQACRF KCLR GMLKEGVRLDRVRGGRQKY+R P++  
Sbjct: 110 SIEYSCPASNECEITKRRRKACQACRFTKCLRVGMLKEGVRLDRVRGGRQKYKRRPEVDP 169

Query: 59  -----------LSQQWPPNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINS 107
                      L+    P K+   +  N ++  LL+ EPE L    +    D  L  + +
Sbjct: 170 LPFPGPFPAGPLAVAGGPRKTAAPV--NALVSHLLVVEPEKLYAMPDPAGPDGHLPAVAT 227

Query: 108 LSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRF 167
           L DL+DRE+V  I WAK IPGF+ LSL+DQM +LQS W E+L L +A RSLP    ++ F
Sbjct: 228 LCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLP-LQDELAF 286

Query: 168 ASDLVLDERQARECGFSEI 186
           A DLVLDE  AR  G  E+
Sbjct: 287 AEDLVLDEEGARAAGLGEL 305

Binds to an ERR-alpha response element (ERRE) containing a single consensus half-site, 5'-TNAAGGTCA-3'. Can bind to the medium-chain acyl coenzyme A dehydrogenase (MCAD) response element NRRE-1 and may act as an important regulator of MCAD promoter. Binds to the C1 region of the lactoferrin gene promoter. Requires dimerization and the coactivator, PGC-1A, for full activity. The ERRalpha/PGC1alpha complex is a regulator of energy metabolism.

Homo sapiens (taxid: 9606)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	312
242021609	448	retinoid X receptor, putative [Pediculus	0.871	0.607	0.508	4e-86
259906648	401	estrogen receptor-like protein [Teleogry	0.871	0.678	0.502	2e-83
345496190	438	PREDICTED: steroid hormone receptor ERR2	0.846	0.602	0.5	2e-79
340714311	430	PREDICTED: steroid hormone receptor ERR2	0.846	0.613	0.5	5e-78
340714309	434	PREDICTED: steroid hormone receptor ERR2	0.846	0.608	0.5	6e-78
383863647	434	PREDICTED: steroid hormone receptor ERR2	0.846	0.608	0.497	9e-78
242117914	434	estrogen-related receptor [Apis mellifer	0.846	0.608	0.5	1e-77
380025663	434	PREDICTED: steroid hormone receptor ERR2	0.846	0.608	0.5	1e-77
345496188	450	PREDICTED: steroid hormone receptor ERR2	0.846	0.586	0.482	1e-76
307201567	426	Steroid hormone receptor ERR2 [Harpegnat	0.846	0.619	0.488	1e-75

>gi|242021609|ref|XP_002431237.1| retinoid X receptor, putative [Pediculus humanus corporis] gi|212516486|gb|EEB18499.1| retinoid X receptor, putative [Pediculus humanus corporis]

 Score =  324 bits (830), Expect = 4e-86,   Method: Compositional matrix adjust.
 Identities = 174/342 (50%), Positives = 217/342 (63%), Gaps = 70/342 (20%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL-- 58
           NIEYTCPA+NDCEINKRRRKACQACRFQKCLR GMLKEGVRLDRVRGGRQKYRRN D   
Sbjct: 147 NIEYTCPAANDCEINKRRRKACQACRFQKCLRMGMLKEGVRLDRVRGGRQKYRRNTDTPY 206

Query: 59  -LSQQWPPNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELV 117
            +    P    +PSLE+NK+LEAL L EP++  +  +   +DP ++T+N LSDLYD+ELV
Sbjct: 207 QIHSMLPLKPYLPSLEDNKILEALSLNEPDISVMAQDISNADPAVRTLNILSDLYDQELV 266

Query: 118 CIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQ 177
            II WAK IPGF DL+LNDQMRLLQSTWAEILTLT+ YRSLP   G+++FA+D   DE+ 
Sbjct: 267 KIITWAKHIPGFLDLTLNDQMRLLQSTWAEILTLTVTYRSLPG-TGELKFAADFSFDEKM 325

Query: 178 ARECGFSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTI 237
           ARECG  +IYQ   H       ++E+L         ++    +Y + +            
Sbjct: 326 ARECGAMDIYQHCMHIVE----RQEKL---------NITKEEYYIIKA------------ 360

Query: 238 QVYSGYRQTGACGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVL------------ 285
                         LVLANSDV++D+   LKK R++ILS+L DC+ VL            
Sbjct: 361 --------------LVLANSDVRIDDLPPLKKLRDNILSALADCVAVLRPNTTSLHMNHL 406

Query: 286 ---------------RFWSTVHKDGKVLMNKLFVEMLEAYLR 312
                          RFW+ VH++GKV MNKLF+EMLE+Y+R
Sbjct: 407 LLCLPALRQADYINRRFWTAVHREGKVYMNKLFIEMLESYIR 448

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|259906648|gb|ACW84414.1| estrogen receptor-like protein [Teleogryllus emma]

 Score =  315 bits (807), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 171/340 (50%), Positives = 212/340 (62%), Gaps = 68/340 (20%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
           NIEYTCPA+NDCEINKRRRKACQACRFQKCLR GMLKEGVRLDRVRGGRQKYRRNPDL  
Sbjct: 102 NIEYTCPAANDCEINKRRRKACQACRFQKCLRMGMLKEGVRLDRVRGGRQKYRRNPDLPY 161

Query: 61  Q-QWPPNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCI 119
           Q Q    + + SL+ENKML+AL  CEP++L    +T   D  L+ +++LSDLYDRELV +
Sbjct: 162 QVQAFMPRPVLSLDENKMLKALTSCEPDLLLASPDTSIVDLELRVVSTLSDLYDRELVGV 221

Query: 120 IGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAR 179
           I WAK IPGFT+L+LNDQMRLLQSTWAEILTL +A+RSL    GK+RFA+D  LDE+ AR
Sbjct: 222 ISWAKLIPGFTELTLNDQMRLLQSTWAEILTLALAFRSLGQ-GGKLRFAADFSLDEKLAR 280

Query: 180 ECGFSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQV 239
           +C   E+YQ   H                                         +R  ++
Sbjct: 281 DCSVLEVYQHCMH---------------------------------------IVERLERL 301

Query: 240 YSGYRQTGACGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVL-------------- 285
                +      LVLANSDV++D+ ++LKKFR++IL++L DC+ V+              
Sbjct: 302 AIAEEEYYVLKALVLANSDVRMDDLAALKKFRDTILAALSDCVAVVRSSSASHHMQQLLL 361

Query: 286 -------------RFWSTVHKDGKVLMNKLFVEMLEAYLR 312
                        R+W+ VH++GK  MNKLFVEMLEA  R
Sbjct: 362 CLPALRQADQVIRRYWTAVHREGKAPMNKLFVEMLEANFR 401

Source: Teleogryllus emma

Species: Teleogryllus emma

Genus: Teleogryllus

Family: Gryllidae

Order: Orthoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345496190|ref|XP_001604033.2| PREDICTED: steroid hormone receptor ERR2 isoform 1 [Nasonia vitripennis]

 Score =  301 bits (772), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 168/336 (50%), Positives = 205/336 (61%), Gaps = 72/336 (21%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
           NIEYTCPA+ +CEINKRRRKACQACRFQKCLR+GMLKEGVRLDRVRGGRQKYRR+ D   
Sbjct: 144 NIEYTCPANGECEINKRRRKACQACRFQKCLRQGMLKEGVRLDRVRGGRQKYRRSTD--- 200

Query: 61  QQWPPNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCII 120
             + P K+I +LE+NKM+EAL+ CEP+ML V + +   D   + +  LSDLYDRELV II
Sbjct: 201 -PYVPGKTI-TLEDNKMVEALISCEPDMLQVSTLSHTLDTDQRVLGQLSDLYDRELVGII 258

Query: 121 GWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE 180
           GWAKQIPGF+ L LNDQMRLLQSTWAEILT ++A+RS+P+ +GK+RFA D  LDER ARE
Sbjct: 259 GWAKQIPGFSSLPLNDQMRLLQSTWAEILTFSLAWRSIPN-SGKLRFAQDFTLDERLARE 317

Query: 181 CGFSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVY 240
           C   E+Y                                         C    +R  ++ 
Sbjct: 318 CHCLELYTH---------------------------------------CMQIVERVQRLS 338

Query: 241 SGYRQTGACGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLR-------------- 286
               +      L+L NSD KLDE  +L +FR+SIL SL DC+  +R              
Sbjct: 339 LAREEFYVLKALILTNSDAKLDEPHALHRFRDSILGSLSDCVSAVRPGQALRANQNMFLV 398

Query: 287 -------------FWSTVHKDGKVLMNKLFVEMLEA 309
                        FWS+V++ GKV MNKLFVEMLEA
Sbjct: 399 LPGLRQADGIVRKFWSSVYRTGKVPMNKLFVEMLEA 434

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340714311|ref|XP_003395673.1| PREDICTED: steroid hormone receptor ERR2-like isoform 2 [Bombus terrestris] gi|350417321|ref|XP_003491365.1| PREDICTED: steroid hormone receptor ERR2-like isoform 2 [Bombus impatiens]

 Score =  297 bits (760), Expect = 5e-78,   Method: Compositional matrix adjust.
 Identities = 168/336 (50%), Positives = 205/336 (61%), Gaps = 72/336 (21%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
           NIEYTCPA+ +CEINKRRRKACQACRFQKCLR+GMLKEGVRLDRVRGGRQKYRR+ D   
Sbjct: 136 NIEYTCPANGECEINKRRRKACQACRFQKCLRQGMLKEGVRLDRVRGGRQKYRRSTD--- 192

Query: 61  QQWPPNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCII 120
             + P K+ P LE+NKMLEAL  CEP+ML V + +   D   + +  LSDLYDRELV II
Sbjct: 193 -PYTPVKTAP-LEDNKMLEALAACEPDMLQVSNISHTLDTDQRVLGQLSDLYDRELVGII 250

Query: 121 GWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE 180
           GWAKQIPGF+ L+LNDQMRLLQSTWAEILT ++A+RS+P+  G++RFA D  LDER ARE
Sbjct: 251 GWAKQIPGFSSLALNDQMRLLQSTWAEILTFSLAWRSMPN-NGRLRFAQDFTLDERLARE 309

Query: 181 CGFSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVY 240
           C  +E+Y                                         C    +R  ++ 
Sbjct: 310 CHCTELYTH---------------------------------------CIQIVERLQRLG 330

Query: 241 SGYRQTGACGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCI------------------ 282
               +      L+LANSD + DE  +L +FR+SIL+SL DC+                  
Sbjct: 331 LTREEYYVLKALILANSDARSDEPQALYRFRDSILNSLSDCMATVRPGQALRATQNMFLV 390

Query: 283 ---------YVLRFWSTVHKDGKVLMNKLFVEMLEA 309
                     V RFWS+V++ GKV MNKLFVEMLEA
Sbjct: 391 LPSLRQVDGIVRRFWSSVYRTGKVPMNKLFVEMLEA 426

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340714309|ref|XP_003395672.1| PREDICTED: steroid hormone receptor ERR2-like isoform 1 [Bombus terrestris] gi|350417319|ref|XP_003491364.1| PREDICTED: steroid hormone receptor ERR2-like isoform 1 [Bombus impatiens]

 Score =  296 bits (759), Expect = 6e-78,   Method: Compositional matrix adjust.
 Identities = 168/336 (50%), Positives = 205/336 (61%), Gaps = 72/336 (21%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
           NIEYTCPA+ +CEINKRRRKACQACRFQKCLR+GMLKEGVRLDRVRGGRQKYRR+ D   
Sbjct: 140 NIEYTCPANGECEINKRRRKACQACRFQKCLRQGMLKEGVRLDRVRGGRQKYRRSTD--- 196

Query: 61  QQWPPNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCII 120
             + P K+ P LE+NKMLEAL  CEP+ML V + +   D   + +  LSDLYDRELV II
Sbjct: 197 -PYTPVKTAP-LEDNKMLEALAACEPDMLQVSNISHTLDTDQRVLGQLSDLYDRELVGII 254

Query: 121 GWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE 180
           GWAKQIPGF+ L+LNDQMRLLQSTWAEILT ++A+RS+P+  G++RFA D  LDER ARE
Sbjct: 255 GWAKQIPGFSSLALNDQMRLLQSTWAEILTFSLAWRSMPN-NGRLRFAQDFTLDERLARE 313

Query: 181 CGFSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVY 240
           C  +E+Y                                         C    +R  ++ 
Sbjct: 314 CHCTELYTH---------------------------------------CIQIVERLQRLG 334

Query: 241 SGYRQTGACGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCI------------------ 282
               +      L+LANSD + DE  +L +FR+SIL+SL DC+                  
Sbjct: 335 LTREEYYVLKALILANSDARSDEPQALYRFRDSILNSLSDCMATVRPGQALRATQNMFLV 394

Query: 283 ---------YVLRFWSTVHKDGKVLMNKLFVEMLEA 309
                     V RFWS+V++ GKV MNKLFVEMLEA
Sbjct: 395 LPSLRQVDGIVRRFWSSVYRTGKVPMNKLFVEMLEA 430

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383863647|ref|XP_003707291.1| PREDICTED: steroid hormone receptor ERR2-like [Megachile rotundata]

 Score =  296 bits (757), Expect = 9e-78,   Method: Compositional matrix adjust.
 Identities = 167/336 (49%), Positives = 205/336 (61%), Gaps = 72/336 (21%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
           NIEYTCPA+ +CEINKRRRKACQACRFQKCLR+GMLKEGVRLDRVRGGRQKYRR+ D   
Sbjct: 140 NIEYTCPANGECEINKRRRKACQACRFQKCLRQGMLKEGVRLDRVRGGRQKYRRSTD--- 196

Query: 61  QQWPPNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCII 120
             + P K+ P LE+NKMLEAL  CEP+ML V + +   D   + +  LSDLYDRELV II
Sbjct: 197 -PYTPVKTAP-LEDNKMLEALAACEPDMLQVSNLSHTLDTDQRVLGQLSDLYDRELVGII 254

Query: 121 GWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE 180
           GWAKQIPGF+ L+LNDQMRLLQSTWAEILT ++A+RS+P+  G++RFA D  LDER ARE
Sbjct: 255 GWAKQIPGFSGLALNDQMRLLQSTWAEILTFSLAWRSMPN-NGRLRFAQDFTLDERLARE 313

Query: 181 CGFSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVY 240
           C  +E+Y                                         C    +R  ++ 
Sbjct: 314 CHCTELYTH---------------------------------------CIQIVERLQRLG 334

Query: 241 SGYRQTGACGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCI------------------ 282
               +      L+LANSD + DE  +L +FR++IL+SL DC+                  
Sbjct: 335 LTREEYYMLKALILANSDARSDEPQALYRFRDTILNSLSDCVAAIRPGQALRATQNMFLV 394

Query: 283 ---------YVLRFWSTVHKDGKVLMNKLFVEMLEA 309
                     V RFWS+V++ GKV MNKLFVEMLEA
Sbjct: 395 LPSLRQVDGIVRRFWSSVYRTGKVPMNKLFVEMLEA 430

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242117914|ref|NP_001155988.1| estrogen-related receptor [Apis mellifera] gi|153793268|gb|ABS50436.1| estrogen-related receptor [Apis mellifera]

 Score =  296 bits (757), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 168/336 (50%), Positives = 204/336 (60%), Gaps = 72/336 (21%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
           NIEYTCPA+ +CEINKRRRKACQACRFQKCLR+GMLKEGVRLDRVRGGRQKYRR+ D   
Sbjct: 140 NIEYTCPANGECEINKRRRKACQACRFQKCLRQGMLKEGVRLDRVRGGRQKYRRSTD--- 196

Query: 61  QQWPPNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCII 120
             + P K  P LE+NKMLEAL  CEP+ML V + +   D   + +  LSDLYDRELV II
Sbjct: 197 -PYTPVKPAP-LEDNKMLEALAACEPDMLQVSNISHTLDTDQRVLGQLSDLYDRELVGII 254

Query: 121 GWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE 180
           GWAKQIPGF+ L+LNDQMRLLQSTWAEILT ++A+RS+P+  G++RFA D  LDER ARE
Sbjct: 255 GWAKQIPGFSSLALNDQMRLLQSTWAEILTFSLAWRSMPN-NGRLRFAQDFTLDERLARE 313

Query: 181 CGFSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVY 240
           C  +E+Y                                         C    +R  ++ 
Sbjct: 314 CHCTELYTH---------------------------------------CIQIVERLQRLG 334

Query: 241 SGYRQTGACGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCI------------------ 282
               +      L+LANSD + DE  +L +FR+SIL+SL DC+                  
Sbjct: 335 LTREEYYVLKALILANSDARSDEPQALYRFRDSILNSLSDCMAAVRPGQALRATQNMFLV 394

Query: 283 ---------YVLRFWSTVHKDGKVLMNKLFVEMLEA 309
                     V RFWS+V++ GKV MNKLFVEMLEA
Sbjct: 395 LPSLRQVDGIVRRFWSSVYRTGKVPMNKLFVEMLEA 430

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380025663|ref|XP_003696588.1| PREDICTED: steroid hormone receptor ERR2-like [Apis florea]

 Score =  295 bits (756), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 168/336 (50%), Positives = 204/336 (60%), Gaps = 72/336 (21%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
           NIEYTCPA+ +CEINKRRRKACQACRFQKCLR+GMLKEGVRLDRVRGGRQKYRR+ D   
Sbjct: 140 NIEYTCPANGECEINKRRRKACQACRFQKCLRQGMLKEGVRLDRVRGGRQKYRRSTD--- 196

Query: 61  QQWPPNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCII 120
             + P K  P LE+NKMLEAL  CEP+ML V + +   D   + +  LSDLYDRELV II
Sbjct: 197 -PYTPVKPAP-LEDNKMLEALAACEPDMLQVSNISHTLDTDQRVLGQLSDLYDRELVGII 254

Query: 121 GWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE 180
           GWAKQIPGF+ L+LNDQMRLLQSTWAEILT ++A+RS+P+  G++RFA D  LDER ARE
Sbjct: 255 GWAKQIPGFSSLALNDQMRLLQSTWAEILTFSLAWRSMPN-NGRLRFAQDFTLDERLARE 313

Query: 181 CGFSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVY 240
           C  +E+Y                                         C    +R  ++ 
Sbjct: 314 CHCTELYTH---------------------------------------CIQIVERLQRLG 334

Query: 241 SGYRQTGACGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCI------------------ 282
               +      L+LANSD + DE  +L +FR+SIL+SL DC+                  
Sbjct: 335 LTREEYYVLKALILANSDARSDEPQALYRFRDSILNSLSDCMAAVRPGQALRATQNMFLV 394

Query: 283 ---------YVLRFWSTVHKDGKVLMNKLFVEMLEA 309
                     V RFWS+V++ GKV MNKLFVEMLEA
Sbjct: 395 LPSLRQVDGIVRRFWSSVYRTGKVPMNKLFVEMLEA 430

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345496188|ref|XP_003427670.1| PREDICTED: steroid hormone receptor ERR2 isoform 2 [Nasonia vitripennis]

 Score =  293 bits (749), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 168/348 (48%), Positives = 204/348 (58%), Gaps = 84/348 (24%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
           NIEYTCPA+ +CEINKRRRKACQACRFQKCLR+GMLKEGVRLDRVRGGRQKYRR+ D   
Sbjct: 144 NIEYTCPANGECEINKRRRKACQACRFQKCLRQGMLKEGVRLDRVRGGRQKYRRSTD--- 200

Query: 61  QQWPPNKSIPSLE------------ENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSL 108
             + P K+I +LE             NKM+EAL+ CEP+ML V + +   D   + +  L
Sbjct: 201 -PYVPGKTI-TLEANVGSAGYAEAINNKMVEALISCEPDMLQVSTLSHTLDTDQRVLGQL 258

Query: 109 SDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFA 168
           SDLYDRELV IIGWAKQIPGF+ L LNDQMRLLQSTWAEILT ++A+RS+P+ +GK+RFA
Sbjct: 259 SDLYDRELVGIIGWAKQIPGFSSLPLNDQMRLLQSTWAEILTFSLAWRSIPN-SGKLRFA 317

Query: 169 SDLVLDERQARECGFSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEA 228
            D  LDER AREC   E+Y                                         
Sbjct: 318 QDFTLDERLARECHCLELYTH--------------------------------------- 338

Query: 229 CKAFFKRTIQVYSGYRQTGACGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLR-- 286
           C    +R  ++     +      L+L NSD KLDE  +L +FR+SIL SL DC+  +R  
Sbjct: 339 CMQIVERVQRLSLAREEFYVLKALILTNSDAKLDEPHALHRFRDSILGSLSDCVSAVRPG 398

Query: 287 -------------------------FWSTVHKDGKVLMNKLFVEMLEA 309
                                    FWS+V++ GKV MNKLFVEMLEA
Sbjct: 399 QALRANQNMFLVLPGLRQADGIVRKFWSSVYRTGKVPMNKLFVEMLEA 446

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307201567|gb|EFN81329.1| Steroid hormone receptor ERR2 [Harpegnathos saltator]

 Score =  289 bits (739), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 164/336 (48%), Positives = 203/336 (60%), Gaps = 72/336 (21%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
           NIEYTCPA+ +CEINKRRRKACQACRFQKCLR+GMLKEGVRLDRVRGGRQKYRR+ D   
Sbjct: 133 NIEYTCPANGECEINKRRRKACQACRFQKCLRQGMLKEGVRLDRVRGGRQKYRRSTD--- 189

Query: 61  QQWPPNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCII 120
             + P KS  +LE+NKM+EAL  CEP+ML V + +   +   + +  LSDLYDRELV II
Sbjct: 190 -PYTPVKST-TLEDNKMVEALTACEPDMLQVSNISHTLETDQRVLGQLSDLYDRELVGII 247

Query: 121 GWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE 180
           GWAKQIPGF+ L+LNDQ+RLLQSTWAEILT T+A+RS P+ +G++RFA D  LDER A E
Sbjct: 248 GWAKQIPGFSSLALNDQIRLLQSTWAEILTFTLAWRSTPN-SGRLRFAQDFTLDERLAHE 306

Query: 181 CGFSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVY 240
           C   ++Y                                         C    +R  ++ 
Sbjct: 307 CHCMDLYTH---------------------------------------CIQIVERIQRLG 327

Query: 241 SGYRQTGACGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVL--------------- 285
               +      L+LANSD + DE  +L +FR++IL+SL DC+ V+               
Sbjct: 328 LTREEYYMLKALILANSDARSDEPQALYRFRDTILNSLSDCVAVVRPGQALRATQNMFLV 387

Query: 286 ------------RFWSTVHKDGKVLMNKLFVEMLEA 309
                       RFWS+V K GKV MNKLFVEMLEA
Sbjct: 388 LPSLRQADGIVRRFWSSVFKTGKVPMNKLFVEMLEA 423

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	312
UNIPROTKB|F1NBB9	438	ESRRB "Uncharacterized protein	0.634	0.452	0.530	1.1e-54
ZFIN|ZDB-GENE-990415-68	436	esrra "estrogen-related recept	0.589	0.422	0.557	4.8e-54
ZFIN|ZDB-GENE-030821-2	508	esrrga "estrogen-related recep	0.644	0.395	0.511	3.3e-53
UNIPROTKB|F1NBB5	393	ESRRG "Uncharacterized protein	0.644	0.511	0.511	3.7e-52
UNIPROTKB|Q5UKY7	435	ESRRG "Nuclear receptor subfam	0.644	0.462	0.514	3.7e-52
UNIPROTKB|E1BC39	450	ESRRG "Uncharacterized protein	0.644	0.446	0.514	3.7e-52
UNIPROTKB|E2R7U1	458	ESRRG "Uncharacterized protein	0.644	0.438	0.514	3.7e-52
UNIPROTKB|J9NWD9	435	ESRRG "Uncharacterized protein	0.644	0.462	0.514	3.7e-52
UNIPROTKB|P62508	458	ESRRG "Estrogen-related recept	0.644	0.438	0.514	3.7e-52
MGI|MGI:1347056	458	Esrrg "estrogen-related recept	0.644	0.438	0.514	3.7e-52

UNIPROTKB|F1NBB9 ESRRB "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 520 (188.1 bits), Expect = 1.1e-54, Sum P(2) = 1.1e-54
 Identities = 112/211 (53%), Positives = 138/211 (65%)

Query:     1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPD--- 57
             NIEY+CPA+N+CEI KRRRK+CQACRF KCL+ GMLKEGVRLDRVRGGRQKY+R  D   
Sbjct:   139 NIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRLDSES 198

Query:    58 --LLSQQWPPNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRE 115
                LS Q PP    P     K++  LL+ EPE +    +    +  ++ + +L DL DRE
Sbjct:   199 STYLSLQIPPPAKKPL---TKIVSHLLVAEPEKIYAMPDPTMPESDIKALTTLCDLADRE 255

Query:   116 LVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDE 175
             LV IIGWAK IPGF++LSL DQM LLQS W EIL L I YRSLP+   K+ +A D ++DE
Sbjct:   256 LVVIIGWAKHIPGFSNLSLGDQMSLLQSAWMEILILGIVYRSLPY-EDKLVYAEDYIMDE 314

Query:   176 RQARECGFSEIY----QQVKHSGSLDGIKEE 202
               +R  G  E+Y    Q V+    L   KEE
Sbjct:   315 EHSRLTGLLELYLAILQLVRRYKKLKVEKEE 345

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

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

GO:0005496 "steroid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0000980 "RNA polymerase II distal enhancer sequence-specific DNA binding" evidence=IEA

GO:0001831 "trophectodermal cellular morphogenesis" evidence=IEA

GO:0001834 "trophectodermal cell proliferation" evidence=IEA

GO:0001892 "embryonic placenta development" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IEA

GO:0019827 "stem cell maintenance" evidence=IEA

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

ZFIN|ZDB-GENE-990415-68 esrra "estrogen-related receptor alpha" [Danio rerio (taxid:7955)]

 Score = 523 (189.2 bits), Expect = 4.8e-54, Sum P(2) = 4.8e-54
 Identities = 107/192 (55%), Positives = 133/192 (69%)

Query:     1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
             NIEY+CPASN+CEI KRRRKACQACRF KCL+ GMLKEGVRLDRVRGGRQKY+R P++ +
Sbjct:   131 NIEYSCPASNECEITKRRRKACQACRFTKCLKVGMLKEGVRLDRVRGGRQKYKRRPEVEN 190

Query:    61 QQWPPNKSIPSLEENK------MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDR 114
               +  +  IP  +E +      ++  LL+ EPE L    +  Q D   +T+ +L DL DR
Sbjct:   191 ATYQ-SAPIPLRKEGEKGSSSIIVSHLLVAEPEKLFAMPDPLQPDTAQRTLTTLCDLADR 249

Query:   115 ELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLD 174
             ELV IIGWAK IPGF  LSL DQM +LQS W E+L L +AYRSL  C  ++ FA D VLD
Sbjct:   250 ELVVIIGWAKHIPGFLSLSLADQMSVLQSVWLEVLVLGVAYRSLG-CEDEVVFAEDFVLD 308

Query:   175 ERQARECGFSEI 186
             E  +R  G +E+
Sbjct:   309 EEMSRVAGLTEL 320

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

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IEA;IC

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0005496 "steroid binding" evidence=IEA

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

GO:0046872 "metal ion binding" evidence=IEA

GO:0042074 "cell migration involved in gastrulation" evidence=IMP

ZFIN|ZDB-GENE-030821-2 esrrga "estrogen-related receptor gamma a" [Danio rerio (taxid:7955)]

 Score = 500 (181.1 bits), Expect = 3.3e-53, Sum P(2) = 3.3e-53
 Identities = 110/215 (51%), Positives = 138/215 (64%)

Query:     1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRR-----N 55
             NIEY+CPA+N+CEI KRRRK+CQACRF KCL  GM++EGVRLDRVRGGRQKY+R     N
Sbjct:   202 NIEYSCPATNECEITKRRRKSCQACRFMKCLTVGMMREGVRLDRVRGGRQKYKRRIDAEN 261

Query:    56 PDLLSQQW--PPNKSIP--SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDL 111
                L+ Q   PP K  P   L +NK++  LL+ EPE +    +    D  ++ + +L DL
Sbjct:   262 SPYLNPQLALPPKKPFPFGCLADNKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDL 321

Query:   112 YDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDL 171
              DRELV  IGWAK IPGF+ LSL DQM LLQS W EIL L + YRSL     K+ +A D 
Sbjct:   322 ADRELVVNIGWAKHIPGFSTLSLADQMSLLQSAWMEILILRVVYRSLSF-EDKLVYAEDY 380

Query:   172 VLDERQARECGFSE----IYQQVKHSGSLDGIKEE 202
             ++DE Q++  G  +    I Q VK   S+   KEE
Sbjct:   381 IMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEE 415

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

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0005496 "steroid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;IC

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|F1NBB5 ESRRG "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 497 (180.0 bits), Expect = 3.7e-52, Sum P(2) = 3.7e-52
 Identities = 109/213 (51%), Positives = 137/213 (64%)

Query:     1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRR-----N 55
             NIEY+CPA+N+CEI KRRRK+CQACRF KCL+ GMLKEGVRLDRVRGGRQKY+R     N
Sbjct:    91 NIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRIDAEN 150

Query:    56 PDLLSQQW--PPNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYD 113
                L+ Q   P  K      +NK++  LL+ EPE +    +    D  ++ + +L DL D
Sbjct:   151 SPYLNPQLVQPAKKPWAIFTDNKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLAD 210

Query:   114 RELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVL 173
             RELV IIGWAK IPGF+ LSL DQM LLQS W EIL L + YRSL     ++ +A D ++
Sbjct:   211 RELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSF-EDELVYAEDYIM 269

Query:   174 DERQARECGFSE----IYQQVKHSGSLDGIKEE 202
             DE Q++  G  +    I Q VK   S+   KEE
Sbjct:   270 DEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEE 302

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

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

GO:0005496 "steroid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

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

UNIPROTKB|Q5UKY7 ESRRG "Nuclear receptor subfamily 3 group B member 3" [Gallus gallus (taxid:9031)]

 Score = 497 (180.0 bits), Expect = 3.7e-52, Sum P(2) = 3.7e-52
 Identities = 107/208 (51%), Positives = 137/208 (65%)

Query:     1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
             NIEY+CPA+N+CEI KRRRK+CQACRF KCL+ GMLKEGVRLDRVRGGRQKY+R  D  +
Sbjct:   136 NIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRIDAEN 195

Query:    61 QQW-PPNKSIPSLEE-NKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVC 118
               +  P    P+ +  NK++  LL+ EPE +    +    D  ++ + +L DL DRELV 
Sbjct:   196 SPYLNPQLVQPAKKPYNKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVV 255

Query:   119 IIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQA 178
             IIGWAK IPGF+ LSL DQM LLQS W EIL L + YRSL     ++ +A D ++DE Q+
Sbjct:   256 IIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSF-EDELVYAEDYIMDEDQS 314

Query:   179 RECGFSE----IYQQVKHSGSLDGIKEE 202
             +  G  +    I Q VK   S+   KEE
Sbjct:   315 KLAGLLDLNNAILQLVKKYKSMKLEKEE 342

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

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

GO:0005496 "steroid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

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

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

UNIPROTKB|E1BC39 ESRRG "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 497 (180.0 bits), Expect = 3.7e-52, Sum P(2) = 3.7e-52
 Identities = 107/208 (51%), Positives = 137/208 (65%)

Query:     1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
             NIEY+CPA+N+CEI KRRRK+CQACRF KCL+ GMLKEGVRLDRVRGGRQKY+R  D  +
Sbjct:   151 NIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRIDAEN 210

Query:    61 QQW-PPNKSIPSLEE-NKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVC 118
               +  P    P+ +  NK++  LL+ EPE +    +    D  ++ + +L DL DRELV 
Sbjct:   211 SPYLNPQLVQPAKKPYNKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVV 270

Query:   119 IIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQA 178
             IIGWAK IPGF+ LSL DQM LLQS W EIL L + YRSL     ++ +A D ++DE Q+
Sbjct:   271 IIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSF-EDELVYADDYIMDEDQS 329

Query:   179 RECGFSE----IYQQVKHSGSLDGIKEE 202
             +  G  +    I Q VK   S+   KEE
Sbjct:   330 KLAGLLDLNNAILQLVKKYKSMKLEKEE 357

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

GO:0005634 "nucleus" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005496 "steroid binding" evidence=IEA

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

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

UNIPROTKB|E2R7U1 ESRRG "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 497 (180.0 bits), Expect = 3.7e-52, Sum P(2) = 3.7e-52
 Identities = 107/208 (51%), Positives = 137/208 (65%)

Query:     1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
             NIEY+CPA+N+CEI KRRRK+CQACRF KCL+ GMLKEGVRLDRVRGGRQKY+R  D  +
Sbjct:   159 NIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRIDAEN 218

Query:    61 QQW-PPNKSIPSLEE-NKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVC 118
               +  P    P+ +  NK++  LL+ EPE +    +    D  ++ + +L DL DRELV 
Sbjct:   219 SPYLNPQLVQPAKKPYNKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVV 278

Query:   119 IIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQA 178
             IIGWAK IPGF+ LSL DQM LLQS W EIL L + YRSL     ++ +A D ++DE Q+
Sbjct:   279 IIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSF-EDELVYADDYIMDEDQS 337

Query:   179 RECGFSE----IYQQVKHSGSLDGIKEE 202
             +  G  +    I Q VK   S+   KEE
Sbjct:   338 KLAGLLDLNNAILQLVKKYKSMKLEKEE 365

GO:0005634 "nucleus" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005496 "steroid binding" evidence=IEA

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

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

UNIPROTKB|J9NWD9 ESRRG "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 497 (180.0 bits), Expect = 3.7e-52, Sum P(2) = 3.7e-52
 Identities = 107/208 (51%), Positives = 137/208 (65%)

Query:     1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
             NIEY+CPA+N+CEI KRRRK+CQACRF KCL+ GMLKEGVRLDRVRGGRQKY+R  D  +
Sbjct:   136 NIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRIDAEN 195

Query:    61 QQW-PPNKSIPSLEE-NKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVC 118
               +  P    P+ +  NK++  LL+ EPE +    +    D  ++ + +L DL DRELV 
Sbjct:   196 SPYLNPQLVQPAKKPYNKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVV 255

Query:   119 IIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQA 178
             IIGWAK IPGF+ LSL DQM LLQS W EIL L + YRSL     ++ +A D ++DE Q+
Sbjct:   256 IIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSF-EDELVYADDYIMDEDQS 314

Query:   179 RECGFSE----IYQQVKHSGSLDGIKEE 202
             +  G  +    I Q VK   S+   KEE
Sbjct:   315 KLAGLLDLNNAILQLVKKYKSMKLEKEE 342

GO:0005634 "nucleus" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005496 "steroid binding" evidence=IEA

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

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

UNIPROTKB|P62508 ESRRG "Estrogen-related receptor gamma" [Homo sapiens (taxid:9606)]

 Score = 497 (180.0 bits), Expect = 3.7e-52, Sum P(2) = 3.7e-52
 Identities = 107/208 (51%), Positives = 137/208 (65%)

Query:     1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
             NIEY+CPA+N+CEI KRRRK+CQACRF KCL+ GMLKEGVRLDRVRGGRQKY+R  D  +
Sbjct:   159 NIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRIDAEN 218

Query:    61 QQW-PPNKSIPSLEE-NKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVC 118
               +  P    P+ +  NK++  LL+ EPE +    +    D  ++ + +L DL DRELV 
Sbjct:   219 SPYLNPQLVQPAKKPYNKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVV 278

Query:   119 IIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQA 178
             IIGWAK IPGF+ LSL DQM LLQS W EIL L + YRSL     ++ +A D ++DE Q+
Sbjct:   279 IIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSF-EDELVYADDYIMDEDQS 337

Query:   179 RECGFSE----IYQQVKHSGSLDGIKEE 202
             +  G  +    I Q VK   S+   KEE
Sbjct:   338 KLAGLLDLNNAILQLVKKYKSMKLEKEE 365

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

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

GO:0005496 "steroid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

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

GO:0050682 "AF-2 domain binding" evidence=ISS

GO:0005515 "protein binding" evidence=IPI

GO:0005654 "nucleoplasm" evidence=TAS

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

GO:0010467 "gene expression" evidence=TAS

MGI|MGI:1347056 Esrrg "estrogen-related receptor gamma" [Mus musculus (taxid:10090)]

 Score = 497 (180.0 bits), Expect = 3.7e-52, Sum P(2) = 3.7e-52
 Identities = 107/208 (51%), Positives = 137/208 (65%)

Query:     1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
             NIEY+CPA+N+CEI KRRRK+CQACRF KCL+ GMLKEGVRLDRVRGGRQKY+R  D  +
Sbjct:   159 NIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRIDAEN 218

Query:    61 QQW-PPNKSIPSLEE-NKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVC 118
               +  P    P+ +  NK++  LL+ EPE +    +    D  ++ + +L DL DRELV 
Sbjct:   219 SPYLNPQLVQPAKKPYNKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVV 278

Query:   119 IIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQA 178
             IIGWAK IPGF+ LSL DQM LLQS W EIL L + YRSL     ++ +A D ++DE Q+
Sbjct:   279 IIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSF-EDELVYADDYIMDEDQS 337

Query:   179 RECGFSE----IYQQVKHSGSLDGIKEE 202
             +  G  +    I Q VK   S+   KEE
Sbjct:   338 KLAGLLDLNNAILQLVKKYKSMKLEKEE 365

GO:0003677 "DNA binding" evidence=NAS

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

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

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

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

GO:0005496 "steroid binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005516 "calmodulin binding" evidence=NAS

GO:0005634 "nucleus" evidence=NAS

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

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

GO:0007275 "multicellular organismal development" evidence=NAS

GO:0008270 "zinc ion binding" evidence=IEA

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

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

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

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

GO:0046872 "metal ion binding" evidence=IEA

GO:0048384 "retinoic acid receptor signaling pathway" 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)
P62510	ERR3_RAT	No assigned EC number	0.3930	0.9262	0.6310	yes	N/A
P62509	ERR3_MOUSE	No assigned EC number	0.3930	0.9262	0.6310	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	312
cd06946	221	cd06946, NR_LBD_ERR, The ligand binding domain of	7e-70
cd07068	221	cd07068, NR_LBD_ER_like, The ligand binding domain	4e-64
cd07170	97	cd07170, NR_DBD_ERR, DNA-binding domain of estroge	3e-34
cd06949	235	cd06949, NR_LBD_ER, Ligand binding domain of Estro	2e-23
cd07074	248	cd07074, NR_LBD_PR, Ligand binding domain of the p	1e-18
cd07155	75	cd07155, NR_DBD_ER_like, DNA-binding domain of est	1e-18
cd07167	93	cd07167, NR_DBD_Lrh-1_like, The DNA-binding domain	2e-18
cd07170	97	cd07170, NR_DBD_ERR, DNA-binding domain of estroge	4e-18
cd06947	246	cd06947, NR_LBD_GR_Like, Ligand binding domain of	7e-18
cd06916	72	cd06916, NR_DBD_like, DNA-binding domain of nuclea	8e-18
cd07155	75	cd07155, NR_DBD_ER_like, DNA-binding domain of est	6e-17
pfam00104	186	pfam00104, Hormone_recep, Ligand-binding domain of	2e-16
cd07076	247	cd07076, NR_LBD_GR, Ligand binding domain of the g	6e-16
pfam00105	70	pfam00105, zf-C4, Zinc finger, C4 type (two domain	2e-15
cd06916	72	cd06916, NR_DBD_like, DNA-binding domain of nuclea	5e-15
pfam00105	70	pfam00105, zf-C4, Zinc finger, C4 type (two domain	6e-15
cd07168	90	cd07168, NR_DBD_DHR4_like, DNA-binding domain of e	7e-15
cd06930	165	cd06930, NR_LBD_F2, Ligand-binding domain of nucle	1e-14
cd06961	85	cd06961, NR_DBD_TR, DNA-binding domain of thyroid	1e-14
cd07075	248	cd07075, NR_LBD_MR, Ligand binding domain of the m	2e-14
cd07073	246	cd07073, NR_LBD_AR, Ligand binding domain of the n	4e-14
cd07171	82	cd07171, NR_DBD_ER, DNA-binding domain of estrogen	1e-13
cd07171	82	cd07171, NR_DBD_ER, DNA-binding domain of estrogen	2e-13
smart00399	70	smart00399, ZnF_C4, c4 zinc finger in nuclear horm	3e-13
cd06945	239	cd06945, NR_LBD_Nurr1_like, The ligand binding dom	6e-13
cd07166	89	cd07166, NR_DBD_REV_ERB, DNA-binding domain of REV	9e-13
smart00399	70	smart00399, ZnF_C4, c4 zinc finger in nuclear horm	3e-12
cd06969	75	cd06969, NR_DBD_NGFI-B, DNA-binding domain of the	3e-12
cd07158	73	cd07158, NR_DBD_Ppar_like, The DNA-binding domain	4e-12
cd06960	76	cd06960, NR_DBD_HNF4A, DNA-binding domain of hepto	5e-12
cd06937	231	cd06937, NR_LBD_RAR, The ligand binding domain (LB	5e-12
cd06157	168	cd06157, NR_LBD, The ligand binding domain of nucl	6e-12
cd06943	207	cd06943, NR_LBD_RXR_like, The ligand binding domai	8e-12
cd06961	85	cd06961, NR_DBD_TR, DNA-binding domain of thyroid	2e-11
cd06960	76	cd06960, NR_DBD_HNF4A, DNA-binding domain of hepto	2e-11
cd06967	87	cd06967, NR_DBD_TR2_like, DNA-binding domain of th	3e-11
cd07169	90	cd07169, NR_DBD_GCNF_like, DNA-binding domain of G	3e-11
cd06965	84	cd06965, NR_DBD_Ppar, DNA-binding domain of peroxi	3e-11
cd06959	73	cd06959, NR_DBD_EcR_like, The DNA-binding domain o	4e-11
cd06964	85	cd06964, NR_DBD_RAR, DNA-binding domain of retinoi	4e-11
cd07167	93	cd07167, NR_DBD_Lrh-1_like, The DNA-binding domain	5e-11
cd07156	72	cd07156, NR_DBD_VDR_like, The DNA-binding domain o	6e-11
cd07168	90	cd07168, NR_DBD_DHR4_like, DNA-binding domain of e	1e-10
cd06969	75	cd06969, NR_DBD_NGFI-B, DNA-binding domain of the	1e-10
cd07179	74	cd07179, 2DBD_NR_DBD2, The second DNA-binding doma	1e-10
cd07165	81	cd07165, NR_DBD_DmE78_like, DNA-binding domain of	1e-10
cd06964	85	cd06964, NR_DBD_RAR, DNA-binding domain of retinoi	3e-10
cd07160	101	cd07160, NR_DBD_LXR, DNA-binding domain of Liver X	4e-10
cd06956	77	cd06956, NR_DBD_RXR, DNA-binding domain of retinoi	6e-10
cd07172	78	cd07172, NR_DBD_GR_PR, DNA-binding domain of gluco	6e-10
cd07169	90	cd07169, NR_DBD_GCNF_like, DNA-binding domain of G	7e-10
cd06956	77	cd06956, NR_DBD_RXR, DNA-binding domain of retinoi	9e-10
cd06967	87	cd06967, NR_DBD_TR2_like, DNA-binding domain of th	1e-09
cd07157	86	cd07157, 2DBD_NR_DBD1, The first DNA-binding domai	1e-09
cd07071	238	cd07071, NR_LBD_Nurr1, The ligand binding domain o	1e-09
cd06931	222	cd06931, NR_LBD_HNF4_like, The ligand binding doma	2e-09
cd07348	238	cd07348, NR_LBD_NGFI-B, The ligand binding domain	2e-09
cd07164	78	cd07164, NR_DBD_PNR_like_1, DNA-binding domain of	3e-09
smart00430	163	smart00430, HOLI, Ligand binding domain of hormone	3e-09
cd07164	78	cd07164, NR_DBD_PNR_like_1, DNA-binding domain of	5e-09
cd07156	72	cd07156, NR_DBD_VDR_like, The DNA-binding domain o	6e-09
cd06962	84	cd06962, NR_DBD_FXR, DNA-binding domain of Farneso	8e-09
cd06966	94	cd06966, NR_DBD_CAR, DNA-binding domain of constit	1e-08
cd06958	73	cd06958, NR_DBD_COUP_TF, DNA-binding domain of chi	1e-08
cd07173	82	cd07173, NR_DBD_AR, DNA-binding domain of androgen	1e-08
cd07161	91	cd07161, NR_DBD_EcR, DNA-binding domain of Ecdyson	1e-08
cd07179	74	cd07179, 2DBD_NR_DBD2, The second DNA-binding doma	3e-08
cd07165	81	cd07165, NR_DBD_DmE78_like, DNA-binding domain of	3e-08
cd07162	87	cd07162, NR_DBD_PXR, DNA-binding domain of pregnan	3e-08
cd06968	95	cd06968, NR_DBD_ROR, DNA-binding domain of Retinoi	4e-08
cd07154	73	cd07154, NR_DBD_PNR_like, The DNA-binding domain o	5e-08
cd06970	92	cd06970, NR_DBD_PNR, DNA-binding domain of the pho	5e-08
cd06968	95	cd06968, NR_DBD_ROR, DNA-binding domain of Retinoi	7e-08
cd07172	78	cd07172, NR_DBD_GR_PR, DNA-binding domain of gluco	1e-07
cd06958	73	cd06958, NR_DBD_COUP_TF, DNA-binding domain of chi	1e-07
cd06963	73	cd06963, NR_DBD_GR_like, The DNA binding domain of	1e-07
cd07154	73	cd07154, NR_DBD_PNR_like, The DNA-binding domain o	2e-07
cd06955	107	cd06955, NR_DBD_VDR, DNA-binding domain of vitamin	2e-07
cd07157	86	cd07157, 2DBD_NR_DBD1, The first DNA-binding domai	3e-07
cd07069	241	cd07069, NR_LBD_Lrh-1, The ligand binding domain o	3e-07
cd07163	92	cd07163, NR_DBD_TLX, DNA-binding domain of Tailles	3e-07
cd06955	107	cd06955, NR_DBD_VDR, DNA-binding domain of vitamin	4e-07
cd06963	73	cd06963, NR_DBD_GR_like, The DNA binding domain of	5e-07
cd06948	236	cd06948, NR_LBD_COUP-TF, Ligand binding domain of	5e-07
cd06965	84	cd06965, NR_DBD_Ppar, DNA-binding domain of peroxi	7e-07
cd07158	73	cd07158, NR_DBD_Ppar_like, The DNA-binding domain	8e-07
cd06966	94	cd06966, NR_DBD_CAR, DNA-binding domain of constit	9e-07
cd06950	206	cd06950, NR_LBD_Tlx_PNR_like, The ligand binding d	9e-07
cd06957	82	cd06957, NR_DBD_PNR_like_2, DNA-binding domain of	1e-06
cd06944	237	cd06944, NR_LBD_Ftz-F1_like, The ligand binding do	2e-06
cd07072	239	cd07072, NR_LBD_DHR38_like, Ligand binding domain	2e-06
cd07166	89	cd07166, NR_DBD_REV_ERB, DNA-binding domain of REV	3e-06
cd07070	237	cd07070, NR_LBD_SF-1, The ligand binding domain of	5e-06
cd07173	82	cd07173, NR_DBD_AR, DNA-binding domain of androgen	6e-06
cd07162	87	cd07162, NR_DBD_PXR, DNA-binding domain of pregnan	6e-06
cd07163	92	cd07163, NR_DBD_TLX, DNA-binding domain of Tailles	6e-06
cd06957	82	cd06957, NR_DBD_PNR_like_2, DNA-binding domain of	6e-06
cd06929	174	cd06929, NR_LBD_F1, Ligand-binding domain of nucle	7e-06
cd06970	92	cd06970, NR_DBD_PNR, DNA-binding domain of the pho	1e-05
cd06953	213	cd06953, NR_LBD_DHR4_like, The ligand binding doma	4e-05
cd06933	238	cd06933, NR_LBD_VDR, The ligand binding domain of	4e-05
cd07161	91	cd07161, NR_DBD_EcR, DNA-binding domain of Ecdyson	7e-05
cd06951	222	cd06951, NR_LBD_Dax1_like, The ligand binding doma	8e-05
cd06962	84	cd06962, NR_DBD_FXR, DNA-binding domain of Farneso	6e-04
cd06954	236	cd06954, NR_LBD_LXR, The ligand binding domain of	9e-04
cd06941	195	cd06941, NR_LBD_DmE78_like, The ligand binding dom	0.001
cd06959	73	cd06959, NR_DBD_EcR_like, The DNA-binding domain o	0.002
cd07160	101	cd07160, NR_DBD_LXR, DNA-binding domain of Liver X	0.002

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

 Score =  216 bits (551), Expect = 7e-70
 Identities = 94/265 (35%), Positives = 126/265 (47%), Gaps = 76/265 (28%)

Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
           +L  LL+ EP+ L    +    D  ++ + +LSDL DRELV IIGWAK IPGF+ LSLND
Sbjct: 1   ILSHLLVAEPDKLFAMPDPALPDSDIKALTTLSDLADRELVVIIGWAKHIPGFSSLSLND 60

Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIY----QQVKH 192
           QM LLQS W EILTL + +RSLP   G++ FA D +LDE  ARE G  E+Y    Q V+ 
Sbjct: 61  QMSLLQSAWMEILTLGVVFRSLP-FNGELVFAEDFILDEELAREAGLLELYSACLQLVRR 119

Query: 193 SGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTL 252
              L   KEE                  Y +      KA                    L
Sbjct: 120 LQRLRLEKEE------------------YVL-----LKA--------------------L 136

Query: 253 VLANSDVKL-DEFSSLKKFRNSILSSLGDCIY---------------------------V 284
            LANSD    ++  ++++ R+++L +L D                               
Sbjct: 137 ALANSDSVHIEDVEAVRQLRDALLEALSDYEAGRHPGEAPRRAGQLLLTLPLLRQTDGKA 196

Query: 285 LRFWSTVHKDGKVLMNKLFVEMLEA 309
            RF+  V ++GKV M+KLF+EMLEA
Sbjct: 197 RRFFYGVKREGKVPMHKLFLEMLEA 221

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

 Score =  201 bits (513), Expect = 4e-64
 Identities = 95/264 (35%), Positives = 129/264 (48%), Gaps = 74/264 (28%)

Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
           +L ALL+ EP+ L   ++    D  +  + +LSDL DRELV II WAK IPGF+DLSLND
Sbjct: 1   LLSALLVAEPDKLYAMNDPTGPDTEVSLLATLSDLADRELVHIISWAKHIPGFSDLSLND 60

Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKHSGS- 195
           QM LLQS W EIL L + +RSLPH  GK+ FA DL+LD  QAR  G  EI+  +      
Sbjct: 61  QMHLLQSAWLEILMLGLVWRSLPH-PGKLVFAPDLLLDREQARVEGLLEIFDMLLQLVRR 119

Query: 196 --LDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLV 253
               G++ EE    +CL                   KA                    ++
Sbjct: 120 FRELGLQREEY---VCL-------------------KA--------------------II 137

Query: 254 LANSDVK-LDEFSSLKKFRNSILSSLGDCIY---------------------------VL 285
           LANSDV+ L++  ++++ R++IL +L D                               +
Sbjct: 138 LANSDVRHLEDREAVQQLRDAILDALVDVEAKRHGSQQPRRLAQLLLLLPHLRQASNKGV 197

Query: 286 RFWSTVHKDGKVLMNKLFVEMLEA 309
           R   +V  +GKV M KLF+EMLEA
Sbjct: 198 RHLYSVKCEGKVPMYKLFLEMLEA 221

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

 Score =  120 bits (302), Expect = 3e-34
 Identities = 46/58 (79%), Positives = 52/58 (89%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL 58
          NIEY+CPA+N+CEI KRRRK+CQACRF KCL+ GMLKEGVRLDRVRGGRQKY+R  D 
Sbjct: 38 NIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRIDA 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|132747 cd06949, NR_LBD_ER, Ligand binding domain of Estrogen receptor, which are activated by the hormone 17beta-estradiol (estrogen)

 Score = 95.6 bits (238), Expect = 2e-23
 Identities = 51/118 (43%), Positives = 73/118 (61%), Gaps = 8/118 (6%)

Query: 77  MLEALLLCEPEMLTVR--SETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSL 134
           ++ ALL  EP  +        P ++ +L  +  L++L DRELV +I WAK+IPGF DLSL
Sbjct: 6   LISALLEAEPPHIYSEYDPTRPFTEASL--MMLLTNLADRELVHMINWAKKIPGFVDLSL 63

Query: 135 NDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQQV 190
           +DQ+ LL+S W E+L L + +RS+ H  GK+ FA DL+LD  Q   C  G  EI+  +
Sbjct: 64  HDQVHLLESAWLELLMLGLVWRSMEH-PGKLLFAPDLLLDRNQGS-CVEGMVEIFDML 119

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

 Score = 83.1 bits (205), Expect = 1e-18
 Identities = 31/108 (28%), Positives = 67/108 (62%), Gaps = 1/108 (0%)

Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
           ++  L+  EP+++    +  + +     + SL+ L +R+L+ ++ W+K +PGF +L ++D
Sbjct: 2   LINLLMSIEPDVVYAGYDNTKPETPSSLLTSLNQLCERQLLSVVKWSKSLPGFRNLHIDD 61

Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGF 183
           Q+ L+Q +W  ++   + +RS  H +G+ + FA DL+L+E++ +E  F
Sbjct: 62  QITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSF 109

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

>gnl|CDD|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 = 78.3 bits (193), Expect = 1e-18
 Identities = 30/44 (68%), Positives = 41/44 (93%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
          N+ Y+CP++++CE++K+RRK+CQACR QKCL+ GMLKEGVRLDR
Sbjct: 32 NLGYSCPSTSECEVDKKRRKSCQACRLQKCLKVGMLKEGVRLDR 75

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

>gnl|CDD|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 = 78.3 bits (193), Expect = 2e-18
 Identities = 28/51 (54%), Positives = 35/51 (68%)

Query: 3  EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYR 53
           YTC  + +C+I+K +RK C  CRFQKCL  GM  E VR DR+RGGR K+ 
Sbjct: 34 RYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMRGGRNKFG 84

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

 Score = 77.6 bits (191), Expect = 4e-18
 Identities = 31/34 (91%), Positives = 34/34 (100%)

Query: 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
           P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQ
Sbjct: 3   PKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQ 36

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

 Score = 80.9 bits (200), Expect = 7e-18
 Identities = 39/117 (33%), Positives = 67/117 (57%), Gaps = 4/117 (3%)

Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
           +L  L   EPE++    +  Q D T + ++SL+ L +R+LV ++ WAK +PGF +L L+D
Sbjct: 2   LLSVLEAIEPEVVYAGYDNSQPDTTARLLSSLNRLGERQLVSVVKWAKALPGFRNLHLDD 61

Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGKI-RFASDLVLDERQARECGFSEIYQQVKH 192
           QM L+Q +W  ++   + +RS  H   ++  FA DLV +E++  +   S +Y     
Sbjct: 62  QMTLIQYSWMSLMVFALGWRSYKHVNSQMLYFAPDLVFNEQRMHQ---SAMYSLCLG 115

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

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

 Score = 76.1 bits (188), Expect = 8e-18
 Identities = 26/41 (63%), Positives = 30/41 (73%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR 41
          N+EYTCPA  +C I+KR R  CQACR +KCL  GM KE VR
Sbjct: 32 NLEYTCPAGGNCVIDKRNRNRCQACRLKKCLAVGMRKEAVR 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|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 = 73.7 bits (181), Expect = 6e-17
 Identities = 30/41 (73%), Positives = 32/41 (78%)

Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGAC 249
           CLVCGD+ASG+HYGVASCEACKAFFKRTIQ   GY      
Sbjct: 1   CLVCGDIASGYHYGVASCEACKAFFKRTIQGNLGYSCPSTS 41

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

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

 Score = 75.5 bits (186), Expect = 2e-16
 Identities = 31/89 (34%), Positives = 56/89 (62%)

Query: 104 TINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAG 163
            +N L ++++R+L+ ++ WAK+ PGF +LSL+DQ+ LL+S+W E L L +A RS      
Sbjct: 1   GLNELFEIWERDLLLVVEWAKRFPGFRELSLDDQLALLKSSWFEWLRLELASRSAECEKD 60

Query: 164 KIRFASDLVLDERQARECGFSEIYQQVKH 192
            + F++ L LD  + +    + I +Q++ 
Sbjct: 61  DLLFSNGLYLDRDELKSIEVNYINEQIRQ 89

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

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

 Score = 75.7 bits (186), Expect = 6e-16
 Identities = 39/117 (33%), Positives = 67/117 (57%), Gaps = 4/117 (3%)

Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
           ++  L + EPE+L    ++   D T + +++L+ L  R++V  + WAK IPGF +L L+D
Sbjct: 2   LVSLLEVIEPEVLYSGYDSSVPDSTWRIMSTLNMLGGRQVVAAVKWAKAIPGFRNLHLDD 61

Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGKIR-FASDLVLDERQARECGFSEIYQQVKH 192
           QM LLQ +W  ++   + +RS     G +  FA DL+++E++        +Y Q KH
Sbjct: 62  QMTLLQYSWMFLMAFALGWRSYRQSNGNLLCFAPDLIINEQRMT---LPCMYDQCKH 115

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

 Score = 69.5 bits (171), Expect = 2e-15
 Identities = 22/32 (68%), Positives = 26/32 (81%)

Query: 207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
            LC VCGD ASG+HYGV +CE CK FF+R+IQ
Sbjct: 1   ELCKVCGDKASGYHYGVLTCEGCKGFFRRSIQ 32

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

 Score = 68.4 bits (168), Expect = 5e-15
 Identities = 19/30 (63%), Positives = 25/30 (83%)

Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
           C VCGD ASG+HYGV +CE CK FF+R+++
Sbjct: 1   CAVCGDKASGYHYGVLTCEGCKGFFRRSVR 30

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 = 68.0 bits (167), Expect = 6e-15
 Identities = 22/37 (59%), Positives = 25/37 (67%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLK 37
          NI YTCP + DC I+KR R  CQ CR +KCL  GM K
Sbjct: 34 NIVYTCPFNKDCVIDKRNRNRCQYCRLKKCLEVGMSK 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|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 = 68.4 bits (167), Expect = 7e-15
 Identities = 26/48 (54%), Positives = 31/48 (64%)

Query: 4  YTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQK 51
          YTC     CEI K +R  CQ CRF+KC+RKGM+   VR DR+ GGR  
Sbjct: 43 YTCVGDGRCEITKAQRNRCQYCRFRKCIRKGMMLAAVREDRMPGGRNS 90

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

 Score = 70.3 bits (173), Expect = 1e-14
 Identities = 27/75 (36%), Positives = 44/75 (58%), Gaps = 1/75 (1%)

Query: 113 DRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHC-AGKIRFASDL 171
           DR L   + WAK +P F +L L+DQ+ LLQ++WAE+L L +A RS+    +  +  +  L
Sbjct: 9   DRVLFKTVDWAKNLPAFRNLPLDDQLTLLQNSWAELLLLGLAQRSVHFELSELLLPSPLL 68

Query: 172 VLDERQARECGFSEI 186
           V+   +    G +E+
Sbjct: 69  VILTEREALLGLAEL 83

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

 Score = 67.4 bits (165), Expect = 1e-14
 Identities = 23/51 (45%), Positives = 31/51 (60%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQK 51
           + Y+C     CEI+K  R  CQ CRF+KC+  GM K+ V  DR RG ++K
Sbjct: 33 KLSYSCKGEGKCEIDKVTRNQCQECRFKKCIAVGMAKDLVLDDRKRGAKRK 83

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

 Score = 71.1 bits (174), Expect = 2e-14
 Identities = 31/109 (28%), Positives = 62/109 (56%), Gaps = 1/109 (0%)

Query: 81  LLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRL 140
           L   EPE++    ++ + D     +++L+ L  ++++ ++ WAK +PGF +L L DQ+ L
Sbjct: 6   LENIEPEIVYAGYDSSKPDTAENLLSTLNRLAGKQMIQVVKWAKVLPGFRNLPLEDQITL 65

Query: 141 LQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQ 188
           +Q +W  + +  +++RS  H   + + FA DLV +E +  +    E+ Q
Sbjct: 66  IQYSWMCLSSFALSWRSYKHTNSQFLYFAPDLVFNEERMHQSAMYELCQ 114

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

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

 Score = 70.4 bits (172), Expect = 4e-14
 Identities = 36/114 (31%), Positives = 67/114 (58%), Gaps = 7/114 (6%)

Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
           +LEA+   EP ++    +  Q D     ++SL++L +R+LV ++ WAK +PGF +L ++D
Sbjct: 5   VLEAI---EPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDD 61

Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQ 189
           QM ++Q +W  ++   + +RS  +   + + FA DLV +E +  +   S +Y Q
Sbjct: 62  QMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHK---SRMYSQ 112

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

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

 Score = 64.9 bits (158), Expect = 1e-13
 Identities = 24/44 (54%), Positives = 32/44 (72%)

Query: 3  EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR 46
          +Y CPA+N C I+K RRK+CQACR +KC   GM+K G+R +R  
Sbjct: 39 DYICPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRRERRG 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|143545 cd07171, NR_DBD_ER, DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers

 Score = 64.5 bits (157), Expect = 2e-13
 Identities = 24/39 (61%), Positives = 28/39 (71%)

Query: 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY 243
               C VC D ASG+HYGV SCE CKAFFKR+IQ ++ Y
Sbjct: 2   DTHFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDY 40

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

 Score = 63.7 bits (156), Expect = 3e-13
 Identities = 23/31 (74%), Positives = 26/31 (83%)

Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
           LC VCGD ASGFH+GV SC ACKAFF+RT+ 
Sbjct: 1   LCCVCGDHASGFHFGVCSCRACKAFFRRTVN 31

Length = 70

>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 = 66.7 bits (163), Expect = 6e-13
 Identities = 33/91 (36%), Positives = 44/91 (48%), Gaps = 5/91 (5%)

Query: 87  EMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWA 146
           E +      P S      +    DL    +  I  WA++IPGF DL   DQ  LL+S + 
Sbjct: 29  ENVDPVPPKPDSQQ----VQQFYDLLTGSVDVIRQWAEKIPGFKDLHREDQDLLLESAFL 84

Query: 147 EILTLTIAYRSLPHCAGKIRFASDLVLDERQ 177
           E+  L +AYRS P   GK+ F + LVL   Q
Sbjct: 85  ELFVLRLAYRSNP-VDGKLVFCNGLVLHRLQ 114

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

 Score = 62.6 bits (152), Expect = 9e-13
 Identities = 25/38 (65%), Positives = 29/38 (76%)

Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ 245
           LC VCGD ASGFHYGV +CE CK FF+R+IQ    YR+
Sbjct: 5   LCKVCGDKASGFHYGVHACEGCKGFFRRSIQQKIQYRK 42

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

 Score = 60.6 bits (148), Expect = 3e-12
 Identities = 19/38 (50%), Positives = 23/38 (60%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE 38
            +Y C   N+C INKR R  C+ACR +KCL  GM  E
Sbjct: 33 RYKYRCDRKNNCSINKRYRCRCRACRLKKCLGVGMDPE 70

Length = 70

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

 Score = 60.9 bits (148), Expect = 3e-12
 Identities = 24/41 (58%), Positives = 31/41 (75%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR 41
          N +Y C A+ +C ++KRRR  CQ CRFQKCL+ GM+KE VR
Sbjct: 34 NAKYVCLANKNCPVDKRRRNRCQYCRFQKCLQVGMVKEVVR 74

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

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

 Score = 60.3 bits (146), Expect = 4e-12
 Identities = 26/37 (70%), Positives = 28/37 (75%)

Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ 245
           C VCGD ASGFHYGV SCE CK FF+RTIQ    YR+
Sbjct: 1   CKVCGDKASGFHYGVHSCEGCKGFFRRTIQHNLTYRR 37

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

 Score = 60.3 bits (147), Expect = 5e-12
 Identities = 18/29 (62%), Positives = 22/29 (75%)

Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTI 237
           C VCGD A+G HYGV SC  CK FF+R++
Sbjct: 1   CAVCGDRATGKHYGVLSCNGCKGFFRRSV 29

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

 Score = 64.1 bits (156), Expect = 5e-12
 Identities = 40/139 (28%), Positives = 67/139 (48%), Gaps = 7/139 (5%)

Query: 82  LLCEPEMLTVRSETPQSDPT-LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRL 140
            LC+    T  S   Q     L   +  S+L  + ++ I+ +AK++PGFT L++ DQ+ L
Sbjct: 16  SLCQLGKYTTNSSADQRVRLDLGLWDKFSELSTKCIIKIVEFAKRLPGFTTLTIADQITL 75

Query: 141 LQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQV-KHSGSLDGI 199
           L++   +IL L I  R  P     + F+  L L+  Q    GF  +   V   +  L  +
Sbjct: 76  LKAACLDILILRICTRYTPEQD-TMTFSDGLTLNRTQMHNAGFGPLTDLVFTFANQLLPL 134

Query: 200 KEEE----LPRRLCLVCGD 214
           + ++    L   +CL+CGD
Sbjct: 135 EMDDTEIGLLSAICLICGD 153

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

 Score = 62.7 bits (153), Expect = 6e-12
 Identities = 27/60 (45%), Positives = 38/60 (63%)

Query: 106 NSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKI 165
             L +L  R+L+ I+ WAK IPGF +L L DQ+ LL+S W E+L L +AYRS  +    +
Sbjct: 1   ELLCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLL 60

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

 Score = 63.1 bits (154), Expect = 8e-12
 Identities = 36/117 (30%), Positives = 62/117 (52%), Gaps = 8/117 (6%)

Query: 76  KMLEALLLCEPEMLTVRSETPQSDP--TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLS 133
           ++LEA L  EP     +SE     P      ++++    D++L  ++ WAK+IP F++L 
Sbjct: 6   RILEAELAVEP-----KSEAVAMVPPEYRDPVSNICQAADKQLFQLVEWAKRIPHFSELP 60

Query: 134 LNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQV 190
           L+DQ+ LL++ W E+L    A+RS+      I  A+ L L    A + G   I+ ++
Sbjct: 61  LDDQVILLRAGWNELLIAAFAHRSI-AVKDGILLATGLHLHRNSAHQAGVGAIFDRI 116

The ligand binding domain of the retinoid X receptor (RXR) and Ultraspiracle (USP): This family includes two evolutionary related nuclear receptors: retinoid X receptor (RXR) and Ultraspiracle (USP). RXR is a nuclear receptor in mammalian and USP is its counterpart in invertebrates. The native ligand of retinoid X receptor is 9-cis retinoic acid (RA). RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. RXRs can play different roles in these heterodimers. It acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, functioning as a receptor for 9-cis RA, independently of other nuclear receptors. Ultraspiracle (USP) plays similar roles as DNA binding partner of other nuclear rec eptors in invertebrates. USP has no known high-affinity ligand and is thought to be a silent component in the heterodimeric complex with partner receptors. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, RXR and USP have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 207

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

 Score = 59.0 bits (143), Expect = 2e-11
 Identities = 18/31 (58%), Positives = 24/31 (77%)

Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
            C+VCGD A+G+HY   +CE CK FF+RT+Q
Sbjct: 1   PCVVCGDKATGYHYRCITCEGCKGFFRRTVQ 31

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

 Score = 58.7 bits (143), Expect = 2e-11
 Identities = 20/45 (44%), Positives = 28/45 (62%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV 45
          N  YTC    +C ++K +R AC+ CRF+KCL  GM  E V+ +R 
Sbjct: 32 NRTYTCRFGGNCVVDKDKRNACRYCRFKKCLEVGMDPEAVQNERD 76

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 = 58.6 bits (142), Expect = 3e-11
 Identities = 27/48 (56%), Positives = 31/48 (64%), Gaps = 2/48 (4%)

Query: 204 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY--RQTGAC 249
            P  LC+VCGD ASG HYG  SCE CK FFKR+I+   GY  R +  C
Sbjct: 1   QPVELCVVCGDKASGRHYGAVSCEGCKGFFKRSIRKNLGYSCRGSKDC 48

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|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 = 58.7 bits (142), Expect = 3e-11
 Identities = 19/48 (39%), Positives = 30/48 (62%)

Query: 4  YTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQK 51
          Y C    +C +++++R  CQ CR  KCL+ GM ++ +R D + GGR K
Sbjct: 43 YRCSRDKNCVMSRKQRNRCQYCRLLKCLQMGMNRKAIREDGMPGGRNK 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|143523 cd06965, NR_DBD_Ppar, DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers

 Score = 58.3 bits (141), Expect = 3e-11
 Identities = 22/31 (70%), Positives = 25/31 (80%)

Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
            C VCGD ASGFHYGV +CE CK FF+RTI+
Sbjct: 1   ECRVCGDKASGFHYGVHACEGCKGFFRRTIR 31

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|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 = 57.8 bits (140), Expect = 4e-11
 Identities = 21/31 (67%), Positives = 25/31 (80%)

Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
            C+VCGD ASGFHYGV SCE CK FF+R++ 
Sbjct: 1   NCVVCGDKASGFHYGVLSCEGCKGFFRRSVT 31

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

 Score = 58.0 bits (140), Expect = 4e-11
 Identities = 19/32 (59%), Positives = 26/32 (81%)

Query: 207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
           + C VC D +SG+HYGV++CE CK FF+R+IQ
Sbjct: 5   KPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQ 36

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|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 = 58.2 bits (141), Expect = 5e-11
 Identities = 20/30 (66%), Positives = 25/30 (83%)

Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
           C VCGD  SG+HYG+ +CE+CK FFKRT+Q
Sbjct: 1   CPVCGDKVSGYHYGLLTCESCKGFFKRTVQ 30

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|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 = 57.0 bits (138), Expect = 6e-11
 Identities = 21/38 (55%), Positives = 25/38 (65%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE 38
             +TCP + DCEI K  R+ CQACR +KCL  GM KE
Sbjct: 32 KARFTCPFNGDCEITKDNRRHCQACRLKKCLDIGMKKE 69

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|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 = 56.8 bits (137), Expect = 1e-10
 Identities = 20/38 (52%), Positives = 28/38 (73%)

Query: 201 EEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
           +E+   +LC +C D A+G HYG+ +CE CK FFKRT+Q
Sbjct: 1   DEDESPKLCSICEDKATGLHYGIITCEGCKGFFKRTVQ 38

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

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

 Score = 56.7 bits (137), Expect = 1e-10
 Identities = 29/65 (44%), Positives = 37/65 (56%), Gaps = 13/65 (20%)

Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVKLDEFSSL 267
           LC VCGD A+  HYGV +CE CK FFKRT+Q  + Y        + LAN +  +D     
Sbjct: 2   LCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKY--------VCLANKNCPVD----- 48

Query: 268 KKFRN 272
           K+ RN
Sbjct: 49  KRRRN 53

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|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 = 56.4 bits (136), Expect = 1e-10
 Identities = 18/42 (42%), Positives = 25/42 (59%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRL 42
          +  Y CP   +C I    R AC++CRF++CL  GM K G R+
Sbjct: 32 SNSYVCPGGQNCAITPATRNACKSCRFRRCLAVGMSKTGSRI 73

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|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 = 56.4 bits (136), Expect = 1e-10
 Identities = 24/36 (66%), Positives = 27/36 (75%)

Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244
           C VCGD ASG+HYGV SCE CK FF+R+IQ    YR
Sbjct: 1   CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYR 36

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

 Score = 55.7 bits (134), Expect = 3e-10
 Identities = 24/44 (54%), Positives = 26/44 (59%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
          N+ YTC    +C INK  R  CQ CR QKC   GM KE VR DR
Sbjct: 38 NMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDR 81

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

 Score = 56.0 bits (135), Expect = 4e-10
 Identities = 20/30 (66%), Positives = 24/30 (80%)

Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTI 237
           +C VCGD ASGFHY V SCE CK FF+R++
Sbjct: 20  VCSVCGDKASGFHYNVLSCEGCKGFFRRSV 49

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

 Score = 54.5 bits (131), Expect = 6e-10
 Identities = 24/44 (54%), Positives = 28/44 (63%), Gaps = 2/44 (4%)

Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY--RQTGAC 249
           +C +CGD ASG HYGV SCE CK FFKRT++    Y  R    C
Sbjct: 2   ICAICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDC 45

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

 Score = 54.5 bits (131), Expect = 6e-10
 Identities = 21/39 (53%), Positives = 28/39 (71%)

Query: 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY 243
           P+++CLVC D ASG HYGV +C +CK FFKR ++    Y
Sbjct: 1   PQKICLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNY 39

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|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 = 54.9 bits (132), Expect = 7e-10
 Identities = 21/31 (67%), Positives = 25/31 (80%)

Query: 207 RLCLVCGDVASGFHYGVASCEACKAFFKRTI 237
           R CL+CGD A+G HYG+ SCE CK FFKR+I
Sbjct: 7   RTCLICGDRATGLHYGIISCEGCKGFFKRSI 37

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

 Score = 54.1 bits (130), Expect = 9e-10
 Identities = 22/41 (53%), Positives = 29/41 (70%)

Query: 4  YTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
          YTC  + DC I+KR+R  CQ CR+QKCL  GM +E V+ +R
Sbjct: 37 YTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER 77

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

>gnl|CDD|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 = 54.0 bits (130), Expect = 1e-09
 Identities = 22/44 (50%), Positives = 27/44 (61%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
          N+ Y+C  S DC INK  R  CQ CR QKCL  GM  + V+ +R
Sbjct: 37 NLGYSCRGSKDCVINKHHRNRCQYCRLQKCLAMGMKSDSVQCER 80

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|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 = 54.0 bits (130), Expect = 1e-09
 Identities = 19/43 (44%), Positives = 23/43 (53%)

Query: 3  EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV 45
             CP    C I+K+ R  CQACR++KCL  GM   G R  R 
Sbjct: 38 ISECPNGGKCIIDKKNRTKCQACRYRKCLNVGMSLGGPRYGRR 80

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

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

 Score = 57.0 bits (137), Expect = 1e-09
 Identities = 40/118 (33%), Positives = 58/118 (49%), Gaps = 9/118 (7%)

Query: 75  NKMLEALLLCEPEMLTVRSETPQSDPTLQT-------INSLSDLYDRELVCIIGWAKQIP 127
           + ++ A +   P M ++     Q++P  Q        I    DL    +  I GWA++IP
Sbjct: 6   SALVRAHVDSNPAMTSLDYSRFQANPDYQMSGDDTQHIQQFYDLLTGSMEIIRGWAEKIP 65

Query: 128 GFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSE 185
           GFTDL   DQ  L +S + E+  L +AYRS P   GK+ F + +VL   Q    GF E
Sbjct: 66  GFTDLPKADQDLLFESAFLELFVLRLAYRSNP-VEGKLIFCNGVVLHRLQCVR-GFGE 121

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

 Score = 56.2 bits (136), Expect = 2e-09
 Identities = 28/84 (33%), Positives = 49/84 (58%), Gaps = 7/84 (8%)

Query: 83  LCEPEMLTVRSETP----QSDPTLQTINSLSDLYD---RELVCIIGWAKQIPGFTDLSLN 135
           L + E L+ +  +P      D   + I S++D+ +   ++L+ ++ WAK IP F +L L+
Sbjct: 5   LLQAEALSRQQSSPIPTCSGDIRPKKIASINDVCESMKQQLLVLVEWAKYIPAFCELPLD 64

Query: 136 DQMRLLQSTWAEILTLTIAYRSLP 159
           DQ+ LL++   E L L +A RS+P
Sbjct: 65  DQVALLRAHAGEHLLLGVARRSMP 88

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

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

 Score = 56.4 bits (136), Expect = 2e-09
 Identities = 30/73 (41%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 105 INSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGK 164
           I    DL    L  I  WA++IPGF+D    DQ  LL+S + E+  L +AYRS P   GK
Sbjct: 43  IQQFYDLLSGSLEVIRKWAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNPE-EGK 101

Query: 165 IRFASDLVLDERQ 177
           + F + +VL   Q
Sbjct: 102 LIFCNGVVLHRTQ 114

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

>gnl|CDD|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 = 52.9 bits (127), Expect = 3e-09
 Identities = 18/44 (40%), Positives = 28/44 (63%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
          N+ Y C  +  C ++  RR  CQACRF+KCL+  M ++ V+ +R
Sbjct: 32 NLAYVCKENGSCVVDVARRNQCQACRFKKCLQVNMNRDAVQHER 75

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

 Score = 54.7 bits (132), Expect = 3e-09
 Identities = 27/67 (40%), Positives = 38/67 (56%), Gaps = 1/67 (1%)

Query: 113 DRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLV 172
           +R+L+  + WAK  PGF +LSL DQ+ LL+S W E+L L +AYRS+      +  A D  
Sbjct: 2   ERQLLLTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKELL-LAPDGT 60

Query: 173 LDERQAR 179
                A 
Sbjct: 61  YIRPDAV 67

Length = 163

>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 = 52.1 bits (125), Expect = 5e-09
 Identities = 20/30 (66%), Positives = 24/30 (80%)

Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
           C VCGD ASG HYGV SC+ C+ FFKR+I+
Sbjct: 1   CRVCGDRASGKHYGVPSCDGCRGFFKRSIR 30

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|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 = 51.6 bits (124), Expect = 6e-09
 Identities = 15/30 (50%), Positives = 23/30 (76%)

Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
           C VCGD A+G+H+   +CE CK FF+R+++
Sbjct: 1   CGVCGDRATGYHFNAMTCEGCKGFFRRSMK 30

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

 Score = 51.5 bits (123), Expect = 8e-09
 Identities = 20/37 (54%), Positives = 27/37 (72%)

Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244
           LC+VCGD ASG+HY   +CE CK FF+R+I   + Y+
Sbjct: 3   LCVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVYK 39

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

 Score = 51.7 bits (124), Expect = 1e-08
 Identities = 18/36 (50%), Positives = 21/36 (58%)

Query: 3  EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE 38
          E+ CP +  CEIN   R+ CQ CR  KC   GM KE
Sbjct: 36 EFKCPFNESCEINVVTRRFCQKCRLDKCFAIGMKKE 71

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

>gnl|CDD|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 = 51.0 bits (122), Expect = 1e-08
 Identities = 18/30 (60%), Positives = 25/30 (83%)

Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
           C+VCGD +SG HYG  +CE CK+FFKR+++
Sbjct: 1   CVVCGDKSSGKHYGQFTCEGCKSFFKRSVR 30

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

 Score = 51.1 bits (122), Expect = 1e-08
 Identities = 19/31 (61%), Positives = 24/31 (77%)

Query: 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKR 235
           P++ CL+CGD ASG HYG  +C +CK FFKR
Sbjct: 2   PQKTCLICGDEASGCHYGALTCGSCKVFFKR 32

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

 Score = 51.0 bits (122), Expect = 1e-08
 Identities = 19/30 (63%), Positives = 24/30 (80%)

Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTI 237
           LCLVCGD ASG+HY   +CE CK FF+R++
Sbjct: 3   LCLVCGDRASGYHYNALTCEGCKGFFRRSV 32

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|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 = 49.8 bits (119), Expect = 3e-08
 Identities = 18/36 (50%), Positives = 23/36 (63%)

Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244
           C VCG  +SGFH+G  +CE CK FF+RT    + Y 
Sbjct: 1   CRVCGGKSSGFHFGALTCEGCKGFFRRTELSSNSYV 36

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|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 = 49.9 bits (119), Expect = 3e-08
 Identities = 22/45 (48%), Positives = 26/45 (57%)

Query: 2  IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR 46
          IEY C     CEI +  R  CQ CRF+KCL  GM K+ VR  R+ 
Sbjct: 33 IEYRCLRDGKCEIIRLNRNRCQYCRFKKCLAAGMSKDSVRYGRIP 77

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

 Score = 50.3 bits (120), Expect = 3e-08
 Identities = 19/38 (50%), Positives = 21/38 (55%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE 38
          N    CP    C I K  R+ CQACR +KCL  GM KE
Sbjct: 33 NARLCCPFQKGCVITKSNRRQCQACRLRKCLSIGMKKE 70

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

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

 Score = 49.8 bits (119), Expect = 4e-08
 Identities = 22/40 (55%), Positives = 27/40 (67%), Gaps = 3/40 (7%)

Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQ---VYSGYRQ 245
           C +CGD +SG HYGV +CE CK FF+R+ Q    YS  RQ
Sbjct: 8   CKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVSYSCPRQ 47

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

 Score = 49.1 bits (117), Expect = 5e-08
 Identities = 21/44 (47%), Positives = 29/44 (65%), Gaps = 3/44 (6%)

Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQ---VYSGYRQTGAC 249
           C VCGD +SG HYGV +C+ C  FFKR+I+   +Y+     G+C
Sbjct: 1   CKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNLLYTCKAGNGSC 44

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

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

 Score = 49.6 bits (118), Expect = 5e-08
 Identities = 22/48 (45%), Positives = 29/48 (60%), Gaps = 3/48 (6%)

Query: 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ---VYSGYRQTGAC 249
           P  LC VCGD +SG HYG+ +C  C  FFKR+++   +Y     TG C
Sbjct: 5   PGLLCRVCGDTSSGKHYGIYACNGCSGFFKRSVRRKLIYRCQAGTGMC 52

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

 Score = 49.1 bits (117), Expect = 7e-08
 Identities = 19/47 (40%), Positives = 28/47 (59%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG 47
          N+ Y+CP   +C I++  R  CQ CR QKCL  GM ++ V+  R+  
Sbjct: 39 NVSYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSK 85

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

 Score = 48.3 bits (115), Expect = 1e-07
 Identities = 19/39 (48%), Positives = 23/39 (58%)

Query: 4  YTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRL 42
          Y C   NDC I+K RRK C ACR +KCL+ GM     + 
Sbjct: 39 YLCAGRNDCIIDKIRRKNCPACRLRKCLQAGMNLGARKT 77

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|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 = 47.9 bits (114), Expect = 1e-07
 Identities = 18/41 (43%), Positives = 27/41 (65%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR 41
          N+ YTC  + +C I++  R  CQ CR +KCL+ GM +E V+
Sbjct: 32 NLTYTCRGNRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQ 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|143521 cd06963, NR_DBD_GR_like, The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers

 Score = 47.6 bits (113), Expect = 1e-07
 Identities = 20/35 (57%), Positives = 24/35 (68%)

Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY 243
           CL+CGD ASG HYGV +C +CK FFKR  +    Y
Sbjct: 1   CLICGDEASGCHYGVLTCGSCKVFFKRAAEGQHNY 35

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

 Score = 47.2 bits (112), Expect = 2e-07
 Identities = 21/42 (50%), Positives = 27/42 (64%), Gaps = 1/42 (2%)

Query: 1  NIEYTCPASN-DCEINKRRRKACQACRFQKCLRKGMLKEGVR 41
          N+ YTC A N  C ++K RR  CQACR +KCL   M K+ V+
Sbjct: 32 NLLYTCKAGNGSCVVDKARRNQCQACRLKKCLEVSMNKDAVQ 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|143513 cd06955, NR_DBD_VDR, DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers

 Score = 48.0 bits (114), Expect = 2e-07
 Identities = 19/40 (47%), Positives = 27/40 (67%)

Query: 4  YTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLD 43
          +TCP + DC I K  R+ CQACR ++C+  GM+KE +  D
Sbjct: 43 FTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTD 82

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|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 = 47.1 bits (112), Expect = 3e-07
 Identities = 17/27 (62%), Positives = 20/27 (74%)

Query: 209 CLVCGDVASGFHYGVASCEACKAFFKR 235
           C VCG+ A+GFH+G   CEACK FF R
Sbjct: 3   CQVCGEPAAGFHHGAYVCEACKKFFMR 29

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

 Score = 50.4 bits (120), Expect = 3e-07
 Identities = 29/90 (32%), Positives = 49/90 (54%), Gaps = 10/90 (11%)

Query: 81  LLLCEPEMLTVRS------ETPQSDPT----LQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           LL CEP+   V++      +  Q++ +    L T   +  + D+ L  I+ WA+    F 
Sbjct: 8   LLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLFSIVEWARSSIFFR 67

Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPH 160
           +L ++DQM+LLQ+ W+E+L L   YR + H
Sbjct: 68  ELKVDDQMKLLQNCWSELLILDHIYRQVVH 97

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

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

 Score = 47.5 bits (113), Expect = 3e-07
 Identities = 17/30 (56%), Positives = 23/30 (76%)

Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
           C VCGD +SG HYG+ +C+ C  FFKR+I+
Sbjct: 9   CKVCGDRSSGKHYGIYACDGCSGFFKRSIR 38

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

 Score = 47.6 bits (113), Expect = 4e-07
 Identities = 17/32 (53%), Positives = 25/32 (78%)

Query: 207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
           R+C VCGD A+GFH+   +CE CK FF+R+++
Sbjct: 7   RICGVCGDRATGFHFNAMTCEGCKGFFRRSMK 38

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

 Score = 46.1 bits (109), Expect = 5e-07
 Identities = 19/39 (48%), Positives = 23/39 (58%)

Query: 4  YTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRL 42
          Y C   NDC I+K RRK C ACR +KC + GM     +L
Sbjct: 35 YLCAGRNDCIIDKIRRKNCPACRLRKCYQAGMTLGARKL 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|132746 cd06948, NR_LBD_COUP-TF, Ligand binding domain of chicken ovalbumin upstream promoter transcription factors, a member of the nuclear receptor family

 Score = 49.8 bits (119), Expect = 5e-07
 Identities = 20/55 (36%), Positives = 33/55 (60%)

Query: 105 INSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLP 159
           I+++ +L  R L   + WA+ IP F DL + DQ+ LL+ +W+E+  L  A   +P
Sbjct: 32  IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLSWSELFVLNAAQCCMP 86

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

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

 Score = 45.9 bits (109), Expect = 7e-07
 Identities = 20/45 (44%), Positives = 26/45 (57%), Gaps = 3/45 (6%)

Query: 2  IEY-TCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV 45
          + Y  C  S  C+I+K+ R  CQ CRFQKCL  GM    +R  R+
Sbjct: 34 LVYKPCDLS--CKIHKKSRNKCQYCRFQKCLNVGMSHNAIRFGRM 76

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

 Score = 45.6 bits (108), Expect = 8e-07
 Identities = 18/42 (42%), Positives = 23/42 (54%), Gaps = 1/42 (2%)

Query: 1  NIEYT-CPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR 41
          N+ Y  C     C I ++ R  CQ CRF+KCL  GM +  VR
Sbjct: 32 NLTYRRCLNGGKCVIQRKNRNRCQYCRFKKCLSVGMSRNAVR 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|143524 cd06966, NR_DBD_CAR, DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers

 Score = 46.3 bits (110), Expect = 9e-07
 Identities = 15/29 (51%), Positives = 23/29 (79%)

Query: 207 RLCLVCGDVASGFHYGVASCEACKAFFKR 235
           ++C VCGD A G+++   +CE+CKAFF+R
Sbjct: 1   KICGVCGDKALGYNFNAITCESCKAFFRR 29

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

 Score = 48.4 bits (116), Expect = 9e-07
 Identities = 18/40 (45%), Positives = 25/40 (62%)

Query: 120 IGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLP 159
           + WAK IP F+ L   DQ+ LL+ +W+E+  L  A  SLP
Sbjct: 43  VKWAKSIPAFSTLPFRDQLILLEESWSELFLLGAAQWSLP 82

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|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 = 45.1 bits (107), Expect = 1e-06
 Identities = 16/30 (53%), Positives = 21/30 (70%)

Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
           C VCGD + G HYGV  C+ C  FFKR+++
Sbjct: 1   CKVCGDKSYGKHYGVYCCDGCSCFFKRSVR 30

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

 Score = 47.7 bits (114), Expect = 2e-06
 Identities = 20/48 (41%), Positives = 31/48 (64%)

Query: 113 DRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPH 160
           D+ L  I+ WA+    F +L ++DQM+LLQ+ W+E+L L   YR + H
Sbjct: 48  DQTLFSIVEWARNSVFFKELKVDDQMKLLQNCWSELLVLDHIYRQVHH 95

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

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

 Score = 47.5 bits (113), Expect = 2e-06
 Identities = 28/90 (31%), Positives = 43/90 (47%), Gaps = 8/90 (8%)

Query: 93  SETPQSDPTLQTINSLSDLYDRELVC-----IIGWAKQIPGFTDLSLNDQMRLLQSTWAE 147
            E    +P +     +   Y   L+      I  +A++IPGF DL   DQ  L QS   E
Sbjct: 29  REPSPLEPPMSEAEKVQQFYS--LLTSSIDVIKTFAEKIPGFPDLCKEDQELLFQSASLE 86

Query: 148 ILTLTIAYRSLPHCAGKIRFASDLVLDERQ 177
           +  L +AYR+ P    K+ F + +VL ++Q
Sbjct: 87  LFVLRLAYRTAPE-DTKLTFCNGVVLHKQQ 115

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

 Score = 44.5 bits (105), Expect = 3e-06
 Identities = 22/54 (40%), Positives = 30/54 (55%), Gaps = 2/54 (3%)

Query: 1  NIEY-TCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYR 53
           I+Y  C  +  C I +  R  CQ CRF+KCL  GM ++ VR  R+   R+K R
Sbjct: 37 KIQYRKCTKNETCSIMRINRNRCQYCRFKKCLAVGMSRDAVRFGRIP-KREKAR 89

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

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

 Score = 46.5 bits (110), Expect = 5e-06
 Identities = 25/88 (28%), Positives = 39/88 (44%), Gaps = 8/88 (9%)

Query: 81  LLLCEPEMLTVRS--------ETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDL 132
           LL  EP+   VR+                      L  + D+  + I+ WA++   F +L
Sbjct: 8   LLQLEPDEDQVRARILGCLQEPQKSRPDQPAPFGLLCRMADQTFISIVDWARRCMVFKEL 67

Query: 133 SLNDQMRLLQSTWAEILTLTIAYRSLPH 160
            + DQM LLQ+ W+E+L     YR + H
Sbjct: 68  EVADQMTLLQNCWSELLVFDHIYRQVQH 95

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

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

 Score = 43.4 bits (102), Expect = 6e-06
 Identities = 18/44 (40%), Positives = 26/44 (59%)

Query: 3  EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR 46
          +Y C + NDC I+K RRK C +CR +KC   GM     +L ++ 
Sbjct: 39 KYLCASRNDCTIDKFRRKNCPSCRLRKCFEAGMTLGARKLKKLG 82

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

 Score = 43.4 bits (102), Expect = 6e-06
 Identities = 15/31 (48%), Positives = 23/31 (74%)

Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
           +C VCGD A+G+H+   +CE CK FF+R ++
Sbjct: 1   ICRVCGDRATGYHFNAMTCEGCKGFFRRAMK 31

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

 Score = 43.6 bits (103), Expect = 6e-06
 Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 2/46 (4%)

Query: 1  NIEYTCPASN--DCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
          N +Y C +     C ++K  R  C+ACR +KC   GM K+ V+ +R
Sbjct: 40 NRQYVCKSKGQGGCPVDKTHRNQCRACRLKKCFEVGMNKDAVQHER 85

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

>gnl|CDD|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 = 43.2 bits (102), Expect = 6e-06
 Identities = 20/45 (44%), Positives = 26/45 (57%), Gaps = 1/45 (2%)

Query: 1  NIEYTCPASN-DCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
           I YTC A N +C ++K RR  C  CR QKC   GM +  V+ +R
Sbjct: 32 GIIYTCIAGNGNCVVDKARRNWCPFCRLQKCFAVGMNRAAVQEER 76

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

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

 Score = 45.3 bits (108), Expect = 7e-06
 Identities = 21/74 (28%), Positives = 31/74 (41%), Gaps = 1/74 (1%)

Query: 119 IIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQA 178
           ++ +AK+IPGF +LS  DQ+ LL+    EIL L  A          + F           
Sbjct: 18  VVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATL-YDPEKNSLTFGDGKGNSRDVL 76

Query: 179 RECGFSEIYQQVKH 192
              GF E  + +  
Sbjct: 77  LNGGFGEFIEPLFE 90

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|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 = 42.6 bits (100), Expect = 1e-05
 Identities = 19/42 (45%), Positives = 27/42 (64%), Gaps = 1/42 (2%)

Query: 4  YTCPA-SNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
          Y C A +  C ++K  R  CQACR +KCL+ GM K+ V+ +R
Sbjct: 43 YRCQAGTGMCPVDKAHRNQCQACRLKKCLQAGMNKDAVQNER 84

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

 Score = 43.5 bits (103), Expect = 4e-05
 Identities = 23/81 (28%), Positives = 34/81 (41%), Gaps = 5/81 (6%)

Query: 80  ALLLCEPEMLTVRSETPQSDPTLQTINSLSDLY----DRELVCIIGWAKQIPGFTDLSLN 135
            LL+ E     + +     D        L  L     D  L   I W K++P FT+LS+ 
Sbjct: 1   QLLVAEDLEPLI-TPMLIEDGATVDQAELFALLCRLGDELLFRQIQWTKKLPFFTELSIK 59

Query: 136 DQMRLLQSTWAEILTLTIAYR 156
           D   LL + WAE++ L+    
Sbjct: 60  DHTHLLTTKWAELILLSTITV 80

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

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

 Score = 43.8 bits (103), Expect = 4e-05
 Identities = 21/50 (42%), Positives = 32/50 (64%)

Query: 102 LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTL 151
           L  +  L+DL    +  +IG+AK IPGF DL+  DQ+ LL+S+  E++ L
Sbjct: 36  LSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEVIML 85

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

 Score = 40.6 bits (95), Expect = 7e-05
 Identities = 16/40 (40%), Positives = 21/40 (52%)

Query: 4  YTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLD 43
          Y C     CE++   R+ CQ CR +KCL  GM  E V  +
Sbjct: 38 YHCKYGRACEMDMYMRRKCQECRLKKCLSVGMRPECVVPE 77

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

 Score = 42.9 bits (101), Expect = 8e-05
 Identities = 17/44 (38%), Positives = 28/44 (63%)

Query: 116 LVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLP 159
           L+  I + + +P FT L  +DQ+RLL+ +WA +L L +A   +P
Sbjct: 32  LLKTIRFVRNLPCFTYLPPDDQLRLLRRSWAPLLLLGLAQDKVP 75

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

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

 Score = 38.0 bits (88), Expect = 6e-04
 Identities = 16/38 (42%), Positives = 21/38 (55%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE 38
          N  Y C    +CE++   R+ CQ CR +KC   GML E
Sbjct: 35 NAVYKCKNGGNCEMDMYMRRKCQECRLRKCKEMGMLAE 72

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

 Score = 39.7 bits (93), Expect = 9e-04
 Identities = 16/38 (42%), Positives = 26/38 (68%)

Query: 119 IIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYR 156
           I+ +AKQ+PGF  L+  DQ+ LL+++  E++ L  A R
Sbjct: 59  IVDFAKQLPGFLTLTREDQIALLKASTIEVMLLETARR 96

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

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

 Score = 39.3 bits (92), Expect = 0.001
 Identities = 16/48 (33%), Positives = 31/48 (64%)

Query: 107 SLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIA 154
            LS+     +  ++ +AK+IPGF DLS +DQ+ L+++ + E+  + I+
Sbjct: 6   QLSEALTPSVQRVVEFAKRIPGFCDLSQDDQLLLIKAGFFEVWLVRIS 53

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|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 = 35.9 bits (83), Expect = 0.002
 Identities = 14/38 (36%), Positives = 19/38 (50%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE 38
             Y C   N CE++   R+ CQ CR +KC   GM  +
Sbjct: 33 GAVYACKFGNKCEMDMYMRRKCQECRLRKCKAAGMRPD 70

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

 Score = 36.8 bits (85), Expect = 0.002
 Identities = 13/38 (34%), Positives = 21/38 (55%)

Query: 3  EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGV 40
          +Y C     C+++   R+ CQ CR +KC   GM ++ V
Sbjct: 54 QYVCKNGGKCQMDMYMRRKCQECRLRKCREAGMREQCV 91

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	312
KOG4215|consensus	432		100.0
KOG4217|consensus	605		100.0
KOG4218|consensus	475		100.0
cd06949	235	NR_LBD_ER Ligand binding domain of Estrogen recept	99.97
cd06947	246	NR_LBD_GR_Like Ligand binding domain of nuclear ho	99.97
cd06937	231	NR_LBD_RAR The ligand binding domain (LBD) of reti	99.96
cd06946	221	NR_LBD_ERR The ligand binding domain of estrogen r	99.96
cd06944	237	NR_LBD_Ftz-F1_like The ligand binding domain of FT	99.96
cd07076	247	NR_LBD_GR Ligand binding domain of the glucocortic	99.96
KOG4216|consensus	479		99.96
cd07348	238	NR_LBD_NGFI-B The ligand binding domain of Nurr1,	99.96
cd07073	246	NR_LBD_AR Ligand binding domain of the nuclear rec	99.96
cd07069	241	NR_LBD_Lrh-1 The ligand binding domain of the live	99.96
cd07070	237	NR_LBD_SF-1 The ligand binding domain of nuclear r	99.96
cd07068	221	NR_LBD_ER_like The ligand binding domain of estrog	99.96
cd07072	239	NR_LBD_DHR38_like Ligand binding domain of DHR38_l	99.96
cd07071	238	NR_LBD_Nurr1 The ligand binding domain of Nurr1, a	99.96
cd06935	243	NR_LBD_TR The ligand binding domain of thyroid hor	99.95
cd06945	239	NR_LBD_Nurr1_like The ligand binding domain of Nur	99.95
cd07075	248	NR_LBD_MR Ligand binding domain of the mineralocor	99.95
cd06948	236	NR_LBD_COUP-TF Ligand binding domain of chicken ov	99.95
cd07074	248	NR_LBD_PR Ligand binding domain of the progesteron	99.95
cd07349	222	NR_LBD_SHP The ligand binding domain of DAX1 prote	99.94
cd06941	195	NR_LBD_DmE78_like The ligand binding domain of Dro	99.94
cd06954	236	NR_LBD_LXR The ligand binding domain of Liver X re	99.93
cd07350	232	NR_LBD_Dax1 The ligand binding domain of DAX1 prot	99.93
cd06951	222	NR_LBD_Dax1_like The ligand binding domain of DAX1	99.93
cd06931	222	NR_LBD_HNF4_like The ligand binding domain of hept	99.93
cd06939	241	NR_LBD_ROR_like The ligand binding domain of Retin	99.93
cd06932	259	NR_LBD_PPAR The ligand binding domain of peroxisom	99.92
cd06940	189	NR_LBD_REV_ERB The ligand binding domain of REV-ER	99.92
cd06933	238	NR_LBD_VDR The ligand binding domain of vitamin D	99.92
cd06938	231	NR_LBD_EcR The ligand binding domain (LBD) of the	99.92
cd06950	206	NR_LBD_Tlx_PNR_like The ligand binding domain of T	99.91
cd06934	226	NR_LBD_PXR_like The ligand binding domain of xenob	99.91
cd06943	207	NR_LBD_RXR_like The ligand binding domain of the r	99.9
cd06952	222	NR_LBD_TR2_like The ligand binding domain of the o	99.9
cd06929	174	NR_LBD_F1 Ligand-binding domain of nuclear recepto	99.89
cd06930	165	NR_LBD_F2 Ligand-binding domain of nuclear recepto	99.89
cd06936	221	NR_LBD_Fxr The ligand binding domain of Farnesoid	99.88
cd06953	213	NR_LBD_DHR4_like The ligand binding domain of orph	99.88
cd06942	191	NR_LBD_Sex_1_like The ligand binding domain of Cae	99.85
cd06157	168	NR_LBD The ligand binding domain of nuclear recept	99.76
smart00430	163	HOLI Ligand binding domain of hormone receptors.	99.74
PF00104	203	Hormone_recep: Ligand-binding domain of nuclear ho	99.73
cd06961	85	NR_DBD_TR DNA-binding domain of thyroid hormone re	99.55
cd07170	97	NR_DBD_ERR DNA-binding domain of estrogen related	99.54
KOG4846|consensus	538		99.52
cd07169	90	NR_DBD_GCNF_like DNA-binding domain of Germ cell n	99.51
cd07167	93	NR_DBD_Lrh-1_like The DNA-binding domain of Lrh-1	99.5
cd07168	90	NR_DBD_DHR4_like DNA-binding domain of ecdysone-in	99.5
cd06967	87	NR_DBD_TR2_like DNA-binding domain of the TR2 and	99.49
cd07164	78	NR_DBD_PNR_like_1 DNA-binding domain of the photor	99.49
cd06964	85	NR_DBD_RAR DNA-binding domain of retinoic acid rec	99.48
cd06956	77	NR_DBD_RXR DNA-binding domain of retinoid X recept	99.48
cd07155	75	NR_DBD_ER_like DNA-binding domain of estrogen rece	99.47
cd07165	81	NR_DBD_DmE78_like DNA-binding domain of Drosophila	99.46
cd06960	76	NR_DBD_HNF4A DNA-binding domain of heptocyte nucle	99.46
cd06957	82	NR_DBD_PNR_like_2 DNA-binding domain of the photor	99.46
cd07171	82	NR_DBD_ER DNA-binding domain of estrogen receptors	99.45
cd07160	101	NR_DBD_LXR DNA-binding domain of Liver X receptors	99.44
cd07163	92	NR_DBD_TLX DNA-binding domain of Tailless (TLX) is	99.44
cd06962	84	NR_DBD_FXR DNA-binding domain of Farnesoid X recep	99.43
cd07166	89	NR_DBD_REV_ERB DNA-binding domain of REV-ERB recep	99.43
cd06970	92	NR_DBD_PNR DNA-binding domain of the photoreceptor	99.43
cd06968	95	NR_DBD_ROR DNA-binding domain of Retinoid-related	99.42
cd07161	91	NR_DBD_EcR DNA-binding domain of Ecdysone receptor	99.42
cd06966	94	NR_DBD_CAR DNA-binding domain of constitutive andr	99.41
cd06969	75	NR_DBD_NGFI-B DNA-binding domain of the orphan nuc	99.41
cd06958	73	NR_DBD_COUP_TF DNA-binding domain of chicken ovalb	99.39
cd06916	72	NR_DBD_like DNA-binding domain of nuclear receptor	99.38
cd07179	74	2DBD_NR_DBD2 The second DNA-binding domain (DBD) o	99.38
cd07157	86	2DBD_NR_DBD1 The first DNA-binding domain (DBD) of	99.38
cd07156	72	NR_DBD_VDR_like The DNA-binding domain of vitamin	99.37
cd07162	87	NR_DBD_PXR DNA-binding domain of pregnane X recept	99.37
cd07154	73	NR_DBD_PNR_like The DNA-binding domain of the phot	99.37
cd06955	107	NR_DBD_VDR DNA-binding domain of vitamin D recepto	99.37
cd06959	73	NR_DBD_EcR_like The DNA-binding domain of Ecdysone	99.37
cd06963	73	NR_DBD_GR_like The DNA binding domain of GR_like n	99.36
cd07158	73	NR_DBD_Ppar_like The DNA-binding domain of peroxis	99.35
cd06965	84	NR_DBD_Ppar DNA-binding domain of peroxisome proli	99.32
cd07172	78	NR_DBD_GR_PR DNA-binding domain of glucocorticoid	99.32
cd07173	82	NR_DBD_AR DNA-binding domain of androgen receptor	99.29
smart00399	70	ZnF_C4 c4 zinc finger in nuclear hormone receptors	99.22
PF00105	70	zf-C4: Zinc finger, C4 type (two domains); InterPr	99.12
KOG4846|consensus	538		98.9
KOG4215|consensus	432		98.65
cd07161	91	NR_DBD_EcR DNA-binding domain of Ecdysone receptor	98.64
cd06956	77	NR_DBD_RXR DNA-binding domain of retinoid X recept	98.63
cd07170	97	NR_DBD_ERR DNA-binding domain of estrogen related	98.63
cd06959	73	NR_DBD_EcR_like The DNA-binding domain of Ecdysone	98.6
cd07172	78	NR_DBD_GR_PR DNA-binding domain of glucocorticoid	98.6
cd07173	82	NR_DBD_AR DNA-binding domain of androgen receptor	98.59
cd07171	82	NR_DBD_ER DNA-binding domain of estrogen receptors	98.58
cd06963	73	NR_DBD_GR_like The DNA binding domain of GR_like n	98.56
cd07155	75	NR_DBD_ER_like DNA-binding domain of estrogen rece	98.56
cd07179	74	2DBD_NR_DBD2 The second DNA-binding domain (DBD) o	98.55
cd07168	90	NR_DBD_DHR4_like DNA-binding domain of ecdysone-in	98.53
cd07156	72	NR_DBD_VDR_like The DNA-binding domain of vitamin	98.53
cd07160	101	NR_DBD_LXR DNA-binding domain of Liver X receptors	98.53
cd07162	87	NR_DBD_PXR DNA-binding domain of pregnane X recept	98.53
cd07169	90	NR_DBD_GCNF_like DNA-binding domain of Germ cell n	98.52
cd06961	85	NR_DBD_TR DNA-binding domain of thyroid hormone re	98.52
cd07167	93	NR_DBD_Lrh-1_like The DNA-binding domain of Lrh-1	98.5
cd06958	73	NR_DBD_COUP_TF DNA-binding domain of chicken ovalb	98.5
cd07158	73	NR_DBD_Ppar_like The DNA-binding domain of peroxis	98.49
smart00399	70	ZnF_C4 c4 zinc finger in nuclear hormone receptors	98.48
cd06962	84	NR_DBD_FXR DNA-binding domain of Farnesoid X recep	98.46
cd06955	107	NR_DBD_VDR DNA-binding domain of vitamin D recepto	98.45
cd06964	85	NR_DBD_RAR DNA-binding domain of retinoic acid rec	98.44
cd06969	75	NR_DBD_NGFI-B DNA-binding domain of the orphan nuc	98.44
cd06966	94	NR_DBD_CAR DNA-binding domain of constitutive andr	98.43
cd06968	95	NR_DBD_ROR DNA-binding domain of Retinoid-related	98.43
cd07164	78	NR_DBD_PNR_like_1 DNA-binding domain of the photor	98.42
KOG4217|consensus	605		98.41
cd06970	92	NR_DBD_PNR DNA-binding domain of the photoreceptor	98.41
cd07163	92	NR_DBD_TLX DNA-binding domain of Tailless (TLX) is	98.4
cd07154	73	NR_DBD_PNR_like The DNA-binding domain of the phot	98.4
cd06965	84	NR_DBD_Ppar DNA-binding domain of peroxisome proli	98.39
cd07165	81	NR_DBD_DmE78_like DNA-binding domain of Drosophila	98.39
cd06957	82	NR_DBD_PNR_like_2 DNA-binding domain of the photor	98.38
cd06960	76	NR_DBD_HNF4A DNA-binding domain of heptocyte nucle	98.36
cd07166	89	NR_DBD_REV_ERB DNA-binding domain of REV-ERB recep	98.35
cd06967	87	NR_DBD_TR2_like DNA-binding domain of the TR2 and	98.33
cd07157	86	2DBD_NR_DBD1 The first DNA-binding domain (DBD) of	98.32
PF00105	70	zf-C4: Zinc finger, C4 type (two domains); InterPr	98.31
KOG4216|consensus	479		98.31
cd06916	72	NR_DBD_like DNA-binding domain of nuclear receptor	98.31
KOG4218|consensus	475		98.2

>KOG4215|consensus

Probab=100.00  E-value=3.8e-46  Score=322.91  Aligned_cols=254  Identities=26%  Similarity=0.393  Sum_probs=201.2

Q ss_pred             CceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccccccccccCCCCCccCCCCCCCCCCchhHHHHHH-
Q psy11505          1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEENKMLE-   79 (312)
Q Consensus         1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-   79 (312)
                      +..|+|+++++|.|||..||.|||||||||+++||++||||.+|++++.++.......        ..  ......++. 
T Consensus        53 ~~~YtCRF~k~C~VDKdkRNaCRyCRfqKC~~aGMK~eAiQnERDrIg~Rr~~~~~~n--------~~--~~~id~L~~a  122 (432)
T KOG4215|consen   53 NHQYTCRFNKQCVVDKDKRNACRYCRFQKCVRAGMKREAIQNERDRIGSRRPSYEAGN--------EN--SPSIDALVQA  122 (432)
T ss_pred             cceeeeeccccccccchhhhhhhHhhHHHHHHhcccHHhhhcccccccccCCCCCCCC--------CC--chhHHHHHhH
Confidence            3579999999999999999999999999999999999999999999987543222111        00  111112211 


Q ss_pred             -----HHHh----cCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHH
Q psy11505         80 -----ALLL----CEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILT  150 (312)
Q Consensus        80 -----~l~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~  150 (312)
                           .+..    ..+... .......++....+..++++...+++...|||||.+|.|.+|+.+||++|||+...++.+
T Consensus       123 E~~~~q~~~srs~~~~~~~-~d~r~~~~n~~~at~~Dv~eSm~qqLlllVEWAK~i~~F~el~l~DqvaLLk~~a~~hll  201 (432)
T KOG4215|consen  123 EALVRQLRSSRSGGVPGID-GDIRQGPPNKKIATENDVCESMKQQLLLLVEWAKYIPPFCELPLDDQVALLKAHAGQHLL  201 (432)
T ss_pred             HHHHhhhhccccccCcCcc-hhhhcCccccccccHHHHHHHHHHHHHHHHHHHHhccchhcCCchhHHHHHHccchhhhh
Confidence                 1111    001000 000011234456778899999999999999999999999999999999999999999999


Q ss_pred             HhhhhhcccCCCCeeEecccchhhHHhhhhcc----cchhhhhhcccCccCCCCccccCCceeeeeCCCCcccccccccc
Q psy11505        151 LTIAYRSLPHCAGKIRFASDLVLDERQARECG----FSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASC  226 (312)
Q Consensus       151 L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~~~----~~~~~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~  226 (312)
                      |..++||.-.++ .++++|+.+++++......    ..+++++++.++++|++|+.||                      
T Consensus       202 Lg~a~RSm~l~~-v~ll~N~~v~~~~~~~~~eis~v~~RIiDElv~Pmr~L~md~~Ey----------------------  258 (432)
T KOG4215|consen  202 LGAAFRSMHLKD-VCLLNNTYVLHRHAPDLPEISRVAPRIIDELVNPMRRLQMDEIEY----------------------  258 (432)
T ss_pred             hhhhhccccccc-eEEecCceeeccCCCChHHHHHHHHHHHHHHhhHHHHhccchHHH----------------------
Confidence            999999999976 6778888887765443322    3678899999999999999999                      


Q ss_pred             hhHHHHHHHHhhhcccceecCCCCceeecCCCCc-ccchH--HHHHHHHHHHHHhHhHHHHH-------hh---------
Q psy11505        227 EACKAFFKRTIQVYSGYRQTGACGTLVLANSDVK-LDEFS--SLKKFRNSILSSLGDCIYVL-------RF---------  287 (312)
Q Consensus       227 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-l~~~~--~~~~~~~~~~~~l~~~~~~~-------~~---------  287 (312)
                                          ++||||++|+||++ |++++  .|+++|++++.+|.+||.-+       ||         
T Consensus       259 --------------------~cLKAi~FfdP~akGis~~s~~~I~~aR~~vl~sLe~yi~d~q~~d~~~R~g~LLLllPs  318 (432)
T KOG4215|consen  259 --------------------VCLKAIAFFDPDAKGLSDPSQIRIREARNRVLKSLEAYISDRQPYDAPGRFGNLLLLLPS  318 (432)
T ss_pred             --------------------HHHHHHHhcCccccccCCchHhHHHHHHHHHHHHHHHHHhhcCccccccchhhHHHHHHH
Confidence                                99999999999998 99999  79999999999999999765       33         


Q ss_pred             -----------hhccccCCccchhHHHHHHHh
Q psy11505        288 -----------WSTVHKDGKVLMNKLFVEMLE  308 (312)
Q Consensus       288 -----------~~~~~~~~~~~~~~~~~~~~~  308 (312)
                                 ..+.+++|.+.+++|+.||+.
T Consensus       319 LqsIt~qliE~iqlaklFGla~vDsll~e~~l  350 (432)
T KOG4215|consen  319 LQSITQQLIEQIQLAKLFGLAKVDSLLQEFLL  350 (432)
T ss_pred             HHHHHHHHHHHHHHHHHhhhhhHhHHHHHhhc
Confidence                       445699999999999999984

>KOG4217|consensus

Probab=100.00  E-value=5.7e-37  Score=273.14  Aligned_cols=262  Identities=30%  Similarity=0.465  Sum_probs=202.0

Q ss_pred             CceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccccccccccCCCCCccCCCCCCCCCCchhHHHHHHH
Q psy11505          1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEENKMLEA   80 (312)
Q Consensus         1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~   80 (312)
                      |.+|+|..+++|+|||..||+||||||||||+|||-+|.|+.+-.++++.+...++... .+.+|+++  ......++..
T Consensus       303 naKYvClanKnCPVDKRrRnRCQyCRfQKCL~VGMVKEVVRtdSLkGRRGRLpSKpKs~-q~sppSpP--i~LltalvrA  379 (605)
T KOG4217|consen  303 NAKYVCLANKNCPVDKRRRNRCQYCRFQKCLAVGMVKEVVRTDSLKGRRGRLPSKPKSR-QPSPPSPP--ISLLTALVRA  379 (605)
T ss_pred             CCeeEeecCCCCCcchhhhhhchhhhHhHHHHhhhhhhheeccccccccCCCCCCCCCC-CCCCCCCc--hHHHHHHHHH
Confidence            56899999999999999999999999999999999999999988777766655554443 11112111  1112334444


Q ss_pred             HHhcCccccccc--CCCC----CCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhh
Q psy11505         81 LLLCEPEMLTVR--SETP----QSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIA  154 (312)
Q Consensus        81 l~~~~~~~~~~~--~~~~----~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a  154 (312)
                      +....+....+.  ...+    ........+..+.++..-.+..+-.||.++|+|.+|+.+||..||..+++++++|+.|
T Consensus       380 h~Dstp~~~~ldys~~q~~~~~~~~tdA~~vqqfy~lLtgsl~virk~aekiPgf~el~paDq~lLlesaflelfvlRlA  459 (605)
T KOG4217|consen  380 HVDSTPSTMTLDYSRFQELVPHFSGTDALHVQQFYDLLTGSLEVIRKWAEKIPGFAELPPADQDLLLESAFLELFVLRLA  459 (605)
T ss_pred             hhcCCCCcchhhHHHhccccccccccHHHHHHHHHHHhhhhHHHHHHHHHhCcCcccCChhhHHHHHHHHHHHHHHHHHH
Confidence            444444211111  1111    2223445567778888888999999999999999999999999999999999999999


Q ss_pred             hhcccCCCCeeEecccchhhHHhhhhcccchhhhhhcccCc---cCCCCccccCCceeeeeCCCCcccccccccchhHHH
Q psy11505        155 YRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKHSGS---LDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKA  231 (312)
Q Consensus       155 ~rs~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~i~~~~~---~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~  231 (312)
                      ||+.+..+ +++|++|.++++.+... ++++|++.|..+.+   .|++|-.-|                           
T Consensus       460 yRs~~~e~-kliFcsG~vlhr~qC~r-gfgewidsi~~FS~~l~~l~idi~Af---------------------------  510 (605)
T KOG4217|consen  460 YRSNPSED-KLIFCSGLVLHRLQCLR-GFGEWIDSIREFSRSLHSLNIDISAF---------------------------  510 (605)
T ss_pred             HhcCCCCC-eEEEecchhhhHHHHHH-HHHHHHHHHHHHHHHhhhchhhHHHH---------------------------
Confidence            99999887 89999999999977644 66799999998877   677777777                           


Q ss_pred             HHHHHhhhcccceecCCCCceeecCCCCcccchHHHHHHHHHHHHHhHhHHHHH--------------------hh----
Q psy11505        232 FFKRTIQVYSGYRQTGACGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVL--------------------RF----  287 (312)
Q Consensus       232 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~--------------------~~----  287 (312)
                                     +++.|+.+..---+|.++.+|+++|+++..+|++|+..+                    |.    
T Consensus       511 ---------------acL~aLa~iTErhGL~epkrVeelqnkIi~~LKDHvt~~~~~~~k~~~lSrllgklpeLr~l~tq  575 (605)
T KOG4217|consen  511 ---------------ACLSALALITERHGLKEPKRVEELQNKIINCLKDHVTGSAGKLAKPVYLSRLLGKLPELRTLCTQ  575 (605)
T ss_pred             ---------------HHHHHHHhhhhhhcCCCcchHHHHHHHHHHHHHHHhhhcccccccchHHHHHhhhhHHHHHHHHH
Confidence                           899999988876669999999999999999999999554                    11    


Q ss_pred             ----hhccccCCccchhHHHHHHHhh
Q psy11505        288 ----WSTVHKDGKVLMNKLFVEMLEA  309 (312)
Q Consensus       288 ----~~~~~~~~~~~~~~~~~~~~~~  309 (312)
                          ++.-++.+.||.+.++..|+..
T Consensus       576 gLqrifyLklEdlvp~p~iidklf~d  601 (605)
T KOG4217|consen  576 GLQRIFYLKLEDLVPPPAIIDKLFLD  601 (605)
T ss_pred             hhhhhhcccHhhccCchhhhhhhhhc
Confidence                2224778888888888888753

>KOG4218|consensus

Probab=100.00  E-value=2.1e-34  Score=247.78  Aligned_cols=166  Identities=25%  Similarity=0.338  Sum_probs=136.9

Q ss_pred             HHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCC-CeeEecccchhhHHh-hhh
Q psy11505        103 QTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCA-GKIRFASDLVLDERQ-ARE  180 (312)
Q Consensus       103 ~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~-~~l~~~~g~~~~~~~-~~~  180 (312)
                      ..+.-.+.+.+..+..+|+||++--.|.+|+.+||++||+++|.++.++...|+-..++. +.+.+.+|.-++-.. +..
T Consensus       274 ~~fgl~c~mAdqtl~sIV~WAr~~~~F~eL~vdDQM~LLQncWselli~DhiyrqV~hgkegsi~lvtGqeV~~~~vA~q  353 (475)
T KOG4218|consen  274 EKFGLSCQMADQTLKSIVIWARNDQLFSELSVDDQMILLQNCWSELLIVDHIYRQVHHGKEGSIKLVTGQEVPVGLVALQ  353 (475)
T ss_pred             hhhhhhhhhhHhHHHHHHHHHhhhhHHHhcchhhHHHHHHHhhHHHHHHHHHHHHHhcCcccceEEecCCcccchhHhhh
Confidence            344555778889999999999999999999999999999999999999999999998876 567776665443221 112


Q ss_pred             ccc--ch---hhhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeec
Q psy11505        181 CGF--SE---IYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLA  255 (312)
Q Consensus       181 ~~~--~~---~~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  255 (312)
                      +|.  ..   -.++++..++.|++|..||                                          +++|.|+||
T Consensus       354 ags~l~tlvs~aqelV~~Lr~lqfd~~ef------------------------------------------vclkFl~LF  391 (475)
T KOG4218|consen  354 AGSLLQTLVSSAQELVIRLRNLQFDNFEF------------------------------------------VCLKFLALF  391 (475)
T ss_pred             hhhHHHHHHHHHHHHHHHHHhcCCccchh------------------------------------------hHHHHHHHH
Confidence            221  12   2355666677999999999                                          999999999


Q ss_pred             CCCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------------------------hhhhccccCCccchhHHHHHHHh
Q psy11505        256 NSDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------------------------RFWSTVHKDGKVLMNKLFVEMLE  308 (312)
Q Consensus       256 ~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------------------------~~~~~~~~~~~~~~~~~~~~~~~  308 (312)
                      +-|.+ |++...|+++|++...+|.+|....                          ++++.+++.+.+|-++|+.||+.
T Consensus       392 sld~kfLenf~lv~~~qe~~naaLldyt~c~yp~~~~kF~qllL~L~eiRa~smqa~eyly~khl~~~~p~nnllieml~  471 (475)
T KOG4218|consen  392 SLDMKFLENFELVRRLQEDSNAALLDYTSCCYPNWEQKFPQLLLVLEEIRATSMQAAEYLYTKHLQVPAPQNNLLIEMLT  471 (475)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCccccchHHHHhh
Confidence            99999 9999999999999999999986432                          45778899999999999999998


Q ss_pred             hh
Q psy11505        309 AY  310 (312)
Q Consensus       309 ~~  310 (312)
                      |.
T Consensus       472 Ak  473 (475)
T KOG4218|consen  472 AK  473 (475)
T ss_pred             cc
Confidence            84

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

Probab=99.97  E-value=5.8e-31  Score=227.70  Aligned_cols=194  Identities=32%  Similarity=0.486  Sum_probs=162.7

Q ss_pred             HHHHHHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhh
Q psy11505         74 ENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTI  153 (312)
Q Consensus        74 ~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~  153 (312)
                      .+.++..+...+|...........++.....+..++++.++.+..+|+|||++|+|.+|+.+||+.|+|++|+++++++.
T Consensus         3 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~la~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w~el~~L~~   82 (235)
T cd06949           3 AEQLISALLEAEPPHIYSEYDPTRPFTEASLMMLLTNLADRELVHMINWAKKIPGFVDLSLHDQVHLLESAWLELLMLGL   82 (235)
T ss_pred             HHHHHHHHHHhCCCcCcCCCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHhHHHHHHHHH
Confidence            34567788888887655554444566678889999999999999999999999999999999999999999999999999


Q ss_pred             hhhcccCCCCeeEecccchhhHHhhh-hcccchhhhhhccc---CccCCCCccccCCceeeeeCCCCcccccccccchhH
Q psy11505        154 AYRSLPHCAGKIRFASDLVLDERQAR-ECGFSEIYQQVKHS---GSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEAC  229 (312)
Q Consensus       154 a~rs~~~~~~~l~~~~g~~~~~~~~~-~~~~~~~~~~i~~~---~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~  229 (312)
                      ||++.+..+ .+.+.+|..++..... ..+..++++.++.+   +.+|++|++||                         
T Consensus        83 a~rs~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~Ey-------------------------  136 (235)
T cd06949          83 VWRSMEHPG-KLLFAPDLLLDRNQGSCVEGMVEIFDMLLATASRFRELQLQREEY-------------------------  136 (235)
T ss_pred             HHHhcCCCC-eEEeeCCceecHHHhhhcccHHHHHHHHHHHHHHHHHhCCCHHHH-------------------------
Confidence            999998866 7888888877766543 34445555555544   44999999999                         


Q ss_pred             HHHHHHHhhhcccceecCCCCceeecCCCCc------ccchHHHHHHHHHHHHHhHhHHHHH------------------
Q psy11505        230 KAFFKRTIQVYSGYRQTGACGTLVLANSDVK------LDEFSSLKKFRNSILSSLGDCIYVL------------------  285 (312)
Q Consensus       230 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~------l~~~~~~~~~~~~~~~~l~~~~~~~------------------  285 (312)
                                       +++|||+|||||++      ++++++|+++|++++.||.+|+..+                  
T Consensus       137 -----------------alLKAIvLfnpd~~g~~~~~l~~~~~Ve~lq~~~~~aL~~y~~~~~~~~p~~~~Rf~~LLl~L  199 (235)
T cd06949         137 -----------------VCLKAIILLNSSVYTFLLESLESRRQVQRLLDKITDALVHACSKRGLSLQQQSRRLAQLLLIL  199 (235)
T ss_pred             -----------------HHHHHHHHcCCCcCCcccccccCHHHHHHHHHHHHHHHHHHHHhcCCCCCCcccHHHHHHHhc
Confidence                             99999999999985      5688999999999999999998743                  


Q ss_pred             -----------hhhhccccCCccchhHHHHHHHhhh
Q psy11505        286 -----------RFWSTVHKDGKVLMNKLFVEMLEAY  310 (312)
Q Consensus       286 -----------~~~~~~~~~~~~~~~~~~~~~~~~~  310 (312)
                                 +++++++++|.+|+++|+.|||+||
T Consensus       200 p~LR~l~~~~~e~l~~~k~~~~~~~~~Ll~Eml~~~  235 (235)
T cd06949         200 SHIRHVSNKGMEHLYSMKCKNVVPLYDLLLEMLDAH  235 (235)
T ss_pred             hHHHHhhHHHHHHHHHHHhCCCCChHHHHHHHhcCC
Confidence                       3467789999999999999999986

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

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

Probab=99.97  E-value=6.6e-30  Score=221.55  Aligned_cols=192  Identities=27%  Similarity=0.460  Sum_probs=156.7

Q ss_pred             HHHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhh
Q psy11505         77 MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYR  156 (312)
Q Consensus        77 ~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~r  156 (312)
                      ++..+...+|...........++.....+..+++|.++++..+|+|||++|+|.+|+.+||++|||++|+++++++.|||
T Consensus         2 ~~~~l~~~ep~~~~~~~~~~~p~~~~~~~~~l~ela~~~L~~~VeWAK~iPgF~~L~~~DQi~LLk~~w~ElliL~~a~r   81 (246)
T cd06947           2 LLSVLEAIEPEVVYAGYDNSQPDTTARLLSSLNRLGERQLVSVVKWAKALPGFRNLHLDDQMTLIQYSWMSLMVFALGWR   81 (246)
T ss_pred             HHHHHHhcCCCcccCCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHh
Confidence            45667777886655555555666677889999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCC-CeeEecccchhhHHhhhhcccchhh---hhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHH
Q psy11505        157 SLPHCA-GKIRFASDLVLDERQARECGFSEIY---QQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAF  232 (312)
Q Consensus       157 s~~~~~-~~l~~~~g~~~~~~~~~~~~~~~~~---~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~  232 (312)
                      +++... +.+.+++|..++++.....+..++.   .++...+++|++|++||                            
T Consensus        82 s~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~L~ld~~E~----------------------------  133 (246)
T cd06947          82 SYKHVNSQMLYFAPDLVFNEQRMHQSAMYSLCLGMRQISQEFVRLQVTYEEF----------------------------  133 (246)
T ss_pred             hccCCCCCeEEecCCeeecHHHhhhccHHHHHHHHHHHHHHHHhcCCCHHHH----------------------------
Confidence            998765 3477788888777665554544443   34455566999999999                            


Q ss_pred             HHHHhhhcccceecCCCCceeecCC-CCc-ccchHHHHHHHHHHHHHhHhHHHHH---------hh--------------
Q psy11505        233 FKRTIQVYSGYRQTGACGTLVLANS-DVK-LDEFSSLKKFRNSILSSLGDCIYVL---------RF--------------  287 (312)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~~~~l~~~-~~~-l~~~~~~~~~~~~~~~~l~~~~~~~---------~~--------------  287 (312)
                                    +|+|||+|||| |++ |+++++|+++|++++.||.+|+..+         ||              
T Consensus       134 --------------acLKAIvLfn~~d~~gL~~~~~Ve~lqe~i~~AL~~yi~~~~~~~~~~~~Rf~kLLllLp~Lr~i~  199 (246)
T cd06947         134 --------------LCMKVLLLLSTIPKDGLKSQAAFDEMRMNYIKELRKAIVKREKNSSQSWQRFYQLTKLLDSMHDLV  199 (246)
T ss_pred             --------------HHHHHHHHcCCCccccccCHHHHHHHHHHHHHHHHHHHHHhCCCCcccchHHHHHHHhhhhHHHHH
Confidence                          99999999999 787 9999999999999999999999753         22              


Q ss_pred             ------hhcc---ccCCccchhHHHHHHHhhh
Q psy11505        288 ------WSTV---HKDGKVLMNKLFVEMLEAY  310 (312)
Q Consensus       288 ------~~~~---~~~~~~~~~~~~~~~~~~~  310 (312)
                            ++..   +..++|++++|+.||++++
T Consensus       200 ~~~~e~~~~~~~~~~~~~v~~~~ll~ei~~~~  231 (246)
T cd06947         200 KNLLQFCFYTFIQSHALSVEFPEMLVEIISDQ  231 (246)
T ss_pred             HHHHHHHHHHHhhcCCCccccHHHHHHHHHcc
Confidence                  2222   3345689999999999976

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

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

Probab=99.96  E-value=5.8e-30  Score=220.89  Aligned_cols=167  Identities=26%  Similarity=0.380  Sum_probs=149.1

Q ss_pred             chhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhh
Q psy11505        100 PTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAR  179 (312)
Q Consensus       100 ~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~  179 (312)
                      .....+..+++...+.+..+|+|||++|+|.+|+.+||++|||++|.++++++.|+++.+..+ .+.+.+|..+++....
T Consensus        35 ~~~~~~~~l~e~~~~~l~~~V~wAK~iPgF~~L~~~DQi~LLk~~w~El~~L~~a~~~~~~~~-~l~~~~~~~~~~~~~~  113 (231)
T cd06937          35 LDLGLWDKFSELSTKCIIKIVEFAKRLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQD-TMTFSDGLTLNRTQMH  113 (231)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhcCCccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCC-eEEecCCceecHHHHh
Confidence            356778899999999999999999999999999999999999999999999999999988776 7899999888887776


Q ss_pred             hcccchhhhhhcccCc---cCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecC
Q psy11505        180 ECGFSEIYQQVKHSGS---LDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLAN  256 (312)
Q Consensus       180 ~~~~~~~~~~i~~~~~---~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  256 (312)
                      ..+.++++++++.+..   +|++|++||                                          +|+|||+||+
T Consensus       114 ~~~~~~~~~~~~~~~~~l~~L~ld~~E~------------------------------------------alLkAivLf~  151 (231)
T cd06937         114 NAGFGPLTDLVFTFANQLLPLEMDDTEI------------------------------------------GLLSAICLIC  151 (231)
T ss_pred             hcChHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHcC
Confidence            6666666666666544   999999999                                          9999999999


Q ss_pred             CCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------------------------hhhhccccCCccchhHHHHHHHhh
Q psy11505        257 SDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------------------------RFWSTVHKDGKVLMNKLFVEMLEA  309 (312)
Q Consensus       257 ~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------------------------~~~~~~~~~~~~~~~~~~~~~~~~  309 (312)
                      ||++ +.++.+|+++||+++.||.+|+..+                          ..++++++.|.+||++|+.|||+.
T Consensus       152 pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~p~rf~kLLl~Lp~LR~l~~~~~e~l~~~k~~~~~~~~~Ll~Eml~~  231 (231)
T cd06937         152 GDRQDLEEPDRVEKLQEPLLEALKIYARKRRPDKPHMFPKMLMKITDLRSISAKGAERVITLKMEIPGPMPPLISEMLEN  231 (231)
T ss_pred             CCCccCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHhHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHhcC
Confidence            9998 9999999999999999999999865                          235667999999999999999973

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

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

Probab=99.96  E-value=9.8e-30  Score=218.87  Aligned_cols=189  Identities=46%  Similarity=0.739  Sum_probs=155.9

Q ss_pred             HHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhc
Q psy11505         78 LEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRS  157 (312)
Q Consensus        78 l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs  157 (312)
                      +..+...+|...........+......+..++++..++++.+|+|||++|+|.+|+.+||++|+|++|+++++++.||++
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Ve~aK~lp~F~~L~~~DQi~LLk~~~~el~lL~~a~~s   81 (221)
T cd06946           2 LSHLLVAEPDKLFAMPDPALPDSDIKALTTLSDLADRELVVIIGWAKHIPGFSSLSLNDQMSLLQSAWMEILTLGVVFRS   81 (221)
T ss_pred             hHHHhhcCCccccCCCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            34556667765544444444455677899999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCeeEecccchhhHHhhhhcccchhhh---hhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHH
Q psy11505        158 LPHCAGKIRFASDLVLDERQARECGFSEIYQ---QVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFK  234 (312)
Q Consensus       158 ~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~---~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~  234 (312)
                      ++.++ .+.+++|...++......+..++.+   ++...+++|++|++||                              
T Consensus        82 ~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~l~~~E~------------------------------  130 (221)
T cd06946          82 LPFNG-ELVFAEDFILDEELAREAGLLELYSACLQLVRRLQRLRLEKEEY------------------------------  130 (221)
T ss_pred             cCCCC-ceeecCCeEEcHHHHhhcCHHHHHHHHHHHHHHHHHcCCCHHHH------------------------------
Confidence            99875 6778777766655544444444333   4455566999999999                              


Q ss_pred             HHhhhcccceecCCCCceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH---------------------------h
Q psy11505        235 RTIQVYSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL---------------------------R  286 (312)
Q Consensus       235 ~~~~~~~~~~~~~~~~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~---------------------------~  286 (312)
                                  ++++||+|||||+. +.+..+|+++|++|+.||.+||..+                           .
T Consensus       131 ------------~lLkai~L~npd~~~l~~~~~v~~~q~~~~~aL~~y~~~~~~~~~p~Rf~~LL~~l~~Lr~~~~~~~e  198 (221)
T cd06946         131 ------------VLLKALALANSDSVHIEDVEAVRQLRDALLEALSDYEAGRHPGEAPRRAGQLLLTLPLLRQTDGKARR  198 (221)
T ss_pred             ------------HHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcchhHHHHHHhhchhHHHHHHHHHH
Confidence                        99999999999987 9999999999999999999999744                           2


Q ss_pred             hhhccccCCccchhHHHHHHHhh
Q psy11505        287 FWSTVHKDGKVLMNKLFVEMLEA  309 (312)
Q Consensus       287 ~~~~~~~~~~~~~~~~~~~~~~~  309 (312)
                      +++.+++.|.+|+++|+.|||+|
T Consensus       199 ~l~~~~~~~~~~~~~Ll~eml~~  221 (221)
T cd06946         199 FFYGVKREGKVPMHKLFLEMLEA  221 (221)
T ss_pred             HHHHHHhcCCCCHHHHHHHHhcC
Confidence            35567899999999999999975

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-

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

Probab=99.96  E-value=5.4e-30  Score=222.21  Aligned_cols=168  Identities=27%  Similarity=0.424  Sum_probs=145.0

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCC-CCeeEecccchhhHHhhh
Q psy11505        101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHC-AGKIRFASDLVLDERQAR  179 (312)
Q Consensus       101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~-~~~l~~~~g~~~~~~~~~  179 (312)
                      ....+..++++..+.+..+|+|||++|+|.+|+.+||+.|+|++|+++++|+.+|+++..+ .+.+.+++|..++.....
T Consensus        36 ~~~~~~~~~~~a~~~l~~~VewaK~lp~F~~L~~~DQi~LLk~~w~el~~L~~a~rs~~~~~~~~l~~~~g~~~~~~~~~  115 (237)
T cd06944          36 ELDTFGLMCKMADQTLFSIVEWARNSVFFKELKVDDQMKLLQNCWSELLVLDHIYRQVHHGKEDSILLVTGQEVDLSTLA  115 (237)
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHhCCChhcCCHHHHHHHHHHHhHHHHHHHHHHHhcccCCCCceeecCCCccchhhhh
Confidence            4457789999999999999999999999999999999999999999999999999999886 568999999877665432


Q ss_pred             h-cc--cchhh---hhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCcee
Q psy11505        180 E-CG--FSEIY---QQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLV  253 (312)
Q Consensus       180 ~-~~--~~~~~---~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  253 (312)
                      . .+  ..++.   .++...+++|++|++||                                          +++|||+
T Consensus       116 ~~~~~~~~~~~~~i~~~~~~l~~L~ld~~E~------------------------------------------~lLkaIi  153 (237)
T cd06944         116 SQAGLGLSSLVDRAQELVNKLRELQFDRQEF------------------------------------------VCLKFLI  153 (237)
T ss_pred             hhccccHHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHH
Confidence            2 11  22333   44555566999999999                                          9999999


Q ss_pred             ecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------------------------hhhhccccCCccchhHHHHHH
Q psy11505        254 LANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------------------------RFWSTVHKDGKVLMNKLFVEM  306 (312)
Q Consensus       254 l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------------------------~~~~~~~~~~~~~~~~~~~~~  306 (312)
                      |||||++ +++++.|+++|++|..||.+|+..+                          .+++++++.|.+|+++|+.||
T Consensus       154 L~npd~~gL~~~~~Ve~~q~~~~~aL~~y~~~~~~~~~~Rf~~LL~~Lp~Lr~is~~~~e~l~~~~l~g~~~~~~Ll~em  233 (237)
T cd06944         154 LFNPDVKGLENRQLVESVQEQVNAALLDYTLCNYPQQTDKFGQLLLRLPEIRAISMQAEEYLYYKHLNGEVPCNNLLIEM  233 (237)
T ss_pred             HcCCCcCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccHHHHHHHHhHHHHHHHHHHHHHHHhcccCCCCcHHHHHHHH
Confidence            9999998 9999999999999999999999765                          346778999999999999999


Q ss_pred             Hhhh
Q psy11505        307 LEAY  310 (312)
Q Consensus       307 ~~~~  310 (312)
                      |+|+
T Consensus       234 l~~~  237 (237)
T cd06944         234 LHAK  237 (237)
T ss_pred             HcCC
Confidence            9874

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

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

Probab=99.96  E-value=2e-29  Score=217.57  Aligned_cols=190  Identities=28%  Similarity=0.416  Sum_probs=160.5

Q ss_pred             HHHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhh
Q psy11505         77 MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYR  156 (312)
Q Consensus        77 ~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~r  156 (312)
                      ++..+...+|.......+...++.....+.++++..+++++.+|+|||++|+|.+|+.+||++|||++|.++++++.|||
T Consensus         2 ~~~~l~~~ep~~~~~~~d~~~p~~~~~~~~~l~~la~r~L~~~VeWAK~IPgF~~L~l~DQi~LLk~sW~Ellvl~~a~r   81 (247)
T cd07076           2 LVSLLEVIEPEVLYSGYDSSVPDSTWRIMSTLNMLGGRQVVAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMAFALGWR   81 (247)
T ss_pred             HHHHHHHcCCCcccCCCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHh
Confidence            35667777888777776777777778889999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCC-eeEecccchhhHHhhhhcccchh---hhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHH
Q psy11505        157 SLPHCAG-KIRFASDLVLDERQARECGFSEI---YQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAF  232 (312)
Q Consensus       157 s~~~~~~-~l~~~~g~~~~~~~~~~~~~~~~---~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~  232 (312)
                      +++..++ .+.+++|..+++......+..++   +.++...+++|++|++||                            
T Consensus        82 s~~~~~~~~l~fa~~~~~~~~~~~~~~~~~~~~~l~e~~~~~r~L~ld~~Ef----------------------------  133 (247)
T cd07076          82 SYRQSNGNLLCFAPDLIINEQRMTLPCMYDQCKHMLYVSSELHRLQVSYEEY----------------------------  133 (247)
T ss_pred             ccCCCCCceEEecCCeeecHHHHhhhhHHHHHHHHHHHHHHHHHcCCCHHHH----------------------------
Confidence            9998663 47888999888776655444443   334555666999999999                            


Q ss_pred             HHHHhhhcccceecCCCCceeecCC-CCc-ccchHHHHHHHHHHHHHhHhHHHHH---------hhh-------------
Q psy11505        233 FKRTIQVYSGYRQTGACGTLVLANS-DVK-LDEFSSLKKFRNSILSSLGDCIYVL---------RFW-------------  288 (312)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~~~~l~~~-~~~-l~~~~~~~~~~~~~~~~l~~~~~~~---------~~~-------------  288 (312)
                                    +|+|||+|||| |++ |+++++|+++|++++.+|.+||..+         ||.             
T Consensus       134 --------------acLKAIvLfnp~d~~GL~~~~~Ve~lqe~~~~aL~~yi~~~~p~~~~~~~RF~kLLllLp~Lr~i~  199 (247)
T cd07076         134 --------------LCMKTLLLLSTVPKDGLKSQELFDEIRMTYIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEVV  199 (247)
T ss_pred             --------------HHHHHHHhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCcchhhhHHHHHHHHHHHHHHHH
Confidence                          99999999999 887 9999999999999999999999854         441             


Q ss_pred             -----hccccCCccchhHHHHHHHh
Q psy11505        289 -----STVHKDGKVLMNKLFVEMLE  308 (312)
Q Consensus       289 -----~~~~~~~~~~~~~~~~~~~~  308 (312)
                           ++.+.+|.+|+..++.||+.
T Consensus       200 ~~~~ef~~~~~~~~~~~~~~~~ml~  224 (247)
T cd07076         200 ENLLNFCFQTFLDKTMSIEFPEMLA  224 (247)
T ss_pred             HHHHHHHHHHhcccchhhhhHHHHH
Confidence                 33577899988888888875

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

>KOG4216|consensus

Probab=99.96  E-value=8.1e-31  Score=229.14  Aligned_cols=138  Identities=20%  Similarity=0.247  Sum_probs=113.7

Q ss_pred             HHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhhccc
Q psy11505        104 TINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGF  183 (312)
Q Consensus       104 ~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~~~~  183 (312)
                      .|+....-....|..+|||||.+++|.+|+.+||+.|||...+|+.+.+.+..+..... .+.+.... .+.......+.
T Consensus       283 mWe~cA~~lt~~IQ~vVEFAK~I~GFM~L~Q~dQI~LLKaGsfEv~lvrm~r~~~v~~n-tV~~e~~~-~g~~~f~a~~~  360 (479)
T KOG4216|consen  283 MWELCAIKLTPAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSFEVVLVRMCRAFDVDNN-TVYFEGKY-AGPEVFYALGC  360 (479)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhHhhccCccceEEeeecCceeeeHHHHHHhhccccc-ceeecccc-cchhheeccCh
Confidence            35555555567899999999999999999999999999999999999988866555544 55554443 33344445566


Q ss_pred             chhhhhhcccCc---cCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCCCCc
Q psy11505        184 SEIYQQVKHSGS---LDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVK  260 (312)
Q Consensus       184 ~~~~~~i~~~~~---~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  260 (312)
                      .+++++++.+..   .|++++.|+                                          +++.|+||.+||+.
T Consensus       361 ~elis~vf~~~ksL~~Lq~te~Ei------------------------------------------AL~~alVL~~~~r~  398 (479)
T KOG4216|consen  361 EELISRVFEFGKSLCSLQLTEDEI------------------------------------------ALFSALVLMSADRS  398 (479)
T ss_pred             HHHHHHHHhhhHHHHhhccCcHHH------------------------------------------HHHHHHHhhCCccc
Confidence            778899998876   899999999                                          99999999999998


Q ss_pred             -ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505        261 -LDEFSSLKKFRNSILSSLGDCIYVL  285 (312)
Q Consensus       261 -l~~~~~~~~~~~~~~~~l~~~~~~~  285 (312)
                       |.+..+|+++++.+..||++.+..+
T Consensus       399 gl~e~~ki~~lq~~~~~a~qhvl~kn  424 (479)
T KOG4216|consen  399 GLQEKVKIEKLQQKIQLALQHVLQKN  424 (479)
T ss_pred             cccchHHHHHHHHHHHHHHHHHHHhc
Confidence             9999999999999999999987655

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

Probab=99.96  E-value=4.2e-29  Score=215.50  Aligned_cols=165  Identities=24%  Similarity=0.373  Sum_probs=146.9

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhh
Q psy11505        101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE  180 (312)
Q Consensus       101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~  180 (312)
                      ....+..+++.....+..+|+|||++|+|.+|+.+||++|||++|.++++|+.||++.+..+ .+++++|..+++.+. .
T Consensus        39 ~~~~~~~~~el~t~~l~~iVewAK~iPgF~~L~~~DQi~LLk~~w~El~vL~~a~r~~~~~~-~l~f~~~~~~~r~~~-~  116 (238)
T cd07348          39 DASDIQQFYDLLSGSLEVIRKWAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNPEEG-KLIFCNGVVLHRTQC-V  116 (238)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHccCCCccCCChHHHHHHHHHHHHHHHHHHHHHHcCCCCC-eEEeeCCeeecHHHH-H
Confidence            34668999999999999999999999999999999999999999999999999999998866 799999998887664 4


Q ss_pred             cccchhhhhhcccCc---cCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCC
Q psy11505        181 CGFSEIYQQVKHSGS---LDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANS  257 (312)
Q Consensus       181 ~~~~~~~~~i~~~~~---~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  257 (312)
                      .+.+++++.++++..   +|++|++||                                          +|+|||+|| |
T Consensus       117 ~~~~~~~~~i~ef~~~l~~L~ld~~E~------------------------------------------a~LkAIvLf-~  153 (238)
T cd07348         117 RGFGDWIDSILEFSQSLHRMNLDVSAF------------------------------------------SCLAALVII-T  153 (238)
T ss_pred             hhHHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHc-C
Confidence            566677777776655   999999999                                          999999999 7


Q ss_pred             CCc-ccchHHHHHHHHHHHHHhHhHHHHH----------------------------hhhhccccCCccchhHHHHHHHh
Q psy11505        258 DVK-LDEFSSLKKFRNSILSSLGDCIYVL----------------------------RFWSTVHKDGKVLMNKLFVEMLE  308 (312)
Q Consensus       258 ~~~-l~~~~~~~~~~~~~~~~l~~~~~~~----------------------------~~~~~~~~~~~~~~~~~~~~~~~  308 (312)
                      |++ |+++++|+++||+++.||.+|+..+                            +.+++.++.|.+||++|+.||++
T Consensus       154 Dr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~p~~p~rf~kLLl~Lp~LRsl~~~~~e~lf~~kl~~~~~~~pLl~e~~~  233 (238)
T cd07348         154 DRHGLKEPKRVEELQNRLISCLKEHVSGSASEPQRPNCLSRLLGKLPELRTLCTQGLQRIFYLKLEDLVPPPPIVDKIFM  233 (238)
T ss_pred             CCcCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHh
Confidence            998 9999999999999999999999763                            23566799999999999999998


Q ss_pred             hh
Q psy11505        309 AY  310 (312)
Q Consensus       309 ~~  310 (312)
                      +-
T Consensus       234 ~~  235 (238)
T cd07348         234 DT  235 (238)
T ss_pred             cc
Confidence            64

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

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

Probab=99.96  E-value=6e-29  Score=215.56  Aligned_cols=190  Identities=24%  Similarity=0.409  Sum_probs=151.3

Q ss_pred             HHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhc
Q psy11505         78 LEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRS  157 (312)
Q Consensus        78 l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs  157 (312)
                      ++.+...||...........++.....+.+++++.+++++.+|+|||++|+|.+|+.+||+.|||++|.++++|+.||++
T Consensus         3 ~~~l~~~ep~~~~~~~~~~~~~~~~~~~~~l~~la~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~w~ElliL~~a~rs   82 (246)
T cd07073           3 LNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRS   82 (246)
T ss_pred             HHHHhhcCCccccCCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHcCCCccCCCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            44455566665544444444555667789999999999999999999999999999999999999999999999999999


Q ss_pred             ccCC-CCeeEecccchhhHHhhhhcccchhh---hhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHH
Q psy11505        158 LPHC-AGKIRFASDLVLDERQARECGFSEIY---QQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFF  233 (312)
Q Consensus       158 ~~~~-~~~l~~~~g~~~~~~~~~~~~~~~~~---~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~  233 (312)
                      ++.. .+.+.+++|..+++......+..+..   .++...+++|++|.+||                             
T Consensus        83 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~L~ld~~Ey-----------------------------  133 (246)
T cd07073          83 FTNVNSRMLYFAPDLVFNEYRMHKSRMYSQCVRMRHLSQEFGWLQITPQEF-----------------------------  133 (246)
T ss_pred             cccCCCCeEEecCCeeechhhhccccHHHHHHHHHHHHHHHHHcCCCHHHH-----------------------------
Confidence            9874 45688988887776654443433433   34445555899999999                             


Q ss_pred             HHHhhhcccceecCCCCceeecCC-CCc-ccchHHHHHHHHHHHHHhHhHHHHH---------hh---------------
Q psy11505        234 KRTIQVYSGYRQTGACGTLVLANS-DVK-LDEFSSLKKFRNSILSSLGDCIYVL---------RF---------------  287 (312)
Q Consensus       234 ~~~~~~~~~~~~~~~~~~~~l~~~-~~~-l~~~~~~~~~~~~~~~~l~~~~~~~---------~~---------------  287 (312)
                                   +|+|||+|||| |++ |+++++|+.+|++++.||.+|+..+         ||               
T Consensus       134 -------------acLKAIiLfnp~d~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~~~~~Rf~kLLl~Lp~LRsi~~  200 (246)
T cd07073         134 -------------LCMKALLLFSIIPVDGLKNQKFFDELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPIAR  200 (246)
T ss_pred             -------------HHHHHHHHcCCCCcccccCHHHHHHHHHHHHHHHHHHHHhcCCCCcccchHHHHHHHHHHHHHHHHH
Confidence                         99999999999 887 9999999999999999999999653         33               


Q ss_pred             ---hhcccc-----CCccchhHHHHHHHhh
Q psy11505        288 ---WSTVHK-----DGKVLMNKLFVEMLEA  309 (312)
Q Consensus       288 ---~~~~~~-----~~~~~~~~~~~~~~~~  309 (312)
                         +++.++     .|+++|++||.||++.
T Consensus       201 ~~~~~~~~l~~~~~~~~~~~~pll~ei~~~  230 (246)
T cd07073         201 ELHQFTFDLLIKSHMVSVDFPEMMAEIISV  230 (246)
T ss_pred             HHHHHHHHHhCccccCccCccHHHHHHHHh
Confidence               122333     4556899999999984

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

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

Probab=99.96  E-value=3.2e-29  Score=217.31  Aligned_cols=168  Identities=27%  Similarity=0.399  Sum_probs=143.4

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCC-CCeeEecccchhhHHhh-
Q psy11505        101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHC-AGKIRFASDLVLDERQA-  178 (312)
Q Consensus       101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~-~~~l~~~~g~~~~~~~~-  178 (312)
                      ....+..++++.++.+..+|+|||++|+|.+|+.+||+.|||++|.++++++.+|++.++. .+.+.+++|..++.... 
T Consensus        38 ~~~~~~~i~~~a~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~w~EllvL~~a~~s~~~~~~~~~ll~~~~~~~~~~~~  117 (241)
T cd07069          38 KLSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIA  117 (241)
T ss_pred             ccchHHHHHHHHHHHHHHHHHHHhhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCeeEecCCCccCchhhh
Confidence            4567789999999999999999999999999999999999999999999999999998765 35788888876553321 


Q ss_pred             --hhcccc---hhhhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCcee
Q psy11505        179 --RECGFS---EIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLV  253 (312)
Q Consensus       179 --~~~~~~---~~~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  253 (312)
                        ...+..   +.+.++...+++|++|.+||                                          +++|||+
T Consensus       118 ~~~~~~~~~~~~~~~e~~~~lr~L~ld~~E~------------------------------------------a~LKaiv  155 (241)
T cd07069         118 SQAGATLNNLMSHAQELVAKLRSLQFDQREF------------------------------------------VCLKFLV  155 (241)
T ss_pred             hhhhhHHHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHH
Confidence              111222   33445666677999999999                                          9999999


Q ss_pred             ecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------------------------hhhhccccCCccchhHHHHHH
Q psy11505        254 LANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------------------------RFWSTVHKDGKVLMNKLFVEM  306 (312)
Q Consensus       254 l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------------------------~~~~~~~~~~~~~~~~~~~~~  306 (312)
                      |||||++ +.+.++|+++|++++.||.+|+..+                          +.++++++.|.+|+++|+.||
T Consensus       156 Lfnpd~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~Rf~kLLl~Lp~LR~is~~~~e~l~~~~l~g~~~~~~Ll~Em  235 (241)
T cd07069         156 LFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEM  235 (241)
T ss_pred             HcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHhHHHHHhhHHHHHHHHhccccCCCcHHHHHHHH
Confidence            9999998 9999999999999999999999765                          336778999999999999999


Q ss_pred             Hhhh
Q psy11505        307 LEAY  310 (312)
Q Consensus       307 ~~~~  310 (312)
                      |+|+
T Consensus       236 l~~~  239 (241)
T cd07069         236 LHAK  239 (241)
T ss_pred             Hhcc
Confidence            9986

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=99.96  E-value=3e-29  Score=217.30  Aligned_cols=168  Identities=24%  Similarity=0.380  Sum_probs=143.6

Q ss_pred             chhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCC-CCeeEecccchhhHHhh
Q psy11505        100 PTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHC-AGKIRFASDLVLDERQA  178 (312)
Q Consensus       100 ~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~-~~~l~~~~g~~~~~~~~  178 (312)
                      .....+..++++..+.++.+|+|||++|+|.+|+.+||+.|||++|.++++|..|||+++.. .+.+.+++|..+.....
T Consensus        35 ~~~~~~~~l~~~a~~~L~~~VeWaK~lP~F~~L~~~DQi~LLk~~w~el~vL~~a~rs~~~~~~~~l~~~~g~~~~~~~~  114 (237)
T cd07070          35 DQPAPFGLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQHGKEGSILLVTGQEVELSTV  114 (237)
T ss_pred             CcccHHHHHHHHHHHHHHHHHHHHHhCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCceeecCCCeechhHH
Confidence            34566889999999999999999999999999999999999999999999999999999765 35788888877664432


Q ss_pred             h-hccc--chh---hhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCce
Q psy11505        179 R-ECGF--SEI---YQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTL  252 (312)
Q Consensus       179 ~-~~~~--~~~---~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  252 (312)
                      . ..+.  ..+   +.++...+++|++|++||                                          +++|||
T Consensus       115 ~~~~~~~~~~~~~~~~e~~~kl~~L~ld~~Ey------------------------------------------~~LkaI  152 (237)
T cd07070         115 AAQAGSLLHSLVLRAQELVLQLHALQLDRQEF------------------------------------------VCLKFL  152 (237)
T ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHhCCCHHHH------------------------------------------HHHHHH
Confidence            2 2221  121   245666677999999999                                          999999


Q ss_pred             eecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------------------------hhhhccccCCccchhHHHHH
Q psy11505        253 VLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------------------------RFWSTVHKDGKVLMNKLFVE  305 (312)
Q Consensus       253 ~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------------------------~~~~~~~~~~~~~~~~~~~~  305 (312)
                      +|||||++ ++++++|+++|++++.||.+||..+                          +++++++++|.+|+++|+.|
T Consensus       153 iLfnpd~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~Rf~kLLl~Lp~LRsis~~~~e~l~~~~l~g~~~~~~Ll~e  232 (237)
T cd07070         153 ILFSLDVKFLNNHSLVKDAQEKANAALLDYTLCHYPHCGDKFQQLLLRLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIE  232 (237)
T ss_pred             HhcCCCccCCCCHHHHHHHHHHHHHHHHHHHHhcCCCcchHHHHHHHHhHHHHHhhHHHHHHHHHhcccCCCcHHHHHHH
Confidence            99999998 9999999999999999999998764                          44778899999999999999


Q ss_pred             HHhh
Q psy11505        306 MLEA  309 (312)
Q Consensus       306 ~~~~  309 (312)
                      ||++
T Consensus       233 ml~~  236 (237)
T cd07070         233 MLQA  236 (237)
T ss_pred             HhcC
Confidence            9987

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).

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

Probab=99.96  E-value=7.6e-29  Score=213.24  Aligned_cols=184  Identities=47%  Similarity=0.711  Sum_probs=153.3

Q ss_pred             hcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCC
Q psy11505         83 LCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCA  162 (312)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~  162 (312)
                      ..+|...........+......+..++++..+.+..+|+|+|++|+|.+|+.+||+.|+|++|++++++..||++++.+.
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~vewaK~lp~F~~L~~~DQi~LLk~~~~~~~~l~~a~~s~~~~~   86 (221)
T cd07068           7 VAEPDKLYAMNDPTGPDTEVSLLATLSDLADRELVHIISWAKHIPGFSDLSLNDQMHLLQSAWLEILMLGLVWRSLPHPG   86 (221)
T ss_pred             hhCCCcccCCCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHhhHHHHHHHHHHhhcCCCC
Confidence            34443333333344556677889999999999999999999999999999999999999999999999999999998877


Q ss_pred             CeeEecccchhhHHhhhhcccchhhh---hhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhh
Q psy11505        163 GKIRFASDLVLDERQARECGFSEIYQ---QVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQV  239 (312)
Q Consensus       163 ~~l~~~~g~~~~~~~~~~~~~~~~~~---~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  239 (312)
                       .+.+++|.+++++.....+..++.+   ++...+++|++|++||                                   
T Consensus        87 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~-----------------------------------  130 (221)
T cd07068          87 -KLVFAPDLLLDREQARVEGLLEIFDMLLQLVRRFRELGLQREEY-----------------------------------  130 (221)
T ss_pred             -eEEeCCCceECHHHHhhccHHHHHHHHHHHHHHHHHcCCCHHHH-----------------------------------
Confidence             7888888877766554445444333   4455566999999999                                   


Q ss_pred             cccceecCCCCceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH---------------------------hhhhcc
Q psy11505        240 YSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL---------------------------RFWSTV  291 (312)
Q Consensus       240 ~~~~~~~~~~~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~---------------------------~~~~~~  291 (312)
                             +++|||++||||++ |+++..|++.|++|+.+|.+|+..+                           ++++.+
T Consensus       131 -------~lLkaIil~npd~~~L~~~~~V~~~q~~~~~aL~~y~~~~~~~~~~~Rf~~LL~~l~~Lr~~~~~~~e~l~~~  203 (221)
T cd07068         131 -------VCLKAIILANSDVRHLEDREAVQQLRDAILDALVDVEAKRHGSQQPRRLAQLLLLLPHLRQASNKGVRHLYSV  203 (221)
T ss_pred             -------HHHHHHHHcCCCccCccCHHHHHHHHHHHHHHHHHHHHHhCCCccccHHHHHHHhccHHHHHHHHHHHHHHHH
Confidence                   99999999999998 9999999999999999999998755                           335567


Q ss_pred             ccCCccchhHHHHHHHhh
Q psy11505        292 HKDGKVLMNKLFVEMLEA  309 (312)
Q Consensus       292 ~~~~~~~~~~~~~~~~~~  309 (312)
                      ++.|.+|+++|+.||++|
T Consensus       204 k~~~~~~~~~Ll~e~l~~  221 (221)
T cd07068         204 KCEGKVPMYKLFLEMLEA  221 (221)
T ss_pred             HHcCCccHHHHHHHHhcC
Confidence            999999999999999986

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

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

Probab=99.96  E-value=1.7e-28  Score=211.85  Aligned_cols=167  Identities=24%  Similarity=0.335  Sum_probs=145.8

Q ss_pred             CchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhh
Q psy11505         99 DPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQA  178 (312)
Q Consensus        99 ~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~  178 (312)
                      ......++.+.+.....+..+|+|||++|+|.+|+.+||+.|||++|+++++|+.||++.+..+ .+.+++|..+++.+.
T Consensus        38 ~~~~~~~~~~~~l~t~~i~~iv~wAK~IPgF~~L~~~DQi~LLk~~w~Ell~L~~a~r~~~~~~-~l~~~~g~~~~~~~~  116 (239)
T cd07072          38 MSEAEKVQQFYSLLTSSIDVIKTFAEKIPGFPDLCKEDQELLFQSASLELFVLRLAYRTAPEDT-KLTFCNGVVLHKQQC  116 (239)
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHHHHHHhHHHHHHHHHHHHccCCCC-eEEeeCCeeecHHHH
Confidence            3456678999999999999999999999999999999999999999999999999999998865 799999988887765


Q ss_pred             hhcccchhhhhhcccC---ccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeec
Q psy11505        179 RECGFSEIYQQVKHSG---SLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLA  255 (312)
Q Consensus       179 ~~~~~~~~~~~i~~~~---~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  255 (312)
                      .. +++++++.++++.   ++|++|++||                                          +|++||+||
T Consensus       117 ~~-~~~~~~~~i~ef~~~l~~L~ld~~E~------------------------------------------a~LkAivLf  153 (239)
T cd07072         117 QR-SFGDWLHAILEFSKSLHAMDIDISAF------------------------------------------ACLCALTLI  153 (239)
T ss_pred             Hh-hHHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHh
Confidence            43 5566666665554   4899999999                                          999999999


Q ss_pred             CCCCc-ccchHHHHHHHHHHHHHhHhHHHHH----------------------------hhhhccccCCccchhHHHHHH
Q psy11505        256 NSDVK-LDEFSSLKKFRNSILSSLGDCIYVL----------------------------RFWSTVHKDGKVLMNKLFVEM  306 (312)
Q Consensus       256 ~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~----------------------------~~~~~~~~~~~~~~~~~~~~~  306 (312)
                      + |++ |.++++|+++|++++.+|.+|+..+                            +.+++.++.|.+|+++|+.||
T Consensus       154 ~-dr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~~~~rf~kLLl~Lp~LRsl~~~~~e~lf~~k~~~~~p~~~Ll~Em  232 (239)
T cd07072         154 T-ERHGLKEPHKVEQLQMKIISSLRDHVTYNAEAQKKPHYFSRLLGKLPELRSLSVQGLQRIFYLKLEDLVPAPPLIENM  232 (239)
T ss_pred             C-CCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcccccHHHHHHHHhHHHHhhHHHHHHHHHHHHcCCCCCCcHHHHHH
Confidence            5 887 9999999999999999999999743                            235667999999999999999


Q ss_pred             Hhhh
Q psy11505        307 LEAY  310 (312)
Q Consensus       307 ~~~~  310 (312)
                      +.+-
T Consensus       233 ~~~~  236 (239)
T cd07072         233 FVAS  236 (239)
T ss_pred             Hhcc
Confidence            9863

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).

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

Probab=99.96  E-value=1.8e-28  Score=211.82  Aligned_cols=165  Identities=27%  Similarity=0.381  Sum_probs=145.0

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhh
Q psy11505        101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE  180 (312)
Q Consensus       101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~  180 (312)
                      ....+..+++.....+..+|+|||++|+|.+|+.+||++|||++|+++++++.|+++.+..+ .+.+++|..+++.+. .
T Consensus        39 ~~~~~~~~~e~~~~~i~~iVewAK~iPgF~~L~~~DQi~LLk~~~~Ell~L~~a~~~~~~~~-~l~~~~g~~~~~~~~-~  116 (238)
T cd07071          39 DTQHIQQFYDLLTGSMEIIRGWAEKIPGFTDLPKADQDLLFESAFLELFVLRLAYRSNPVEG-KLIFCNGVVLHRLQC-V  116 (238)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCC-ceEeeCCceechhhh-h
Confidence            45678999999999999999999999999999999999999999999999999999998866 799999988876653 4


Q ss_pred             cccchhhhhhcccCc---cCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCC
Q psy11505        181 CGFSEIYQQVKHSGS---LDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANS  257 (312)
Q Consensus       181 ~~~~~~~~~i~~~~~---~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  257 (312)
                      .+.+++++.++++..   +|++|++||                                          +|++||+|| +
T Consensus       117 ~~~~~~~~~i~ef~~~l~~L~ld~~E~------------------------------------------alLkAIvLf-~  153 (238)
T cd07071         117 RGFGEWIDSIVEFSSNLQNMNIDISAF------------------------------------------SCIAALAMV-T  153 (238)
T ss_pred             hcHHHHHHHHHHHHHHHHhcCCCHHHH------------------------------------------HHHHHHHHc-C
Confidence            466667777766554   899999999                                          999999999 5


Q ss_pred             CCc-ccchHHHHHHHHHHHHHhHhHHHHH----------------------------hhhhccccCCccchhHHHHHHHh
Q psy11505        258 DVK-LDEFSSLKKFRNSILSSLGDCIYVL----------------------------RFWSTVHKDGKVLMNKLFVEMLE  308 (312)
Q Consensus       258 ~~~-l~~~~~~~~~~~~~~~~l~~~~~~~----------------------------~~~~~~~~~~~~~~~~~~~~~~~  308 (312)
                      |++ |+++++|+++||+++.||.+|+..+                            +.+++.++.|.+|+++|+.||+.
T Consensus       154 D~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~p~~~~rf~kLLl~Lp~LRsl~~~~~e~l~~~k~~~~~p~~~Ll~e~~~  233 (238)
T cd07071         154 ERHGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLGKLPELRTLCTQGLQRIFYLKLEDLVPPPAIIDKLFL  233 (238)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCCcccHHHHHHHHhHHHHHHHHHHHHHHHHHHcCCCCCCcHHHHHHHH
Confidence            887 9999999999999999999999743                            23556789999999999999997


Q ss_pred             hh
Q psy11505        309 AY  310 (312)
Q Consensus       309 ~~  310 (312)
                      +-
T Consensus       234 ~~  235 (238)
T cd07071         234 DT  235 (238)
T ss_pred             hh
Confidence            64

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

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

Probab=99.95  E-value=2.1e-28  Score=212.80  Aligned_cols=164  Identities=20%  Similarity=0.347  Sum_probs=146.6

Q ss_pred             chhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhh
Q psy11505        100 PTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAR  179 (312)
Q Consensus       100 ~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~  179 (312)
                      .....+..+++.....+..+|+|||++|+|.+|+.+||+.|||++|+++++++.|+++.+..+ .+.+++|..+.++...
T Consensus        49 ~~~~~~~~~~~~~~~~l~~iVefAK~iPgF~~L~~~DQi~LLk~~~~ElliL~~a~~~~~~~~-~~~~~~~~~~~~~~~~  127 (243)
T cd06935          49 VDLEAFSHFTKIITPAITRVVDFAKKLPMFTELPCEDQIILLKGCCMEIMSLRAAVRYDPESE-TLTLSGEMAVTREQLK  127 (243)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHhcCCccccCChHHHHHHHHHhHHHHHHHHHHHHhCcCCC-eEEeeCCeEeeHHHHH
Confidence            356789999999999999999999999999999999999999999999999999999877765 7999999988888777


Q ss_pred             hcccchhhhhhcccCc---cCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecC
Q psy11505        180 ECGFSEIYQQVKHSGS---LDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLAN  256 (312)
Q Consensus       180 ~~~~~~~~~~i~~~~~---~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  256 (312)
                      ..+.+++.+.++.++.   +|++|++||                                          ++++||+|||
T Consensus       128 ~~~~~~~~~~i~~f~~~l~~L~ld~~E~------------------------------------------alLkAivLf~  165 (243)
T cd06935         128 NGGLGVVSDAIFDLGVSLSSFNLDDTEV------------------------------------------ALLQAVLLMS  165 (243)
T ss_pred             hcChHHHHHHHHHHHHHHHhcCCCHHHH------------------------------------------HHHHHHHHhC
Confidence            7777777777776654   999999999                                          9999999999


Q ss_pred             CCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------------------------hhhhccccCCccch-hHHHHHH
Q psy11505        257 SDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------------------------RFWSTVHKDGKVLM-NKLFVEM  306 (312)
Q Consensus       257 ~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------------------------~~~~~~~~~~~~~~-~~~~~~~  306 (312)
                      ||++ |+++++|+++|++++.||.+|+..+                          +.+++.++.|..|+ ++|+.||
T Consensus       166 pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~rf~kLL~~L~~LR~i~~~~~e~l~~~k~~~~~~~~~~L~~Em  243 (243)
T cd06935         166 SDRPGLACVERIEKLQDSFLLAFEHYINYRKHHVPHFWPKLLMKVTDLRMIGACHASRFLHMKVECPTELFPPLFLEV  243 (243)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCChhhhcC
Confidence            9998 9999999999999999999999765                          22455788999995 9999987

The ligand binding domain (LBD) of thyroid hormone receptors: Thyroid hormone receptors are members of a superfamily of nuclear receptors. Thyroid hormone receptors (TR) mediate the actions of thyroid hormones, which play critical roles in growth, development, and homeostasis in mammals. They regulate overall metabolic rate, cholesterol and triglyceride levels, and heart rate, and affect mood. TRs are expressed from two separate genes (alpha and beta) in human and each gene generates two isoforms of the receptor through differential promoter usage or splicing. TRalpha functions in the heart to regulate heart rate and rhythm and TRbeta is active in the liver and other tissues. The unliganded TRs function as transcription repressors, by binding to thyroid hormone response elements (TRE) predominantly as homodimers, or as heterodimers with retinoid X-receptors (RXR), a

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

Probab=99.95  E-value=3.2e-28  Score=210.94  Aligned_cols=166  Identities=27%  Similarity=0.343  Sum_probs=147.2

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhh
Q psy11505        101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE  180 (312)
Q Consensus       101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~  180 (312)
                      ....+..+++.....+..+|+|||++|+|.+|+.+||+.|||++|+++++++.|+++.+..+ .+.+++|..+++.+. .
T Consensus        39 ~~~~~~~~~~~~~~~l~~iv~wAK~IPgF~~L~~~DQi~LLk~~w~El~~L~~a~r~~~~~~-~l~~~~~~~~~~~~~-~  116 (239)
T cd06945          39 DSQQVQQFYDLLTGSVDVIRQWAEKIPGFKDLHREDQDLLLESAFLELFVLRLAYRSNPVDG-KLVFCNGLVLHRLQC-V  116 (239)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCC-ceEeeCCceecHHHH-H
Confidence            45678999999999999999999999999999999999999999999999999999998866 799999988877664 3


Q ss_pred             cccchhhhhhcccCc---cCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCC
Q psy11505        181 CGFSEIYQQVKHSGS---LDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANS  257 (312)
Q Consensus       181 ~~~~~~~~~i~~~~~---~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  257 (312)
                      .+..++++.++.+..   +|++|++||                                          ++++||+||+|
T Consensus       117 ~~~~~~~~~i~~f~~~l~~L~ld~~E~------------------------------------------~~LkaivL~~p  154 (239)
T cd06945         117 RGFGEWLDSILAFSSSLQSLLLDDISA------------------------------------------FCCLALLLLIT  154 (239)
T ss_pred             HhHHHHHHHHHHHHHHHHHHhCChHHH------------------------------------------HHHHHHHHhCC
Confidence            456677787777544   799999999                                          99999999999


Q ss_pred             CCc-ccchHHHHHHHHHHHHHhHhHHHHH----------------------------hhhhccccCCccchhHHHHHHHh
Q psy11505        258 DVK-LDEFSSLKKFRNSILSSLGDCIYVL----------------------------RFWSTVHKDGKVLMNKLFVEMLE  308 (312)
Q Consensus       258 ~~~-l~~~~~~~~~~~~~~~~l~~~~~~~----------------------------~~~~~~~~~~~~~~~~~~~~~~~  308 (312)
                      |++ |.++++|+++|++++.+|.+|+..+                            +.+++.++.|.+||++|+.||++
T Consensus       155 D~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~~~rf~kLLl~Lp~LR~ls~~~~e~l~~~k~~~~~~~~~Ll~e~~~  234 (239)
T cd06945         155 ERHGLKEPKKVEELQNKIISCLRDHVTSNYPGQDKPNRLSKLLLKLPELRTLSKKGLQRIFFLKLEDLLPPPPLIDKRFL  234 (239)
T ss_pred             CccccCCHHHHHHHHHHHHHHHHHHHHHhCCCcccccHHHHHHHHhHHHHHHHHHHHHHHHHHHccCCCCCChHHHHHHH
Confidence            998 9999999999999999999999754                            22556799999999999999997


Q ss_pred             hh
Q psy11505        309 AY  310 (312)
Q Consensus       309 ~~  310 (312)
                      .-
T Consensus       235 ~~  236 (239)
T cd06945         235 DT  236 (239)
T ss_pred             hc
Confidence            53

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

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

Probab=99.95  E-value=7.9e-28  Score=207.81  Aligned_cols=165  Identities=24%  Similarity=0.427  Sum_probs=137.9

Q ss_pred             HHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhc
Q psy11505         78 LEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRS  157 (312)
Q Consensus        78 l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs  157 (312)
                      +..+...++...........++.....+..+++..++.+..+|+|||++|+|.+|+.+||++|||++|.++++++.+||+
T Consensus         3 ~~~l~~~e~~~~~~~~~~~~p~~~~~~~~~l~ela~~~L~~iVeWAK~IPgF~~L~~~DQi~LLk~~w~EllvL~~a~rs   82 (248)
T cd07075           3 VMVLENIEPEIVYAGYDSSKPDTAENLLSTLNRLAGKQMIQVVKWAKVLPGFRNLPLEDQITLIQYSWMCLSSFALSWRS   82 (248)
T ss_pred             HHHHhhcCCCcccCCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            34455566655555555555666677899999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCC-CeeEecccchhhHHhhhhcccchhhh---hhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHH
Q psy11505        158 LPHCA-GKIRFASDLVLDERQARECGFSEIYQ---QVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFF  233 (312)
Q Consensus       158 ~~~~~-~~l~~~~g~~~~~~~~~~~~~~~~~~---~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~  233 (312)
                      ++... +.+.+++|..++.......+..++.+   ++...+++|++|++||                             
T Consensus        83 ~~~~~~~~l~fa~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~L~Ld~~E~-----------------------------  133 (248)
T cd07075          83 YKHTNSQFLYFAPDLVFNEERMHQSAMYELCQGMHQISLQFVRLQLTFEEY-----------------------------  133 (248)
T ss_pred             cCCCCCceEEecCCccccHHHHhhccHHHHHHHHHHHHHHHHHcCCCHHHH-----------------------------
Confidence            98865 45888888888877766656555433   4444555999999999                             


Q ss_pred             HHHhhhcccceecCCCCceeecCCC-Cc-ccchHHHHHHHHHHHHHhHhHHHH
Q psy11505        234 KRTIQVYSGYRQTGACGTLVLANSD-VK-LDEFSSLKKFRNSILSSLGDCIYV  284 (312)
Q Consensus       234 ~~~~~~~~~~~~~~~~~~~~l~~~~-~~-l~~~~~~~~~~~~~~~~l~~~~~~  284 (312)
                                   +|+|||+||||| ++ |+++++|+++|++++.||.+|+..
T Consensus       134 -------------acLKAIvLfn~d~~~gL~~~~~Ve~lqe~~~~aL~~yi~~  173 (248)
T cd07075         134 -------------TIMKVLLLLSTIPKDGLKSQAAFEEMRTNYIKELRKMVTK  173 (248)
T ss_pred             -------------HHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence                         999999999997 56 999999999999999999999984

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

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

Probab=99.95  E-value=4.2e-28  Score=210.40  Aligned_cols=167  Identities=23%  Similarity=0.359  Sum_probs=141.6

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhh
Q psy11505        101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE  180 (312)
Q Consensus       101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~  180 (312)
                      ....++.++++..+.++.+|+|||++|+|.+|+.+||+.|||++|+++++|+.|+++.+...+.+.+++|..........
T Consensus        28 ~~~~~~~l~~~a~~~L~~~VewaK~lp~F~~L~~~DQi~LLk~~w~el~lL~~a~~s~~~~~~~~~~~~g~~~~~~~~~~  107 (236)
T cd06948          28 NIMGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLSWSELFVLNAAQCCMPLHVAPLLAAAGLHASPMSADR  107 (236)
T ss_pred             ccchHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHhhHHHHHHHHHHHcccccchhhhhccccccCccchhh
Confidence            34668999999999999999999999999999999999999999999999999999999887677777777554322111


Q ss_pred             -ccc---chhhhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecC
Q psy11505        181 -CGF---SEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLAN  256 (312)
Q Consensus       181 -~~~---~~~~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  256 (312)
                       ...   .+.+.++...+++|++|++||                                          +++|||+|||
T Consensus       108 ~~~~~~~~~~~~~l~~~l~~L~ld~~E~------------------------------------------~lLkaiiL~n  145 (236)
T cd06948         108 VVAFMDHIRIFQEQVEKLKALHVDSAEF------------------------------------------SCLKAIVLFT  145 (236)
T ss_pred             HhHHHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHcC
Confidence             111   122445566677999999999                                          9999999999


Q ss_pred             CCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------------------------hhhhccccCCccchhHHHHHHHhh
Q psy11505        257 SDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------------------------RFWSTVHKDGKVLMNKLFVEMLEA  309 (312)
Q Consensus       257 ~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------------------------~~~~~~~~~~~~~~~~~~~~~~~~  309 (312)
                      ||++ |++.++|+++|++|+.||.+|+..+                          ..+++++++|.+|+++|+.|||++
T Consensus       146 pd~~~L~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LLl~Lp~Lr~is~~~~e~l~~~~l~g~~~~~~ll~e~l~~  225 (236)
T cd06948         146 SDACGLSDPAHIESLQEKSQCALEEYVRTQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDMLLS  225 (236)
T ss_pred             cccccccCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHhccHHHHHHhhcccccCCCcHHHHHHHHHhC
Confidence            9997 9999999999999999999999865                          236678999999999999999986

The ligand binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs): COUP-TFs are orphan members of the steroid/thyroid hormone receptor superfamily. They are expressed in many tissues and are involved in the regulation of several important biological processes, such as neurogenesis, organogenesis, cell fate determination, and metabolic homeostasis. In mammals two isoforms named COUP-TFI and COUP-TFII have been identified. Both genes show an exceptional homology and overlapping expression patterns, suggesting that they may serve redundant functions. Although COUP-TF was originally characterized as a transcriptional activator of the chicken ovalbumin gene, COUP-TFs are generally considered to be repressors of transcription for other nuclear hormone receptors, such as retinoic acid receptor (RAR), thyroid hormone

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

Probab=99.95  E-value=2.1e-27  Score=204.99  Aligned_cols=167  Identities=25%  Similarity=0.510  Sum_probs=140.2

Q ss_pred             HHHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhh
Q psy11505         77 MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYR  156 (312)
Q Consensus        77 ~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~r  156 (312)
                      +++.+...||...........++.....+..+++..+++++.+|+|||++|+|.+|+.+||++|+|++|++++++..|||
T Consensus         2 ~~~~l~~~ep~~~~~~~d~~~p~~~~~~~~~l~~la~r~L~~vVeWAK~lPgF~~L~~~DQi~LLk~sw~ellvL~~a~r   81 (248)
T cd07074           2 LINLLMSIEPDVVYAGYDNTKPETPSSLLTSLNQLCERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWR   81 (248)
T ss_pred             HhHHHHHhCCCcccCCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence            46677888887777766666677777889999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCC-CeeEecccchhhHHhhhhcccchhh---hhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHH
Q psy11505        157 SLPHCA-GKIRFASDLVLDERQARECGFSEIY---QQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAF  232 (312)
Q Consensus       157 s~~~~~-~~l~~~~g~~~~~~~~~~~~~~~~~---~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~  232 (312)
                      |++.+. +.+.+++|..+++......+..+..   .++...+.++++|++||                            
T Consensus        82 S~~~~~~~~l~fa~d~~~~~~~~~~~~~~~~~~~m~e~~~~~~~L~ld~~Ey----------------------------  133 (248)
T cd07074          82 SYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEF----------------------------  133 (248)
T ss_pred             hhccCCCCeEEecCCcccchhhhhhccHHHHHHHHHHHHHHHHHcCCCHHHH----------------------------
Confidence            998864 4567877777776654333333322   23555666999999999                            


Q ss_pred             HHHHhhhcccceecCCCCceeecCC-CCc-ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505        233 FKRTIQVYSGYRQTGACGTLVLANS-DVK-LDEFSSLKKFRNSILSSLGDCIYVL  285 (312)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~~~~l~~~-~~~-l~~~~~~~~~~~~~~~~l~~~~~~~  285 (312)
                                    +|+|||+|||| |++ |+++++|+++|++|..+|.+||..+
T Consensus       134 --------------~cLKAIvLfnp~d~~gL~~q~~Ve~lR~~y~~aL~~yi~~~  174 (248)
T cd07074         134 --------------LCMKALLLLNTIPLEGLRSQTQFDEMRSSYIRELIKAIGLR  174 (248)
T ss_pred             --------------HHHHHHHHCCCCcCCCCCCHHHHHHHHHHHHHHHHHHHHHc
Confidence                          99999999999 777 9999999999999999999997644

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

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

Probab=99.94  E-value=1e-27  Score=205.09  Aligned_cols=164  Identities=18%  Similarity=0.153  Sum_probs=132.0

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCe---------eEecccc
Q psy11505        101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGK---------IRFASDL  171 (312)
Q Consensus       101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~---------l~~~~g~  171 (312)
                      ....++.+++...+.++.+|+|||++|+|.+|+.+||+.|||++|.++++|+.||++.+.....         +.+. |.
T Consensus        17 ~~~~~~~ice~a~~~L~~~V~WAK~iP~F~~L~~~DQi~LLk~~W~EL~iL~laq~s~~~~~~~~~~~~~~~~~l~~-~~   95 (222)
T cd07349          17 CLCTPHRTCREASDVLVKTVAFMRNLPSFWQLPPQDQLLLLQNCWGPLFLLGLAQDRVTFEVAEAPVPSMLKKILLE-GQ   95 (222)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHhcCCCcccCChHHHHHHHHHccHHHHHHHHHHHccccccccccchhHHHHHHhc-cc
Confidence            3456788899999999999999999999999999999999999999999999999997765421         1122 11


Q ss_pred             hhhHHh--hhhcc----cchhhhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505        172 VLDERQ--ARECG----FSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ  245 (312)
Q Consensus       172 ~~~~~~--~~~~~----~~~~~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (312)
                      ......  ....+    ....+.++...+++|++|++||                                         
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~~l~e~~~~l~~L~ld~~Ey-----------------------------------------  134 (222)
T cd07349          96 SSSGGSGQPDRPQPSLAAVQWLQCCLNKFWSLDLSPKEY-----------------------------------------  134 (222)
T ss_pred             ccccccchhhhhhhHHHHHHHHHHHHHHHHHcCCCHHHH-----------------------------------------
Confidence            111000  00001    1123455666677999999999                                         


Q ss_pred             cCCCCceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------------------------hhhhccccCCccc
Q psy11505        246 TGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------------------------RFWSTVHKDGKVL  298 (312)
Q Consensus       246 ~~~~~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------------------------~~~~~~~~~~~~~  298 (312)
                       +++|||+|||||++ +++.++|+.+|++++.||.+|+...                          +.+++++++|.+|
T Consensus       135 -a~LkaivLf~pd~~gl~~~~~V~~lqe~~~~aL~~~~~~~~p~~~~r~~kLLl~Lp~LR~i~~~~ie~lff~~~~g~~~  213 (222)
T cd07349         135 -AYLKGTILFNPDVPGLTASSHVGHLQQEAQWALCEVLEPLHPQDQGRFARILLTASTLKSIPPSLITDLFFRPIIGDAD  213 (222)
T ss_pred             -HHHHHHHHcCCCcccCCCHHHHHHHHHHHHHHHHHHHHHHCCCcccHHHHHHHHhHHHhcCCHHHHHHHhCccccCCCc
Confidence             99999999999998 9999999999999999999999765                          3478889999999


Q ss_pred             hhHHHHHHH
Q psy11505        299 MNKLFVEML  307 (312)
Q Consensus       299 ~~~~~~~~~  307 (312)
                      |++|+.|||
T Consensus       214 i~~Ll~eml  222 (222)
T cd07349         214 IAELLGDML  222 (222)
T ss_pred             HHHHHHHhC
Confidence            999999996

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.

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

Probab=99.94  E-value=7.4e-27  Score=197.23  Aligned_cols=162  Identities=21%  Similarity=0.266  Sum_probs=134.9

Q ss_pred             HHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhhccc
Q psy11505        104 TINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGF  183 (312)
Q Consensus       104 ~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~~~~  183 (312)
                      .|..+.+..+..+..+|+|||++|+|++|+.+||+.|+|++|+++++++.++++.+..+ .+.+.+|..++.+.....+.
T Consensus         3 ~w~~~~~~~~~~l~~iI~waK~iP~F~~L~~~DQi~LLk~~~~el~ll~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~   81 (195)
T cd06941           3 LWQQLSEALTPSVQRVVEFAKRIPGFCDLSQDDQLLLIKAGFFEVWLVRISRLINSKSG-SITFDDGISISRQQLDIIYD   81 (195)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHcCCCC-eEEecCCeEeeHHHHHhccc
Confidence            57888999999999999999999999999999999999999999999999987666544 79999998887665433222


Q ss_pred             chhhhhhcc---cCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCCCCc
Q psy11505        184 SEIYQQVKH---SGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVK  260 (312)
Q Consensus       184 ~~~~~~i~~---~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  260 (312)
                      .++.+.+..   .+++|++|++||                                          ++++||+||+||++
T Consensus        82 ~~~~~~~~~~~~~l~~L~ld~~E~------------------------------------------allkAi~Lf~pd~~  119 (195)
T cd06941          82 SDFVKALFEFSDSFNSLGLSDTEV------------------------------------------ALFCAVVLLSPDRI  119 (195)
T ss_pred             hHHHHHHHHHHHHHHhcCCCHHHH------------------------------------------HHHHHHHHcCCCCC
Confidence            344444444   455999999999                                          99999999999997


Q ss_pred             -ccchHHHHHHHHHHHHHhHhHHHHH------hh--------------------hh-ccccCCccchhHHHHHHHh
Q psy11505        261 -LDEFSSLKKFRNSILSSLGDCIYVL------RF--------------------WS-TVHKDGKVLMNKLFVEMLE  308 (312)
Q Consensus       261 -l~~~~~~~~~~~~~~~~l~~~~~~~------~~--------------------~~-~~~~~~~~~~~~~~~~~~~  308 (312)
                       ++++++|+++|++++.+|.+|+..+      ||                    +. +++..+.+++++|+.||+|
T Consensus       120 gl~~~~~Ve~lq~~~~~aL~~~i~~~~p~~~~rf~~Ll~~Lp~Lr~l~~~~~e~l~~~~~~~~~~~~p~L~~E~~~  195 (195)
T cd06941         120 GLSEPKKVAILQDRVLEALKVQVSRNRPAEAQLFASLLMKIPELRSIGAKHQMHLDWYRVNWPLLRLPPLFAEIYD  195 (195)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHhHHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHhcC
Confidence             9999999999999999999998755      22                    22 3455677899999999986

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

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

Probab=99.93  E-value=3.1e-26  Score=199.05  Aligned_cols=164  Identities=19%  Similarity=0.279  Sum_probs=138.2

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhh
Q psy11505        101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE  180 (312)
Q Consensus       101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~  180 (312)
                      ....+..+.+|....+..+|+|||++|+|..|+.+||+.|||++|+++++++.|+++.+..+ .+.+++|..++++....
T Consensus        41 ~~~~~~~~~~~~~~~i~~~VefaK~lP~F~~L~~~DQi~LLK~~~~el~iL~~a~~~~~~~~-~~~~~~g~~~~~~~~~~  119 (236)
T cd06954          41 RQQRFAHFTELAILSVQEIVDFAKQLPGFLTLTREDQIALLKASTIEVMLLETARRYNPESE-AITFLKDFPYSRDDFAR  119 (236)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCCCCcccCChHHHHHHHHHhHHHHHHHHHHHHhcCCCC-eEEeeCCccccHHHHHH
Confidence            34678899999999999999999999999999999999999999999999999988766654 89999998877765543


Q ss_pred             ccc-chhhhhhc---ccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecC
Q psy11505        181 CGF-SEIYQQVK---HSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLAN  256 (312)
Q Consensus       181 ~~~-~~~~~~i~---~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  256 (312)
                      .+. .++.+.+.   ..+++|++|++||                                          ++++||+|||
T Consensus       120 ~~~~~~~~~~i~~~~~~l~~L~ld~~E~------------------------------------------~lL~aivLf~  157 (236)
T cd06954         120 AGLQVEFINPIFEFSKSMRELQLDDAEY------------------------------------------ALLIAINIFS  157 (236)
T ss_pred             hcChHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHhhcc
Confidence            332 34544444   4455999999999                                          9999999999


Q ss_pred             CCCc-ccchHHHHHHHHHHHHHhHhHHHHH------h--------------------hhhccccCCccchhHHHHHHHh
Q psy11505        257 SDVK-LDEFSSLKKFRNSILSSLGDCIYVL------R--------------------FWSTVHKDGKVLMNKLFVEMLE  308 (312)
Q Consensus       257 ~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~------~--------------------~~~~~~~~~~~~~~~~~~~~~~  308 (312)
                      ||++ |++.++|+++|++++.+|.+|+..+      |                    .++..++.+ .++++|+.||++
T Consensus       158 pd~~gL~~~~~V~~lQ~~~~~aL~~y~~~~~p~~~~rf~klL~~L~~Lr~l~~~~~e~l~~~k~~~-~~~~~L~~El~~  235 (236)
T cd06954         158 ADRPNVQDHHRVERLQETYVEALHSYIKIKRPSDRLMFPRMLMKLVSLRTLSSVHSEQVFALRLQD-KKLPPLLSEIWD  235 (236)
T ss_pred             CCcccCCCHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCCCcHHHHHhc
Confidence            9998 9999999999999999999999755      2                    234456655 689999999987

The ligand binding domain of Liver X receptors: Liver X receptors (LXRs) belong to a family of nuclear receptors of ligand-activated transcription factors. LXRs operate as cholesterol sensors which protect from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. Upon ligand binding a conformational change leads to recruitment of co-factors, which stimulates expression of target genes. Among the LXR target genes are several genes involved in cholesterol efflux from peripheral tissues such as the ATP-binding-cassette transporters ABCA1, ABCG1 and ApoE. There are two LXR isoforms in mammals, LXRalpha and LXRbeta. LXRalpha is expressed mainly in the liver, intestine, kidney, splee

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

Probab=99.93  E-value=1.5e-26  Score=199.04  Aligned_cols=162  Identities=19%  Similarity=0.226  Sum_probs=130.0

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccc----hhhHH
Q psy11505        101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDL----VLDER  176 (312)
Q Consensus       101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~----~~~~~  176 (312)
                      +...++.+++...+.++.+|+|||++|+|.+|+.+||+.|||++|.++++|+.|+++.+.....+ +.++.    .....
T Consensus        17 ~l~~~~~~ce~a~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~W~El~iL~~a~~s~~~~~~~~-~~~~~~~~~l~~~~   95 (232)
T cd07350          17 TLKSPQVTCKAASAVLVKTLRFVKGVPCFQELPLDDQLVLVRSCWAPLLVLGLAQDGVDFETVET-SEPSMLQRILTTRP   95 (232)
T ss_pred             ccCCHHHHHHHHHHHHHHHHHHHHhCcCcccCChHHHHHHHHHhhHHHHHHHHHHHcCCCccccc-cchhHHHHHHhccc
Confidence            45567888999999999999999999999999999999999999999999999999988875221 21111    00000


Q ss_pred             -----------------hhhhccc------chhhhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHH
Q psy11505        177 -----------------QARECGF------SEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFF  233 (312)
Q Consensus       177 -----------------~~~~~~~------~~~~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~  233 (312)
                                       .....+.      .+.+.++...+++|++|++||                             
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~e~~~~l~~L~ld~~E~-----------------------------  146 (232)
T cd07350          96 PPTSGAEPGEPQALPQMPQAEASHLPSAADIRAIKAFLAKCWSLDISTKEY-----------------------------  146 (232)
T ss_pred             ccccccccccccccccccchhhccccHHHHHHHHHHHHHHHHHcCCCHHHH-----------------------------
Confidence                             0000010      123455556666999999999                             


Q ss_pred             HHHhhhcccceecCCCCceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------------------------h
Q psy11505        234 KRTIQVYSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------------------------R  286 (312)
Q Consensus       234 ~~~~~~~~~~~~~~~~~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------------------------~  286 (312)
                                   +++|||+|||||++ |.++++|+++|++++.+|.+|+...                          .
T Consensus       147 -------------a~LkAivLf~pD~~~L~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~rf~kLLl~Lp~LRsi~~~~iE  213 (232)
T cd07350         147 -------------AYLKGTVLFNPDLPGLQCVQYIQGLQWEAQQALNEHVRMIHRGDQARFAKLNIALSLLRAINANVIA  213 (232)
T ss_pred             -------------HHHHHHHHhCCCcccCCCHHHHHHHHHHHHHHHHHHHHhhCCChhhHHHHHHHHhHHHHccCHHHHH
Confidence                         99999999999998 9999999999999999999999855                          3


Q ss_pred             hhhccccCCccchhHHHHH
Q psy11505        287 FWSTVHKDGKVLMNKLFVE  305 (312)
Q Consensus       287 ~~~~~~~~~~~~~~~~~~~  305 (312)
                      .+++++++|.+||++|+.|
T Consensus       214 ~lff~~l~g~v~i~~ll~E  232 (232)
T cd07350         214 ELFFRPIIGTVNMDDMLLE  232 (232)
T ss_pred             HHhccccCCCCcHHHHhcC
Confidence            4778899999999999875

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

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

Probab=99.93  E-value=1.3e-26  Score=198.82  Aligned_cols=162  Identities=18%  Similarity=0.165  Sum_probs=129.0

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCC---------eeEecccc
Q psy11505        101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAG---------KIRFASDL  171 (312)
Q Consensus       101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~---------~l~~~~g~  171 (312)
                      .....+.+++...+.+..+|+|||++|+|.+|+.+||+.|||++|.++++|+.|+++.+.+..         .+...++.
T Consensus        17 ~~~~~~~~ce~a~~~L~~~V~wAK~iP~F~~L~~~DQi~LLk~~w~El~iL~~a~~s~~~~~~~~~~~~~~~~~~~~~~~   96 (222)
T cd06951          17 QLCAPQMVCRAASQVLLKTIRFVRNLPCFTYLPPDDQLRLLRRSWAPLLLLGLAQDKVPFDTVEVPAPSILCEILTGAEM   96 (222)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHhCCCcccCChHHHHHHHHHHhHHHHHHHHHHHhccccccccccchHHHHHHhcccc
Confidence            345678899999999999999999999999999999999999999999999999999887542         11222222


Q ss_pred             hhhHHhh--hhcc------cchhhhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccc
Q psy11505        172 VLDERQA--RECG------FSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY  243 (312)
Q Consensus       172 ~~~~~~~--~~~~------~~~~~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  243 (312)
                      .......  ...+      ..+.+.++...+++|++|++||                                       
T Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~l~~L~ld~~Ey---------------------------------------  137 (222)
T cd06951          97 HWGGTPPPTLTMPPCIPLADVQDIQQFLMKCWSLDLDCKEY---------------------------------------  137 (222)
T ss_pred             ccccccccccccchhhHHHHHHHHHHHHHHHHHcCCCHHHH---------------------------------------
Confidence            2211110  0001      1122445555666999999999                                       


Q ss_pred             eecCCCCceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------------------------hhhhccccCCc
Q psy11505        244 RQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------------------------RFWSTVHKDGK  296 (312)
Q Consensus       244 ~~~~~~~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------------------------~~~~~~~~~~~  296 (312)
                         +++|||+|||||++ + ++++|+++|++++.+|.+|+..+                          +.+++++++|.
T Consensus       138 ---a~LkAivLfnpD~~gl-~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~Rf~kLLl~Lp~LRsl~~~~~e~lff~~~~g~  213 (222)
T cd06951         138 ---AYLKGAVLFTPVPPLL-CPHYIEALQKEAQQALNEHTMMTRPLEQLRSARLLLMLSLLRGIKTEPVTELFFRPIIGN  213 (222)
T ss_pred             ---HHHHHHHHhCCCCCcc-CHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHhHHhhcCCHHHHHHHhCccccCC
Confidence               99999999999998 9 99999999999999999999765                          34778899999


Q ss_pred             cchhHHHHH
Q psy11505        297 VLMNKLFVE  305 (312)
Q Consensus       297 ~~~~~~~~~  305 (312)
                      +||++++.|
T Consensus       214 ~~i~~ll~~  222 (222)
T cd06951         214 VSMDDVLLQ  222 (222)
T ss_pred             CcHHHHhcC
Confidence            999999865

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.

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

Probab=99.93  E-value=1.2e-25  Score=193.83  Aligned_cols=163  Identities=26%  Similarity=0.385  Sum_probs=140.4

Q ss_pred             chhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhh
Q psy11505        100 PTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAR  179 (312)
Q Consensus       100 ~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~  179 (312)
                      .+..+..++++++..++..+++|+|+||+|+.|+.+||+.|+|++|++++++..||++++.++ .+++++|.+++.....
T Consensus        29 ~~~~~~~~~~~~~~~~l~~~vewak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~s~~~~~-~l~~~~g~~~~~~~~~  107 (222)
T cd06931          29 KKIASINDVCESMKQQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGVARRSMPYKD-ILLLGNDLIIPRHCPE  107 (222)
T ss_pred             cccCCHHHHHHHHHHHHHHHHHHHHhCCccccCChHHHHHHHHHHHHHHHHHHHHHhccCCCC-eeeeCCCccccccccc
Confidence            467789999999999999999999999999999999999999999999999999999987655 7888988877654322


Q ss_pred             hccc----chhhhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeec
Q psy11505        180 ECGF----SEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLA  255 (312)
Q Consensus       180 ~~~~----~~~~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  255 (312)
                       .+.    .++++.+...+.+|++|++||                                          ++++||++|
T Consensus       108 -~~~~~~~~~~~~~~~~~l~~L~l~~~E~------------------------------------------~lLkaiil~  144 (222)
T cd06931         108 -PEISRVANRILDELVLPLRDLNIDDNEY------------------------------------------ACLKAIVFF  144 (222)
T ss_pred             -chHHHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHc
Confidence             222    233455666777999999999                                          999999999


Q ss_pred             CCCCc-ccchHHHHHHHHHHHHHhHhHHHHH------h--------------------hhhccccCCccchhHHHHHH
Q psy11505        256 NSDVK-LDEFSSLKKFRNSILSSLGDCIYVL------R--------------------FWSTVHKDGKVLMNKLFVEM  306 (312)
Q Consensus       256 ~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~------~--------------------~~~~~~~~~~~~~~~~~~~~  306 (312)
                      +||++ +++.++++++|++++.+|.+|+...      |                    .+...+++|.+|+++|+.||
T Consensus       145 ~p~~~~ls~~~~i~~~r~~~~~aL~~y~~~~~~~~~~Rf~~LL~~l~~lr~~~~~~~e~l~~~~lf~~~~~~~L~~e~  222 (222)
T cd06931         145 DPDAKGLSDPQKIKRLRFQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFARLFGVAKIDNLLQEM  222 (222)
T ss_pred             CCCccCCCCHHHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCcHHHHHhhC
Confidence            99998 9999999999999999999998543      2                    34557999999999999986

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

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

Probab=99.93  E-value=1.2e-25  Score=194.93  Aligned_cols=163  Identities=18%  Similarity=0.254  Sum_probs=136.5

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhh
Q psy11505        101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE  180 (312)
Q Consensus       101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~  180 (312)
                      ....|..+.+.....+..+|+|||++|+|.+|+.+||++|||++|+++++++.|+++.+... .+.+. |...+++....
T Consensus        46 ~~~~~~~~~~~~t~~i~~vVefAK~IPgF~~L~~~DQi~LLk~~~~Ellll~~a~~~~~~~~-~~~~~-~~~~~~~~~~~  123 (241)
T cd06939          46 REEMWQLCAEKITEAIQYVVEFAKRIPGFMELCQNDQIVLLKAGSLEVVLVRMSRAFNPSNN-TVLFD-GKYAPIDLFKS  123 (241)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhCCCCC-EEEEC-CccccHHHHHH
Confidence            55789999999999999999999999999999999999999999999999999977665544 66664 44566666666


Q ss_pred             cccchhhhhhcccCc---cCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCC
Q psy11505        181 CGFSEIYQQVKHSGS---LDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANS  257 (312)
Q Consensus       181 ~~~~~~~~~i~~~~~---~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  257 (312)
                      .+.+++++.++.++.   +|++|++||                                          ++++||+||+|
T Consensus       124 ~~~~~~~~~~~~f~~~l~~L~ld~~E~------------------------------------------all~AivL~~p  161 (241)
T cd06939         124 LGCDDLISAVFDFAKSLCELKLTEDEI------------------------------------------ALFSALVLISA  161 (241)
T ss_pred             cCcHHHHHHHHHHHHHHHhcCCCHHHH------------------------------------------HHHHHHHHhcC
Confidence            666677777766655   899999999                                          99999999999


Q ss_pred             CCc-ccchHHHHHHHHHHHHHhHhHHHHH-------------------------hhhhccccC----CccchhHHHHHHH
Q psy11505        258 DVK-LDEFSSLKKFRNSILSSLGDCIYVL-------------------------RFWSTVHKD----GKVLMNKLFVEML  307 (312)
Q Consensus       258 ~~~-l~~~~~~~~~~~~~~~~l~~~~~~~-------------------------~~~~~~~~~----~~~~~~~~~~~~~  307 (312)
                      |++ |.++++|+++|++++.||.+|+..+                         +.+...+..    +..++++|+.||+
T Consensus       162 Dr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~rf~kLL~~Lp~LR~l~~~~~e~l~~~k~~~p~~~~~~~ppL~~Elf  241 (241)
T cd06939         162 DRPGLQEKRKVEKLQQKIELALRHVLQKNHGDDTILTKLLAKMPTLRALCSLHMEKLQKFKQSYPDIVHLEFPPLYKELF  241 (241)
T ss_pred             CCcCCCCHHHHHHHHHHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcccCCCCcHHHhhC
Confidence            998 9999999999999999999999764                         223444555    3457899999985

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

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

Probab=99.92  E-value=3.8e-25  Score=193.76  Aligned_cols=165  Identities=16%  Similarity=0.194  Sum_probs=133.8

Q ss_pred             chhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEeccc-chhhHHhh
Q psy11505        100 PTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASD-LVLDERQA  178 (312)
Q Consensus       100 ~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g-~~~~~~~~  178 (312)
                      .....|..+.......+..+|+|||++|+|.+|+.+||++|||++|++++++..+.+...  + .+++++| .+..++..
T Consensus        60 ~~~~~~~~~~~~~~~~i~~vVewAK~IPgF~~L~~~DQi~LLk~~~~Ellil~~a~~~~~--~-~~~~~~~~~~~~~~~~  136 (259)
T cd06932          60 IRIRLFQRCQVRSVETIRELTEFAKSLPGFRNLDLNDQVTLLKYGVHEVIFTMLASLYNK--D-GLLFPEGNGYVTREFL  136 (259)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCChhHHHHHHHHhhHHHHHHHHHHhcCC--C-CeEEeCCCEEeeHHHH
Confidence            456678888888889999999999999999999999999999999999999999976432  2 4666554 44555554


Q ss_pred             hhcc--cchhhhhhcccC---ccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCcee
Q psy11505        179 RECG--FSEIYQQVKHSG---SLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLV  253 (312)
Q Consensus       179 ~~~~--~~~~~~~i~~~~---~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  253 (312)
                      ...+  ..++++.++.++   .+|++|++||                                          ++++||+
T Consensus       137 ~~~~~~~~~~~~~~~e~~~~l~~L~ld~~E~------------------------------------------alLkAiv  174 (259)
T cd06932         137 ESLRKPFCDIMEPKFEFAEKFNALELTDSEL------------------------------------------ALFCAVI  174 (259)
T ss_pred             HHhcccHHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHH
Confidence            4433  245666555544   4899999999                                          9999999


Q ss_pred             ecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH------hh--------------------hhc-cccCCccchhHHHHH
Q psy11505        254 LANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL------RF--------------------WST-VHKDGKVLMNKLFVE  305 (312)
Q Consensus       254 l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~------~~--------------------~~~-~~~~~~~~~~~~~~~  305 (312)
                      ||+||++ |.++++|+++|++++.||.+|+..+      ||                    +.. +...|.+++++|+.|
T Consensus       175 Lf~pDr~gL~~~~~Ve~lQe~~~~aL~~~i~~~~p~~~~rf~kLLl~L~~LRsl~~~~~e~l~~~k~~~~~~~~~pLl~E  254 (259)
T cd06932         175 ILSPDRPGLINRKPVERIQEHVLQALELQLKKNHPDSPQLFAKLLQKMVDLRQLVTDHVQMVQQIKKTETDASLPPLLQE  254 (259)
T ss_pred             HhCCCcccCcCHHHHHHHHHHHHHHHHHHHhhhCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCCcHHHH
Confidence            9999998 9999999999999999999999876      22                    232 345678999999999


Q ss_pred             HHhh
Q psy11505        306 MLEA  309 (312)
Q Consensus       306 ~~~~  309 (312)
                      |++.
T Consensus       255 i~~~  258 (259)
T cd06932         255 IYKD  258 (259)
T ss_pred             Hhhc
Confidence            9975

The ligand binding domain (LBD) of peroxisome proliferator-activated receptors (PPAR): Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily of ligand-activated transcription factors. PPARs play important roles in regulating cellular differentiation, development and lipid metabolism. Activated PPAR forms a heterodimer with the retinoid X receptor (RXR) that binds to the hormone response element located upstream of the peroxisome proliferator responsive genes and interacts with co-activators. There are three subtypes of peroxisome proliferator activated receptors, alpha, beta (or delta), and gamma, each with a distinct tissue distribution. Several essential fatty acids, oxidized lipids and prostaglandin J derivatives can bind and activate PPAR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, P

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

Probab=99.92  E-value=4.4e-25  Score=185.02  Aligned_cols=143  Identities=20%  Similarity=0.290  Sum_probs=127.8

Q ss_pred             chhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhh
Q psy11505        100 PTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAR  179 (312)
Q Consensus       100 ~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~  179 (312)
                      .....|+.+.+..+..+..+|+|||++|+|.+|+.+||+.|||++|+++++++.++++....+ .+.+.+|..++++...
T Consensus         9 ~~~~~~~~~~~~~~~~i~~~V~waK~iPgF~~L~~~DQi~LLk~~w~Ell~L~~a~~~~~~~~-~l~~~~~~~~~~~~~~   87 (189)
T cd06940           9 SGHEIWEEFSMSFTPAVREVVEFAKRIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFDAKER-SVTFLSGQKYSVDDLH   87 (189)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCChhhHHHHHHHhhHHHHHHHHHHHhccCCC-eEEecCCcEEcHHHHH
Confidence            355778999999999999999999999999999999999999999999999999998776655 7889899888877766


Q ss_pred             hcccchhhhhhcccCc---cCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecC
Q psy11505        180 ECGFSEIYQQVKHSGS---LDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLAN  256 (312)
Q Consensus       180 ~~~~~~~~~~i~~~~~---~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  256 (312)
                      ..+..++++.++.+..   +|++|++||                                          ++++||+|||
T Consensus        88 ~~~~~~~~~~~~~~~~~l~~L~ld~~E~------------------------------------------a~LkAivLf~  125 (189)
T cd06940          88 SMGAGDLLNSMFDFSEKLNSLQLSDEEM------------------------------------------GLFTAVVLVS  125 (189)
T ss_pred             HcCcHHHHHHHHHHHHHHHhcCCCHHHH------------------------------------------HHHHHHHHhC
Confidence            6666677776666554   999999999                                          9999999999


Q ss_pred             CCCc-ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505        257 SDVK-LDEFSSLKKFRNSILSSLGDCIYVL  285 (312)
Q Consensus       257 ~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~  285 (312)
                      ||++ +.++++|+++|++++.+|.+|+...
T Consensus       126 pd~~~L~~~~~Ve~lq~~~~~aL~~~~~~~  155 (189)
T cd06940         126 ADRSGLENVNLVEALQETLIRALRTLIAKN  155 (189)
T ss_pred             CCCcCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            9998 9999999999999999999999865

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

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

Probab=99.92  E-value=6.7e-25  Score=190.23  Aligned_cols=143  Identities=22%  Similarity=0.311  Sum_probs=115.0

Q ss_pred             chhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecc-cchhhHHhh
Q psy11505        100 PTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFAS-DLVLDERQA  178 (312)
Q Consensus       100 ~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~-g~~~~~~~~  178 (312)
                      .+...+..+++.....+..+|+|||++|+|.+|+.+||+.|||++|+++++++.++. ++..+..+.+++ +..+.....
T Consensus        34 ~~~~l~~~l~~l~~~~l~~iI~wAK~iPgF~~L~~~DQi~LLk~~~~ElliL~~~~~-~~~~~~~~~~~~~~~~~~~~~~  112 (238)
T cd06933          34 VRLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEVIMLRSNQS-FSLDDMSWTCGSPDFKYKVSDV  112 (238)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHcCCCccccCChHHHHHHHHHhHHHHHHHHHHHh-cCcCCCeeEecCCceeecHHHH
Confidence            356778899999999999999999999999999999999999999999999998875 444443455443 333344333


Q ss_pred             hhcccc-hhhhhhcc---cCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceee
Q psy11505        179 RECGFS-EIYQQVKH---SGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVL  254 (312)
Q Consensus       179 ~~~~~~-~~~~~i~~---~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  254 (312)
                      ...+.. ++.+.+..   .+++|++|++||                                          +|++||+|
T Consensus       113 ~~~g~~~~~~~~l~~~~~~l~~L~ld~~E~------------------------------------------alLkAivL  150 (238)
T cd06933         113 TKAGHSLELLEPLVKFQVGLKKLNLHEEEH------------------------------------------VLLMAICI  150 (238)
T ss_pred             HHccCcHHHHHHHHHHHHHHHhcCCCHHHH------------------------------------------HHHHHHHH
Confidence            333322 34444433   455999999999                                          99999999


Q ss_pred             cCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505        255 ANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  285 (312)
Q Consensus       255 ~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~  285 (312)
                      ||||++ |.++++|+++||+++.||.+|+..+
T Consensus       151 f~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~  182 (238)
T cd06933         151 LSPDRPGVQDHALIEAIQDRLSDTLQTYIRCR  182 (238)
T ss_pred             HCCCCCCCcchHHHHHHHHHHHHHHHHHHHhc
Confidence            999998 9999999999999999999999765

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

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

Probab=99.92  E-value=7.7e-25  Score=189.45  Aligned_cols=164  Identities=18%  Similarity=0.260  Sum_probs=137.4

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhh
Q psy11505        101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE  180 (312)
Q Consensus       101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~  180 (312)
                      ....+..++++....+..+|+|+|++|+|..|+.+||+.|+|++|+++++++.|+++... .+.+.+++|..+.++....
T Consensus        37 ~~~~~~~~~~~~~~~i~~iIefaK~lp~F~~L~~~DQi~LLK~~~~el~~L~~a~~~~~~-~~~~~f~~g~~~~~~~~~~  115 (231)
T cd06938          37 SDMRFRHITEMTILTVQLIVEFAKRLPGFDKLSREDQITLLKACSSEVMMLRVARRYDAK-TDSIVFANNQPYTRDSYRK  115 (231)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHhcCCccccCChhHHHHHHHHHHHHHHHHHHHHHhCCC-CCeEEeeCCEEecHHHHhh
Confidence            346788999999999999999999999999999999999999999999999999876554 4589999998877776555


Q ss_pred             cccchhhhhhc---ccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCC
Q psy11505        181 CGFSEIYQQVK---HSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANS  257 (312)
Q Consensus       181 ~~~~~~~~~i~---~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  257 (312)
                      .+.+++.+.++   ..+.+|++|++||                                          ++++||+||++
T Consensus       116 ~~~~~~~~~l~~~~~~l~~L~ld~~E~------------------------------------------~lL~AI~Lf~d  153 (231)
T cd06938         116 AGMGDSAEDLFRFCRAMCSMKVDNAEY------------------------------------------ALLTAIVIFSD  153 (231)
T ss_pred             cCHHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHccC
Confidence            56555555554   4455999999999                                          99999999985


Q ss_pred             CCcccchHHHHHHHHHHHHHhHhHHHHH-------hh--------------------hhccccCCccchhHHHHHHHh
Q psy11505        258 DVKLDEFSSLKKFRNSILSSLGDCIYVL-------RF--------------------WSTVHKDGKVLMNKLFVEMLE  308 (312)
Q Consensus       258 ~~~l~~~~~~~~~~~~~~~~l~~~~~~~-------~~--------------------~~~~~~~~~~~~~~~~~~~~~  308 (312)
                      ..+|+++..|+++|++|..+|.+|+..+       ||                    ++..++. ..++++|+.|++|
T Consensus       154 ~~~L~~~~~Ve~~Q~~~~~aL~~y~~~~~~~~~~~rf~kLL~~L~~Lr~l~~~~~e~~~~~k~~-~~~~~pl~~Ei~d  230 (231)
T cd06938         154 RPGLLQPKKVEKIQEIYLEALRAYVDNRRPPSQRVIFAKLLSILTELRTLGNQNSEMCFSLKLK-NRKLPPFLAEIWD  230 (231)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCCcHHHHHhC
Confidence            4449999999999999999999999765       22                    3445667 5689999999986

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

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

Probab=99.91  E-value=8e-25  Score=186.01  Aligned_cols=143  Identities=23%  Similarity=0.321  Sum_probs=117.1

Q ss_pred             chhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhh
Q psy11505        100 PTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAR  179 (312)
Q Consensus       100 ~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~  179 (312)
                      ......+.+++++.+.++.+|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+.....+..+++........ 
T Consensus        23 ~~~~~~~~~~~~a~~~L~~~VewaK~ip~F~~L~~~DQi~LLk~~w~el~iL~~a~~s~~~~~~~ll~~~~~~~~~~~~-  101 (206)
T cd06950          23 SYEVSPESVCESAARLLFMAVKWAKSIPAFSTLPFRDQLILLEESWSELFLLGAAQWSLPLDSCPLLAVPGLSPDNTEA-  101 (206)
T ss_pred             ccccCHHHHHHHHHHHHHHHHHHHHhCCccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCcceeecCCcccccccch-
Confidence            3556788999999999999999999999999999999999999999999999999999887664344444443322111 


Q ss_pred             hcccc---hhhhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecC
Q psy11505        180 ECGFS---EIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLAN  256 (312)
Q Consensus       180 ~~~~~---~~~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  256 (312)
                      .....   ..+.++...+++|++|++||                                          +++|||+|||
T Consensus       102 ~~~~~~~~~~i~~~~~~~~~L~ld~~Ey------------------------------------------alLKai~L~n  139 (206)
T cd06950         102 ERTFLSEVRALQETLSRFRQLRVDATEF------------------------------------------ACLKAIVLFK  139 (206)
T ss_pred             hhHHHHHHHHHHHHHHHHHHhCCCHHHH------------------------------------------HHHHHHHHhC
Confidence            11111   23445555667999999999                                          9999999999


Q ss_pred             CCCc-ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505        257 SDVK-LDEFSSLKKFRNSILSSLGDCIYVL  285 (312)
Q Consensus       257 ~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~  285 (312)
                      ||++ +++.++|+++|++++.||.+|+..+
T Consensus       140 pd~~~L~~~~~Ve~lq~~~~~aL~~y~~~~  169 (206)
T cd06950         140 PETRGLKDPAQVEALQDQAQLMLNKHIRTR  169 (206)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            9998 9999999999999999999999765

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

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

Probab=99.91  E-value=1.4e-24  Score=186.73  Aligned_cols=140  Identities=19%  Similarity=0.239  Sum_probs=115.0

Q ss_pred             hHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhhc
Q psy11505        102 LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC  181 (312)
Q Consensus       102 ~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~~  181 (312)
                      ...+..+++.....+..+|+|||++|+|.+|+.+||++|||++|+++++++.++++....+ .+.. +|..+........
T Consensus        34 ~~~~~~~~~~~~~~l~~iV~wAK~iPgF~~L~~~DQi~LLk~~~~Ellil~~~~~~~~~~~-~~~~-~~~~~~~~~~~~~  111 (226)
T cd06934          34 FSLLPHFADLTTYMIKQIIKFAKDLPYFRSLPIEDQISLLKGATFEICQIRFNTVFNEETG-TWEC-GPLTYCIEDAARA  111 (226)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHhcCCcccccCCcchHHHHHHHhHHHHHHHHHHHHhcccCC-eEee-CCEeecHHHHHHc
Confidence            5567888999999999999999999999999999999999999999999999988777543 4444 4444433334444


Q ss_pred             ccch-hhhhh---cccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCC
Q psy11505        182 GFSE-IYQQV---KHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANS  257 (312)
Q Consensus       182 ~~~~-~~~~i---~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  257 (312)
                      ++.. +.+.+   ...+++|++|++||                                          ++++||+||||
T Consensus       112 g~~~~~~~~~~~~~~~l~~L~ld~~E~------------------------------------------alLkAivLf~p  149 (226)
T cd06934         112 GFQQLLLEPLLRFHYTLRKLQLQEEEY------------------------------------------VLMQAMSLFSP  149 (226)
T ss_pred             cchHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHhCC
Confidence            5443 33333   34455999999999                                          99999999999


Q ss_pred             CCc-ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505        258 DVK-LDEFSSLKKFRNSILSSLGDCIYVL  285 (312)
Q Consensus       258 ~~~-l~~~~~~~~~~~~~~~~l~~~~~~~  285 (312)
                      |++ |.+.++|+++|++++.||.+|+..+
T Consensus       150 Dr~gL~~~~~Ve~lQe~~~~aL~~yi~~~  178 (226)
T cd06934         150 DRPGVTQHDVIDQLQEKMALTLKSYIDSK  178 (226)
T ss_pred             CCcCCcChHHHHHHHHHHHHHHHHHHHHc
Confidence            998 9999999999999999999999765

The ligand binding domain of xenobiotic receptors: This xenobiotic receptor family includes pregnane X receptor (PXR), constitutive androstane receptor (CAR) and other related nuclear receptors. They function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The nuclear receptor pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. The ligand binding domain of PXR shows remarkable flexibility to accommodate both large and small molecules. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and elimination of

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

Probab=99.90  E-value=2.5e-24  Score=183.65  Aligned_cols=140  Identities=28%  Similarity=0.466  Sum_probs=122.6

Q ss_pred             HHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhhcc
Q psy11505        103 QTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECG  182 (312)
Q Consensus       103 ~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~~~  182 (312)
                      ..+..++++....+..+|+|+|++|+|.+|+.+||+.|+|++|++++++..||+++...+ .+++++|..+.++.....+
T Consensus        30 ~~~~~~~~~~~~~l~~~Iewak~lp~F~~L~~~DQ~~LLk~~~~e~~~l~~a~~s~~~~~-~~~~~~~~~~~~~~~~~~~  108 (207)
T cd06943          30 DPVSNICQAADKQLFQLVEWAKRIPHFSELPLDDQVILLRAGWNELLIAAFAHRSIAVKD-GILLATGLHLHRNSAHQAG  108 (207)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHhCchhhccChhhhHHHHHHHHHHHHHHHHHHHccCCCC-eeEecCCceeccchhhhcc
Confidence            456799999999999999999999999999999999999999999999999999998866 6888888777665544444


Q ss_pred             cchh----hhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCCC
Q psy11505        183 FSEI----YQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSD  258 (312)
Q Consensus       183 ~~~~----~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  258 (312)
                      ...+    ++++...+++|++|++||                                          +++|||+|||||
T Consensus       109 ~~~~~~~~~~~~~~~l~~L~ld~~E~------------------------------------------~lLkaI~L~~pd  146 (207)
T cd06943         109 VGAIFDRILTELVVKMRDLKMDRTEL------------------------------------------GCLRAIILFNPD  146 (207)
T ss_pred             chHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHhcCCC
Confidence            4443    445555677999999999                                          999999999999


Q ss_pred             Cc-ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505        259 VK-LDEFSSLKKFRNSILSSLGDCIYVL  285 (312)
Q Consensus       259 ~~-l~~~~~~~~~~~~~~~~l~~~~~~~  285 (312)
                      ++ |++++.|+++|++|+.+|.+|+..+
T Consensus       147 ~~~L~~~~~v~~~q~~~~~aL~~y~~~~  174 (207)
T cd06943         147 VKGLKSRQEVESLREKVYASLEEYCRQK  174 (207)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            97 9999999999999999999999765

The ligand binding domain of the retinoid X receptor (RXR) and Ultraspiracle (USP): This family includes two evolutionary related nuclear receptors: retinoid X receptor (RXR) and Ultraspiracle (USP). RXR is a nuclear receptor in mammalian and USP is its counterpart in invertebrates. The native ligand of retinoid X receptor is 9-cis retinoic acid (RA). RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. RXRs can play different roles in these heterodimers. It acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, func

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

Probab=99.90  E-value=5.7e-24  Score=183.23  Aligned_cols=171  Identities=20%  Similarity=0.250  Sum_probs=134.4

Q ss_pred             CCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhH
Q psy11505         96 PQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDE  175 (312)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~  175 (312)
                      |...+....+..+++++.+++..+++|+|++|+|..|+.+||+.|+|++|.+++++..++++.+...+.+..+.+.+...
T Consensus        14 ~~~~~~~~~~~~~~~~a~~~l~~~v~wak~iP~F~~L~~~DQ~~LLk~~w~el~lL~~~~~~~~~~~~~~~~~~~~~~~~   93 (222)
T cd06952          14 PSPMPSYLNVHYICESASRLLFLSIHWARSIPAFQALGAETQTSLVRACWPELFTLGLAQCSQQLSLPTILAAIINHLQT   93 (222)
T ss_pred             CCCCcccCCHHHHHHHHHHHHHHHHHHHHhCCchhhCChHHHHHHHHHHhHHHHHHHHHHHhcccCchHHhhhhhhhhhh
Confidence            34445556688999999999999999999999999999999999999999999999999888766654333333222211


Q ss_pred             H----hhhhcccchh------hhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505        176 R----QARECGFSEI------YQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ  245 (312)
Q Consensus       176 ~----~~~~~~~~~~------~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (312)
                      .    .........+      +..+...+++|++|++||                                         
T Consensus        94 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~-----------------------------------------  132 (222)
T cd06952          94 SIQQDKLSADKVKQVMEHINKLQEFVNSMQKLDVDDHEY-----------------------------------------  132 (222)
T ss_pred             hHhcCCCchhhhHHHHHHHHHHHHHHHHHHHcCCCHHHH-----------------------------------------
Confidence            1    1111111111      234455666999999999                                         


Q ss_pred             cCCCCceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------------------------hhhhccccCCccc
Q psy11505        246 TGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------------------------RFWSTVHKDGKVL  298 (312)
Q Consensus       246 ~~~~~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------------------------~~~~~~~~~~~~~  298 (312)
                       +++|||+||+||++ +++.+.++++|++++.+|.+|+..+                          +.+++.+++|.+|
T Consensus       133 -~~LkaiiLf~~d~~~l~~~~~v~~lq~~i~~aL~~y~~~~~p~~~~R~~klLl~Lp~Lr~~~~~~~e~l~~~~~~g~~~  211 (222)
T cd06952         133 -AYLKAIVLFSPDHPGQELRQQIEKLQEKALMELRDYVGKTYPEDEYRLSKLLLRLPPLRSLSPAITEELFFAGLIGNVQ  211 (222)
T ss_pred             -HHHHHHHHhCCCCcCCcCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHhHHhhhcCHHHHHHHhcccccCCCc
Confidence             99999999999998 9999999999999999999999654                          3366789999999


Q ss_pred             hhHHHHHHHh
Q psy11505        299 MNKLFVEMLE  308 (312)
Q Consensus       299 ~~~~~~~~~~  308 (312)
                      +++++..+|-
T Consensus       212 ~~~ll~~~~~  221 (222)
T cd06952         212 IDSVIPYILR  221 (222)
T ss_pred             HHHHHHHHHh
Confidence            9999999873

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

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

Probab=99.89  E-value=2.8e-23  Score=172.41  Aligned_cols=139  Identities=22%  Similarity=0.341  Sum_probs=120.0

Q ss_pred             HHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhhccc
Q psy11505        104 TINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGF  183 (312)
Q Consensus       104 ~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~~~~  183 (312)
                      .+..+++..+..+..+|+|||++|+|..|+.+||+.|+|++|+++++++.++++.+. .+.+.+++|...+.......+.
T Consensus         3 ~~~~~~~~~~~~l~~~v~~ak~ip~F~~L~~~Dq~~Llk~~~~~l~~l~~a~~~~~~-~~~~~~~~~~~~~~~~~~~~~~   81 (174)
T cd06929           3 KFDHFTEIMTVAIRRVVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATLYDPE-KNSLTFGDGKGNSRDVLLNGGF   81 (174)
T ss_pred             HHHHHHHHHHHHHHHHHhhccCCcCcccCChhHHHHHHHhcHHHHHHHHHHHHhccc-CCeEEecCCceecHHHHHHccc
Confidence            578889999999999999999999999999999999999999999999999866554 4589999998766655444455


Q ss_pred             chhhhhhcc---cCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCCCCc
Q psy11505        184 SEIYQQVKH---SGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVK  260 (312)
Q Consensus       184 ~~~~~~i~~---~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  260 (312)
                      .++.+.+..   .+++|++|++||                                          ++++||+|||||+.
T Consensus        82 ~~~~~~~~~~~~~l~~L~l~~~E~------------------------------------------~llkai~l~~pd~~  119 (174)
T cd06929          82 GEFIEPLFEFAEKMNKLQLDDNEY------------------------------------------ALLTAIVLFSPDRP  119 (174)
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHhCCCcc
Confidence            555555444   455999999999                                          99999999999997


Q ss_pred             -ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505        261 -LDEFSSLKKFRNSILSSLGDCIYVL  285 (312)
Q Consensus       261 -l~~~~~~~~~~~~~~~~l~~~~~~~  285 (312)
                       ++++..|++.|+++..+|.+|+..+
T Consensus       120 ~l~~~~~v~~~q~~~~~aL~~y~~~~  145 (174)
T cd06929         120 GLQDVDTVEKLQERLLEALQRYLKVN  145 (174)
T ss_pred             cCcCHHHHHHHHHHHHHHHHHHHHhc
Confidence             9999999999999999999999765

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

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

Probab=99.89  E-value=3.4e-23  Score=170.37  Aligned_cols=138  Identities=28%  Similarity=0.410  Sum_probs=118.8

Q ss_pred             hhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCC-CeeEecccchhhHHhhhhcccc
Q psy11505        106 NSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCA-GKIRFASDLVLDERQARECGFS  184 (312)
Q Consensus       106 ~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~-~~l~~~~g~~~~~~~~~~~~~~  184 (312)
                      +.++++..+.+..+|||||++|+|.+|+.+||+.|+|++|.+++++..||++++.+. +.+.+++|..++.......+..
T Consensus         2 ~~~~~~~~~~l~~~ie~ak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (165)
T cd06930           2 ESLCELADRVLFKTVDWAKNLPAFRNLPLDDQLTLLQNSWAELLLLGLAQRSVHFELSELLLPSPLLVILTEREALLGLA   81 (165)
T ss_pred             hhHHHHHHHHHHHHHHHHHcCCccccCChHHHHHHHHHHHHHHHHHHHHHHHhccCCCcceeecCCcccchhhhhhhhHH
Confidence            467889999999999999999999999999999999999999999999999998853 5788888887776544332322


Q ss_pred             h---hhhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCCCCc-
Q psy11505        185 E---IYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVK-  260 (312)
Q Consensus       185 ~---~~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-  260 (312)
                      +   .+..+...+.+|++|++||                                          ++++||++|+||++ 
T Consensus        82 ~~~~~~~~~~~~l~~L~l~~~E~------------------------------------------~lLkai~l~~p~~~~  119 (165)
T cd06930          82 ELVQRLQELLSKLRSLQLDPKEY------------------------------------------ACLKAIVLFNPDLPG  119 (165)
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHcCCCCCC
Confidence            2   3345566667999999999                                          99999999999997 


Q ss_pred             ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505        261 LDEFSSLKKFRNSILSSLGDCIYVL  285 (312)
Q Consensus       261 l~~~~~~~~~~~~~~~~l~~~~~~~  285 (312)
                      +++.+.+++.|++++.+|.+|+..+
T Consensus       120 l~~~~~v~~~q~~~~~aL~~~~~~~  144 (165)
T cd06930         120 LKNQQQVEELQEKAQQALQEYIRKR  144 (165)
T ss_pred             CcCHHHHHHHHHHHHHHHHHHHHhh
Confidence            9999999999999999999999754

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).

>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=99.88  E-value=5.1e-23  Score=176.65  Aligned_cols=137  Identities=18%  Similarity=0.238  Sum_probs=109.4

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccc-hhhHHhhh
Q psy11505        101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDL-VLDERQAR  179 (312)
Q Consensus       101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~-~~~~~~~~  179 (312)
                      ....+..+++|....+..+|+|||++|+|.+|+.+||+.|||++|+++++++.|+.+...      +++|. .+......
T Consensus        34 ~~~~~~~~~e~a~~~l~~~IefaK~iP~F~~L~~~DQi~LLk~~~~el~iL~~a~~~~~~------~~~~~~~~~~~~~~  107 (221)
T cd06936          34 PEENFLILTEMATSHVQVLVEFTKGLPGFETLDHEDQIALLKGSAVEAMFLRSAQIYNKK------LPAGHADLLEERIR  107 (221)
T ss_pred             HhHHHHHHHHHHHHHHHHHHHHHhCCCchhhCChhHHHHHHHHhHHHHHHHHHHHHhccc------ccCCCchhhHHHHH
Confidence            357899999999999999999999999999999999999999999999999988554321      22222 11111112


Q ss_pred             hcc-cchhhhhhccc---CccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeec
Q psy11505        180 ECG-FSEIYQQVKHS---GSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLA  255 (312)
Q Consensus       180 ~~~-~~~~~~~i~~~---~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  255 (312)
                      ..+ ..++++.++.+   +.+|++|++||                                          ++++||++|
T Consensus       108 ~~~~~~e~~~~i~~~~~kl~~L~l~~~E~------------------------------------------~lLkaIvL~  145 (221)
T cd06936         108 SSGISDEFITPMFNFYKSMGELKMTQEEY------------------------------------------ALLTAITIL  145 (221)
T ss_pred             hccchHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHh
Confidence            222 23455555444   44999999999                                          999999999


Q ss_pred             CCCCc-ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505        256 NSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  285 (312)
Q Consensus       256 ~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~  285 (312)
                      |||++ |++++.|+.+|++|+.||.+||...
T Consensus       146 npd~~gL~~~~~Ve~~Q~~~~~aL~~y~~~~  176 (221)
T cd06936         146 FPDRPYLKDKEAVEKLQEPLLDLLQKFCKLY  176 (221)
T ss_pred             cCCCcCCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            99998 9999999999999999999999765

The ligand binding domain (LBD) of Farnesoid X receptor: Farnesoid X receptor (FXR) is a member of the nuclear receptor superfamily of ligand-activated transcription factors. FXR is highly expressed in the liver, the intestine, the kidney, and the adrenals. FXR plays key roles in the regulation of bile acid, cholesterol, triglyceride, and glucose metabolism. Evidences show that it also regulates liver regeneration. Upon binding of ligands, such as bile acid, an endogenous ligand, FXRs bind to FXR response elements (FXREs) either as a monomer or as a heterodimer with retinoid X receptor (RXR), and regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. There are two FXR genes (FXRalpha and FXRbeta) in mammals. A single FXRalpha gene encodes four isoforms resulting from differential use of prom

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

Probab=99.88  E-value=4.6e-23  Score=176.01  Aligned_cols=146  Identities=21%  Similarity=0.215  Sum_probs=114.3

Q ss_pred             CCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeE----ecccch
Q psy11505         97 QSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIR----FASDLV  172 (312)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~----~~~g~~  172 (312)
                      .+......+..+++...+.+..+|+|||++|+|.+|+.+||+.|+|++|+++++++.||++++.+...+.    .+.|.-
T Consensus        21 ~~~~~~~~~~~l~~la~~~l~~~I~waK~lp~F~~L~~~DQi~LLk~~w~el~iL~~a~~s~~~~~~~l~~~~~~~~~~~  100 (213)
T cd06953          21 ATVDQAELFALLCRLGDELLFRQIQWTKKLPFFTELSIKDHTHLLTTKWAELILLSTITVASLQNLGLLQDCLSKYLPSE  100 (213)
T ss_pred             CCcchhhHHHHHHHHHHHHHHHHHHHHhcCCchhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHhhhccCCch
Confidence            3344567889999999999999999999999999999999999999999999999999999986532111    111110


Q ss_pred             hhHHhhhhcccchhhh---hhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCC
Q psy11505        173 LDERQARECGFSEIYQ---QVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGAC  249 (312)
Q Consensus       173 ~~~~~~~~~~~~~~~~---~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  249 (312)
                      ...... .....++.+   ++...+++|++|++||                                          +++
T Consensus       101 ~~~~~~-~~~~~~~~~~i~~l~~~l~~L~ld~eEy------------------------------------------~lL  137 (213)
T cd06953         101 DELERF-GDEGGEVVERLTYLLAKFRQLKVSNEEY------------------------------------------VCL  137 (213)
T ss_pred             hhHHHH-HhhHHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHH
Confidence            000000 111223333   4445556999999999                                          999


Q ss_pred             CceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505        250 GTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  285 (312)
Q Consensus       250 ~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~  285 (312)
                      |||+|||||++ +++.++|+++|++|..+|.+|+..+
T Consensus       138 kAIvLfnpd~~gLs~~~~Ve~lQ~~~~~aL~~y~~~~  174 (213)
T cd06953         138 KVINFLNQDIDGLTNASQLESLQKRYWYVLQDFTELN  174 (213)
T ss_pred             HHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999998 9999999999999999999999755

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

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

Probab=99.85  E-value=1.5e-21  Score=164.15  Aligned_cols=137  Identities=14%  Similarity=0.143  Sum_probs=112.8

Q ss_pred             HHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhh-hcc
Q psy11505        104 TINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAR-ECG  182 (312)
Q Consensus       104 ~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~-~~~  182 (312)
                      .|..+.+...+.+..+|+|+|++|+|..|+.+||+.|+|++|+++++++.++++.+.   .+.+++|..+...... ..+
T Consensus         3 ~w~~~~~~~~~~i~~~IefaK~iPgF~~L~~~DQi~LLk~~~~e~~ll~~~~~~~~~---~~~~~~g~~~~~~~~~~~~~   79 (191)
T cd06942           3 AWGHFAHEFEMHIQEIVQFVKSIPGFNQLSGEDRAQLLKGNMFPLYLLRLSRDYNNE---GTVLCDFRPVEFASLLSQLL   79 (191)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCcccCChhHHHHHHHHHHHHHHHHHHHHHhCcC---CeEEeCCccccHHHHHHhcc
Confidence            578889999999999999999999999999999999999999999999877554444   3566667665544321 222


Q ss_pred             cchhhhhhcc---cCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCCC-
Q psy11505        183 FSEIYQQVKH---SGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSD-  258 (312)
Q Consensus       183 ~~~~~~~i~~---~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~-  258 (312)
                      ..++++++..   .+.+|++|++||                                          ++++||++|+|| 
T Consensus        80 ~~~~~~~~~~~~~~l~~L~l~~~E~------------------------------------------~lL~Aivl~~pd~  117 (191)
T cd06942          80 HGKLIDEMLQFANKILTLNLTNAEL------------------------------------------ALLCAAELLQPDS  117 (191)
T ss_pred             hHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHhCCCC
Confidence            3455554444   445999999999                                          999999999999 


Q ss_pred             -Cc-ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505        259 -VK-LDEFSSLKKFRNSILSSLGDCIYVL  285 (312)
Q Consensus       259 -~~-l~~~~~~~~~~~~~~~~l~~~~~~~  285 (312)
                       ++ ++++++|+.+|+.+..+|.+|+..+
T Consensus       118 ~~~~l~~~~~v~~~q~~l~~~L~~~~~~~  146 (191)
T cd06942         118 LGIQLEETAKSNLQLSVLFQFLKSVLFKD  146 (191)
T ss_pred             CCCCccchHHHHHHHHHHHHHHHHHHHhc
Confidence             87 9999999999999999999999754

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

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

Probab=99.76  E-value=1.2e-18  Score=143.04  Aligned_cols=137  Identities=28%  Similarity=0.426  Sum_probs=113.5

Q ss_pred             hHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccch---hhHHhhhh---
Q psy11505        107 SLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLV---LDERQARE---  180 (312)
Q Consensus       107 ~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~---~~~~~~~~---  180 (312)
                      .+.+++..++..+++|++++|+|+.|+.+||+.|+|++|+++++|+.+|+++..+......+++..   ........   
T Consensus         2 ~~~~~~~~~~~~~i~~~~~~~~f~~L~~~dq~~Llk~~~~~~~~L~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (168)
T cd06157           2 LLCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLLLAPNGGHTDDDKEDEMKLLLK   81 (168)
T ss_pred             cHHHHHHHHHHHHHHHHHcCCchhcCChHHHHHHHHHHhHHHHHHHHHHHHHhcCCCcEEeecccccccCchHHHHHhHH
Confidence            467899999999999999999999999999999999999999999999999999885555544432   11111111   


Q ss_pred             cccchhhhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCCCCc
Q psy11505        181 CGFSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVK  260 (312)
Q Consensus       181 ~~~~~~~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  260 (312)
                      ....+.+..+...+.+|++|++||                                          ++++||++|+|+.+
T Consensus        82 ~~~~~~~~~~~~~~~~L~l~~~E~------------------------------------------~~l~ai~l~~~~~~  119 (168)
T cd06157          82 GELIRLLFEFVNPLRALKLDDEEY------------------------------------------ALLKAIVLFSPDRK  119 (168)
T ss_pred             HHHHHHHHHHHHHHHHhCCCHHHH------------------------------------------HHHHHHHHhCCCCC
Confidence            112345566777777999999999                                          99999999999985


Q ss_pred             --ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505        261 --LDEFSSLKKFRNSILSSLGDCIYVL  285 (312)
Q Consensus       261 --l~~~~~~~~~~~~~~~~l~~~~~~~  285 (312)
                        ......+++.|+++..+|..|+...
T Consensus       120 ~s~~~~~~~~~~~~~~~~~L~~y~~~~  146 (168)
T cd06157         120 ESLEDRKIVEELQERLLEALQDYLRKN  146 (168)
T ss_pred             CCccCHHHHHHHHHHHHHHHHHHHHHh
Confidence              7888899999999999999999665

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=99.74  E-value=1.1e-18  Score=142.44  Aligned_cols=131  Identities=25%  Similarity=0.348  Sum_probs=109.7

Q ss_pred             HHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhh------hcccchh
Q psy11505        113 DRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAR------ECGFSEI  186 (312)
Q Consensus       113 ~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~------~~~~~~~  186 (312)
                      ..++..+++|++++|+|.+|+.+||+.|+|++|.++++++.++++++.+.+.+.+++|.........      .......
T Consensus         2 ~~~~~~~~~~~~~~~~f~~L~~~dq~~Llk~~~~~~~~l~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (163)
T smart00430        2 ERDLLLAVEWAKTFPFFRELSQEDKLILLKHFWFEWLLLESAYRSAKMKKSLLLLPDGTFIDNDKVDLLRKLFSPFLDRI   81 (163)
T ss_pred             hhHHHHHHHHHHhChhHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEeCCCcccCcchhHHHHHHHHHHHHHH
Confidence            4678999999999999999999999999999999999999999999988765666766655432211      1122345


Q ss_pred             hhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCCCCc-ccch-
Q psy11505        187 YQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVK-LDEF-  264 (312)
Q Consensus       187 ~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-l~~~-  264 (312)
                      ++.+...+.+|++|++||                                          ++++|+++|+||.+ +++. 
T Consensus        82 ~~~~~~~l~~L~l~~~E~------------------------------------------~~l~ai~l~~~~~~~l~~~~  119 (163)
T smart00430       82 LQELVKPLRELKLDDEEY------------------------------------------ALLKAILLFNPAGPGLSEEG  119 (163)
T ss_pred             HHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHcChhhhhhChHH
Confidence            667777788999999999                                          99999999999987 8888 


Q ss_pred             -HHHHHHHHHHHHHhHhHHHHH
Q psy11505        265 -SSLKKFRNSILSSLGDCIYVL  285 (312)
Q Consensus       265 -~~~~~~~~~~~~~l~~~~~~~  285 (312)
                       ..++++|+.+..+|.+|+..+
T Consensus       120 ~~~~~~~~~~~~~~L~~y~~~~  141 (163)
T smart00430      120 KEILEKLQEKLANALHDYYLKN  141 (163)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHc
Confidence             789999999999999999654

>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=99.73  E-value=1.1e-17  Score=141.74  Aligned_cols=143  Identities=29%  Similarity=0.508  Sum_probs=119.4

Q ss_pred             CCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHh
Q psy11505         98 SDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQ  177 (312)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~  177 (312)
                      ...+..++.++.+++...+..+++|++++|+|.+|+.+||+.|+|++|+++++|+.++++.....+.+.+++|...+...
T Consensus        12 ~~~~~~~~~~~~~~~~~~~~~~v~~~k~~p~f~~L~~~dk~~Llk~~~~~~~~l~~~~~s~~~~~~~~~~~~~~~~~~~~   91 (203)
T PF00104_consen   12 QELRPATFEDLCEIWRRELRLIVDWAKSFPEFSELSMEDKIALLKSSWFELFILELAYRSYQCNQDQLMFPNGTFIDKDS   91 (203)
T ss_dssp             SSSHHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGS-HHHHHHHHHHHHHHHHHHHHHHHEEHTTTTEEEETTTEEEEHHH
T ss_pred             CCCcHhhHHHHHHHHHHHHHHHHHHHHhCcCHHhhhhhhhhhHHhhhcccccchhhhhhhcccccccccccccccccccc
Confidence            44577889999999999999999999999999999999999999999999999999999995444689999998876554


Q ss_pred             hhhc---ccch---hhhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCc
Q psy11505        178 AREC---GFSE---IYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGT  251 (312)
Q Consensus       178 ~~~~---~~~~---~~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  251 (312)
                      ....   ...+   .+..+...+.++++|++||                                          ++++|
T Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~l~l~~~E~------------------------------------------~~l~~  129 (203)
T PF00104_consen   92 FDDFITGIFSEFIQYMNEVLRPFRRLKLDEEEF------------------------------------------ALLKA  129 (203)
T ss_dssp             HHHTSTTTHHHHHHHHHHHHHHHHHTT-BHHHH------------------------------------------HHHHH
T ss_pred             cccccccccccchhHHHHHHHHHHHhhhhhHHH------------------------------------------HHHHH
Confidence            4333   1222   3345555677999999999                                          99999


Q ss_pred             eeecCCCCc-cc-chHH-HHHHHHHHHHHhHhHH
Q psy11505        252 LVLANSDVK-LD-EFSS-LKKFRNSILSSLGDCI  282 (312)
Q Consensus       252 ~~l~~~~~~-l~-~~~~-~~~~~~~~~~~l~~~~  282 (312)
                      +++++||.. ++ +... +++.|+++..+|.+|+
T Consensus       130 l~l~~~~~~~~~~~~~~~~~~~r~~~~~~L~~y~  163 (203)
T PF00104_consen  130 LILFNPDYPGLSEETREIVEELRDRIIQALHSYY  163 (203)
T ss_dssp             HHHSSTTSTTHS-SHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhhhcccccccccchhHHHHHHHHHHHHHHHHHH
Confidence            999999987 66 5555 9999999999999999

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 ....

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

Probab=99.55  E-value=1.6e-15  Score=109.51  Aligned_cols=51  Identities=45%  Similarity=0.931  Sum_probs=46.6

Q ss_pred             CceeEcCCCCCcccccccccccccCchhHHHHhcccccccccccccccccc
Q psy11505          1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQK   51 (312)
Q Consensus         1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~~~~   51 (312)
                      +..|.|..+++|.|+...|+.||+|||+||++|||++++||.+|++.++++
T Consensus        33 ~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~~~~~   83 (85)
T cd06961          33 KLSYSCKGEGKCEIDKVTRNQCQECRFKKCIAVGMAKDLVLDDRKRGAKRK   83 (85)
T ss_pred             CCccccCCCCccccCccccccCccchhhhhhhccCCHHHcccccCcccccc
Confidence            357999999999999999999999999999999999999999999876654

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

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

Probab=99.54  E-value=2.9e-15  Score=110.37  Aligned_cols=52  Identities=83%  Similarity=1.525  Sum_probs=47.1

Q ss_pred             ceeEcCCCCCcccccccccccccCchhHHHHhcccccccccccccccccccc
Q psy11505          2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYR   53 (312)
Q Consensus         2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~~~~~~   53 (312)
                      ..|.|.++++|.|++..|+.||+|||+|||+|||++++||.+|+..++++..
T Consensus        39 ~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~vq~~r~~~~~~~~~   90 (97)
T cd07170          39 IEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQKYK   90 (97)
T ss_pred             CceeecCCCccccCcccCccCCccccchhhhcCCCHHHcccccCCCCCCCcc
Confidence            5699999999999999999999999999999999999999999887765543

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

>KOG4846|consensus

Probab=99.52  E-value=3.9e-15  Score=132.08  Aligned_cols=48  Identities=40%  Similarity=0.890  Sum_probs=43.2

Q ss_pred             Ccee-EcCCCCCcccccccccccccCchhHHHHhccccccccccccccc
Q psy11505          1 NIEY-TCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG   48 (312)
Q Consensus         1 ~~~Y-~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~   48 (312)
                      |..| .|.+..+|.|.+..||+||+|||+|||+|||+++||+..+++..
T Consensus       166 kI~YrrClk~e~C~I~R~nRNRCQ~CRfKKCL~vGMSrDaVRFG~m~~r  214 (538)
T KOG4846|consen  166 KIDYRRCLKQEVCEIKRENRNRCQYCRFKKCLDVGMSRDAVRFGQMKFR  214 (538)
T ss_pred             hhhHHHHhhhhceehhhhccchhhhhhHHHHHhcccchhhhhhcccccc
Confidence            4578 69999999999999999999999999999999999998876543

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

Probab=99.51  E-value=4.5e-15  Score=108.15  Aligned_cols=49  Identities=37%  Similarity=0.888  Sum_probs=45.9

Q ss_pred             ceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccccccc
Q psy11505          2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQ   50 (312)
Q Consensus         2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~~~   50 (312)
                      ..|.|..+++|.|+...|..||+|||+|||+|||++++||.+|++++++
T Consensus        41 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~~~~   89 (90)
T cd07169          41 RVYRCSRDKNCVMSRKQRNRCQYCRLLKCLQMGMNRKAIREDGMPGGRN   89 (90)
T ss_pred             CceecCCCCcccccccccccccccchhhhccccCCHHHhccccCCCCCC
Confidence            5799999999999999999999999999999999999999999988765

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).

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

Probab=99.50  E-value=5.8e-15  Score=107.92  Aligned_cols=52  Identities=54%  Similarity=1.059  Sum_probs=47.2

Q ss_pred             CceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccccccccc
Q psy11505          1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKY   52 (312)
Q Consensus         1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~~~~~   52 (312)
                      +..|+|..+++|.|+...|+.|++|||+|||+|||++++||.+|.++++.+.
T Consensus        32 ~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~Vq~~r~~~~~~~~   83 (93)
T cd07167          32 KKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMRGGRNKF   83 (93)
T ss_pred             CCccccCCCCccccCccccCcCCCcccchhhhccCCHHHhhhcccCCCcccc
Confidence            3579999999999999999999999999999999999999999987776553

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

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

Probab=99.50  E-value=6.6e-15  Score=107.35  Aligned_cols=50  Identities=52%  Similarity=1.028  Sum_probs=45.9

Q ss_pred             CceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccccccc
Q psy11505          1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQ   50 (312)
Q Consensus         1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~~~   50 (312)
                      +..|.|..+++|.|+...|..||+|||+|||+|||++++||.+|+++++.
T Consensus        40 ~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R~~~~~~   89 (90)
T cd07168          40 KRVYTCVGDGRCEITKAQRNRCQYCRFRKCIRKGMMLAAVREDRMPGGRN   89 (90)
T ss_pred             CCCccCCCCCCccccccccccccccchhhhhhcCCCHHHhhcccCCCCCC
Confidence            35789999999999999999999999999999999999999999887653

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

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

Probab=99.49  E-value=9.1e-15  Score=105.93  Aligned_cols=46  Identities=46%  Similarity=0.884  Sum_probs=43.2

Q ss_pred             ceeEcCCCCCcccccccccccccCchhHHHHhcccccccccccccc
Q psy11505          2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG   47 (312)
Q Consensus         2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~   47 (312)
                      ..|+|.++++|.|++..|..||+|||+|||+|||++++||.+|++.
T Consensus        38 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~R~~~   83 (87)
T cd06967          38 LGYSCRGSKDCVINKHHRNRCQYCRLQKCLAMGMKSDSVQCERKPI   83 (87)
T ss_pred             CCcccCCCCccccCccccccCccchhhhhhHcCCCHHHhccccCCC
Confidence            5789999999999999999999999999999999999999999764

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

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

Probab=99.49  E-value=9.8e-15  Score=103.86  Aligned_cols=45  Identities=38%  Similarity=0.910  Sum_probs=42.5

Q ss_pred             ceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccc
Q psy11505          2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR   46 (312)
Q Consensus         2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~   46 (312)
                      ..|+|..+++|.|++..|..||+|||+|||+|||++++||.+|++
T Consensus        33 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~   77 (78)
T cd07164          33 LAYVCKENGSCVVDVARRNQCQACRFKKCLQVNMNRDAVQHERAP   77 (78)
T ss_pred             CCccCCCCCcccccCcccccCccchhhhhhHhcCCHHHhccCCCC
Confidence            578999999999999999999999999999999999999999874

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

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

Probab=99.48  E-value=1.1e-14  Score=105.03  Aligned_cols=45  Identities=51%  Similarity=0.933  Sum_probs=42.4

Q ss_pred             ceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccc
Q psy11505          2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR   46 (312)
Q Consensus         2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~   46 (312)
                      ..|.|..+++|.|++..|..||+|||+|||+|||++++||.+|++
T Consensus        39 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~R~~   83 (85)
T cd06964          39 MVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNK   83 (85)
T ss_pred             CCeECCCCCccccCCcccccCccchhhhhhhhCCCHHHhhccccC
Confidence            569999999999999999999999999999999999999999865

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

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

Probab=99.48  E-value=9.6e-15  Score=103.54  Aligned_cols=44  Identities=50%  Similarity=1.051  Sum_probs=41.1

Q ss_pred             CceeEcCCCCCcccccccccccccCchhHHHHhccccccccccc
Q psy11505          1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR   44 (312)
Q Consensus         1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r   44 (312)
                      +..|+|..+++|.|++..|+.||+|||+|||+|||++++||.+|
T Consensus        34 ~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r   77 (77)
T cd06956          34 DLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER   77 (77)
T ss_pred             CCccccCCCCccccCCCccccCccchhHHHhHhCCCHHHhccCC
Confidence            35799999999999999999999999999999999999999875

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

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

Probab=99.47  E-value=1.4e-14  Score=102.29  Aligned_cols=43  Identities=67%  Similarity=1.421  Sum_probs=40.7

Q ss_pred             ceeEcCCCCCcccccccccccccCchhHHHHhccccccccccc
Q psy11505          2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR   44 (312)
Q Consensus         2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r   44 (312)
                      ..|.|..+++|.|++..|..||+|||+|||+|||++++||.+|
T Consensus        33 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r   75 (75)
T cd07155          33 LGYSCPSTSECEVDKKRRKSCQACRLQKCLKVGMLKEGVRLDR   75 (75)
T ss_pred             CceeCCcCCCcccCCcccccCccchhhhhhHhCCCHHHcccCC
Confidence            5799999999999999999999999999999999999999875

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

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

Probab=99.46  E-value=1.7e-14  Score=103.32  Aligned_cols=46  Identities=48%  Similarity=0.957  Sum_probs=43.1

Q ss_pred             ceeEcCCCCCcccccccccccccCchhHHHHhcccccccccccccc
Q psy11505          2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG   47 (312)
Q Consensus         2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~   47 (312)
                      ..|.|..+++|.|++..|..|++|||+|||+|||++++||.+|++.
T Consensus        33 ~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~V~~~r~~~   78 (81)
T cd07165          33 IEYRCLRDGKCEIIRLNRNRCQYCRFKKCLAAGMSKDSVRYGRIPN   78 (81)
T ss_pred             CceeCCCCCCccccccccccccchhhhhcccccCCHHHcccCCCCc
Confidence            5799999999999999999999999999999999999999998763

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,

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

Probab=99.46  E-value=1.9e-14  Score=102.00  Aligned_cols=44  Identities=43%  Similarity=0.887  Sum_probs=41.4

Q ss_pred             ceeEcCCCCCcccccccccccccCchhHHHHhcccccccccccc
Q psy11505          2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV   45 (312)
Q Consensus         2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~   45 (312)
                      ..|.|..+++|.|+...|..|++|||+|||+|||++++||.+|+
T Consensus        33 ~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~   76 (76)
T cd06960          33 RTYTCRFGGNCVVDKDKRNACRYCRFKKCLEVGMDPEAVQNERD   76 (76)
T ss_pred             CceeCCCCCcccccCcccccCccchhhhhhhcCCCHHHcccCCC
Confidence            57899999999999999999999999999999999999999874

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

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

Probab=99.46  E-value=1.9e-14  Score=103.18  Aligned_cols=46  Identities=39%  Similarity=0.785  Sum_probs=42.1

Q ss_pred             ceeEcC-CCCCcccccccccccccCchhHHHHhcccccccccccccc
Q psy11505          2 IEYTCP-ASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG   47 (312)
Q Consensus         2 ~~Y~C~-~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~   47 (312)
                      ..|.|. .+++|.|+...|+.||+|||+||++|||++++||.+|++.
T Consensus        33 ~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~p~   79 (82)
T cd06957          33 IIYTCIAGNGNCVVDKARRNWCPFCRLQKCFAVGMNRAAVQEERGPR   79 (82)
T ss_pred             CceEccCccCCCccCCCccCcccCcchhhcccccCCHHHhccccCcC
Confidence            579999 5789999999999999999999999999999999988654

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

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

Probab=99.45  E-value=2.7e-14  Score=102.18  Aligned_cols=43  Identities=56%  Similarity=1.200  Sum_probs=40.7

Q ss_pred             ceeEcCCCCCcccccccccccccCchhHHHHhccccccccccc
Q psy11505          2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR   44 (312)
Q Consensus         2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r   44 (312)
                      ..|+|.++++|.|+...|+.||+|||+|||+|||++++|+.+|
T Consensus        38 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~~   80 (82)
T cd07171          38 NDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRRER   80 (82)
T ss_pred             CceeCCCCCccccCCcccccCccchhHHHhHhcCCHHHHHHhh
Confidence            5799999999999999999999999999999999999999875

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

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

Probab=99.44  E-value=3e-14  Score=105.73  Aligned_cols=45  Identities=29%  Similarity=0.703  Sum_probs=42.2

Q ss_pred             ceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccc
Q psy11505          2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR   46 (312)
Q Consensus         2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~   46 (312)
                      ..|.|..+++|.|+...|..||+|||+|||+|||++++||.+|+.
T Consensus        53 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~~~   97 (101)
T cd07160          53 AQYVCKNGGKCQMDMYMRRKCQECRLRKCREAGMREQCVLSEEQI   97 (101)
T ss_pred             CccccCCCCccccCCcccccCccchhHHHHHhCCCHHHhcChhhh
Confidence            579999999999999999999999999999999999999998864

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

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

Probab=99.44  E-value=3.8e-14  Score=103.82  Aligned_cols=46  Identities=35%  Similarity=0.833  Sum_probs=41.9

Q ss_pred             ceeEcCC--CCCcccccccccccccCchhHHHHhcccccccccccccc
Q psy11505          2 IEYTCPA--SNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG   47 (312)
Q Consensus         2 ~~Y~C~~--~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~   47 (312)
                      ..|.|..  +++|.|++..|..||+|||+||++|||++++||.+|++.
T Consensus        41 ~~~~C~~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~r~p~   88 (92)
T cd07163          41 RQYVCKSKGQGGCPVDKTHRNQCRACRLKKCFEVGMNKDAVQHERGPR   88 (92)
T ss_pred             CCcCCCCCCCCCCccCCCccccCccchhhhhhhhcCCHHHhhcccCcC
Confidence            5789987  479999999999999999999999999999999988753

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).

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

Probab=99.43  E-value=3.7e-14  Score=101.96  Aligned_cols=46  Identities=35%  Similarity=0.732  Sum_probs=42.1

Q ss_pred             CceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccc
Q psy11505          1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR   46 (312)
Q Consensus         1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~   46 (312)
                      +..|.|.++++|.|+...|+.||+|||+|||+|||++++|+.++..
T Consensus        35 ~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~~   80 (84)
T cd06962          35 NAVYKCKNGGNCEMDMYMRRKCQECRLRKCKEMGMLAECLLTEIQC   80 (84)
T ss_pred             CCceecCCCCcCccCccccccCccchhhHHHHhCCChHHccCHHHH
Confidence            3579999999999999999999999999999999999999987653

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

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

Probab=99.43  E-value=2.9e-14  Score=103.73  Aligned_cols=47  Identities=40%  Similarity=0.910  Sum_probs=42.9

Q ss_pred             cee-EcCCCCCcccccccccccccCchhHHHHhccccccccccccccc
Q psy11505          2 IEY-TCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG   48 (312)
Q Consensus         2 ~~Y-~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~   48 (312)
                      ..| .|..+++|.|++..|..|++|||+|||+|||++++||.+|++..
T Consensus        38 ~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~~~~   85 (89)
T cd07166          38 IQYRKCTKNETCSIMRINRNRCQYCRFKKCLAVGMSRDAVRFGRIPKR   85 (89)
T ss_pred             CcchhhccCCcccccccccccccchhhhhcccccCCHHHhcCCCCCCc
Confidence            568 59999999999999999999999999999999999999987643

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

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

Probab=99.43  E-value=4.5e-14  Score=103.13  Aligned_cols=47  Identities=40%  Similarity=0.858  Sum_probs=42.7

Q ss_pred             CceeEcCCC-CCcccccccccccccCchhHHHHhcccccccccccccc
Q psy11505          1 NIEYTCPAS-NDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG   47 (312)
Q Consensus         1 ~~~Y~C~~~-~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~   47 (312)
                      +..|+|..+ ++|.|+...|..||+|||+|||+|||++++||.+|++.
T Consensus        40 ~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R~~~   87 (92)
T cd06970          40 KLIYRCQAGTGMCPVDKAHRNQCQACRLKKCLQAGMNKDAVQNERQPR   87 (92)
T ss_pred             CCCceeecCCCcCccCCCccccCccchhhHhhHhCCCHHHcccccCcc
Confidence            357999985 89999999999999999999999999999999998754

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

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

Probab=99.42  E-value=4.6e-14  Score=103.83  Aligned_cols=47  Identities=38%  Similarity=0.950  Sum_probs=43.3

Q ss_pred             ceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccccc
Q psy11505          2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG   48 (312)
Q Consensus         2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~   48 (312)
                      ..|.|..+++|.|+...|+.||+|||+||++|||++++||.+|.+.+
T Consensus        40 ~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~V~~~r~~~~   86 (95)
T cd06968          40 VSYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSKK   86 (95)
T ss_pred             CceecCCCcccccccCCceeccccchhhcccccCChhhcccCcCChh
Confidence            57999999999999999999999999999999999999999886544

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

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

Probab=99.42  E-value=4.4e-14  Score=103.08  Aligned_cols=46  Identities=35%  Similarity=0.686  Sum_probs=42.5

Q ss_pred             ceeEcCCCCCcccccccccccccCchhHHHHhcccccccccccccc
Q psy11505          2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG   47 (312)
Q Consensus         2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~   47 (312)
                      ..|.|..+++|.|+...|+.||+|||+|||+|||++++||.+++..
T Consensus        36 ~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~~~   81 (91)
T cd07161          36 AVYHCKYGRACEMDMYMRRKCQECRLKKCLSVGMRPECVVPESQCA   81 (91)
T ss_pred             CceecCCCCccccCccccccCccchhhHHhHcCCCHHHcCchhhhh
Confidence            5799999999999999999999999999999999999999987543

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

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

Probab=99.41  E-value=2.3e-14  Score=105.31  Aligned_cols=49  Identities=37%  Similarity=0.778  Sum_probs=45.0

Q ss_pred             ceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccccccc
Q psy11505          2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQ   50 (312)
Q Consensus         2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~~~   50 (312)
                      ..|.|..+++|.|+...|..|++|||+|||+|||++++||.+|+..++.
T Consensus        35 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~r~~~~~r   83 (94)
T cd06966          35 KEFKCPFNESCEINVVTRRFCQKCRLDKCFAIGMKKEWIMSEEDKSEKR   83 (94)
T ss_pred             CccccCCCCccccCccccccCccchhhhCcccCCCHHHccchhhhhHHH
Confidence            4799999999999999999999999999999999999999998776554

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

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

Probab=99.41  E-value=7.4e-14  Score=98.47  Aligned_cols=41  Identities=56%  Similarity=1.112  Sum_probs=38.4

Q ss_pred             ceeEcCCCCCcccccccccccccCchhHHHHhccccccccc
Q psy11505          2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRL   42 (312)
Q Consensus         2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~   42 (312)
                      ..|+|..+++|.|++..|+.||+|||+|||+|||++++||.
T Consensus        35 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~   75 (75)
T cd06969          35 AKYVCLANKNCPVDKRRRNRCQYCRFQKCLQVGMVKEVVRT   75 (75)
T ss_pred             CcccCCcCCccccCCcccccCcccHhHHHHHhCCCHHHccC
Confidence            57899999999999999999999999999999999999873

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

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

Probab=99.39  E-value=1.2e-13  Score=96.88  Aligned_cols=40  Identities=43%  Similarity=1.036  Sum_probs=38.0

Q ss_pred             ceeEcCCCCCcccccccccccccCchhHHHHhcccccccc
Q psy11505          2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR   41 (312)
Q Consensus         2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq   41 (312)
                      ..|+|..+++|.|++..|+.||+|||+|||+|||++++||
T Consensus        33 ~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   72 (73)
T cd06958          33 LTYTCRGNRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQ   72 (73)
T ss_pred             CceeCCCCCcCccCCcccccCccchhhHhhHhCCCHHHcc
Confidence            5689999999999999999999999999999999999987

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=99.38  E-value=1.4e-13  Score=96.43  Aligned_cols=40  Identities=63%  Similarity=1.222  Sum_probs=37.7

Q ss_pred             ceeEcCCCCCcccccccccccccCchhHHHHhcccccccc
Q psy11505          2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR   41 (312)
Q Consensus         2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq   41 (312)
                      ..|.|..+++|.|+...|..||+|||+|||+|||++++||
T Consensus        33 ~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   72 (72)
T cd06916          33 LEYTCPAGGNCVIDKRNRNRCQACRLKKCLAVGMRKEAVR   72 (72)
T ss_pred             CCccCCCCCccccCCcccccCccchhhHhhHhCCChHHcC
Confidence            5789999999999999999999999999999999999886

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

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

Probab=99.38  E-value=1.5e-13  Score=96.63  Aligned_cols=41  Identities=44%  Similarity=1.058  Sum_probs=38.6

Q ss_pred             ceeEcCCCCCcccccccccccccCchhHHHHhccccccccc
Q psy11505          2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRL   42 (312)
Q Consensus         2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~   42 (312)
                      ..|+|..+++|.|++..|+.||+|||+|||+|||++++|+.
T Consensus        33 ~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~   73 (74)
T cd07179          33 NSYVCPGGQNCAITPATRNACKSCRFRRCLAVGMSKTGSRI   73 (74)
T ss_pred             CcccCCCCCccccCCcccccCccchhHHHHHhCCCHhHeeC
Confidence            57999999999999999999999999999999999999975

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=99.38  E-value=2.1e-13  Score=98.62  Aligned_cols=45  Identities=42%  Similarity=0.852  Sum_probs=41.5

Q ss_pred             ceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccc
Q psy11505          2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR   46 (312)
Q Consensus         2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~   46 (312)
                      ..|.|..+++|.++...|+.||+|||+|||+|||++++++.+|+.
T Consensus        37 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~~~~~~   81 (86)
T cd07157          37 TISECPNGGKCIIDKKNRTKCQACRYRKCLNVGMSLGGPRYGRRS   81 (86)
T ss_pred             ccccCCCCCccccCccccccCccchhhHHhHcCCCcccccccccc
Confidence            378999999999999999999999999999999999999988753

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.

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

Probab=99.37  E-value=1.7e-13  Score=95.91  Aligned_cols=39  Identities=54%  Similarity=1.086  Sum_probs=37.0

Q ss_pred             ceeEcCCCCCcccccccccccccCchhHHHHhccccccc
Q psy11505          2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGV   40 (312)
Q Consensus         2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaV   40 (312)
                      ..|+|..+++|.|++..|+.||+|||+|||+|||++++|
T Consensus        33 ~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v   71 (72)
T cd07156          33 ARFTCPFNGDCEITKDNRRHCQACRLKKCLDIGMKKEMI   71 (72)
T ss_pred             CccccCCCCccccCCcccccCccchhHHHHHhCCCHHHc
Confidence            579999999999999999999999999999999999987

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

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

Probab=99.37  E-value=1e-13  Score=100.55  Aligned_cols=44  Identities=43%  Similarity=0.833  Sum_probs=40.9

Q ss_pred             ceeEcCCCCCcccccccccccccCchhHHHHhcccccccccccc
Q psy11505          2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV   45 (312)
Q Consensus         2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~   45 (312)
                      ..|.|..+++|.|+...|+.|++|||+|||++||++++|+.++.
T Consensus        34 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~~   77 (87)
T cd07162          34 ARLCCPFQKGCVITKSNRRQCQACRLRKCLSIGMKKELIMSDEA   77 (87)
T ss_pred             ceeEcCCCCceecCCcccccCccchhhHHhHhCCCHHHccCHHH
Confidence            57999999999999999999999999999999999999998753

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

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

Probab=99.37  E-value=1.8e-13  Score=96.15  Aligned_cols=41  Identities=46%  Similarity=0.987  Sum_probs=37.7

Q ss_pred             CceeEcC-CCCCcccccccccccccCchhHHHHhcccccccc
Q psy11505          1 NIEYTCP-ASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR   41 (312)
Q Consensus         1 ~~~Y~C~-~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq   41 (312)
                      +..|.|. ++++|.|++..|..||+|||+|||+|||++++||
T Consensus        32 ~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~vq   73 (73)
T cd07154          32 NLLYTCKAGNGSCVVDKARRNQCQACRLKKCLEVSMNKDAVQ   73 (73)
T ss_pred             CCCcccCCCCCCCccCCcccccCccchhhHhhHhCCChHHCC
Confidence            3578999 7789999999999999999999999999999886

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

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

Probab=99.37  E-value=1.3e-13  Score=103.38  Aligned_cols=42  Identities=45%  Similarity=0.971  Sum_probs=39.0

Q ss_pred             ceeEcCCCCCcccccccccccccCchhHHHHhcccccccccc
Q psy11505          2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLD   43 (312)
Q Consensus         2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~   43 (312)
                      ..|.|..+++|.|+...|+.||+|||+|||+|||++++|+.+
T Consensus        41 ~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~   82 (107)
T cd06955          41 ALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTD   82 (107)
T ss_pred             CccccCCCCccccccCCccccccchhHHHHHcCCCchhccCH
Confidence            578999999999999999999999999999999999888776

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

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

Probab=99.37  E-value=2.1e-13  Score=95.68  Aligned_cols=40  Identities=35%  Similarity=0.790  Sum_probs=37.4

Q ss_pred             ceeEcCCCCCcccccccccccccCchhHHHHhcccccccc
Q psy11505          2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR   41 (312)
Q Consensus         2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq   41 (312)
                      ..|.|..+++|.|++..|..||+|||+|||+|||+++.|+
T Consensus        34 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~   73 (73)
T cd06959          34 AVYACKFGNKCEMDMYMRRKCQECRLRKCKAAGMRPDCLL   73 (73)
T ss_pred             CCccCCCCCcCCcCCcccccCccchhHHHHHhCCChhhcC
Confidence            5799999999999999999999999999999999999873

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

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

Probab=99.36  E-value=2.7e-13  Score=95.04  Aligned_cols=40  Identities=45%  Similarity=0.924  Sum_probs=37.4

Q ss_pred             ceeEcCCCCCcccccccccccccCchhHHHHhcccccccc
Q psy11505          2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR   41 (312)
Q Consensus         2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq   41 (312)
                      ..|.|..+++|.|++..|+.||+|||+|||++||+++++.
T Consensus        33 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~a~~   72 (73)
T cd06963          33 HNYLCAGRNDCIIDKIRRKNCPACRLRKCYQAGMTLGARK   72 (73)
T ss_pred             CceeCCCCCccccCCcccccCccchhhHHHHcCCChhhcc
Confidence            5799999999999999999999999999999999999864

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

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

Probab=99.35  E-value=2.6e-13  Score=95.41  Aligned_cols=40  Identities=43%  Similarity=0.998  Sum_probs=37.4

Q ss_pred             cee-EcCCCCCcccccccccccccCchhHHHHhcccccccc
Q psy11505          2 IEY-TCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR   41 (312)
Q Consensus         2 ~~Y-~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq   41 (312)
                      ..| .|..+++|.|++..|..||+|||+|||+|||++++|+
T Consensus        33 ~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   73 (73)
T cd07158          33 LTYRRCLNGGKCVIQRKNRNRCQYCRFKKCLSVGMSRNAVR   73 (73)
T ss_pred             CCcccCCCCCCcCCCccccccCccchhhhhhHccCChHHcC
Confidence            468 7999999999999999999999999999999999885

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=99.32  E-value=3.9e-13  Score=96.80  Aligned_cols=45  Identities=44%  Similarity=0.935  Sum_probs=39.7

Q ss_pred             ceeE-cCCCCCcccccccccccccCchhHHHHhccccccccccccccc
Q psy11505          2 IEYT-CPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG   48 (312)
Q Consensus         2 ~~Y~-C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~   48 (312)
                      ..|. |.++  |.|++..|+.||+|||+||++|||++++||.+|++..
T Consensus        34 ~~~~~C~~~--C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~~~~   79 (84)
T cd06965          34 LVYKPCDLS--CKIHKKSRNKCQYCRFQKCLNVGMSHNAIRFGRMPRV   79 (84)
T ss_pred             CCccccccC--CCcCccccccccchhhhhhhhccCCHHHcccCCCCch
Confidence            4674 9853  9999999999999999999999999999999987643

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

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

Probab=99.32  E-value=7.6e-13  Score=93.84  Aligned_cols=40  Identities=48%  Similarity=0.943  Sum_probs=37.4

Q ss_pred             ceeEcCCCCCcccccccccccccCchhHHHHhcccccccc
Q psy11505          2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR   41 (312)
Q Consensus         2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq   41 (312)
                      ..|+|.++++|.|+...|+.||+|||+|||+|||++.++.
T Consensus        37 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~   76 (78)
T cd07172          37 HNYLCAGRNDCIIDKIRRKNCPACRLRKCLQAGMNLGARK   76 (78)
T ss_pred             CceeCCCCCccccCCcccccCccchhHHHHHhCCCccccc
Confidence            5799999999999999999999999999999999998875

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

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

Probab=99.29  E-value=1.3e-12  Score=93.43  Aligned_cols=43  Identities=42%  Similarity=0.936  Sum_probs=38.4

Q ss_pred             ceeEcCCCCCcccccccccccccCchhHHHHhccccccccccc
Q psy11505          2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR   44 (312)
Q Consensus         2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r   44 (312)
                      ..|.|..+++|.|++..|+.||+|||+|||+|||+++....++
T Consensus        38 ~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~~~~~~   80 (82)
T cd07173          38 QKYLCASRNDCTIDKFRRKNCPSCRLRKCFEAGMTLGARKLKK   80 (82)
T ss_pred             CceecCCCCccccCCCccCcCcchhhhhhhhcCCCcChHHhhc
Confidence            5789999999999999999999999999999999988765443

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

>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors

Probab=99.22  E-value=5.1e-12  Score=88.13  Aligned_cols=37  Identities=51%  Similarity=1.011  Sum_probs=34.5

Q ss_pred             ceeEcCCCCCcccccccccccccCchhHHHHhccccc
Q psy11505          2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE   38 (312)
Q Consensus         2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~e   38 (312)
                      ..|.|..+++|.|++..|+.||+|||+|||+|||+++
T Consensus        34 ~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~   70 (70)
T smart00399       34 YKYRCDRKNNCSINKRYRCRCRACRLKKCLGVGMDPE   70 (70)
T ss_pred             CCeecCCCcccccCCCccccCccCcChhHhhccCcCC
Confidence            4689999999999999999999999999999999974

>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=99.12  E-value=1.5e-11  Score=85.97  Aligned_cols=36  Identities=47%  Similarity=1.089  Sum_probs=29.6

Q ss_pred             ceeEcCCCCCcccccccccccccCchhHHHHhcccc
Q psy11505          2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLK   37 (312)
Q Consensus         2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~   37 (312)
                      ..|.|..+++|.+++..|..|++|||+|||+|||++
T Consensus        35 ~~~~C~~~~~C~i~~~~~~~C~~CRf~KCl~~GM~k   70 (70)
T PF00105_consen   35 KPYKCKKNGNCKIDKDNRRKCRSCRFQKCLEVGMKK   70 (70)
T ss_dssp             CG-STSSSST---STTTTTTSHHHHHHHHHHTTBSG
T ss_pred             ccccccccccccccccCCCEeCcchHHHHHHHCCcC
Confidence            458999999999999999999999999999999974

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 ....

>KOG4846|consensus

Probab=98.90  E-value=4.3e-10  Score=100.39  Aligned_cols=36  Identities=67%  Similarity=1.336  Sum_probs=33.5

Q ss_pred             eeeeeCCCCcccccccccchhHHHHHHHHhhhcccc
Q psy11505        208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY  243 (312)
Q Consensus       208 ~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  243 (312)
                      .|.||||.++||||||..|||||+||||+||--.+|
T Consensus       134 lCkVCgDkASGfHYGV~aCEGCKGFFRRSIQqkI~Y  169 (538)
T KOG4846|consen  134 LCKVCGDKASGFHYGVTACEGCKGFFRRSIQQKIDY  169 (538)
T ss_pred             eehhhccccccceeceeecccchHHHHHHHHHhhhH
Confidence            799999999999999999999999999999766666

>KOG4215|consensus

Probab=98.65  E-value=1e-08  Score=90.52  Aligned_cols=42  Identities=40%  Similarity=0.965  Sum_probs=38.1

Q ss_pred             CCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceec
Q psy11505        205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQT  246 (312)
Q Consensus       205 ~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  246 (312)
                      ....|.||||++.|.|||+.+|.|||+||||+|.+...|+|+
T Consensus        18 ~~~~CaICGDkaTGKHYGA~SCdGCKGFFRRSVrk~~~YtCR   59 (432)
T KOG4215|consen   18 VAEFCAICGDKATGKHYGAISCDGCKGFFRRSVRKNHQYTCR   59 (432)
T ss_pred             ccchhheeCCcccccccceeecCcchHHHHHHHHhcceeeee
Confidence            455699999999999999999999999999999998888654

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

Probab=98.64  E-value=1.6e-08  Score=73.86  Aligned_cols=40  Identities=50%  Similarity=1.100  Sum_probs=35.4

Q ss_pred             ceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceec
Q psy11505        207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQT  246 (312)
Q Consensus       207 ~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  246 (312)
                      +.|.||++.++|+|||+.+|++|++||+|++.....|++.
T Consensus         2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~   41 (91)
T cd07161           2 ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYHCK   41 (91)
T ss_pred             CCCeeCCCcCcceEECceeehhhHHHHHHHhccCCceecC
Confidence            5699999999999999999999999999999866666543

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

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

Probab=98.63  E-value=1.6e-08  Score=71.70  Aligned_cols=38  Identities=58%  Similarity=1.130  Sum_probs=34.2

Q ss_pred             ceeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505        207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR  244 (312)
Q Consensus       207 ~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (312)
                      +.|.||++.++|+|||+.+|++|++||+|++.....|.
T Consensus         1 ~~C~VC~~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~   38 (77)
T cd06956           1 HICAICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYT   38 (77)
T ss_pred             CCCcccCCcCcceEECceeehhHHHHHHHHhhCCCccc
Confidence            36999999999999999999999999999998666664

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

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

Probab=98.63  E-value=1.8e-08  Score=74.39  Aligned_cols=40  Identities=78%  Similarity=1.369  Sum_probs=35.1

Q ss_pred             CceeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505        206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ  245 (312)
Q Consensus       206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (312)
                      ...|.||++.++|+||||.+|++|++||+|+++....|.+
T Consensus         4 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C   43 (97)
T cd07170           4 KRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSC   43 (97)
T ss_pred             CCCCeecCCcCcceEECceeehhhhHHHHHHhccCCceee
Confidence            3569999999999999999999999999999977665543

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

>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=98.60  E-value=1.9e-08  Score=70.57  Aligned_cols=36  Identities=61%  Similarity=1.244  Sum_probs=32.6

Q ss_pred             eeeeeCCCCcccccccccchhHHHHHHHHhhhcccc
Q psy11505        208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY  243 (312)
Q Consensus       208 ~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  243 (312)
                      +|.||++.++++|||+.+|++|++||+|++.....|
T Consensus         1 ~C~vCg~~~~~~hygv~sC~aC~~FFRR~v~~~~~~   36 (73)
T cd06959           1 NCVVCGDKASGFHYGVLSCEGCKGFFRRSVTKGAVY   36 (73)
T ss_pred             CCceeCCcCcceEECceeehhhHHHHHHhhcCCCCc
Confidence            589999999999999999999999999999755555

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

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

Probab=98.60  E-value=2e-08  Score=71.22  Aligned_cols=38  Identities=53%  Similarity=1.124  Sum_probs=34.6

Q ss_pred             ceeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505        207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR  244 (312)
Q Consensus       207 ~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (312)
                      ..|.||++.++++||||.+|++|++||+|++.....|.
T Consensus         3 ~~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~   40 (78)
T cd07172           3 KICLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYL   40 (78)
T ss_pred             CCCeecCCcCcceEECceeehhhHHhHHHHeeCCCcee
Confidence            57999999999999999999999999999998776664

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

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

Probab=98.59  E-value=2.7e-08  Score=71.20  Aligned_cols=38  Identities=50%  Similarity=1.064  Sum_probs=34.2

Q ss_pred             ceeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505        207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR  244 (312)
Q Consensus       207 ~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (312)
                      ..|.||++.++++||||.+|++|++||+|+|.....|.
T Consensus         4 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~   41 (82)
T cd07173           4 KTCLICGDEASGCHYGALTCGSCKVFFKRAAEGKQKYL   41 (82)
T ss_pred             CCCeecCCcCcceEECcchhhhHHHHHHHHhcCCCcee
Confidence            46999999999999999999999999999997666554

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

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

Probab=98.58  E-value=2.4e-08  Score=71.48  Aligned_cols=39  Identities=62%  Similarity=1.125  Sum_probs=34.8

Q ss_pred             ceeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505        207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ  245 (312)
Q Consensus       207 ~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (312)
                      ..|.||++.++++|||+.+|++|++||+|++.....|++
T Consensus         4 ~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C   42 (82)
T cd07171           4 HFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYIC   42 (82)
T ss_pred             CCCeecCCcCcceEECceeehhhHHhHHHHeeCCCceeC
Confidence            579999999999999999999999999999977666643

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

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

Probab=98.56  E-value=2.5e-08  Score=69.84  Aligned_cols=36  Identities=56%  Similarity=1.154  Sum_probs=32.7

Q ss_pred             eeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505        209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR  244 (312)
Q Consensus       209 c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (312)
                      |.||++.++++|||+.+|++|++||+|++.....|.
T Consensus         1 C~VCg~~a~~~hygv~sC~aCk~FFRR~~~~~~~~~   36 (73)
T cd06963           1 CLICGDEASGCHYGVLTCGSCKVFFKRAAEGQHNYL   36 (73)
T ss_pred             CcccCccCcceEECceeehhhhHhHHHhhcCCCcee
Confidence            789999999999999999999999999997666564

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

>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=98.56  E-value=3e-08  Score=69.96  Aligned_cols=37  Identities=81%  Similarity=1.441  Sum_probs=33.0

Q ss_pred             eeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505        209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ  245 (312)
Q Consensus       209 c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (312)
                      |.||++.++++|||+.+|++|++||+|++.....+++
T Consensus         1 C~VC~~~~~g~hygv~sC~aCk~FFRR~~~~~~~~~C   37 (75)
T cd07155           1 CLVCGDIASGYHYGVASCEACKAFFKRTIQGNLGYSC   37 (75)
T ss_pred             CcccCccCcceEEChhhhhhhHHHHHHHhhCCCceeC
Confidence            7899999999999999999999999999976655643

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

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

Probab=98.55  E-value=3.3e-08  Score=69.47  Aligned_cols=36  Identities=50%  Similarity=1.099  Sum_probs=32.9

Q ss_pred             eeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505        209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR  244 (312)
Q Consensus       209 c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (312)
                      |.||++.++++|||+.+|++|++||+|++.....++
T Consensus         1 C~VCg~~~~g~hygv~sC~aC~~FFRR~~~~~~~~~   36 (74)
T cd07179           1 CRVCGGKSSGFHFGALTCEGCKGFFRRTELSSNSYV   36 (74)
T ss_pred             CcccCccCcceEECceeehhHHHHHHHHhhCCCccc
Confidence            789999999999999999999999999997766664

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.

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

Probab=98.53  E-value=4.1e-08  Score=71.67  Aligned_cols=39  Identities=51%  Similarity=1.106  Sum_probs=35.0

Q ss_pred             CceeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505        206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR  244 (312)
Q Consensus       206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (312)
                      ...|.||++.++++|||+.+|++|++||+|++.....|.
T Consensus         6 ~~~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~   44 (90)
T cd07168           6 PKLCSICEDKATGLHYGIITCEGCKGFFKRTVQNKRVYT   44 (90)
T ss_pred             CCCCcccCCcCcceEECceehhhhhHhhhhhhcCCCCcc
Confidence            567999999999999999999999999999997666553

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

>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=98.53  E-value=2.4e-08  Score=69.85  Aligned_cols=36  Identities=42%  Similarity=1.090  Sum_probs=32.7

Q ss_pred             eeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505        209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR  244 (312)
Q Consensus       209 c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (312)
                      |.||++.++++|||+.+|++|++||+|++.....++
T Consensus         1 C~VC~~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~   36 (72)
T cd07156           1 CGVCGDRATGYHFNAMTCEGCKGFFRRSMKRKARFT   36 (72)
T ss_pred             CCccCccCcccEECcceehhhhhhhchhccCcCccc
Confidence            789999999999999999999999999997666554

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

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

Probab=98.53  E-value=2.7e-08  Score=73.90  Aligned_cols=40  Identities=53%  Similarity=1.048  Sum_probs=35.2

Q ss_pred             CceeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505        206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ  245 (312)
Q Consensus       206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (312)
                      ...|.||++.++|+|||+.+|++|++||+|++.....|.+
T Consensus        18 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C   57 (101)
T cd07160          18 NEVCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAQYVC   57 (101)
T ss_pred             CCCCeecCCcCcceEECcceehhhhhhhhhcccccCcccc
Confidence            3569999999999999999999999999999976666643

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

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

Probab=98.53  E-value=3.9e-08  Score=71.38  Aligned_cols=38  Identities=39%  Similarity=0.992  Sum_probs=33.7

Q ss_pred             eeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505        208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ  245 (312)
Q Consensus       208 ~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (312)
                      .|.||++.++++|||+.+|++|++||+|++.....|.+
T Consensus         1 ~C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C   38 (87)
T cd07162           1 ICRVCGDRATGYHFNAMTCEGCKGFFRRAMKRNARLCC   38 (87)
T ss_pred             CCcccCCcCcceEECcceehhhHHHHHhhhccCceeEc
Confidence            48999999999999999999999999999976655543

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

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

Probab=98.52  E-value=5.3e-08  Score=70.99  Aligned_cols=39  Identities=59%  Similarity=1.214  Sum_probs=34.7

Q ss_pred             CceeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505        206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR  244 (312)
Q Consensus       206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (312)
                      ...|.||++.++++|||+.+|++|++||+|++.....|+
T Consensus         6 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~   44 (90)
T cd07169           6 QRTCLICGDRATGLHYGIISCEGCKGFFKRSICNKRVYR   44 (90)
T ss_pred             CCCCeecCCcCcceEECcceehhhHHHHHHHhcCCCcee
Confidence            357999999999999999999999999999997666554

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).

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

Probab=98.52  E-value=4.2e-08  Score=70.86  Aligned_cols=38  Identities=50%  Similarity=1.093  Sum_probs=33.7

Q ss_pred             eeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505        208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ  245 (312)
Q Consensus       208 ~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (312)
                      .|.||++.++++|||+.+|++|++||+|++.....|++
T Consensus         1 ~C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C   38 (85)
T cd06961           1 PCVVCGDKATGYHYRCITCEGCKGFFRRTVQKKLSYSC   38 (85)
T ss_pred             CCceeCCcCcceEEChhhhhhhhHhhHhhhccCCcccc
Confidence            38999999999999999999999999999976666643

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

>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=98.50  E-value=4.3e-08  Score=71.81  Aligned_cols=37  Identities=57%  Similarity=1.186  Sum_probs=33.6

Q ss_pred             eeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505        209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ  245 (312)
Q Consensus       209 c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (312)
                      |.||++.++++||||.+|++|++||+|+|.....|++
T Consensus         1 C~VCg~~a~g~hyGv~sC~aCk~FFRRsv~~~~~~~C   37 (93)
T cd07167           1 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKRYTC   37 (93)
T ss_pred             CcccCccCcceEECchhhhhHHHHHHHHeeCCCcccc
Confidence            7899999999999999999999999999977766643

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

>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=98.50  E-value=4.2e-08  Score=68.79  Aligned_cols=36  Identities=53%  Similarity=1.137  Sum_probs=32.5

Q ss_pred             eeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505        209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR  244 (312)
Q Consensus       209 c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (312)
                      |.||++.++++|||+.+|++|++||+|++.....|.
T Consensus         1 C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~   36 (73)
T cd06958           1 CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYT   36 (73)
T ss_pred             CCccCccCcceEEChhhhhhhhhhhhhhhcCCCcee
Confidence            789999999999999999999999999997665553

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

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

Probab=98.49  E-value=5.3e-08  Score=68.38  Aligned_cols=35  Identities=71%  Similarity=1.330  Sum_probs=32.0

Q ss_pred             eeeeCCCCcccccccccchhHHHHHHHHhhhcccc
Q psy11505        209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY  243 (312)
Q Consensus       209 c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  243 (312)
                      |.||++.++++|||+.+|++|++||+|++.....|
T Consensus         1 C~VCg~~~~g~hyGv~~C~aC~~FFRR~v~~~~~~   35 (73)
T cd07158           1 CKVCGDKASGFHYGVHSCEGCKGFFRRTIQHNLTY   35 (73)
T ss_pred             CcccCccCcceEECcchhhHHHHHHhhhhcCCCCc
Confidence            78999999999999999999999999999766555

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).

>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors

Probab=98.48  E-value=4.6e-08  Score=68.12  Aligned_cols=37  Identities=68%  Similarity=1.338  Sum_probs=33.3

Q ss_pred             eeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505        208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR  244 (312)
Q Consensus       208 ~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (312)
                      .|.||++.++++|||+.+|++|++||+|+|+....+.
T Consensus         1 ~C~vC~~~~~~~hygv~~C~aC~~FFRR~v~~~~~~~   37 (70)
T smart00399        1 LCCVCGDHASGFHFGVCSCRACKAFFRRTVNLRYKYR   37 (70)
T ss_pred             CCeEeCCcCcccEeCCcEechhhhhhhhheeCCCCee
Confidence            4899999999999999999999999999997666553

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

Probab=98.46  E-value=2e-08  Score=72.27  Aligned_cols=38  Identities=53%  Similarity=1.191  Sum_probs=34.1

Q ss_pred             ceeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505        207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR  244 (312)
Q Consensus       207 ~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (312)
                      ..|.||++.++|+|||+.+|++|++||+|++.....|.
T Consensus         2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~   39 (84)
T cd06962           2 ELCVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVYK   39 (84)
T ss_pred             CCCeecCCcCcceEECcceeecceeeeeeeeccCCcee
Confidence            46999999999999999999999999999997665554

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

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

Probab=98.45  E-value=3e-08  Score=74.45  Aligned_cols=40  Identities=43%  Similarity=1.004  Sum_probs=35.4

Q ss_pred             CceeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505        206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ  245 (312)
Q Consensus       206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (312)
                      ...|.||++.++|+|||+.+|++|++||+|+|.....|++
T Consensus         6 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C   45 (107)
T cd06955           6 PRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTC   45 (107)
T ss_pred             CCCCeecCCcCcccEECcceeeeecceecceeccCCcccc
Confidence            4579999999999999999999999999999976666643

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

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

Probab=98.44  E-value=2e-08  Score=72.42  Aligned_cols=39  Identities=51%  Similarity=1.111  Sum_probs=34.4

Q ss_pred             CceeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505        206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR  244 (312)
Q Consensus       206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (312)
                      ...|.|||+.++++|||+.+|++|++||+|++.....|.
T Consensus         4 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~   42 (85)
T cd06964           4 YKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYT   42 (85)
T ss_pred             CCCCcccCCcCcccEECcceeeeeeeEEeeeecCCCCeE
Confidence            357999999999999999999999999999997655553

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

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

Probab=98.44  E-value=2e-08  Score=70.82  Aligned_cols=38  Identities=58%  Similarity=1.092  Sum_probs=33.8

Q ss_pred             ceeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505        207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR  244 (312)
Q Consensus       207 ~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (312)
                      +.|.||++.++++|||+.+|++|++||+|++.....|.
T Consensus         1 ~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~   38 (75)
T cd06969           1 GLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYV   38 (75)
T ss_pred             CCCeecCCcCcceEECcceeeeeeeeeeeeeecCCccc
Confidence            36999999999999999999999999999997665553

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

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

Probab=98.43  E-value=4.1e-08  Score=72.18  Aligned_cols=38  Identities=39%  Similarity=0.949  Sum_probs=34.0

Q ss_pred             eeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505        208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ  245 (312)
Q Consensus       208 ~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (312)
                      .|.||++.++|+|||+.+|++|++||+|++.....|++
T Consensus         2 ~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C   39 (94)
T cd06966           2 ICGVCGDKALGYNFNAITCESCKAFFRRNALKNKEFKC   39 (94)
T ss_pred             CCeeCCCcCcceEECcceeeeehheehhcccCCCcccc
Confidence            59999999999999999999999999999976666643

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

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

Probab=98.43  E-value=9.4e-08  Score=70.38  Aligned_cols=40  Identities=48%  Similarity=0.981  Sum_probs=35.0

Q ss_pred             CceeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505        206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ  245 (312)
Q Consensus       206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (312)
                      ...|.|||+.++|+|||+.+|++|++||+|++.....+.+
T Consensus         5 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C   44 (95)
T cd06968           5 VIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVSYSC   44 (95)
T ss_pred             ccCCcccCCcCcceEECceeehhhHHhhHHheeCCCceec
Confidence            3579999999999999999999999999999976655543

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

>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=98.42  E-value=8e-08  Score=68.32  Aligned_cols=36  Identities=58%  Similarity=1.173  Sum_probs=32.5

Q ss_pred             eeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505        209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR  244 (312)
Q Consensus       209 c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (312)
                      |.||++.++++|||+.+|++|++||+|++.....+.
T Consensus         1 C~VCg~~~~g~hyG~~~C~~C~~FFRR~~~~~~~~~   36 (78)
T cd07164           1 CRVCGDRASGKHYGVPSCDGCRGFFKRSIRRNLAYV   36 (78)
T ss_pred             CcccCccCcceEECcchhhhhhhhhhhhccCCCCcc
Confidence            789999999999999999999999999997655553

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

>KOG4217|consensus

Probab=98.41  E-value=1e-07  Score=86.77  Aligned_cols=64  Identities=44%  Similarity=0.825  Sum_probs=49.2

Q ss_pred             cCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCCCCccc----chHHHHHHH
Q psy11505        196 LDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVKLD----EFSSLKKFR  271 (312)
Q Consensus       196 ~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~----~~~~~~~~~  271 (312)
                      +-.++.+    ..|.||||.+.=-||||-.|||||+||+|++||..+|        +.|-|-+++++    +.-+--++|
T Consensus       263 rs~~~~e----~~CAVCgDnAaCqHYGvRTCEGCKGFFKRTVQKnaKY--------vClanKnCPVDKRrRnRCQyCRfQ  330 (605)
T KOG4217|consen  263 RSSLSAE----GLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKY--------VCLANKNCPVDKRRRNRCQYCRFQ  330 (605)
T ss_pred             ccCCCcc----ceeeecCChHHhhhcCccccccchHHHHHHHhcCCee--------EeecCCCCCcchhhhhhchhhhHh
Confidence            4445554    4699999999999999999999999999999999999        44556666543    333444444

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

Probab=98.41  E-value=2.9e-08  Score=72.58  Aligned_cols=39  Identities=49%  Similarity=1.014  Sum_probs=34.5

Q ss_pred             ceeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505        207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ  245 (312)
Q Consensus       207 ~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (312)
                      ..|.||++.++|+|||+.+|++|++||+|+|+....|.+
T Consensus         7 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C   45 (92)
T cd06970           7 LLCRVCGDTSSGKHYGIYACNGCSGFFKRSVRRKLIYRC   45 (92)
T ss_pred             CCCeecCCcCcccEECccEEeeeeeEeeeeeecCCCcee
Confidence            469999999999999999999999999999976655543

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

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

Probab=98.40  E-value=2.4e-08  Score=73.23  Aligned_cols=40  Identities=45%  Similarity=0.934  Sum_probs=35.4

Q ss_pred             CCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505        205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR  244 (312)
Q Consensus       205 ~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (312)
                      +...|.||++.++|+|||+.+|++|++||+|++.....|.
T Consensus         5 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~   44 (92)
T cd07163           5 LDIPCKVCGDRSSGKHYGIYACDGCSGFFKRSIRRNRQYV   44 (92)
T ss_pred             cCCCCcccCCcCcccEECceeeeeeeeEEeeeecCCCCcC
Confidence            3568999999999999999999999999999997666554

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).

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

Probab=98.40  E-value=2.6e-08  Score=69.87  Aligned_cols=37  Identities=51%  Similarity=1.025  Sum_probs=33.0

Q ss_pred             eeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505        209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ  245 (312)
Q Consensus       209 c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (312)
                      |.||++.++++|||+.+|++|++||+|+++....|.+
T Consensus         1 C~vCg~~~~~~hyGv~sC~aC~~FFRR~v~~~~~~~C   37 (73)
T cd07154           1 CKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNLLYTC   37 (73)
T ss_pred             CcccCccCcceEECcceeeeeeeEeeeeecCCCCccc
Confidence            7899999999999999999999999999976655543

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

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

Probab=98.39  E-value=5.7e-08  Score=69.97  Aligned_cols=36  Identities=64%  Similarity=1.254  Sum_probs=32.7

Q ss_pred             eeeeeCCCCcccccccccchhHHHHHHHHhhhcccc
Q psy11505        208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY  243 (312)
Q Consensus       208 ~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  243 (312)
                      .|.||++.++|+|||+.+|++|++||+|++.....|
T Consensus         1 ~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~   36 (84)
T cd06965           1 ECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLVY   36 (84)
T ss_pred             CCcccCccCcceEEChhhhhhhhhheeeeeecCCCc
Confidence            389999999999999999999999999999766555

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

>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=98.39  E-value=1.6e-07  Score=67.30  Aligned_cols=36  Identities=67%  Similarity=1.328  Sum_probs=32.5

Q ss_pred             eeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505        209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR  244 (312)
Q Consensus       209 c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (312)
                      |.||++.++++|||+.+|++|++||+|++.....+.
T Consensus         1 C~VCg~~~~g~hyG~~sC~aC~~FFRR~~~~~~~~~   36 (81)
T cd07165           1 CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYR   36 (81)
T ss_pred             CCccCccCcceEECchhhhhHHHHHHhHhccCCcee
Confidence            789999999999999999999999999997665553

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,

>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=98.38  E-value=2.2e-08  Score=71.87  Aligned_cols=38  Identities=45%  Similarity=0.925  Sum_probs=33.9

Q ss_pred             eeeeCCCCcccccccccchhHHHHHHHHhhhcccceec
Q psy11505        209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQT  246 (312)
Q Consensus       209 c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  246 (312)
                      |.||++.++|+|||+.+|++|++||+|+|+....|.+.
T Consensus         1 C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~   38 (82)
T cd06957           1 CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKGIIYTCI   38 (82)
T ss_pred             CCccCccCcceEECcceEeeeeeEEEEeecCCCceEcc
Confidence            78999999999999999999999999999876666443

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

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

Probab=98.36  E-value=5.9e-08  Score=68.68  Aligned_cols=36  Identities=53%  Similarity=1.159  Sum_probs=32.5

Q ss_pred             eeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505        209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR  244 (312)
Q Consensus       209 c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (312)
                      |.||++.++++|||+.+|++|++||+|++.....++
T Consensus         1 C~vCg~~~~~~hygv~~C~aC~~FFrR~~~~~~~~~   36 (76)
T cd06960           1 CAVCGDRATGKHYGVLSCNGCKGFFRRSVRKNRTYT   36 (76)
T ss_pred             CCccCccCcccEECcceeeeehheeCccccCCCcee
Confidence            789999999999999999999999999997665554

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

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

Probab=98.35  E-value=7e-08  Score=70.26  Aligned_cols=38  Identities=63%  Similarity=1.209  Sum_probs=33.9

Q ss_pred             CceeeeeCCCCcccccccccchhHHHHHHHHhhhcccc
Q psy11505        206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY  243 (312)
Q Consensus       206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  243 (312)
                      ...|.||++.++|+|||+.+|++|++||+|++.....|
T Consensus         3 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~   40 (89)
T cd07166           3 VVLCKVCGDKASGFHYGVHACEGCKGFFRRSIQQKIQY   40 (89)
T ss_pred             CCCCcccCccCcceEEChhhhhhHhhEecceeEcCCcc
Confidence            35799999999999999999999999999999755555

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

>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=98.33  E-value=5.9e-08  Score=70.35  Aligned_cols=39  Identities=62%  Similarity=1.192  Sum_probs=34.5

Q ss_pred             CceeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505        206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR  244 (312)
Q Consensus       206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (312)
                      ...|.||++.++++|||+.+|++|++||+|+|.....+.
T Consensus         3 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~   41 (87)
T cd06967           3 VELCVVCGDKASGRHYGAVSCEGCKGFFKRSIRKNLGYS   41 (87)
T ss_pred             CCCCeecCCcCCcCEeCcceEeeeeeEeeeeeeCCCCcc
Confidence            357999999999999999999999999999997665553

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

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

Probab=98.32  E-value=5.5e-08  Score=70.33  Aligned_cols=33  Identities=52%  Similarity=1.052  Sum_probs=30.9

Q ss_pred             eeeeeCCCCcccccccccchhHHHHHHHHhhhc
Q psy11505        208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVY  240 (312)
Q Consensus       208 ~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  240 (312)
                      .|.||++.++++|||+.+|++|++||+|++...
T Consensus         2 ~C~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~   34 (86)
T cd07157           2 TCQVCGEPAAGFHHGAYVCEACKKFFMRSSNAI   34 (86)
T ss_pred             CCcccCCcCcccEECcceeeEeeeEEecceecC
Confidence            599999999999999999999999999999754

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.

>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=98.31  E-value=2e-07  Score=64.98  Aligned_cols=36  Identities=58%  Similarity=1.217  Sum_probs=32.8

Q ss_pred             eeeeeCCCCcccccccccchhHHHHHHHHhhhcccc
Q psy11505        208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY  243 (312)
Q Consensus       208 ~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  243 (312)
                      .|.||++.++++|||+.+|++|+.||+|++.....+
T Consensus         2 ~C~VCg~~~~~~~ygv~sC~~C~~FFrR~~~~~~~~   37 (70)
T PF00105_consen    2 KCKVCGDPASGYHYGVLSCNACKMFFRRSVKKKKPY   37 (70)
T ss_dssp             BSTTTSSBESEEETTEEEEHHHHHHHHHHHHTTCG-
T ss_pred             CCeECCCccCcccccccccccceeeeeecccccccc
Confidence            599999999999999999999999999999876665

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 ....

>KOG4216|consensus

Probab=98.31  E-value=2.1e-07  Score=82.95  Aligned_cols=37  Identities=51%  Similarity=1.131  Sum_probs=33.7

Q ss_pred             ceeeeeCCCCcccccccccchhHHHHHHHHhhhcccc
Q psy11505        207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY  243 (312)
Q Consensus       207 ~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  243 (312)
                      --|.||||.+||+||||..|||||+||||+=+-...|
T Consensus        47 IPCKiCGDKSSGiHYGVITCEGCKGFFRRSQ~s~a~Y   83 (479)
T KOG4216|consen   47 IPCKICGDKSSGIHYGVITCEGCKGFFRRSQQSNANY   83 (479)
T ss_pred             EeeeeccCCCCcceeeeEeeccchHhhhhhhhccccc
Confidence            3699999999999999999999999999998766666

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

Probab=98.31  E-value=4.8e-08  Score=68.34  Aligned_cols=36  Identities=56%  Similarity=1.246  Sum_probs=32.5

Q ss_pred             eeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505        209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR  244 (312)
Q Consensus       209 c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (312)
                      |.||++.++++|||+.+|++|++||+|++.....+.
T Consensus         1 C~vC~~~~~~~hygv~sC~aC~~FFRR~~~~~~~~~   36 (72)
T cd06916           1 CAVCGDKASGYHYGVLTCEGCKGFFRRSVRRNLEYT   36 (72)
T ss_pred             CCccCccCcccEECcceeeeeeeeEeEeecCCCCcc
Confidence            789999999999999999999999999997665553

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

>KOG4218|consensus

Probab=98.20  E-value=6.1e-07  Score=78.79  Aligned_cols=43  Identities=51%  Similarity=1.040  Sum_probs=38.4

Q ss_pred             CCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecC
Q psy11505        205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTG  247 (312)
Q Consensus       205 ~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  247 (312)
                      +.+.|.||||.-||+|||.-.||.||+||+|++|.-+-|+|.+
T Consensus        14 l~ElCPVCGDkVSGYHYGLLTCESCKGFFKRTVQNnK~YtC~e   56 (475)
T KOG4218|consen   14 LGELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKQYTCSE   56 (475)
T ss_pred             cccccccccCccccceeeeeehhhhhhHHHHHhhcCcceeccc
Confidence            3566999999999999999999999999999999888886543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	312
2ewp_A	226	Crystal Structure Of Estrogen Related Receptor-3 (E		5e-26
1kv6_A	230	X-Ray Structure Of The Orphan Nuclear Receptor Err3		5e-26
1vjb_A	251	Crystal Structure Of The Ligand-Binding Domain Of T		5e-26
1s9q_A	251	Crystal Structure Of The Ligand-Binding Domain Of T		5e-26
1s9p_A	227	Crystal Structure Of The Ligand-Binding Domain Of T		5e-26
2e2r_A	244	Crystal Structure Of Human Estrogen-Related Recepto		5e-26
2pjl_A	247	Crystal Structure Of Human Estrogen-Related Recepto		3e-25
3d24_A	253	Crystal Structure Of Ligand-Binding Domain Of Estro		1e-24
3k6p_A	248	Estrogen Related Receptor Alpha In Complex With An		3e-24
1xb7_A	247	X-Ray Structure Of Erralpha Lbd In Complex With A P		3e-24
3dzu_A	467	Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp		1e-22
3dzu_A	467	Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp		8e-08
1lo1_A	98	Estrogen Related Receptor 2 Dna Binding Domain In C		5e-21
1lo1_A	98	Estrogen Related Receptor 2 Dna Binding Domain In C		5e-14
1qkt_A	248	Mutant Estrogen Nuclear Receptor Ligand Binding Dom		7e-20
2yat_A	252	Crystal Structure Of Estradiol Derived Metal Chelat		7e-20
1uom_A	254	The Structure Of Estrogen Receptor In Complex With		7e-20
1pcg_A	244	Helix-Stabilized Cyclic Peptides As Selective Inhib		7e-20
3q95_B	260	Crystal Structure Of Human Estrogen Receptor Alpha		2e-19
1zky_A	257	Human Estrogen Receptor Alpha Ligand-Binding Domain		3e-19
2ocf_A	298	Human Estrogen Receptor Alpha Ligand-Binding Domain		3e-19
3uu7_B	251	Crystal Structure Of Hera-Lbd (Y537s) In Complex Wi		3e-19
3hm1_A	253	Crystal Structure Of Human Estrogen Receptor Alpha		3e-19
3q97_A	260	Crystal Structure Of Human Estrogen Receptor Alpha		3e-19
3uu7_A	251	Crystal Structure Of Hera-Lbd (Y537s) In Complex Wi		3e-19
2jfa_B	252	Estrogen Receptor Alpha Lbd In Complex With An Affi		4e-19
1l2i_A	261	Human Estrogen Receptor Alpha Ligand-Binding Domain		5e-19
2qa8_B	258	Crystal Structure Of The Estrogen Receptor Alpha Li		8e-19
2fsz_A	246	A Second Binding Site For Hydroxytamoxifen Within T		8e-19
1err_A	253	Human Estrogen Receptor Ligand-Binding Domain In Co		8e-19
3uuc_A	251	Crystal Structure Of Hera-Lbd (Wt) In Complex With		8e-19
2qzo_B	258	Crystal Structure Of The Estrogen Receptor Alpha Li		8e-19
3q95_A	260	Crystal Structure Of Human Estrogen Receptor Alpha		8e-19
3uua_A	251	Crystal Structure Of Hera-Lbd (Y537s) In Complex Wi		9e-19
3uua_B	251	Crystal Structure Of Hera-Lbd (Y537s) In Complex Wi		1e-18
2bj4_A	252	Estrogen Receptor Alpha Lbd In Complex With A Phage		1e-18
1a52_A	258	Estrogen Receptor Alpha Ligand-Binding Domain Compl		1e-18
3dt3_A	255	Human Estrogen Receptor Alpha Lbd With Gw368 Length		1e-18
3l03_A	253	Crystal Structure Of Human Estrogen Receptor Alpha		1e-18
1ere_A	253	Human Estrogen Receptor Ligand-Binding Domain In Co		1e-18
2iok_A	254	Human Estrogen Receptor Alpha Ligand-binding Domain		1e-18
3erd_A	261	Human Estrogen Receptor Alpha Ligand-Binding Domain		1e-18
2qa8_A	258	Crystal Structure Of The Estrogen Receptor Alpha Li		1e-18
1gwq_A	248	Human Oestrogen Receptor Alpha Ligand-Binding Domai		1e-18
4dma_A	247	Crystal Structure Of Era Lbd In Complex With Ru1001		1e-18
3hlv_A	253	Crystal Structure Of Human Estrogen Receptor Alpha		1e-18
1qku_A	250	Wild Type Estrogen Nuclear Receptor Ligand Binding		1e-18
2p15_A	258	Crystal Structure Of The Er Alpha Ligand Binding Do		1e-18
2qxs_A	258	Crystal Structure Of Antagonizing Mutant 536s Of Th		2e-18
1gwr_A	245	Human Oestrogen Receptor Alpha Ligand-Binding Domai		2e-18
2iog_A	246	Human Estrogen Receptor Alpha Ligand-Binding Domain		2e-18
1g50_A	247	Crystal Structure Of A Wild Type Her Alpha Lbd At 2		2e-18
1sj0_A	248	Human Estrogen Receptor Alpha Ligand-binding Domain		2e-18
1qkn_A	255	Rat Oestrogen Receptor Beta Ligand-Binding Domain I		2e-18
2j7x_A	255	Structure Of Estradiol-bound Estrogen Receptor Beta		2e-18
3ltx_A	243	Crystal Structure Of The Pacific Oyster Estrogen Re		3e-18
3os8_A	258	Estrogen Receptor Length = 258		3e-18
1nde_A	255	Estrogen Receptor Beta With Selective Triazine Modu		7e-18
2i0g_A	257	Benzopyrans Are Selective Estrogen Receptor Beta Ag		7e-18
1qkm_A	255	Human Oestrogen Receptor Beta Ligand-Binding Domain		7e-18
2nv7_A	238	Crystal Structure Of Estrogen Receptor Beta Complex		7e-18
1zaf_A	238	Crystal Structure Of Estrogen Receptor Beta Complex		7e-18
3oll_A	240	Crystal Structure Of Phosphorylated Estrogen Recept		8e-18
2giu_A	241	Human Estrogen Receptor Beta Ligand-Binding Domain		8e-18
1l2j_A	271	Human Estrogen Receptor Beta Ligand-Binding Domain		8e-18
1x76_A	240	Crystal Structure Of Estrogen Receptor Beta Complex		8e-18
1u9e_A	241	Crystal Structure Of Estrogen Receptor Beta Complex		8e-18
2yly_A	240	Sulfonamides As Selective Estrogen Receptor Beta Ag		8e-18
3os8_C	258	Estrogen Receptor Length = 258		1e-17
1yy4_A	268	Crystal Structure Of Estrogen Receptor Beta Complex		1e-17
1x7e_A	245	Crystal Structure Of Estrogen Receptor Alpha Comple		1e-17
3kba_A	253	Progesterone Receptor Bound To Sulfonamide Pyrrolid		1e-15
1a28_A	256	Hormone-Bound Human Progesterone Receptor Ligand-Bi		1e-15
1e3k_A	258	Human Progesteron Receptor Ligand Binding Domain In		1e-15
3g8o_A	263	Progesterone Receptor With Bound Pyrrolidine 1 Leng		1e-15
2w8y_A	260	Ru486 Bound To The Progesterone Receptor In A Desta		1e-15
1sr7_A	259	Progesterone Receptor Hormone Binding Domain With B		1e-15
1sqn_A	261	Progesterone Receptor Ligand Binding Domain With Bo		1e-15
4fne_A	254	X-Ray Crystal Structure Of The Ancestral 3-Keto Ste		2e-15
2q1h_A	250	Ancestral Corticoid Receptor In Complex With Aldost		3e-15
2q3y_A	249	Ancestral Corticiod Receptor In Complex With Doc Le		3e-15
3ry9_A	250	Crystal Structure Of The Resurrected Ancestral Gluc		2e-14
3h52_A	254	Crystal Structure Of The Antagonist Form Of Human G		1e-13
3cld_A	259	Ligand Binding Domain Of The Glucocorticoid Recepto		2e-13
1nhz_A	280	Crystal Structure Of The Antagonist Form Of Glucoco		2e-13
3bqd_A	255	Doubling The Size Of The Glucocorticoid Receptor Li		2e-13
3e7c_A	257	Glucocorticoid Receptor Lbd Bound To Gsk866 Length		2e-13
3mne_A	261	Crystal Structure Of The Agonist Form Of Mouse Gluc		2e-13
3mno_A	261	Crystal Structure Of The Agonist Form Of Mouse Gluc		2e-13
3mnp_A	261	Crystal Structure Of The Agonist Form Of Mouse Gluc		3e-13
1m2z_A	257	Crystal Structure Of A Dimer Complex Of The Human G		4e-13
3vhv_A	260	Mineralocorticoid Receptor Ligand-Binding Domain Wi		5e-13
3vhu_A	294	Mineralocorticoid Receptor Ligand-Binding Domain Wi		6e-13
2aa6_A	275	Mineralocorticoid Receptor S810l Mutant With Bound		6e-13
4e2j_A	250	X-Ray Crystal Structure Of The Ancestral Glucocorti		1e-12
3gn8_A	249	X-Ray Crystal Structure Of Ancgr2 In Complex With D		1e-12
2oax_A	256	Crystal Structure Of The S810l Mutant Mineralocorti		2e-12
1y9r_A	255	Crystal Structure Of The Human Mineralocorticoid Re		2e-12
2a3i_A	253	Structural And Biochemical Mechanisms For The Speci		3e-12
2q60_A	258	Crystal Structure Of The Ligand Binding Domain Of P		3e-12
1i38_A	260	Crystal Structure Of The Rat Androgen Receptor Liga		4e-12
2ax6_A	256	Crystal Structure Of The Androgen Receptor Ligand B		4e-12
2ax9_A	256	Crystal Structure Of The Androgen Receptor Ligand B		4e-12
1i37_A	260	Crystal Structure Of The Rat Androgen Receptor Liga		4e-12
3rll_A	247	Crystal Structure Of The T877a Androgen Receptor Li		4e-12
2q7k_A	257	The Androgen Receptor Prostate Cancer Mutant H874y		4e-12
2aa2_A	275	Mineralocorticoid Receptor With Bound Aldosterone L		4e-12
1e3g_A	263	Human Androgen Receptor Ligand Binding In Complex W		4e-12
1xj7_A	257	Complex Androgen Receptor Lbd And Rac3 Peptide Leng		4e-12
1t73_A	269	Crystal Structure Of The Androgen Receptor Ligand B		4e-12
3rlj_A	247	Crystal Structure Of The Androgen Receptor Ligand B		4e-12
1t5z_A	251	Crystal Structure Of The Androgen Receptor Ligand B		4e-12
2hvc_A	250	The Crystal Structure Of Ligand-Binding Domain (Lbd		4e-12
3l3x_A	250	Crystal Structure Of Dht-Bound Androgen Receptor In		4e-12
2z4j_A	248	Crystal Structure Of Ar Lbd With Shp Peptide Nr Box		4e-12
2oz7_A	249	Crystal Structure Of The Human Androgen Receptor T8		4e-12
1xow_A	249	Crystal Structure Of The Human Androgen Receptor Li		5e-12
2am9_A	266	Crystal Structure Of Human Androgen Receptor Ligand		5e-12
1gs4_A	248	Structural Basis For The Glucocorticoid Response In		1e-11
2abi_A	256	Crystal Structure Of The Human Mineralocorticoid Re		1e-11
1z5x_U	262	Hemipteran Ecdysone Receptor Ligand-Binding Domain		4e-11
1z95_A	246	Crystal Structure Of The Androgen Receptor Ligand-B		1e-10
1hcq_A	84	The Crystal Structure Of The Estrogen Receptor Dna-		1e-10
1hcq_A	84	The Crystal Structure Of The Estrogen Receptor Dna-		1e-08
2ax8_A	256	Crystal Structure Of The Androgen Receptor Ligand B		2e-10
1lbd_A	282	Ligand-Binding Domain Of The Human Nuclear Receptor		2e-10
2ff0_A	102	Solution Structure Of Steroidogenic Factor 1 Dna Bi		4e-10
2ff0_A	102	Solution Structure Of Steroidogenic Factor 1 Dna Bi		7e-08
2gl8_A	241	Human Retinoic Acid Receptor Rxr-Gamma Ligand-Bindi		4e-10
2a66_A	113	Human Liver Receptor Homologue Dna-Binding Domain (		8e-10
2a66_A	113	Human Liver Receptor Homologue Dna-Binding Domain (		8e-08
3a9e_A	240	Crystal Structure Of A Mixed Agonist-Bound Rar-Alph		1e-09
1xdk_A	238	Crystal Structure Of The RarbetaRXRALPHA LIGAND BIN		1e-09
1dkf_A	233	Crystal Structure Of A Heterodimeric Complex Of Rar		2e-09
1xiu_A	230	Crystal Structure Of The Agonist-Bound Ligand-Bindi		2e-09
1rdt_A	242	Crystal Structure Of A New Rexinoid Bound To The Rx		2e-09
3e94_A	244	Crystal Structure Of Rxralpha Ligand Binding Domain		3e-09
3uvv_B	244	Crystal Structure Of The Ligand Binding Domains Of		3e-09
3eyb_A	219	Structural And Functional Insights Into The Ligand		3e-09
1hlz_A	94	Crystal Structure Of The Orphan Nuclear Receptor Re		3e-09
1fby_A	239	Crystal Structure Of The Human Rxr Alpha Ligand Bin		3e-09
1xv9_A	236	Crystal Structure Of CarRXR HETERODIMER BOUND WITH		3e-09
1fm6_A	238	The 2.1 Angstrom Resolution Crystal Structure Of Th		3e-09
3pcu_A	230	Crystal Structure Of Human Retinoic X Receptor Alph		3e-09
1mv9_A	240	Crystal Structure Of The Human Rxr Alpha Ligand Bin		3e-09
3h0a_A	228	Crystal Structure Of Peroxisome Proliferator-Activa		3e-09
1xls_A	232	Crystal Structure Of The Mouse CarRXR LBD HETERODIM		3e-09
3oap_A	231	Crystal Structure Of Human Retinoid X Receptor Alph		3e-09
1hcp_A	76	Dna Recognition By The Oestrogen Receptor: From Sol		1e-08
4aa6_E	71	The Oestrogen Receptor Recognizes An Imperfectly Pa		1e-08
4aa6_A	71	The Oestrogen Receptor Recognizes An Imperfectly Pa		1e-08
3dzu_D	419	Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp		1e-08
1fcy_A	236	Isotype Selectivity Of The Human Retinoic Acid Nucl		2e-08
1cit_A	89	Dna-Binding Mechanism Of The Monomeric Orphan Nucle		2e-08
1cit_A	89	Dna-Binding Mechanism Of The Monomeric Orphan Nucle		5e-08
1ovl_A	271	Crystal Structure Of Nurr1 Lbd Length = 271		2e-08
1fcx_A	235	Isotype Selectivity Of The Human Retinoic Acid Nucl		2e-08
1exa_A	246	Enantiomer Discrimination Illustrated By Crystal St		2e-08
2lbd_A	267	Ligand-Binding Domain Of The Human Retinoic Acid Re		2e-08
2nxx_A	235	Crystal Structure Of The Ligand-Binding Domains Of		3e-08
1ovl_B	271	Crystal Structure Of Nurr1 Lbd Length = 271		4e-08
1lat_A	82	Glucocorticoid Receptor MutantDNA COMPLEX Length =		6e-08
2env_A	88	Solution Sturcture Of The C4-Type Zinc Finger Domai		6e-08
2qw4_A	273	Human Nr4a1 Ligand-Binding Domain Length = 273		8e-08
1h9u_A	224	The Structure Of The Human Retinoid-X-Receptor Beta		8e-08
1uhl_A	236	Crystal Structure Of The Lxralfa-Rxrbeta Lbd Hetero		9e-08
3v3e_B	257	Crystal Structure Of The Human Nur77 Ligand-Binding		9e-08
1yje_A	264	Crystal Structure Of The Rngfi-B Ligand-Binding Dom		1e-07
2han_A	93	Structural Basis Of Heterodimeric Ecdysteroid Recep		1e-07
1ynw_B	99	Crystal Structure Of Vitamin D Receptor And 9-Cis R		1e-07
1r0o_A	86	Crystal Structure Of The Heterodimeric Ecdysone Rec		1e-07
3a9e_B	269	Crystal Structure Of A Mixed Agonist-Bound Rar-Alph		2e-07
4dqm_A	234	Revealing A Marine Natural Product As A Novel Agoni		2e-07
1dkf_B	235	Crystal Structure Of A Heterodimeric Complex Of Rar		2e-07
3kmr_A	266	Crystal Structure Of Raralpha Ligand Binding Domain		2e-07
1xap_A	267	Structure Of The Ligand Binding Domain Of The Retin		2e-07
4hn6_A	114	Gr Dna Binding Domain R460d/d462r - Tslp Ngre Compl		2e-07
1xdk_B	303	Crystal Structure Of The RarbetaRXRALPHA LIGAND BIN		2e-07
1dsz_A	86	Structure Of The RxrRAR DNA-Binding Domain Heterodi		3e-07
1dsz_B	85	Structure Of The RxrRAR DNA-Binding Domain Heterodi		3e-07
2c7a_A	78	Structure Of The Progesterone Receptor-Dna Complex		3e-07
1by4_A	82	Structure And Mechanism Of The Homodimeric Assembly		3e-07
4hn5_A	117	Gr Dna Binding Domain - Tslp Ngre Complex Length =		3e-07
1rxr_A	83	High Resolution Solution Structure Of The Retinoid		3e-07
1hra_A	80	The Solution Structure Of The Human Retinoic Acid R		3e-07
2han_B	119	Structural Basis Of Heterodimeric Ecdysteroid Recep		3e-07
3plz_A	257	Human Lrh1 Lbd Bound To Gr470 Length = 257		3e-07
1yok_A	256	Crystal Structure Of Human Lrh-1 Bound With Tif-2 P		4e-07
1r4i_A	105	Crystal Structure Of Androgen Receptor Dna-Binding		4e-07
1r0n_A	81	Crystal Structure Of Heterodimeric Ecdsyone Recepto		4e-07
3m9e_A	105	Thyroid Hormone Beta Dna Binding Domain Homodimer W		6e-07
2nll_B	103	Retinoid X Receptor-Thyroid Hormone Receptor Dna-Bi		6e-07
1r0n_B	109	Crystal Structure Of Heterodimeric Ecdsyone Recepto		8e-07
1glu_A	81	Crystallographic Analysis Of The Interaction Of The		9e-07
1r4r_B	92	Crystallographic Analysis Of The Interaction Of The		9e-07
1yuc_A	255	Human Nuclear Receptor Liver Receptor Homologue-1,		1e-06
1r4o_A	92	Crystallographic Analysis Of The Interaction Of The		1e-06
1g2n_A	264	Crystal Structure Of The Ligand Binding Domain Of T		1e-06
1zh7_A	243	Structural And Biochemical Basis For Selective Repr		1e-06
1r1k_A	263	Crystal Structure Of The Ligand-Binding Domains Of		1e-06
2nll_A	66	Retinoid X Receptor-Thyroid Hormone Receptor Dna-Bi		2e-06
1pk5_A	248	Crystal Structure Of The Orphan Nuclear Receptor Lr		2e-06
1zdu_A	245	The Crystal Structure Of Human Liver Receptor Homol		2e-06
4dos_A	242	Human Nuclear Receptor Liver Receptor Homologue-1,		2e-06
1ynw_A	110	Crystal Structure Of Vitamin D Receptor And 9-Cis R		4e-06
2gda_A	72	Refined Solution Structure Of The Glucocorticoid Re		4e-06
1gdc_A	72	Refined Solution Structure Of The Glucocorticoid Re		4e-06
1kb2_A	110	Crystal Structure Of Vdr Dna-Binding Domain Bound T		4e-06
3cjw_A	244	Crystal Structure Of The Human Coup-Tfii Ligand Bin		5e-06
3cbb_A	78	Crystal Structure Of Hepatocyte Nuclear Factor 4alp		6e-06
3g9p_B	90	Gr Dna Binding Domain:sgk 16bp Complex-7 Length = 9		7e-06
3tx7_B	352	Crystal Structure Of Lrh-1BETA-Catenin Complex Leng		9e-06
3g6t_A	91	Gr Gamma Dna-Binding Domain:fkbp5 16bp Complex-34 L		1e-05
2ebl_A	89	Solution Structure Of The Zinc Finger, C4-type Doma		1e-05
1rgd_A	71	Structure Refinement Of The Glucocorticoid Receptor		1e-05
2hbh_A	302	Crystal Structure Of Vitamin D Nuclear Receptor Lig		2e-05
4fhh_A	300	Development Of Synthetically Accessible Non-Secoste		3e-05
3f7d_A	244	Sf-1 Lbd Bound By Phosphatidylcholine Length = 244		4e-05
1rjk_A	292	Crystal Structure Of The Rat Vitamin D Receptor Lig		5e-05
1ymt_A	246	Mouse Sf-1 Lbd Length = 246		6e-05
2zl9_A	271	2-Substituted-16-Ene-22-Thia-1alpha,25-Dihydroxy-26		6e-05
2zfx_A	265	Crystal Structure Of The Rat Vitamin D Receptor Lig		6e-05
1yow_A	242	Human Steroidogenic Factor 1 Lbd With Bound Co-Fact		7e-05
3p8x_A	280	Synthesis, Structure, And Biological Activity Of De		8e-05
1yp0_A	239	Structure Of The Steroidogenic Factor-1 Ligand Bind		8e-05
1zdt_A	241	The Crystal Structure Of Human Steroidogenic Factor		9e-05
1s0z_A	263	Crystal Structure Of The Vdr Lbd Complexed To Seoca		9e-05
3b0t_A	254	Human Vdr Ligand Binding Domain In Complex With Max		9e-05
3az1_A	253	Crystal Structure Analysis Of Vitamin D Receptor Le		9e-05
3a2i_A	263	Crystal Structure Of The Human Vitamin D Receptor (		9e-05
3a2j_A	263	Crystal Structure Of The Human Vitamin D Receptor (		9e-05
3m7r_A	253	Crystal Structure Of Vdr H305q Mutant Length = 253		9e-05
1db1_A	259	Crystal Structure Of The Nuclear Receptor For Vitam		9e-05
1lv2_A	229	Hepatocyte Nuclear Factor 4 Is A Transcription Fact		1e-04
3fs1_A	230	Crystal Structure Of Hnf4a Lbd In Complex With The		5e-04
1pzl_A	237	Crystal Structure Of Hnf4a Lbd In Complex With The		6e-04
1m7w_A	250	Hnf4a Ligand Binding Domain With Bound Fatty Acid L		7e-04

>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 =  114 bits (286), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 77/242 (31%), Positives = 119/242 (49%), Gaps = 27/242 (11%)
Query: 75  NKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSL 134
           NK++  LL+ EPE +    +    D  ++ + +L DL DRELV IIGWAK IPGF+ LSL
Sbjct: 3   NKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSL 62
Query: 135 NDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGF----SEIYQQV 190
            DQM LLQS W EIL L + YRSL     ++ +A D ++DE Q++  G     + I Q V
Sbjct: 63  ADQMSLLQSAWMEILILGVVYRSLS-FEDELVYADDYIMDEDQSKLAGLLDLNNAILQLV 121
Query: 191 KHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGA-- 248
           K   S+  +++EE      +   +  S     V + +  +      +Q Y   +      
Sbjct: 122 KKYKSM-KLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPR 180
Query: 249 -CGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLRFWSTVHKDGKVLMNKLFVEML 307
             G +++    ++     +++ F N                  +  +GKV M+KLF+EML
Sbjct: 181 RAGKMLMTLPLLRQTSTKAVQHFYN------------------IKLEGKVPMHKLFLEML 222
Query: 308 EA 309
           EA
Sbjct: 223 EA 224

>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 =  114 bits (286), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 77/242 (31%), Positives = 119/242 (49%), Gaps = 27/242 (11%)
Query: 75  NKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSL 134
           NK++  LL+ EPE +    +    D  ++ + +L DL DRELV IIGWAK IPGF+ LSL
Sbjct: 7   NKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSL 66
Query: 135 NDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGF----SEIYQQV 190
            DQM LLQS W EIL L + YRSL     ++ +A D ++DE Q++  G     + I Q V
Sbjct: 67  ADQMSLLQSAWMEILILGVVYRSLS-FEDELVYADDYIMDEDQSKLAGLLDLNNAILQLV 125
Query: 191 KHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGA-- 248
           K   S+  +++EE      +   +  S     V + +  +      +Q Y   +      
Sbjct: 126 KKYKSM-KLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPR 184
Query: 249 -CGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLRFWSTVHKDGKVLMNKLFVEML 307
             G +++    ++     +++ F N                  +  +GKV M+KLF+EML
Sbjct: 185 RAGKMLMTLPLLRQTSTKAVQHFYN------------------IKLEGKVPMHKLFLEML 226
Query: 308 EA 309
           EA
Sbjct: 227 EA 228

>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 =  114 bits (286), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 77/242 (31%), Positives = 119/242 (49%), Gaps = 27/242 (11%)
Query: 75  NKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSL 134
           NK++  LL+ EPE +    +    D  ++ + +L DL DRELV IIGWAK IPGF+ LSL
Sbjct: 28  NKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSL 87
Query: 135 NDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGF----SEIYQQV 190
            DQM LLQS W EIL L + YRSL     ++ +A D ++DE Q++  G     + I Q V
Sbjct: 88  ADQMSLLQSAWMEILILGVVYRSLS-FEDELVYADDYIMDEDQSKLAGLLDLNNAILQLV 146
Query: 191 KHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGA-- 248
           K   S+  +++EE      +   +  S     V + +  +      +Q Y   +      
Sbjct: 147 KKYKSM-KLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPR 205
Query: 249 -CGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLRFWSTVHKDGKVLMNKLFVEML 307
             G +++    ++     +++ F N                  +  +GKV M+KLF+EML
Sbjct: 206 RAGKMLMTLPLLRQTSTKAVQHFYN------------------IKLEGKVPMHKLFLEML 247
Query: 308 EA 309
           EA
Sbjct: 248 EA 249

>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 =  114 bits (286), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 77/242 (31%), Positives = 119/242 (49%), Gaps = 27/242 (11%)
Query: 75  NKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSL 134
           NK++  LL+ EPE +    +    D  ++ + +L DL DRELV IIGWAK IPGF+ LSL
Sbjct: 28  NKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSL 87
Query: 135 NDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGF----SEIYQQV 190
            DQM LLQS W EIL L + YRSL     ++ +A D ++DE Q++  G     + I Q V
Sbjct: 88  ADQMSLLQSAWMEILILGVVYRSLS-FEDELVYADDYIMDEDQSKLAGLLDLNNAILQLV 146
Query: 191 KHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGA-- 248
           K   S+  +++EE      +   +  S     V + +  +      +Q Y   +      
Sbjct: 147 KKYKSM-KLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPR 205
Query: 249 -CGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLRFWSTVHKDGKVLMNKLFVEML 307
             G +++    ++     +++ F N                  +  +GKV M+KLF+EML
Sbjct: 206 RAGKMLMTLPLLRQTSTKAVQHFYN------------------IKLEGKVPMHKLFLEML 247
Query: 308 EA 309
           EA
Sbjct: 248 EA 249

>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 =  114 bits (286), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 77/242 (31%), Positives = 119/242 (49%), Gaps = 27/242 (11%)
Query: 75  NKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSL 134
           NK++  LL+ EPE +    +    D  ++ + +L DL DRELV IIGWAK IPGF+ LSL
Sbjct: 4   NKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSL 63
Query: 135 NDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGF----SEIYQQV 190
            DQM LLQS W EIL L + YRSL     ++ +A D ++DE Q++  G     + I Q V
Sbjct: 64  ADQMSLLQSAWMEILILGVVYRSLS-FEDELVYADDYIMDEDQSKLAGLLDLNNAILQLV 122
Query: 191 KHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGA-- 248
           K   S+  +++EE      +   +  S     V + +  +      +Q Y   +      
Sbjct: 123 KKYKSM-KLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPR 181
Query: 249 -CGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLRFWSTVHKDGKVLMNKLFVEML 307
             G +++    ++     +++ F N                  +  +GKV M+KLF+EML
Sbjct: 182 RAGKMLMTLPLLRQTSTKAVQHFYN------------------IKLEGKVPMHKLFLEML 223
Query: 308 EA 309
           EA
Sbjct: 224 EA 225

>pdb|2E2R|A Chain A, Crystal Structure Of Human Estrogen-Related Receptor Gamma Ligand Binding Domain Complex With Bisphenol A Length = 244

Iteration: 1
 Score =  114 bits (286), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 77/242 (31%), Positives = 119/242 (49%), Gaps = 27/242 (11%)
Query: 75  NKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSL 134
           NK++  LL+ EPE +    +    D  ++ + +L DL DRELV IIGWAK IPGF+ LSL
Sbjct: 20  NKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSL 79
Query: 135 NDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGF----SEIYQQV 190
            DQM LLQS W EIL L + YRSL     ++ +A D ++DE Q++  G     + I Q V
Sbjct: 80  ADQMSLLQSAWMEILILGVVYRSL-SFEDELVYADDYIMDEDQSKLAGLLDLNNAILQLV 138
Query: 191 KHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGA-- 248
           K   S+  +++EE      +   +  S     V + +  +      +Q Y   +      
Sbjct: 139 KKYKSM-KLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPR 197
Query: 249 -CGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLRFWSTVHKDGKVLMNKLFVEML 307
             G +++    ++     +++ F N                  +  +GKV M+KLF+EML
Sbjct: 198 RAGKMLMTLPLLRQTSTKAVQHFYN------------------IKLEGKVPMHKLFLEML 239
Query: 308 EA 309
           EA
Sbjct: 240 EA 241

>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 =  112 bits (279), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 55/112 (49%), Positives = 71/112 (63%), Gaps = 1/112 (0%)
Query: 75  NKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSL 134
           N ++  LL+ EPE L    +    D  L  + +LSDL+DRE+V  I WAK IPGF+ LSL
Sbjct: 19  NALVSHLLVVEPEKLYAMPDPAGPDGHLPAVATLSDLFDREIVVTISWAKSIPGFSSLSL 78
Query: 135 NDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEI 186
           +DQM +LQS W E+L L +A RSLP    ++ FA DLVLDE  AR  G  E+
Sbjct: 79  SDQMSVLQSVWMEVLVLGVAQRSLP-LQDELAFAEDLVLDEEGARAAGLGEL 129

>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 =  110 bits (274), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/252 (33%), Positives = 118/252 (46%), Gaps = 19/252 (7%)
Query: 65  PNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAK 124
           P  S  +   N ++  LL+ EPE L    +    D  L  + +L DL+DRE+V  I WAK
Sbjct: 15  PRGSKTAAPVNALVSHLLVVEPEKLYAMPDPAGPDGHLPAVATLCDLFDREIVVTISWAK 74
Query: 125 QIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFS 184
            IPGF+ LSL+DQM +LQS W E+L L +A RSLP    ++ FA DLVLDE  AR  G  
Sbjct: 75  SIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLP-LQDELAFAEDLVLDEEGARAAGLG 133
Query: 185 E----IYQQVKHSGSLDGIKEE-ELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQV 239
           E    + Q V+   +L   +EE  L + L L   D     H  +   EA +   +   + 
Sbjct: 134 ELGAALLQLVRRLQALRLEREEYVLLKALALANSD---SVH--IEDAEAVEQLREALHEA 188
Query: 240 YSGYRQTGACGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLRFWSTVHKDGKVLM 299
              Y                   E     +   ++         VL  +  V  +GKV M
Sbjct: 189 LLEYEAG--------RAGPGGGAERRRAGRLLLTLPLLRQTAGKVLAHFYGVKLEGKVPM 240
Query: 300 NKLFVEMLEAYL 311
           +KLF+EMLEA +
Sbjct: 241 HKLFLEMLEAMM 252

>pdb|3K6P|A Chain A, Estrogen Related Receptor Alpha In Complex With An Ether Based Ligand Length = 248

Iteration: 1
 Score =  108 bits (271), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 54/112 (48%), Positives = 70/112 (62%), Gaps = 1/112 (0%)
Query: 75  NKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSL 134
           N ++  LL+ EPE L    +    D  L  + +L DL+DRE+V  I WAK IPGF+ LSL
Sbjct: 20  NALVSHLLVVEPEKLYAMPDPAGPDGHLPAVATLCDLFDREIVVTISWAKSIPGFSSLSL 79
Query: 135 NDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEI 186
           +DQM +LQS W E+L L +A RSLP    ++ FA DLVLDE  AR  G  E+
Sbjct: 80  SDQMSVLQSVWMEVLVLGVAQRSLP-LQDELAFAEDLVLDEEGARAAGLGEL 130

>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 =  108 bits (271), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 54/112 (48%), Positives = 70/112 (62%), Gaps = 1/112 (0%)
Query: 75  NKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSL 134
           N ++  LL+ EPE L    +    D  L  + +L DL+DRE+V  I WAK IPGF+ LSL
Sbjct: 19  NALVSHLLVVEPEKLYAMPDPAGPDGHLPAVATLCDLFDREIVVTISWAKSIPGFSSLSL 78
Query: 135 NDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEI 186
           +DQM +LQS W E+L L +A RSLP    ++ FA DLVLDE  AR  G  E+
Sbjct: 79  SDQMSVLQSVWMEVLVLGVAQRSLP-LQDELAFAEDLVLDEEGARAAGLGEL 129

>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 =  103 bits (257), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 63/192 (32%), Positives = 104/192 (54%), Gaps = 10/192 (5%)
Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
           ++ YTC  + DC I+KR+R  CQ CR+QKCL  GM +E V+ +R RG      RN + + 
Sbjct: 171 DLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRG----KDRNENEVE 226
Query: 61  QQWPPNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQT--INSLSDLYDRELVC 118
                N+ +P     ++LEA L  EP+  T        +P+     + ++    D++L  
Sbjct: 227 STSSANEDMPV---ERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFT 283
Query: 119 IIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQA 178
           ++ WAK+IP F++L L+DQ+ LL++ W E+L  + ++RS+    G I  A+ L +    A
Sbjct: 284 LVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDG-ILLATGLHVHRNSA 342
Query: 179 RECGFSEIYQQV 190
              G   I+ +V
Sbjct: 343 HSAGVGAIFDRV 354

>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 = 54.3 bits (129), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 20/33 (60%), Positives = 26/33 (78%)
Query: 206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
           + +C +CGD +SG HYGV SCE CK FFKRT++
Sbjct: 137 KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVR 169

>pdb|1LO1|A Chain A, Estrogen Related Receptor 2 Dna Binding Domain In Complex With Dna Length = 98

Iteration: 1
 Score = 98.2 bits (243), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 45/57 (78%), Positives = 51/57 (89%)
Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPD 57
          NIEY+CPA+N+CEI KRRRK+CQACRF K L+ GMLKEGVRLDRVRGGRQKY+R  D
Sbjct: 38 NIEYSCPATNECEITKRRRKSCQACRFMKALKVGMLKEGVRLDRVRGGRQKYKRRLD 94

>pdb|1LO1|A Chain A, Estrogen Related Receptor 2 Dna Binding Domain In Complex With Dna Length = 98

Iteration: 1
 Score = 75.1 bits (183), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 31/35 (88%), Positives = 35/35 (100%)
Query: 204 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
           +P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQ
Sbjct: 2   IPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQ 36

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

Iteration: 1
 Score = 94.4 bits (233), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 50/126 (39%), Positives = 77/126 (61%), Gaps = 2/126 (1%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 6   SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 65
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC-GFSEIYQQ 189
           DL+L+DQ+ LL+S W EIL + + +RS+ H  GK+ FA +L+LD  Q +   G  EI+  
Sbjct: 66  DLTLHDQVHLLESAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGKSVEGMVEIFDM 124
Query: 190 VKHSGS 195
           +  + S
Sbjct: 125 LLATSS 130

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

Iteration: 1
 Score = 94.4 bits (233), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 50/126 (39%), Positives = 77/126 (61%), Gaps = 2/126 (1%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 10  SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 69
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC-GFSEIYQQ 189
           DL+L+DQ+ LL+S W EIL + + +RS+ H  GK+ FA +L+LD  Q +   G  EI+  
Sbjct: 70  DLTLHDQVHLLESAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGKSVEGMVEIFDM 128
Query: 190 VKHSGS 195
           +  + S
Sbjct: 129 LLATSS 134

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

Iteration: 1
 Score = 94.4 bits (233), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 50/126 (39%), Positives = 77/126 (61%), Gaps = 2/126 (1%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 10  SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 69
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC-GFSEIYQQ 189
           DL+L+DQ+ LL+S W EIL + + +RS+ H  GK+ FA +L+LD  Q +   G  EI+  
Sbjct: 70  DLTLHDQVHLLESAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGKSVEGMVEIFDM 128
Query: 190 VKHSGS 195
           +  + S
Sbjct: 129 LLATSS 134

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

Iteration: 1
 Score = 94.4 bits (233), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 50/126 (39%), Positives = 77/126 (61%), Gaps = 2/126 (1%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 6   SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 65
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC-GFSEIYQQ 189
           DL+L+DQ+ LL+S W EIL + + +RS+ H  GK+ FA +L+LD  Q +   G  EI+  
Sbjct: 66  DLTLHDQVHLLESAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGKSVEGMVEIFDM 124
Query: 190 VKHSGS 195
           +  + S
Sbjct: 125 LLATSS 130

>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 = 92.4 bits (228), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 49/126 (38%), Positives = 76/126 (60%), Gaps = 2/126 (1%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 15  SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 74
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC-GFSEIYQQ 189
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q +   G  EI+  
Sbjct: 75  DLTLHDQVHLLEXAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGKXVEGMVEIFDM 133
Query: 190 VKHSGS 195
           +  + S
Sbjct: 134 LLATSS 139

>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 = 92.4 bits (228), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 49/126 (38%), Positives = 76/126 (60%), Gaps = 2/126 (1%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 12  SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 71
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC-GFSEIYQQ 189
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q +   G  EI+  
Sbjct: 72  DLTLHDQVHLLEXAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGKXVEGMVEIFDM 130
Query: 190 VKHSGS 195
           +  + S
Sbjct: 131 LLATSS 136

>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 = 92.4 bits (228), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 48/121 (39%), Positives = 74/121 (61%), Gaps = 2/121 (1%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 12  SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 71
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC-GFSEIYQQ 189
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q +   G  EI+  
Sbjct: 72  DLTLHDQVHLLEXAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGKXVEGMVEIFDM 130
Query: 190 V 190
           +
Sbjct: 131 L 131

>pdb|3UU7|B Chain B, Crystal Structure Of Hera-Lbd (Y537s) In Complex With Bisphenol-A Length = 251

Iteration: 1
 Score = 92.4 bits (228), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 49/126 (38%), Positives = 76/126 (60%), Gaps = 2/126 (1%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 8   SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 67
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC-GFSEIYQQ 189
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q +   G  EI+  
Sbjct: 68  DLTLHDQVHLLEXAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGKXVEGMVEIFDM 126
Query: 190 VKHSGS 195
           +  + S
Sbjct: 127 LLATSS 132

>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 = 92.4 bits (228), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 49/126 (38%), Positives = 76/126 (60%), Gaps = 2/126 (1%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 12  SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 71
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC-GFSEIYQQ 189
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q +   G  EI+  
Sbjct: 72  DLTLHDQVHLLEXAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGKXVEGMVEIFDM 130
Query: 190 VKHSGS 195
           +  + S
Sbjct: 131 LLATSS 136

>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 = 92.4 bits (228), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 49/126 (38%), Positives = 76/126 (60%), Gaps = 2/126 (1%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 15  SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 74
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC-GFSEIYQQ 189
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q +   G  EI+  
Sbjct: 75  DLTLHDQVHLLEXAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGKXVEGMVEIFDM 133
Query: 190 VKHSGS 195
           +  + S
Sbjct: 134 LLATSS 139

>pdb|3UU7|A Chain A, Crystal Structure Of Hera-Lbd (Y537s) In Complex With Bisphenol-A Length = 251

Iteration: 1
 Score = 92.4 bits (228), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 49/126 (38%), Positives = 76/126 (60%), Gaps = 2/126 (1%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 8   SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 67
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC-GFSEIYQQ 189
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q +   G  EI+  
Sbjct: 68  DLTLHDQVHLLEXAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGKXVEGMVEIFDM 126
Query: 190 VKHSGS 195
           +  + S
Sbjct: 127 LLATSS 132

>pdb|2JFA|B Chain B, Estrogen Receptor Alpha Lbd In Complex With An Affinity- Selected Corepressor Peptide Length = 252

Iteration: 1
 Score = 91.7 bits (226), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 49/126 (38%), Positives = 76/126 (60%), Gaps = 2/126 (1%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 28  SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 87
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC-GFSEIYQQ 189
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q +   G  EI+  
Sbjct: 88  DLTLHDQVHLLECAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGKXVEGMVEIFDM 146
Query: 190 VKHSGS 195
           +  + S
Sbjct: 147 LLATSS 152

>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 = 91.7 bits (226), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 49/126 (38%), Positives = 76/126 (60%), Gaps = 2/126 (1%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 16  SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 75
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC-GFSEIYQQ 189
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q +   G  EI+  
Sbjct: 76  DLTLHDQVHLLECAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGKXVEGMVEIFDM 134
Query: 190 VKHSGS 195
           +  + S
Sbjct: 135 LLATSS 140

>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 = 90.9 bits (224), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 50/127 (39%), Positives = 77/127 (60%), Gaps = 4/127 (3%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 13  SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 72
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQ 188
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q + C  G  EI+ 
Sbjct: 73  DLTLHDQVHLLEXAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGK-CVEGMVEIFD 130
Query: 189 QVKHSGS 195
            +  + S
Sbjct: 131 MLLATSS 137

>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 = 90.9 bits (224), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 47/111 (42%), Positives = 71/111 (63%), Gaps = 4/111 (3%)
Query: 86  PEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTW 145
           P +L  R   P ++ ++    SL+ L D+ELV +I WAK+IPGF +LSL DQ+RLL+S+W
Sbjct: 22  PHVLISRPSAPFTEASMMM--SLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESSW 79
Query: 146 AEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC-GFSEIYQQVKHSGS 195
            E+L + + +RS+ H  GK+ FA DLVLD  + +   G  EI+  +  + S
Sbjct: 80  MEVLMMGLMWRSIDH-PGKLIFAPDLVLDRDEGKSVEGILEIFDMLLATTS 129

>pdb|1ERR|A Chain A, Human Estrogen Receptor Ligand-Binding Domain In Complex With Raloxifene Length = 253

Iteration: 1
 Score = 90.9 bits (224), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 50/127 (39%), Positives = 77/127 (60%), Gaps = 4/127 (3%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 9   SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 68
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQ 188
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q + C  G  EI+ 
Sbjct: 69  DLTLHDQVHLLEXAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGK-CVEGMVEIFD 126
Query: 189 QVKHSGS 195
            +  + S
Sbjct: 127 MLLATSS 133

>pdb|3UUC|A Chain A, Crystal Structure Of Hera-Lbd (Wt) In Complex With Bisphenol-C Length = 251

Iteration: 1
 Score = 90.9 bits (224), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 50/127 (39%), Positives = 77/127 (60%), Gaps = 4/127 (3%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 8   SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 67
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQ 188
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q + C  G  EI+ 
Sbjct: 68  DLTLHDQVHLLEXAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGK-CVEGMVEIFD 125
Query: 189 QVKHSGS 195
            +  + S
Sbjct: 126 MLLATSS 132

>pdb|2QZO|B Chain B, Crystal Structure Of The Estrogen Receptor Alpha Ligand Binding Domain Complexed With Way-169916 Length = 258

Iteration: 1
 Score = 90.9 bits (224), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 50/127 (39%), Positives = 77/127 (60%), Gaps = 4/127 (3%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 13  SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 72
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQ 188
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q + C  G  EI+ 
Sbjct: 73  DLTLHDQVHLLEXAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGK-CVEGMVEIFD 130
Query: 189 QVKHSGS 195
            +  + S
Sbjct: 131 MLLATSS 137

>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 = 90.9 bits (224), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 50/127 (39%), Positives = 77/127 (60%), Gaps = 4/127 (3%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 15  SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 74
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQ 188
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q + C  G  EI+ 
Sbjct: 75  DLTLHDQVHLLEXAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGK-CVEGMVEIFD 132
Query: 189 QVKHSGS 195
            +  + S
Sbjct: 133 MLLATSS 139

>pdb|3UUA|A Chain A, Crystal Structure Of Hera-Lbd (Y537s) In Complex With Bisphenol-Af Length = 251

Iteration: 1
 Score = 90.9 bits (224), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 50/127 (39%), Positives = 77/127 (60%), Gaps = 4/127 (3%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 8   SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 67
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQ 188
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q + C  G  EI+ 
Sbjct: 68  DLTLHDQVHLLEXAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGK-CVEGMVEIFD 125
Query: 189 QVKHSGS 195
            +  + S
Sbjct: 126 MLLATSS 132

>pdb|3UUA|B Chain B, Crystal Structure Of Hera-Lbd (Y537s) In Complex With Bisphenol-Af Length = 251

Iteration: 1
 Score = 90.5 bits (223), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 50/127 (39%), Positives = 77/127 (60%), Gaps = 4/127 (3%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 8   SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 67
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQ 188
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q + C  G  EI+ 
Sbjct: 68  DLTLHDQVHLLEXAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGK-CVEGMVEIFD 125
Query: 189 QVKHSGS 195
            +  + S
Sbjct: 126 MLLATSS 132

>pdb|2BJ4|A Chain A, Estrogen Receptor Alpha Lbd In Complex With A Phage-Display Derived Peptide Antagonist Length = 252

Iteration: 1
 Score = 90.1 bits (222), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 50/127 (39%), Positives = 77/127 (60%), Gaps = 4/127 (3%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 28  SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 87
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQ 188
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q + C  G  EI+ 
Sbjct: 88  DLTLHDQVHLLECAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGK-CVEGMVEIFD 145
Query: 189 QVKHSGS 195
            +  + S
Sbjct: 146 MLLATSS 152

>pdb|1A52|A Chain A, Estrogen Receptor Alpha Ligand-Binding Domain Complexed To Estradiol Length = 258

Iteration: 1
 Score = 90.1 bits (222), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 50/127 (39%), Positives = 77/127 (60%), Gaps = 4/127 (3%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 13  SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 72
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQ 188
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q + C  G  EI+ 
Sbjct: 73  DLTLHDQVHLLECAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGK-CVEGMVEIFD 130
Query: 189 QVKHSGS 195
            +  + S
Sbjct: 131 MLLATSS 137

>pdb|3DT3|A Chain A, Human Estrogen Receptor Alpha Lbd With Gw368 Length = 255

Iteration: 1
 Score = 90.1 bits (222), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 50/127 (39%), Positives = 77/127 (60%), Gaps = 4/127 (3%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 13  SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 72
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQ 188
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q + C  G  EI+ 
Sbjct: 73  DLTLHDQVHLLECAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGK-CVEGMVEIFD 130
Query: 189 QVKHSGS 195
            +  + S
Sbjct: 131 MLLATSS 137

>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 = 90.1 bits (222), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 50/127 (39%), Positives = 77/127 (60%), Gaps = 4/127 (3%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 12  SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 71
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQ 188
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q + C  G  EI+ 
Sbjct: 72  DLTLHDQVHLLECAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGK-CVEGMVEIFD 129
Query: 189 QVKHSGS 195
            +  + S
Sbjct: 130 MLLATSS 136

>pdb|1ERE|A Chain A, Human Estrogen Receptor Ligand-Binding Domain In Complex With 17beta-Estradiol Length = 253

Iteration: 1
 Score = 90.1 bits (222), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 50/127 (39%), Positives = 77/127 (60%), Gaps = 4/127 (3%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 9   SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 68
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQ 188
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q + C  G  EI+ 
Sbjct: 69  DLTLHDQVHLLECAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGK-CVEGMVEIFD 126
Query: 189 QVKHSGS 195
            +  + S
Sbjct: 127 MLLATSS 133

>pdb|2IOK|A Chain A, Human Estrogen Receptor Alpha Ligand-binding Domain In Complex With Compound 1d Length = 254

Iteration: 1
 Score = 90.1 bits (222), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 50/127 (39%), Positives = 77/127 (60%), Gaps = 4/127 (3%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 9   SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 68
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQ 188
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q + C  G  EI+ 
Sbjct: 69  DLTLHDQVHLLECAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGK-CVEGMVEIFD 126
Query: 189 QVKHSGS 195
            +  + S
Sbjct: 127 MLLATSS 133

>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 = 90.1 bits (222), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 50/127 (39%), Positives = 77/127 (60%), Gaps = 4/127 (3%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 16  SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 75
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQ 188
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q + C  G  EI+ 
Sbjct: 76  DLTLHDQVHLLECAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGK-CVEGMVEIFD 133
Query: 189 QVKHSGS 195
            +  + S
Sbjct: 134 MLLATSS 140

>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 = 90.1 bits (222), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 50/127 (39%), Positives = 77/127 (60%), Gaps = 4/127 (3%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 13  SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 72
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQ 188
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q + C  G  EI+ 
Sbjct: 73  DLTLHDQVHLLECAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGK-CVEGMVEIFD 130
Query: 189 QVKHSGS 195
            +  + S
Sbjct: 131 MLLATSS 137

>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 = 90.1 bits (222), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 50/127 (39%), Positives = 77/127 (60%), Gaps = 4/127 (3%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 9   SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 68
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQ 188
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q + C  G  EI+ 
Sbjct: 69  DLTLHDQVHLLECAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGK-CVEGMVEIFD 126
Query: 189 QVKHSGS 195
            +  + S
Sbjct: 127 MLLATSS 133

>pdb|4DMA|A Chain A, Crystal Structure Of Era Lbd In Complex With Ru100132 Length = 247

Iteration: 1
 Score = 90.1 bits (222), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 50/127 (39%), Positives = 77/127 (60%), Gaps = 4/127 (3%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 7   SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 66
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQ 188
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q + C  G  EI+ 
Sbjct: 67  DLTLHDQVHLLECAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGK-CVEGMVEIFD 124
Query: 189 QVKHSGS 195
            +  + S
Sbjct: 125 MLLATSS 131

>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 = 90.1 bits (222), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 50/127 (39%), Positives = 77/127 (60%), Gaps = 4/127 (3%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 12  SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 71
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQ 188
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q + C  G  EI+ 
Sbjct: 72  DLTLHDQVHLLECAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGK-CVEGMVEIFD 129
Query: 189 QVKHSGS 195
            +  + S
Sbjct: 130 MLLATSS 136

>pdb|1QKU|A Chain A, Wild Type Estrogen Nuclear Receptor Ligand Binding Domain Complexed With Estradiol Length = 250

Iteration: 1
 Score = 90.1 bits (222), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 50/127 (39%), Positives = 77/127 (60%), Gaps = 4/127 (3%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 9   SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 68
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQ 188
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q + C  G  EI+ 
Sbjct: 69  DLTLHDQVHLLECAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGK-CVEGMVEIFD 126
Query: 189 QVKHSGS 195
            +  + S
Sbjct: 127 MLLATSS 133

>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 = 90.1 bits (222), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 50/127 (39%), Positives = 77/127 (60%), Gaps = 4/127 (3%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 13  SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 72
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQ 188
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q + C  G  EI+ 
Sbjct: 73  DLTLHDQVHLLECAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGK-CVEGMVEIFD 130
Query: 189 QVKHSGS 195
            +  + S
Sbjct: 131 MLLATSS 137

>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 = 90.1 bits (222), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 50/127 (39%), Positives = 77/127 (60%), Gaps = 4/127 (3%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 13  SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 72
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQ 188
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q + C  G  EI+ 
Sbjct: 73  DLTLHDQVHLLECAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGK-CVEGMVEIFD 130
Query: 189 QVKHSGS 195
            +  + S
Sbjct: 131 MLLATSS 137

>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 = 90.1 bits (222), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 50/127 (39%), Positives = 77/127 (60%), Gaps = 4/127 (3%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 5   SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 64
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQ 188
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q + C  G  EI+ 
Sbjct: 65  DLTLHDQVHLLECAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGK-CVEGMVEIFD 122
Query: 189 QVKHSGS 195
            +  + S
Sbjct: 123 MLLATSS 129

>pdb|2IOG|A Chain A, Human Estrogen Receptor Alpha Ligand-Binding Domain In Complex With Compound 11f Length = 246

Iteration: 1
 Score = 90.1 bits (222), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 50/127 (39%), Positives = 77/127 (60%), Gaps = 4/127 (3%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 1   SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 60
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQ 188
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q + C  G  EI+ 
Sbjct: 61  DLTLHDQVHLLECAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGK-CVEGMVEIFD 118
Query: 189 QVKHSGS 195
            +  + S
Sbjct: 119 MLLATSS 125

>pdb|1G50|A Chain A, Crystal Structure Of A Wild Type Her Alpha Lbd At 2.9 Angstrom Resolution Length = 247

Iteration: 1
 Score = 89.7 bits (221), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 50/127 (39%), Positives = 77/127 (60%), Gaps = 4/127 (3%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 6   SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 65
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQ 188
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q + C  G  EI+ 
Sbjct: 66  DLTLHDQVHLLECAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGK-CVEGMVEIFD 123
Query: 189 QVKHSGS 195
            +  + S
Sbjct: 124 MLLATSS 130

>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 = 89.7 bits (221), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 50/127 (39%), Positives = 77/127 (60%), Gaps = 4/127 (3%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 3   SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 62
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQ 188
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q + C  G  EI+ 
Sbjct: 63  DLTLHDQVHLLECAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGK-CVEGMVEIFD 120
Query: 189 QVKHSGS 195
            +  + S
Sbjct: 121 MLLATSS 127

>pdb|1QKN|A Chain A, Rat Oestrogen Receptor Beta Ligand-Binding Domain In Complex With Antagonist Raloxifene Length = 255

Iteration: 1
 Score = 89.7 bits (221), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 50/112 (44%), Positives = 72/112 (64%), Gaps = 6/112 (5%)
Query: 86  PEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTW 145
           P +L  R   P ++ ++    SL+ L D+ELV +IGWAK+IPGF +LSL DQ+RLL+S W
Sbjct: 24  PNVLVSRPSMPFTEASMMM--SLTKLADKELVHMIGWAKKIPGFVELSLLDQVRLLESCW 81
Query: 146 AEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQQVKHSGS 195
            E+L + + +RS+ H  GK+ FA DLVLD R   +C  G  EI+  +  + S
Sbjct: 82  MEVLMVGLMWRSIDH-PGKLIFAPDLVLD-RDEGKCVEGILEIFDMLLATTS 131

>pdb|2J7X|A Chain A, Structure Of Estradiol-bound Estrogen Receptor Beta Lbd In Complex With Lxxll Motif From Ncoa5 Length = 255

Iteration: 1
 Score = 89.7 bits (221), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 50/112 (44%), Positives = 72/112 (64%), Gaps = 6/112 (5%)
Query: 86  PEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTW 145
           P +L  R   P ++ ++    SL+ L D+ELV +IGWAK+IPGF +LSL DQ+RLL+S W
Sbjct: 24  PNVLVSRPSMPFTEASMMM--SLTKLADKELVHMIGWAKKIPGFVELSLLDQVRLLESCW 81
Query: 146 AEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQQVKHSGS 195
            E+L + + +RS+ H  GK+ FA DLVLD R   +C  G  EI+  +  + S
Sbjct: 82  MEVLMVGLMWRSIDH-PGKLIFAPDLVLD-RDEGKCVEGILEIFDMLLATTS 131

>pdb|3LTX|A Chain A, Crystal Structure Of The Pacific Oyster Estrogen Receptor Ligand Binding Domain Length = 243

Iteration: 1
 Score = 89.0 bits (219), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 43/92 (46%), Positives = 60/92 (65%), Gaps = 1/92 (1%)
Query: 100 PT-LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSL 158
           PT +  +NSL  L +RELV +I WAK +PG+TDLSL+DQ+ L++  W E+L L  A+RS+
Sbjct: 32  PTKVHLLNSLVKLAERELVHLINWAKNVPGYTDLSLSDQVHLIECCWMELLLLNCAFRSI 91
Query: 159 PHCAGKIRFASDLVLDERQARECGFSEIYQQV 190
            H    + FA DLVLD         +EI++QV
Sbjct: 92  EHGGKSLAFAPDLVLDRSSWSTVEMTEIFEQV 123

>pdb|3OS8|A Chain A, Estrogen Receptor Length = 258

Iteration: 1
 Score = 89.0 bits (219), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 48/126 (38%), Positives = 75/126 (59%), Gaps = 2/126 (1%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 14  SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 73
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC-GFSEIYQQ 189
           DL+ +DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q +   G  EI+  
Sbjct: 74  DLTRHDQVHLLECAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGKXVEGMVEIFDM 132
Query: 190 VKHSGS 195
           +  + S
Sbjct: 133 LLATSS 138

>pdb|1NDE|A Chain A, Estrogen Receptor Beta With Selective Triazine Modulator Length = 255

Iteration: 1
 Score = 87.8 bits (216), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 49/112 (43%), Positives = 71/112 (63%), Gaps = 6/112 (5%)
Query: 86  PEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTW 145
           P +L  R   P ++ ++    SL+ L D+ELV +I WAK+IPGF +LSL DQ+RLL+S W
Sbjct: 32  PHVLISRPSAPFTEASMMM--SLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCW 89
Query: 146 AEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQQVKHSGS 195
            E+L + + +RS+ H  GK+ FA DLVLD R   +C  G  EI+  +  + S
Sbjct: 90  MEVLMMGLMWRSIDH-PGKLIFAPDLVLD-RDEGKCVEGILEIFDMLLATTS 139

>pdb|2I0G|A Chain A, Benzopyrans Are Selective Estrogen Receptor Beta Agonists (Serbas) With Novel Activity In Models Of Benign Prostatic Hyperplasia Length = 257

Iteration: 1
 Score = 87.8 bits (216), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 49/112 (43%), Positives = 71/112 (63%), Gaps = 6/112 (5%)
Query: 86  PEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTW 145
           P +L  R   P ++ ++    SL+ L D+ELV +I WAK+IPGF +LSL DQ+RLL+S W
Sbjct: 30  PHVLISRPSAPFTEASMMM--SLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCW 87
Query: 146 AEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQQVKHSGS 195
            E+L + + +RS+ H  GK+ FA DLVLD R   +C  G  EI+  +  + S
Sbjct: 88  MEVLMMGLMWRSIDH-PGKLIFAPDLVLD-RDEGKCVEGILEIFDMLLATTS 137

>pdb|1QKM|A Chain A, Human Oestrogen Receptor Beta Ligand-Binding Domain In Complex With Partial Agonist Genistein Length = 255

Iteration: 1
 Score = 87.8 bits (216), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 49/112 (43%), Positives = 71/112 (63%), Gaps = 6/112 (5%)
Query: 86  PEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTW 145
           P +L  R   P ++ ++    SL+ L D+ELV +I WAK+IPGF +LSL DQ+RLL+S W
Sbjct: 24  PHVLISRPSAPFTEASMMM--SLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCW 81
Query: 146 AEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQQVKHSGS 195
            E+L + + +RS+ H  GK+ FA DLVLD R   +C  G  EI+  +  + S
Sbjct: 82  MEVLMMGLMWRSIDH-PGKLIFAPDLVLD-RDEGKCVEGILEIFDMLLATTS 131

>pdb|2NV7|A Chain A, Crystal Structure Of Estrogen Receptor Beta Complexed With Way-555 Length = 238

Iteration: 1
 Score = 87.8 bits (216), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 49/112 (43%), Positives = 71/112 (63%), Gaps = 6/112 (5%)
Query: 86  PEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTW 145
           P +L  R   P ++ ++    SL+ L D+ELV +I WAK+IPGF +LSL DQ+RLL+S W
Sbjct: 16  PHVLISRPSAPFTEASMMM--SLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCW 73
Query: 146 AEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQQVKHSGS 195
            E+L + + +RS+ H  GK+ FA DLVLD R   +C  G  EI+  +  + S
Sbjct: 74  MEVLMMGLMWRSIDH-PGKLIFAPDLVLD-RDEGKCVEGILEIFDMLLATTS 123

>pdb|1ZAF|A Chain A, Crystal Structure Of Estrogen Receptor Beta Complexed With 3-Bromo-6-Hydroxy-2-(4-Hydroxy-Phenyl)-Inden-1-One Length = 238

Iteration: 1
 Score = 87.8 bits (216), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 49/112 (43%), Positives = 71/112 (63%), Gaps = 6/112 (5%)
Query: 86  PEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTW 145
           P +L  R   P ++ ++    SL+ L D+ELV +I WAK+IPGF +LSL DQ+RLL+S W
Sbjct: 16  PHVLISRPSAPFTEASMMM--SLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCW 73
Query: 146 AEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQQVKHSGS 195
            E+L + + +RS+ H  GK+ FA DLVLD R   +C  G  EI+  +  + S
Sbjct: 74  MEVLMMGLMWRSIDH-PGKLIFAPDLVLD-RDEGKCVEGILEIFDMLLATTS 123

>pdb|3OLL|A Chain A, Crystal Structure Of Phosphorylated Estrogen Receptor Beta Ligand Binding Domain Length = 240

Iteration: 1
 Score = 87.8 bits (216), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 49/112 (43%), Positives = 71/112 (63%), Gaps = 6/112 (5%)
Query: 86  PEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTW 145
           P +L  R   P ++ ++    SL+ L D+ELV +I WAK+IPGF +LSL DQ+RLL+S W
Sbjct: 18  PHVLISRPSAPFTEASMMM--SLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCW 75
Query: 146 AEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQQVKHSGS 195
            E+L + + +RS+ H  GK+ FA DLVLD R   +C  G  EI+  +  + S
Sbjct: 76  MEVLMMGLMWRSIDH-PGKLIFAPDLVLD-RDEGKCVEGILEIFDMLLATTS 125

>pdb|2GIU|A Chain A, Human Estrogen Receptor Beta Ligand-Binding Domain In Complex With Compound 45 Length = 241

Iteration: 1
 Score = 87.8 bits (216), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 49/112 (43%), Positives = 71/112 (63%), Gaps = 6/112 (5%)
Query: 86  PEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTW 145
           P +L  R   P ++ ++    SL+ L D+ELV +I WAK+IPGF +LSL DQ+RLL+S W
Sbjct: 19  PHVLISRPSAPFTEASMMM--SLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCW 76
Query: 146 AEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQQVKHSGS 195
            E+L + + +RS+ H  GK+ FA DLVLD R   +C  G  EI+  +  + S
Sbjct: 77  MEVLMMGLMWRSIDH-PGKLIFAPDLVLD-RDEGKCVEGILEIFDMLLATTS 126

>pdb|1L2J|A Chain A, Human Estrogen Receptor Beta Ligand-Binding Domain In Complex With (R, R)-5,11-Cis-Diethyl-5,6,11,12-Tetrahydrochrysene-2, 8-Diol Length = 271

Iteration: 1
 Score = 87.8 bits (216), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 49/112 (43%), Positives = 71/112 (63%), Gaps = 6/112 (5%)
Query: 86  PEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTW 145
           P +L  R   P ++ ++    SL+ L D+ELV +I WAK+IPGF +LSL DQ+RLL+S W
Sbjct: 44  PHVLISRPSAPFTEASMMM--SLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCW 101
Query: 146 AEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQQVKHSGS 195
            E+L + + +RS+ H  GK+ FA DLVLD R   +C  G  EI+  +  + S
Sbjct: 102 MEVLMMGLMWRSIDH-PGKLIFAPDLVLD-RDEGKCVEGILEIFDMLLATTS 151

>pdb|1X76|A Chain A, Crystal Structure Of Estrogen Receptor Beta Complexed With Way-697 Length = 240

Iteration: 1
 Score = 87.4 bits (215), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 49/112 (43%), Positives = 71/112 (63%), Gaps = 6/112 (5%)
Query: 86  PEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTW 145
           P +L  R   P ++ ++    SL+ L D+ELV +I WAK+IPGF +LSL DQ+RLL+S W
Sbjct: 18  PHVLISRPSAPFTEASMMM--SLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCW 75
Query: 146 AEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQQVKHSGS 195
            E+L + + +RS+ H  GK+ FA DLVLD R   +C  G  EI+  +  + S
Sbjct: 76  MEVLMMGLMWRSIDH-PGKLIFAPDLVLD-RDEGKCVEGILEIFDMLLATTS 125

>pdb|1U9E|A Chain A, Crystal Structure Of Estrogen Receptor Beta Complexed With Way-397 Length = 241

Iteration: 1
 Score = 87.4 bits (215), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 49/112 (43%), Positives = 71/112 (63%), Gaps = 6/112 (5%)
Query: 86  PEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTW 145
           P +L  R   P ++ ++    SL+ L D+ELV +I WAK+IPGF +LSL DQ+RLL+S W
Sbjct: 18  PHVLISRPSAPFTEASMMM--SLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCW 75
Query: 146 AEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQQVKHSGS 195
            E+L + + +RS+ H  GK+ FA DLVLD R   +C  G  EI+  +  + S
Sbjct: 76  MEVLMMGLMWRSIDH-PGKLIFAPDLVLD-RDEGKCVEGILEIFDMLLATTS 125

>pdb|2YLY|A Chain A, Sulfonamides As Selective Estrogen Receptor Beta Agonists. Length = 240

Iteration: 1
 Score = 87.4 bits (215), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 49/112 (43%), Positives = 71/112 (63%), Gaps = 6/112 (5%)
Query: 86  PEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTW 145
           P +L  R   P ++ ++    SL+ L D+ELV +I WAK+IPGF +LSL DQ+RLL+S W
Sbjct: 19  PHVLISRPSAPFTEASMMM--SLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCW 76
Query: 146 AEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQQVKHSGS 195
            E+L + + +RS+ H  GK+ FA DLVLD R   +C  G  EI+  +  + S
Sbjct: 77  MEVLMMGLMWRSIDH-PGKLIFAPDLVLD-RDEGKCVEGILEIFDMLLATTS 126

>pdb|3OS8|C Chain C, Estrogen Receptor Length = 258

Iteration: 1
 Score = 87.4 bits (215), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 49/127 (38%), Positives = 76/127 (59%), Gaps = 4/127 (3%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 14  SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 73
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQ 188
           DL+ +DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q + C  G  EI+ 
Sbjct: 74  DLTRHDQVHLLECAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGK-CVEGMVEIFD 131
Query: 189 QVKHSGS 195
            +  + S
Sbjct: 132 MLLATSS 138

>pdb|1YY4|A Chain A, Crystal Structure Of Estrogen Receptor Beta Complexed With 1-Chloro-6-(4-Hydroxy-Phenyl)-Naphthalen-2-Ol Length = 268

Iteration: 1
 Score = 87.0 bits (214), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 48/107 (44%), Positives = 70/107 (65%), Gaps = 6/107 (5%)
Query: 86  PEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTW 145
           P +L  R   P ++ ++  + SL+ L D+ELV +I WAK+IPGF +LSL DQ+RLL+S W
Sbjct: 16  PHVLISRPSAPFTEASM--MMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCW 73
Query: 146 AEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQQV 190
            E+L + + +RS+ H  GK+ FA DLVLD R   +C  G  EI+  +
Sbjct: 74  MEVLMMGLMWRSIDH-PGKLIFAPDLVLD-RDEGKCVEGILEIFDML 118

>pdb|1X7E|A Chain A, Crystal Structure Of Estrogen Receptor Alpha Complexed With Way-244 Length = 245

Iteration: 1
 Score = 87.0 bits (214), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 49/127 (38%), Positives = 76/127 (59%), Gaps = 4/127 (3%)
Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 5   SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 64
Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC--GFSEIYQ 188
           DL+L+DQ+ LL+  W EIL + + +RS+ H   K+ FA +L+LD  Q + C  G  EI+ 
Sbjct: 65  DLTLHDQVHLLECAWLEILMIGLVWRSMEHPV-KLLFAPNLLLDRNQGK-CVEGMVEIFD 122
Query: 189 QVKHSGS 195
            +  + S
Sbjct: 123 MLLATSS 129

>pdb|3KBA|A Chain A, Progesterone Receptor Bound To Sulfonamide Pyrrolidine Partial Agonist Length = 253

Iteration: 1
 Score = 80.5 bits (197), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 44/180 (24%), Positives = 93/180 (51%), Gaps = 5/180 (2%)
Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
           ++  L+  EP+++    +  + D +   + SL+ L +R+L+ ++ W+K +PGF +L ++D
Sbjct: 7   LINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDD 66
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEI----YQQVK 191
           Q+ L+Q +W  ++   + +RS  H +G+ + FA DL+L+E++ +E  F  +    +Q  +
Sbjct: 67  QITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQ 126
Query: 192 HSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGT 251
               L   +EE L  ++ L+   +           E  ++ + R +    G RQ G   +
Sbjct: 127 EFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSS 186

>pdb|1A28|A Chain A, Hormone-Bound Human Progesterone Receptor Ligand-Binding Domain Length = 256

Iteration: 1
 Score = 80.5 bits (197), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 44/180 (24%), Positives = 93/180 (51%), Gaps = 5/180 (2%)
Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
           ++  L+  EP+++    +  + D +   + SL+ L +R+L+ ++ W+K +PGF +L ++D
Sbjct: 10  LINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDD 69
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEI----YQQVK 191
           Q+ L+Q +W  ++   + +RS  H +G+ + FA DL+L+E++ +E  F  +    +Q  +
Sbjct: 70  QITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQ 129
Query: 192 HSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGT 251
               L   +EE L  ++ L+   +           E  ++ + R +    G RQ G   +
Sbjct: 130 EFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSS 189

>pdb|1E3K|A Chain A, Human Progesteron Receptor Ligand Binding Domain In Complex With The Ligand Metribolone (R1881) Length = 258

Iteration: 1
 Score = 80.1 bits (196), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 44/180 (24%), Positives = 93/180 (51%), Gaps = 5/180 (2%)
Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
           ++  L+  EP+++    +  + D +   + SL+ L +R+L+ ++ W+K +PGF +L ++D
Sbjct: 12  LINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDD 71
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEI----YQQVK 191
           Q+ L+Q +W  ++   + +RS  H +G+ + FA DL+L+E++ +E  F  +    +Q  +
Sbjct: 72  QITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQ 131
Query: 192 HSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGT 251
               L   +EE L  ++ L+   +           E  ++ + R +    G RQ G   +
Sbjct: 132 EFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSS 191

>pdb|3G8O|A Chain A, Progesterone Receptor With Bound Pyrrolidine 1 Length = 263

Iteration: 1
 Score = 80.1 bits (196), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 44/180 (24%), Positives = 93/180 (51%), Gaps = 5/180 (2%)
Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
           ++  L+  EP+++    +  + D +   + SL+ L +R+L+ ++ W+K +PGF +L ++D
Sbjct: 17  LINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDD 76
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEI----YQQVK 191
           Q+ L+Q +W  ++   + +RS  H +G+ + FA DL+L+E++ +E  F  +    +Q  +
Sbjct: 77  QITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQ 136
Query: 192 HSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGT 251
               L   +EE L  ++ L+   +           E  ++ + R +    G RQ G   +
Sbjct: 137 EFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSS 196

>pdb|2W8Y|A Chain A, Ru486 Bound To The Progesterone Receptor In A Destabilized Agonistic Conformation Length = 260

Iteration: 1
 Score = 80.1 bits (196), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 44/180 (24%), Positives = 93/180 (51%), Gaps = 5/180 (2%)
Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
           ++  L+  EP+++    +  + D +   + SL+ L +R+L+ ++ W+K +PGF +L ++D
Sbjct: 14  LINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDD 73
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEI----YQQVK 191
           Q+ L+Q +W  ++   + +RS  H +G+ + FA DL+L+E++ +E  F  +    +Q  +
Sbjct: 74  QITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQ 133
Query: 192 HSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGT 251
               L   +EE L  ++ L+   +           E  ++ + R +    G RQ G   +
Sbjct: 134 EFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSS 193

>pdb|1SR7|A Chain A, Progesterone Receptor Hormone Binding Domain With Bound Mometasone Furoate Length = 259

Iteration: 1
 Score = 80.1 bits (196), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 44/180 (24%), Positives = 93/180 (51%), Gaps = 5/180 (2%)
Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
           ++  L+  EP+++    +  + D +   + SL+ L +R+L+ ++ W+K +PGF +L ++D
Sbjct: 13  LINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDD 72
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEI----YQQVK 191
           Q+ L+Q +W  ++   + +RS  H +G+ + FA DL+L+E++ +E  F  +    +Q  +
Sbjct: 73  QITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQ 132
Query: 192 HSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGT 251
               L   +EE L  ++ L+   +           E  ++ + R +    G RQ G   +
Sbjct: 133 EFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSS 192

>pdb|1SQN|A Chain A, Progesterone Receptor Ligand Binding Domain With Bound Norethindrone Length = 261

Iteration: 1
 Score = 80.1 bits (196), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 44/180 (24%), Positives = 93/180 (51%), Gaps = 5/180 (2%)
Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
           ++  L+  EP+++    +  + D +   + SL+ L +R+L+ ++ W+K +PGF +L ++D
Sbjct: 15  LINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDD 74
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEI----YQQVK 191
           Q+ L+Q +W  ++   + +RS  H +G+ + FA DL+L+E++ +E  F  +    +Q  +
Sbjct: 75  QITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQ 134
Query: 192 HSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGT 251
               L   +EE L  ++ L+   +           E  ++ + R +    G RQ G   +
Sbjct: 135 EFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSS 194

>pdb|4FNE|A Chain A, X-Ray Crystal Structure Of The Ancestral 3-Keto Steroid Receptor - Doc Complex Length = 254

Iteration: 1
 Score = 79.3 bits (194), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 41/138 (29%), Positives = 77/138 (55%), Gaps = 7/138 (5%)
Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
           ++  L   EPE++    +  Q D T   ++SL+ L +++LV ++ WAK +PGF +L L+D
Sbjct: 8   LISILQAIEPEVVYAGYDNTQPDTTNYLLSSLNRLAEKQLVSVVKWAKALPGFRNLHLDD 67
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEI---YQQVKH 192
           QM L+Q +W  ++   + +RS  H  G+ + FA DL+ +E++ ++    ++    QQ+  
Sbjct: 68  QMTLIQYSWMGLMAFAMGWRSYKHTNGQMLYFAPDLIFNEQRMQQSAMYDLCQGMQQISQ 127
Query: 193 SGSLDGIKEEELPRRLCL 210
                 + +EE    LC+
Sbjct: 128 EFVRLQVTQEEF---LCM 142

>pdb|2Q1H|A Chain A, Ancestral Corticoid Receptor In Complex With Aldosterone Length = 250

Iteration: 1
 Score = 79.0 bits (193), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 37/117 (31%), Positives = 71/117 (60%), Gaps = 4/117 (3%)
Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
           +LEA+   EPE++    +  Q D T   ++SL+ L  +++V ++ WAK +PGF +L L+D
Sbjct: 7   ILEAI---EPEVVYAGYDNSQPDTTNYLLSSLNRLAGKQMVSVVKWAKALPGFRNLHLDD 63
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQVKH 192
           QM L+Q +W  ++  ++ +RS  H  G+ + FA DL+ +E + ++    ++ Q ++ 
Sbjct: 64  QMTLIQYSWMSLMAFSLGWRSYKHTNGQMLYFAPDLIFNEERMQQSAMYDLCQGMRQ 120

>pdb|2Q3Y|A Chain A, Ancestral Corticiod Receptor In Complex With Doc Length = 249

Iteration: 1
 Score = 79.0 bits (193), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 37/117 (31%), Positives = 71/117 (60%), Gaps = 4/117 (3%)
Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
           +LEA+   EPE++    +  Q D T   ++SL+ L  +++V ++ WAK +PGF +L L+D
Sbjct: 7   ILEAI---EPEVVYAGYDNSQPDTTNYLLSSLNRLAGKQMVSVVKWAKALPGFRNLHLDD 63
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQVKH 192
           QM L+Q +W  ++  ++ +RS  H  G+ + FA DL+ +E + ++    ++ Q ++ 
Sbjct: 64  QMTLIQYSWMSLMAFSLGWRSYKHTNGQMLYFAPDLIFNEERMQQSAMYDLCQGMRQ 120

>pdb|3RY9|A Chain A, Crystal Structure Of The Resurrected Ancestral Glucocorticoid Receptor 1 In Complex With Doc Length = 250

Iteration: 1
 Score = 76.6 bits (187), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 43/145 (29%), Positives = 81/145 (55%), Gaps = 7/145 (4%)
Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
           M+  L   EP+++    ++   D T + ++SL+ L  R+++  + WAK +PGF +L L+D
Sbjct: 4   MISILEAIEPDVIYAGYDSTLPDTTNRLLSSLNRLGGRQMISAVKWAKALPGFRNLHLDD 63
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQVKHSGS 195
           QM LLQ +W  ++  ++ +RS  H  G  + FA DL+ +E + ++    E+ + + H  S
Sbjct: 64  QMTLLQYSWMSLMAFSLGWRSYQHTNGNMLYFAPDLIFNEERMQQSSMYELCKGM-HKIS 122
Query: 196 LDGIK-----EEELPRRLCLVCGDV 215
           L+ ++     EE L  ++ L+   V
Sbjct: 123 LEFVRLQVSYEEYLCMKVLLLLSTV 147

>pdb|3H52|A Chain A, Crystal Structure Of The Antagonist Form Of Human Glucocorticoid Receptor Length = 254

Iteration: 1
 Score = 73.6 bits (179), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 37/117 (31%), Positives = 67/117 (57%), Gaps = 4/117 (3%)
Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
           ++  L + EPE+L    ++   D T + + +L+ L  R+++  + WAK IPGF +L L+D
Sbjct: 9   LVSLLEVIEPEVLYAGYDSSVPDSTWRIMTTLNMLGGRQVIAAVKWAKAIPGFRNLHLDD 68
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGKIR-FASDLVLDERQARECGFSEIYQQVKH 192
           QM LLQ +W  ++   + +RS    +  +  FA DL+++E++       ++Y Q KH
Sbjct: 69  QMTLLQYSWMSLMAFALGWRSYRQSSANLLCFAPDLIINEQR---MTLPDMYDQCKH 122

>pdb|3CLD|A Chain A, Ligand Binding Domain Of The Glucocorticoid Receptor Complexed With Fluticazone Furoate Length = 259

Iteration: 1
 Score = 73.2 bits (178), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 40/126 (31%), Positives = 71/126 (56%), Gaps = 5/126 (3%)
Query: 68  SIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIP 127
           ++P L    ++  L + EPE+L    ++   D T + + +L+ L  R+++  + WAK IP
Sbjct: 6   TLPQLTPT-LVSLLEVIEPEVLYAGYDSSVPDSTWRIMTTLNMLGGRQVIAAVKWAKAIP 64
Query: 128 GFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIR-FASDLVLDERQARECGFSEI 186
           GF +L L+DQM LLQ +W  ++   + +RS    +  +  FA DL+++E++    G   +
Sbjct: 65  GFRNLHLDDQMTLLQYSWMYLMAFALGWRSYRQSSANLLCFAPDLIINEQRMTLPG---M 121
Query: 187 YQQVKH 192
           Y Q KH
Sbjct: 122 YDQCKH 127

>pdb|1NHZ|A Chain A, Crystal Structure Of The Antagonist Form Of Glucocorticoid Receptor Length = 280

Iteration: 1
 Score = 73.2 bits (178), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 39/126 (30%), Positives = 71/126 (56%), Gaps = 5/126 (3%)
Query: 68  SIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIP 127
           ++P L    ++  L + EPE+L    ++   D T + + +L+ L  R+++  + WAK IP
Sbjct: 27  TLPQLTPT-LVSLLEVIEPEVLYAGYDSSVPDSTWRIMTTLNMLGGRQVIAAVKWAKAIP 85
Query: 128 GFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIR-FASDLVLDERQARECGFSEI 186
           GF +L L+DQM LLQ +W  ++   + +RS    +  +  FA DL+++E++       ++
Sbjct: 86  GFRNLHLDDQMTLLQYSWMSLMAFALGWRSYRQSSANLLCFAPDLIINEQR---MTLPDM 142
Query: 187 YQQVKH 192
           Y Q KH
Sbjct: 143 YDQCKH 148

>pdb|3BQD|A Chain A, Doubling The Size Of The Glucocorticoid Receptor Ligand Binding Pocket By Deacylcortivazol Length = 255

Iteration: 1
 Score = 73.2 bits (178), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 42/127 (33%), Positives = 70/127 (55%), Gaps = 7/127 (5%)
Query: 68  SIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIP 127
           S+P L    ++  L + EPE+L    ++   D T + + +L+ L  R+++  + WAK IP
Sbjct: 2   SLPQLTPT-LVSLLEVIEPEVLYAGYDSSVPDSTWRIMTTLNMLGGRQVIAAVKWAKAIP 60
Query: 128 GFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIR-FASDLVLDE-RQARECGFSE 185
           GF +L L+DQM LLQ +W  ++   + +RS    +  +  FA DL+++E R    C    
Sbjct: 61  GFRNLHLDDQMTLLQYSWMSLMAFALGWRSYRQSSANLLCFAPDLIINEQRMTLPC---- 116
Query: 186 IYQQVKH 192
           +Y Q KH
Sbjct: 117 MYDQCKH 123

>pdb|3E7C|A Chain A, Glucocorticoid Receptor Lbd Bound To Gsk866 Length = 257

Iteration: 1
 Score = 73.2 bits (178), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 40/126 (31%), Positives = 71/126 (56%), Gaps = 5/126 (3%)
Query: 68  SIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIP 127
           ++P L    ++  L + EPE+L    ++   D T + + +L+ L  R+++  + WAK IP
Sbjct: 4   TLPQLTPT-LVSLLEVIEPEVLYAGYDSSVPDSTWRIMTTLNMLGGRQVIAAVKWAKAIP 62
Query: 128 GFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIR-FASDLVLDERQARECGFSEI 186
           GF +L L+DQM LLQ +W  ++   + +RS    +  +  FA DL+++E++    G   +
Sbjct: 63  GFRNLHLDDQMTLLQYSWMYLMAFALGWRSYRQSSANLLCFAPDLIINEQRMTLPG---M 119
Query: 187 YQQVKH 192
           Y Q KH
Sbjct: 120 YDQCKH 125

>pdb|3MNE|A Chain A, Crystal Structure Of The Agonist Form Of Mouse Glucocorticoid Receptor Stabilized By F608s Mutation At 1.96a Length = 261

Iteration: 1
 Score = 72.8 bits (177), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 41/127 (32%), Positives = 70/127 (55%), Gaps = 7/127 (5%)
Query: 68  SIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIP 127
           ++P L    ++  L + EPE+L    ++   D   + + +L+ L  R+++  + WAK IP
Sbjct: 8   ALPQLTPT-LVSLLEVIEPEVLYAGYDSSVPDSAWRIMTTLNMLGGRQVIAAVKWAKAIP 66
Query: 128 GFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIR-FASDLVLDE-RQARECGFSE 185
           GF +L L+DQM LLQ +W  ++   + +RS    +G +  FA DL+++E R    C    
Sbjct: 67  GFRNLHLDDQMTLLQYSWMSLMAFALGWRSYRQASGNLLCFAPDLIINEQRMTLPC---- 122
Query: 186 IYQQVKH 192
           +Y Q KH
Sbjct: 123 MYDQCKH 129

>pdb|3MNO|A Chain A, Crystal Structure Of The Agonist Form Of Mouse Glucocorticoid Receptor Stabilized By (A611v, F608s) Mutations At 1.55a Length = 261

Iteration: 1
 Score = 72.8 bits (177), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 41/127 (32%), Positives = 70/127 (55%), Gaps = 7/127 (5%)
Query: 68  SIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIP 127
           ++P L    ++  L + EPE+L    ++   D   + + +L+ L  R+++  + WAK IP
Sbjct: 8   ALPQLTPT-LVSLLEVIEPEVLYAGYDSSVPDSAWRIMTTLNMLGGRQVIAAVKWAKAIP 66
Query: 128 GFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIR-FASDLVLDE-RQARECGFSE 185
           GF +L L+DQM LLQ +W  ++   + +RS    +G +  FA DL+++E R    C    
Sbjct: 67  GFRNLHLDDQMTLLQYSWMSLMVFALGWRSYRQASGNLLCFAPDLIINEQRMTLPC---- 122
Query: 186 IYQQVKH 192
           +Y Q KH
Sbjct: 123 MYDQCKH 129

>pdb|3MNP|A Chain A, Crystal Structure Of The Agonist Form Of Mouse Glucocorticoid Receptor Stabilized By (A611v, V708a, E711g) Mutations At 1.50a Length = 261

Iteration: 1
 Score = 72.4 bits (176), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 41/127 (32%), Positives = 70/127 (55%), Gaps = 7/127 (5%)
Query: 68  SIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIP 127
           ++P L    ++  L + EPE+L    ++   D   + + +L+ L  R+++  + WAK IP
Sbjct: 8   ALPQLTPT-LVSLLEVIEPEVLYAGYDSSVPDSAWRIMTTLNMLGGRQVIAAVKWAKAIP 66
Query: 128 GFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIR-FASDLVLDE-RQARECGFSE 185
           GF +L L+DQM LLQ +W  ++   + +RS    +G +  FA DL+++E R    C    
Sbjct: 67  GFRNLHLDDQMTLLQYSWMFLMVFALGWRSYRQASGNLLCFAPDLIINEQRMTLPC---- 122
Query: 186 IYQQVKH 192
           +Y Q KH
Sbjct: 123 MYDQCKH 129

>pdb|1M2Z|A Chain A, Crystal Structure Of A Dimer Complex Of The Human Glucocorticoid Receptor Ligand-Binding Domain Bound To Dexamethasone And A Tif2 Coactivator Motif Length = 257

Iteration: 1
 Score = 72.0 bits (175), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 41/127 (32%), Positives = 70/127 (55%), Gaps = 7/127 (5%)
Query: 68  SIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIP 127
           ++P L    ++  L + EPE+L    ++   D T + + +L+ L  R+++  + WAK IP
Sbjct: 4   TLPQLTPT-LVSLLEVIEPEVLYAGYDSSVPDSTWRIMTTLNMLGGRQVIAAVKWAKAIP 62
Query: 128 GFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIR-FASDLVLDE-RQARECGFSE 185
           GF +L L+DQM LLQ +W  ++   + +RS    +  +  FA DL+++E R    C    
Sbjct: 63  GFRNLHLDDQMTLLQYSWMSLMAFALGWRSYRQSSANLLCFAPDLIINEQRMTLPC---- 118
Query: 186 IYQQVKH 192
           +Y Q KH
Sbjct: 119 MYDQCKH 125

>pdb|3VHV|A Chain A, Mineralocorticoid Receptor Ligand-Binding Domain With Non-Steroidal Antagonist Length = 260

Iteration: 1
 Score = 71.6 bits (174), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 53/213 (24%), Positives = 98/213 (46%), Gaps = 20/213 (9%)
Query: 84  CEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQS 143
            EPE++    ++ + D     +++L+ L  ++++ ++ WAK +PGF +L L DQ+ L+Q 
Sbjct: 21  IEPEIVYAGYDSSKPDTAENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQY 80
Query: 144 TWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQVKHSGSLDGIK-- 200
           +W  +L+  +++RS  H   + + FA DLV +E +  +    E+ Q + H  SL  ++  
Sbjct: 81  SWMSLLSFALSWRSYKHTNSQFLYFAPDLVFNEEKMHQSAMYELCQGM-HQISLQFVRLQ 139
Query: 201 ---EEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANS 257
              EE    ++ L+   +      G+ S  A +    RT  +    +    C      NS
Sbjct: 140 LTFEEYTIMKVLLLLSTIPKD---GLKSQAAFEEM--RTNYIKELRKMVTKCPN----NS 190
Query: 258 DVKLDEFSSLKKFRNSILSSLGD----CIYVLR 286
                 F  L K  +S+   + D    C Y  R
Sbjct: 191 GQSWQRFYQLTKLLDSMHDLVSDLLEFCFYTFR 223

>pdb|3VHU|A Chain A, Mineralocorticoid Receptor Ligand-Binding Domain With Spironolactone Length = 294

Iteration: 1
 Score = 71.2 bits (173), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 34/118 (28%), Positives = 68/118 (57%), Gaps = 2/118 (1%)
Query: 84  CEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQS 143
            EPE++    ++ + D     +++L+ L  ++++ ++ WAK +PGF +L L DQ+ L+Q 
Sbjct: 55  IEPEIVYAGYDSSKPDTAENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQY 114
Query: 144 TWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQVKHSGSLDGIK 200
           +W  +L+  +++RS  H   + + FA DLV +E +  +    E+ Q + H  SL  ++
Sbjct: 115 SWMSLLSFALSWRSYKHTNSQFLYFAPDLVFNEEKMHQSAMYELCQGM-HQISLQFVR 171

>pdb|2AA6|A Chain A, Mineralocorticoid Receptor S810l Mutant With Bound Progesterone Length = 275

Iteration: 1
 Score = 71.2 bits (173), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 34/118 (28%), Positives = 68/118 (57%), Gaps = 2/118 (1%)
Query: 84  CEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQS 143
            EPE++    ++ + D     +++L+ L  ++++ ++ WAK +PGF +L L DQ+ L+Q 
Sbjct: 36  IEPEIVYAGYDSSKPDTAENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQY 95
Query: 144 TWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQVKHSGSLDGIK 200
           +W  +L+  +++RS  H   + + FA DLV +E +  +    E+ Q + H  SL  ++
Sbjct: 96  SWMSLLSFALSWRSYKHTNSQFLYFAPDLVFNEEKMHQSAMYELCQGM-HQISLQFVR 152

>pdb|4E2J|A Chain A, X-Ray Crystal Structure Of The Ancestral Glucocorticoid Receptor 2 Ligand Binding Domain In Complex With Mometasone Furoate And Tif-2 Coactivator Fragment Length = 250

Iteration: 1
 Score = 70.1 bits (170), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/104 (32%), Positives = 63/104 (60%), Gaps = 1/104 (0%)
Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
           ++  L + EPE+L    ++   D + + +++L+ L  R++V  + WAK +PGF +L L+D
Sbjct: 6   LISLLEVIEPEVLYSGYDSTLPDTSTRLMSTLNRLGGRQVVSAVKWAKALPGFRNLHLDD 65
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGKIR-FASDLVLDERQAR 179
           QM LLQ +W  ++  ++ +RS     G +  FA DLV++E + +
Sbjct: 66  QMTLLQYSWMSLMAFSLGWRSYKQSNGNMLCFAPDLVINEERMQ 109

>pdb|3GN8|A Chain A, X-Ray Crystal Structure Of Ancgr2 In Complex With Dexamethasone Length = 249

Iteration: 1
 Score = 70.1 bits (170), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/104 (32%), Positives = 63/104 (60%), Gaps = 1/104 (0%)
Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
           ++  L + EPE+L    ++   D + + +++L+ L  R++V  + WAK +PGF +L L+D
Sbjct: 4   LISLLEVIEPEVLYSGYDSTLPDTSTRLMSTLNRLGGRQVVSAVKWAKALPGFRNLHLDD 63
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGKIR-FASDLVLDERQAR 179
           QM LLQ +W  ++  ++ +RS     G +  FA DLV++E + +
Sbjct: 64  QMTLLQYSWMSLMAFSLGWRSYKQSNGNMLCFAPDLVINEERMQ 107

>pdb|2OAX|A Chain A, Crystal Structure Of The S810l Mutant Mineralocorticoid Receptor Associated With Sc9420 Length = 256

Iteration: 1
 Score = 69.7 bits (169), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 34/118 (28%), Positives = 68/118 (57%), Gaps = 2/118 (1%)
Query: 84  CEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQS 143
            EPE++    ++ + D     +++L+ L  ++++ ++ WAK +PGF +L L DQ+ L+Q 
Sbjct: 17  IEPEIVYAGYDSSKPDTAENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQY 76
Query: 144 TWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQVKHSGSLDGIK 200
           +W  +L+  +++RS  H   + + FA DLV +E +  +    E+ Q + H  SL  ++
Sbjct: 77  SWMCLLSFALSWRSYKHTNSQFLYFAPDLVFNEEKMHQSAMYELCQGM-HQISLQFVR 133

>pdb|1Y9R|A Chain A, Crystal Structure Of The Human Mineralocorticoid Receptor Ligand-Binding Domain Bound To Deoxycorticosterone And Harboring The S810l Mutation Responsible For A Severe Form Of Hypertension Length = 255

Iteration: 1
 Score = 69.3 bits (168), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 34/118 (28%), Positives = 68/118 (57%), Gaps = 2/118 (1%)
Query: 84  CEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQS 143
            EPE++    ++ + D     +++L+ L  ++++ ++ WAK +PGF +L L DQ+ L+Q 
Sbjct: 16  IEPEIVYAGYDSSKPDTAENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQY 75
Query: 144 TWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQVKHSGSLDGIK 200
           +W  +L+  +++RS  H   + + FA DLV +E +  +    E+ Q + H  SL  ++
Sbjct: 76  SWMCLLSFALSWRSYKHTNSQFLYFAPDLVFNEEKMHQSAMYELCQGM-HQISLQFVR 132

>pdb|2A3I|A Chain A, Structural And Biochemical Mechanisms For The Specificity Of Hormone Binding And Coactivator Assembly By Mineralocorticoid Receptor Length = 253

Iteration: 1
 Score = 69.3 bits (168), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 52/213 (24%), Positives = 97/213 (45%), Gaps = 20/213 (9%)
Query: 84  CEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQS 143
            EPE++    ++ + D     +++L+ L  ++++ ++ WAK +PGF +L L DQ+ L+Q 
Sbjct: 14  IEPEIVYAGYDSSKPDTAENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQY 73
Query: 144 TWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQVKHSGSLDGIK-- 200
           +W  + +  +++RS  H   + + FA DLV +E +  +    E+ Q + H  SL  ++  
Sbjct: 74  SWMSLSSFALSWRSYKHTNSQFLYFAPDLVFNEEKMHQSAMYELCQGM-HQISLQFVRLQ 132
Query: 201 ---EEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANS 257
              EE    ++ L+   +      G+ S  A +    RT  +    +    C      NS
Sbjct: 133 LTFEEYTIMKVLLLLSTIPKD---GLKSQAAFEEM--RTNYIKELRKMVTKCPN----NS 183
Query: 258 DVKLDEFSSLKKFRNSILSSLGD----CIYVLR 286
                 F  L K  +S+   + D    C Y  R
Sbjct: 184 GQSWQRFYQLTKLLDSMHDLVSDLLEFCFYTFR 216

>pdb|2Q60|A Chain A, Crystal Structure Of The Ligand Binding Domain Of Polyandrocarpa Misakiensis Rxr In Tetramer In Absence Of Ligand Length = 258

Iteration: 1
 Score = 68.9 bits (167), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 41/128 (32%), Positives = 71/128 (55%), Gaps = 10/128 (7%)
Query: 65  PNKSIPSLEENKMLEALLLCEP--EMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGW 122
           PN  +P    +K+LEA L+ +P  E +    +  ++DP    ++++    DR+LV ++ W
Sbjct: 25  PNDDMPV---DKILEAELISDPKVEQVVPFEQVNENDP----VSNICKAADRQLVTLVEW 77
Query: 123 AKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECG 182
           AK+IP F+ L L DQ+ LL++ W E+L  + ++RS+      I  AS L +    A + G
Sbjct: 78  AKRIPHFSSLPLEDQVILLRAGWNELLIASFSHRSI-DVKDSILLASGLHVHRHSAHQAG 136
Query: 183 FSEIYQQV 190
              I+ +V
Sbjct: 137 VGPIFDRV 144

>pdb|1I38|A Chain A, Crystal Structure Of The Rat Androgen Receptor Ligand Binding Domain T877a Mutant Complex With Dihydrotestosterone Length = 260

Iteration: 1
 Score = 68.9 bits (167), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 35/113 (30%), Positives = 64/113 (56%), Gaps = 4/113 (3%)
Query: 78  LEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQ 137
           L  L   EP ++    +  Q D     ++SL++L +R+LV ++ WAK +PGF +L ++DQ
Sbjct: 15  LNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQ 74
Query: 138 MRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQ 189
           M ++Q +W  ++   + +RS  +   + + FA DLV +E +  +   S +Y Q
Sbjct: 75  MAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHK---SRMYSQ 124

>pdb|2AX6|A Chain A, Crystal Structure Of The Androgen Receptor Ligand Binding Domain T877a Mutant In Complex With Hydroxyflutamide Length = 256

Iteration: 1
 Score = 68.6 bits (166), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 35/114 (30%), Positives = 64/114 (56%), Gaps = 4/114 (3%)
Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
            L  L   EP ++    +  Q D     ++SL++L +R+LV ++ WAK +PGF +L ++D
Sbjct: 10  FLNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDD 69
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQ 189
           QM ++Q +W  ++   + +RS  +   + + FA DLV +E +  +   S +Y Q
Sbjct: 70  QMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHK---SRMYSQ 120

>pdb|2AX9|A Chain A, Crystal Structure Of The Androgen Receptor Ligand Binding Domain In Complex With R-3 Length = 256

Iteration: 1
 Score = 68.6 bits (166), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 35/114 (30%), Positives = 64/114 (56%), Gaps = 4/114 (3%)
Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
            L  L   EP ++    +  Q D     ++SL++L +R+LV ++ WAK +PGF +L ++D
Sbjct: 10  FLNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDD 69
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQ 189
           QM ++Q +W  ++   + +RS  +   + + FA DLV +E +  +   S +Y Q
Sbjct: 70  QMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHK---SRMYSQ 120

>pdb|1I37|A Chain A, Crystal Structure Of The Rat Androgen Receptor Ligand Binding Domain Complex With Dihydrotestosterone Length = 260

Iteration: 1
 Score = 68.6 bits (166), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 35/113 (30%), Positives = 64/113 (56%), Gaps = 4/113 (3%)
Query: 78  LEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQ 137
           L  L   EP ++    +  Q D     ++SL++L +R+LV ++ WAK +PGF +L ++DQ
Sbjct: 15  LNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQ 74
Query: 138 MRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQ 189
           M ++Q +W  ++   + +RS  +   + + FA DLV +E +  +   S +Y Q
Sbjct: 75  MAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHK---SRMYSQ 124

>pdb|3RLL|A Chain A, Crystal Structure Of The T877a Androgen Receptor Ligand Binding Domain In Complex With (S)-N-(4-Cyano-3-(Trifluoromethyl)phenyl)-3-(4- Cyanonaphthalen-1-Yloxy)-2-Hydroxy-2-Methylpropanamide Length = 247

Iteration: 1
 Score = 68.6 bits (166), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 35/113 (30%), Positives = 64/113 (56%), Gaps = 4/113 (3%)
Query: 78  LEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQ 137
           L  L   EP ++    +  Q D     ++SL++L +R+LV ++ WAK +PGF +L ++DQ
Sbjct: 4   LNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQ 63
Query: 138 MRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQ 189
           M ++Q +W  ++   + +RS  +   + + FA DLV +E +  +   S +Y Q
Sbjct: 64  MAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHK---SRMYSQ 113

>pdb|2Q7K|A Chain A, The Androgen Receptor Prostate Cancer Mutant H874y Ligand Binding Domain Bound With Testosterone And An Ar 20-30 Peptide Length = 257

Iteration: 1
 Score = 68.6 bits (166), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 35/114 (30%), Positives = 64/114 (56%), Gaps = 4/114 (3%)
Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
            L  L   EP ++    +  Q D     ++SL++L +R+LV ++ WAK +PGF +L ++D
Sbjct: 11  FLNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDD 70
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQ 189
           QM ++Q +W  ++   + +RS  +   + + FA DLV +E +  +   S +Y Q
Sbjct: 71  QMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHK---SRMYSQ 121

>pdb|2AA2|A Chain A, Mineralocorticoid Receptor With Bound Aldosterone Length = 275

Iteration: 1
 Score = 68.6 bits (166), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 33/118 (27%), Positives = 67/118 (56%), Gaps = 2/118 (1%)
Query: 84  CEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQS 143
            EPE++    ++ + D     +++L+ L  ++++ ++ WAK +PGF +L L DQ+ L+Q 
Sbjct: 36  IEPEIVYAGYDSSKPDTAENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQY 95
Query: 144 TWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQVKHSGSLDGIK 200
           +W  + +  +++RS  H   + + FA DLV +E +  +    E+ Q + H  SL  ++
Sbjct: 96  SWMSLSSFALSWRSYKHTNSQFLYFAPDLVFNEEKMHQSAMYELCQGM-HQISLQFVR 152

>pdb|1E3G|A Chain A, Human Androgen Receptor Ligand Binding In Complex With The Ligand Metribolone (R1881) Length = 263

Iteration: 1
 Score = 68.6 bits (166), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 35/114 (30%), Positives = 64/114 (56%), Gaps = 4/114 (3%)
Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
            L  L   EP ++    +  Q D     ++SL++L +R+LV ++ WAK +PGF +L ++D
Sbjct: 17  FLNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDD 76
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQ 189
           QM ++Q +W  ++   + +RS  +   + + FA DLV +E +  +   S +Y Q
Sbjct: 77  QMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHK---SRMYSQ 127

>pdb|1XJ7|A Chain A, Complex Androgen Receptor Lbd And Rac3 Peptide Length = 257

Iteration: 1
 Score = 68.6 bits (166), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 35/114 (30%), Positives = 64/114 (56%), Gaps = 4/114 (3%)
Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
            L  L   EP ++    +  Q D     ++SL++L +R+LV ++ WAK +PGF +L ++D
Sbjct: 11  FLNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDD 70
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQ 189
           QM ++Q +W  ++   + +RS  +   + + FA DLV +E +  +   S +Y Q
Sbjct: 71  QMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHK---SRMYSQ 121

>pdb|1T73|A Chain A, Crystal Structure Of The Androgen Receptor Ligand Binding Domain In Complex With A Fxxff Motif Length = 269

Iteration: 1
 Score = 68.6 bits (166), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 35/114 (30%), Positives = 64/114 (56%), Gaps = 4/114 (3%)
Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
            L  L   EP ++    +  Q D     ++SL++L +R+LV ++ WAK +PGF +L ++D
Sbjct: 23  FLNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDD 82
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQ 189
           QM ++Q +W  ++   + +RS  +   + + FA DLV +E +  +   S +Y Q
Sbjct: 83  QMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHK---SRMYSQ 133

>pdb|3RLJ|A Chain A, Crystal Structure Of The Androgen Receptor Ligand Binding Domain In Complex With Sarm S-22 Length = 247

Iteration: 1
 Score = 68.6 bits (166), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 35/113 (30%), Positives = 64/113 (56%), Gaps = 4/113 (3%)
Query: 78  LEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQ 137
           L  L   EP ++    +  Q D     ++SL++L +R+LV ++ WAK +PGF +L ++DQ
Sbjct: 4   LNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQ 63
Query: 138 MRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQ 189
           M ++Q +W  ++   + +RS  +   + + FA DLV +E +  +   S +Y Q
Sbjct: 64  MAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHK---SRMYSQ 113

>pdb|1T5Z|A Chain A, Crystal Structure Of The Androgen Receptor Ligand Binding Domain (Lbd) With Dht And A Peptide Derived From Its Physiological Coactivator Ara70 Length = 251

Iteration: 1
 Score = 68.6 bits (166), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 35/114 (30%), Positives = 64/114 (56%), Gaps = 4/114 (3%)
Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
            L  L   EP ++    +  Q D     ++SL++L +R+LV ++ WAK +PGF +L ++D
Sbjct: 5   FLNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDD 64
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQ 189
           QM ++Q +W  ++   + +RS  +   + + FA DLV +E +  +   S +Y Q
Sbjct: 65  QMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHK---SRMYSQ 115

>pdb|2HVC|A Chain A, The Crystal Structure Of Ligand-Binding Domain (Lbd) Of Human Androgen Receptor In Complex With A Selective Modulator Lgd2226 Length = 250

Iteration: 1
 Score = 68.6 bits (166), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 35/114 (30%), Positives = 64/114 (56%), Gaps = 4/114 (3%)
Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
            L  L   EP ++    +  Q D     ++SL++L +R+LV ++ WAK +PGF +L ++D
Sbjct: 5   FLNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDD 64
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQ 189
           QM ++Q +W  ++   + +RS  +   + + FA DLV +E +  +   S +Y Q
Sbjct: 65  QMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHK---SRMYSQ 115

>pdb|3L3X|A Chain A, Crystal Structure Of Dht-Bound Androgen Receptor In Complex With The First Motif Of Steroid Receptor Coactivator 3 Length = 250

Iteration: 1
 Score = 68.6 bits (166), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 35/114 (30%), Positives = 64/114 (56%), Gaps = 4/114 (3%)
Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
            L  L   EP ++    +  Q D     ++SL++L +R+LV ++ WAK +PGF +L ++D
Sbjct: 5   FLNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDD 64
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQ 189
           QM ++Q +W  ++   + +RS  +   + + FA DLV +E +  +   S +Y Q
Sbjct: 65  QMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHK---SRMYSQ 115

>pdb|2Z4J|A Chain A, Crystal Structure Of Ar Lbd With Shp Peptide Nr Box 2 Length = 248

Iteration: 1
 Score = 68.6 bits (166), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 35/113 (30%), Positives = 64/113 (56%), Gaps = 4/113 (3%)
Query: 78  LEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQ 137
           L  L   EP ++    +  Q D     ++SL++L +R+LV ++ WAK +PGF +L ++DQ
Sbjct: 4   LNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQ 63
Query: 138 MRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQ 189
           M ++Q +W  ++   + +RS  +   + + FA DLV +E +  +   S +Y Q
Sbjct: 64  MAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHK---SRMYSQ 113

>pdb|2OZ7|A Chain A, Crystal Structure Of The Human Androgen Receptor T877a Mutant Ligand- Binding Domain With Cyproterone Acetate Length = 249

Iteration: 1
 Score = 68.6 bits (166), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 35/113 (30%), Positives = 64/113 (56%), Gaps = 4/113 (3%)
Query: 78  LEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQ 137
           L  L   EP ++    +  Q D     ++SL++L +R+LV ++ WAK +PGF +L ++DQ
Sbjct: 4   LNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQ 63
Query: 138 MRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQ 189
           M ++Q +W  ++   + +RS  +   + + FA DLV +E +  +   S +Y Q
Sbjct: 64  MAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHK---SRMYSQ 113

>pdb|1XOW|A Chain A, Crystal Structure Of The Human Androgen Receptor Ligand Binding Domain Bound With An Androgen Receptor Nh2- Terminal Peptide, Ar20-30, And R1881 Length = 249

Iteration: 1
 Score = 68.6 bits (166), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 35/113 (30%), Positives = 64/113 (56%), Gaps = 4/113 (3%)
Query: 78  LEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQ 137
           L  L   EP ++    +  Q D     ++SL++L +R+LV ++ WAK +PGF +L ++DQ
Sbjct: 4   LNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQ 63
Query: 138 MRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQ 189
           M ++Q +W  ++   + +RS  +   + + FA DLV +E +  +   S +Y Q
Sbjct: 64  MAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHK---SRMYSQ 113

>pdb|2AM9|A Chain A, Crystal Structure Of Human Androgen Receptor Ligand Binding Domain In Complex With Testosterone Length = 266

Iteration: 1
 Score = 68.6 bits (166), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 35/114 (30%), Positives = 64/114 (56%), Gaps = 4/114 (3%)
Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
            L  L   EP ++    +  Q D     ++SL++L +R+LV ++ WAK +PGF +L ++D
Sbjct: 20  FLNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDD 79
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQ 189
           QM ++Q +W  ++   + +RS  +   + + FA DLV +E +  +   S +Y Q
Sbjct: 80  QMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHK---SRMYSQ 130

>pdb|1GS4|A Chain A, Structural Basis For The Glucocorticoid Response In A Mutant Human Androgen Receptor (Arccr) Derived From An Androgen-Independent Prostate Cancer Length = 248

Iteration: 1
 Score = 67.0 bits (162), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 35/114 (30%), Positives = 63/114 (55%), Gaps = 4/114 (3%)
Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
            L  L   EP ++    +  Q D      +SL++L +R+LV ++ WAK +PGF +L ++D
Sbjct: 4   FLNVLEAIEPGVVCAGHDNNQPDSFAALHSSLNELGERQLVHVVKWAKALPGFRNLHVDD 63
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQ 189
           QM ++Q +W  ++   + +RS  +   + + FA DLV +E +  +   S +Y Q
Sbjct: 64  QMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHK---SRMYSQ 114

>pdb|2ABI|A Chain A, Crystal Structure Of The Human Mineralocorticoid Receptor Ligand-Binding Domain Bound To Deoxycorticosterone Length = 256

Iteration: 1
 Score = 67.0 bits (162), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 33/118 (27%), Positives = 67/118 (56%), Gaps = 2/118 (1%)
Query: 84  CEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQS 143
            EPE++    ++ + D     +++L+ L  ++++ ++ WAK +PGF +L L DQ+ L+Q 
Sbjct: 17  IEPEIVYAGYDSSKPDTAENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQY 76
Query: 144 TWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQVKHSGSLDGIK 200
           +W  + +  +++RS  H   + + FA DLV +E +  +    E+ Q + H  SL  ++
Sbjct: 77  SWMCLSSFALSWRSYKHTNSQFLYFAPDLVFNEEKMHQSAMYELCQGM-HQISLQFVR 133

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

Iteration: 1
 Score = 65.5 bits (158), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 41/115 (35%), Positives = 61/115 (53%), Gaps = 9/115 (7%)
Query: 76  KMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLN 135
           ++LEA L  EP+   + S  P SD        +    DR+L  +I WAK IP FT+L + 
Sbjct: 45  RILEAELRVEPKNEDIDSRDPVSD--------ICQAADRQLYQLIEWAKHIPHFTELPVE 96
Query: 136 DQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQV 190
           DQ+ LL+S W E+L    ++RS+    G I  A+ LV+    A + G   I+ +V
Sbjct: 97  DQVILLKSGWNELLIAGFSHRSMSVKDG-IMLATGLVVHRNCAHQAGVGAIFDRV 150

>pdb|1Z95|A Chain A, Crystal Structure Of The Androgen Receptor Ligand-Binding Domain W741l Mutant Complex With R-Bicalutamide Length = 246

Iteration: 1
 Score = 63.5 bits (153), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 34/113 (30%), Positives = 63/113 (55%), Gaps = 4/113 (3%)
Query: 78  LEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQ 137
           L  L   EP ++    +  Q D     ++SL++L +R+LV ++ WAK +PGF +L ++DQ
Sbjct: 3   LNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQ 62
Query: 138 MRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQ 189
           M ++Q +   ++   + +RS  +   + + FA DLV +E +  +   S +Y Q
Sbjct: 63  MAVIQYSLMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHK---SRMYSQ 112

>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 = 63.5 bits (153), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 28/46 (60%), Positives = 35/46 (76%), Gaps = 1/46 (2%)
Query: 3  EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG 48
          +Y CPA+N C I+K RRK+CQACR +KC   GM+K G+R DR RGG
Sbjct: 40 DYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRKDR-RGG 84

>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 = 57.4 bits (137), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 25/37 (67%), Positives = 29/37 (78%)
Query: 207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY 243
           R C VC D ASG+HYGV SCE CKAFFKR+IQ ++ Y
Sbjct: 5   RYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDY 41

>pdb|2AX8|A Chain A, Crystal Structure Of The Androgen Receptor Ligand Binding Domain W741l Mutant In Complex With S-1 Length = 256

Iteration: 1
 Score = 63.5 bits (153), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 34/114 (29%), Positives = 63/114 (55%), Gaps = 4/114 (3%)
Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
            L  L   EP ++    +  Q D     ++SL++L +R+LV ++ WAK +PGF +L ++D
Sbjct: 10  FLNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDD 69
Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQ 189
           QM ++Q +   ++   + +RS  +   + + FA DLV +E +  +   S +Y Q
Sbjct: 70  QMAVIQYSLMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHK---SRMYSQ 120

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

Iteration: 1
 Score = 63.2 bits (152), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 44/156 (28%), Positives = 79/156 (50%), Gaps = 10/156 (6%)
Query: 37  KEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEENKMLEALLLCEPEMLTVRSETP 96
           +E V+ +R RG      RN + +      N+ +P     ++LEA L  EP+  T      
Sbjct: 22  REAVQEERQRGKD----RNENEVESTSSANEDMPV---ERILEAELAVEPKTETYVEANM 74
Query: 97  QSDPTLQT--INSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIA 154
             +P+     + ++    D++L  ++ WAK+IP F++L L+DQ+ LL++ W E+L  + +
Sbjct: 75  GLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFS 134
Query: 155 YRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQV 190
           +RS+    G I  A+ L +    A   G   I+ +V
Sbjct: 135 HRSIAVKDG-ILLATGLHVHRNSAHSAGVGAIFDRV 169

>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 = 62.4 bits (150), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 34/66 (51%), Positives = 41/66 (62%), Gaps = 4/66 (6%)
Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQK----YRRNP 56
           N  YTC  S  C+I+K +RK C  CRFQKCL  GM  E VR DR+RGGR K    Y+R+ 
Sbjct: 35  NKHYTCTESQSCKIDKTQRKRCPFCRFQKCLTVGMRLEAVRADRMRGGRNKFGPMYKRDR 94
Query: 57  DLLSQQ 62
            L  Q+
Sbjct: 95  ALKQQK 100

>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 = 54.7 bits (130), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 22/36 (61%), Positives = 27/36 (75%)
Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY 243
           LC VCGD  SG+HYG+ +CE+CK FFKRT+Q    Y
Sbjct: 3   LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKHY 38

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

Iteration: 1
 Score = 62.0 bits (149), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 37/118 (31%), Positives = 65/118 (55%), Gaps = 8/118 (6%)
Query: 76  KMLEALLLCEPEMLT---VRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDL 132
           ++LEA L  EP+  +   +  E   +DP    + ++    D++L  ++ WAK+IP F+DL
Sbjct: 16  RILEAELAVEPKTESYGDMNMENSTNDP----VTNICHAADKQLFTLVEWAKRIPHFSDL 71
Query: 133 SLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQV 190
           +L DQ+ LL++ W E+L  + ++RS+    G I  A+ L +    A   G   I+ +V
Sbjct: 72  TLEDQVILLRAGWNELLIASFSHRSVSVQDG-ILLATGLHVHRSSAHSAGVGSIFDRV 128

>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 = 60.8 bits (146), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 33/66 (50%), Positives = 42/66 (63%), Gaps = 4/66 (6%)
Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQK----YRRNP 56
           N  YTC  + +C+I+K +RK C  CRFQKCL  GM  E VR DR+RGGR K    Y+R+ 
Sbjct: 43  NKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMRGGRNKFGPMYKRDR 102
Query: 57  DLLSQQ 62
            L  Q+
Sbjct: 103 ALKQQK 108

>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 = 54.3 bits (129), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 21/31 (67%), Positives = 26/31 (83%)
Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
           LC VCGD  SG+HYG+ +CE+CK FFKRT+Q
Sbjct: 11  LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQ 41

>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 = 60.5 bits (145), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 36/117 (30%), Positives = 63/117 (53%), Gaps = 3/117 (2%)
Query: 76  KMLEALLLCEPEMLTVRSETPQSDPTLQT--INSLSDLYDRELVCIIGWAKQIPGFTDLS 133
           K+LEA L  EP+  T        +P+     + ++    D++L  ++ WAK+IP F++L 
Sbjct: 12  KILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELP 71
Query: 134 LNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQV 190
           L+DQ+ LL++ W E+L  + ++RS+    G I  A+ L +    A   G   I+ +V
Sbjct: 72  LDDQVILLRAGWNELLIASFSHRSIAVKDG-ILLATGLHVHRNSAHSAGVGAIFDRV 127

>pdb|1XDK|A Chain A, Crystal Structure Of The RarbetaRXRALPHA LIGAND BINDING Domain Heterodimer In Complex With 9-Cis Retinoic Acid And A Fragment Of The Trap220 Coactivator Length = 238

Iteration: 1
 Score = 60.5 bits (145), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 36/117 (30%), Positives = 63/117 (53%), Gaps = 3/117 (2%)
Query: 76  KMLEALLLCEPEMLTVRSETPQSDPTLQT--INSLSDLYDRELVCIIGWAKQIPGFTDLS 133
           K+LEA L  EP+  T        +P+     + ++    D++L  ++ WAK+IP F++L 
Sbjct: 10  KILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELP 69
Query: 134 LNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQV 190
           L+DQ+ LL++ W E+L  + ++RS+    G I  A+ L +    A   G   I+ +V
Sbjct: 70  LDDQVILLRAGWNELLIASFSHRSIAVKDG-ILLATGLHVHRNSAHSAGVGAIFDRV 125

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

Iteration: 1
 Score = 60.1 bits (144), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 36/117 (30%), Positives = 63/117 (53%), Gaps = 3/117 (2%)
Query: 76  KMLEALLLCEPEMLTVRSETPQSDPTLQT--INSLSDLYDRELVCIIGWAKQIPGFTDLS 133
           K+LEA L  EP+  T        +P+     + ++    D++L  ++ WAK+IP F++L 
Sbjct: 10  KILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELP 69
Query: 134 LNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQV 190
           L+DQ+ LL++ W E+L  + ++RS+    G I  A+ L +    A   G   I+ +V
Sbjct: 70  LDDQVILLRAGWNELLIASASHRSIAVKDG-ILLATGLHVHRNSAHSAGVGAIFDRV 125

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

Iteration: 1
 Score = 59.7 bits (143), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 37/115 (32%), Positives = 63/115 (54%), Gaps = 7/115 (6%)
Query: 76  KMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLN 135
           ++LEA L  +P++ T      Q DP    + ++    D++L  ++ WAK+IP FT+L L 
Sbjct: 10  QILEAELAVDPKIDTYIDA--QKDP----VTNICQAADKQLFTLVEWAKRIPHFTELPLE 63
Query: 136 DQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQV 190
           DQ+ LL++ W E+L    ++RS+    G I  A+ L +    A + G   I+ +V
Sbjct: 64  DQVILLRAGWNELLIAGFSHRSIMAKDG-ILLATGLHVHRSSAHQAGVGTIFDRV 117

>pdb|1RDT|A Chain A, Crystal Structure Of A New Rexinoid Bound To The Rxralpha Ligand Binding Doamin In The RxralphaPPARGAMMA HETERODIMER Length = 242

Iteration: 1
 Score = 59.7 bits (143), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 35/117 (29%), Positives = 63/117 (53%), Gaps = 3/117 (2%)
Query: 76  KMLEALLLCEPEMLTVRSETPQSDPTLQT--INSLSDLYDRELVCIIGWAKQIPGFTDLS 133
           ++LEA L  EP+  T        +P+     + ++    D++L  ++ WAK+IP F++L 
Sbjct: 14  RILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELP 73
Query: 134 LNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQV 190
           L+DQ+ LL++ W E+L  + ++RS+    G I  A+ L +    A   G   I+ +V
Sbjct: 74  LDDQVILLRAGWNELLIASFSHRSIAVKDG-ILLATGLHVHRNSAHSAGVGAIFDRV 129

>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 = 59.3 bits (142), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 35/117 (29%), Positives = 63/117 (53%), Gaps = 3/117 (2%)
Query: 76  KMLEALLLCEPEMLTVRSETPQSDPTLQT--INSLSDLYDRELVCIIGWAKQIPGFTDLS 133
           ++LEA L  EP+  T        +P+     + ++    D++L  ++ WAK+IP F++L 
Sbjct: 16  RILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELP 75
Query: 134 LNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQV 190
           L+DQ+ LL++ W E+L  + ++RS+    G I  A+ L +    A   G   I+ +V
Sbjct: 76  LDDQVILLRAGWNELLIASFSHRSIAVKDG-ILLATGLHVHRNSAHSAGVGAIFDRV 131

>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 = 59.3 bits (142), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 35/117 (29%), Positives = 63/117 (53%), Gaps = 3/117 (2%)
Query: 76  KMLEALLLCEPEMLTVRSETPQSDPTLQT--INSLSDLYDRELVCIIGWAKQIPGFTDLS 133
           ++LEA L  EP+  T        +P+     + ++    D++L  ++ WAK+IP F++L 
Sbjct: 14  RILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELP 73
Query: 134 LNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQV 190
           L+DQ+ LL++ W E+L  + ++RS+    G I  A+ L +    A   G   I+ +V
Sbjct: 74  LDDQVILLRAGWNELLIASFSHRSIAVKDG-ILLATGLHVHRNSAHSAGVGAIFDRV 129

>pdb|3EYB|A Chain A, Structural And Functional Insights Into The Ligand Binding Domain Of A Non-Duplicated Rxr From The Invertebrate Chordate Amphioxus Length = 219

Iteration: 1
 Score = 59.3 bits (142), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 38/115 (33%), Positives = 65/115 (56%), Gaps = 7/115 (6%)
Query: 76  KMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLN 135
           K+ EA +  EP+   +  E P +DP    + ++    D++LV ++ WAK+IP F+DL ++
Sbjct: 6   KIQEAEMAVEPKDGNM-VEQP-NDP----VTNICQAADKQLVTLVEWAKRIPHFSDLPID 59
Query: 136 DQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQV 190
           DQ+ LL++ W E+L    ++RS+    G I  AS L +    A + G   I+ +V
Sbjct: 60  DQVILLRAGWNELLIAAFSHRSIDVKDG-ILLASGLHVHRSSAHQAGVGTIFDRV 113

>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 = 59.3 bits (142), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 25/38 (65%), Positives = 30/38 (78%)
Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ 245
           LC VCGDVASGFHYGV +CE CK FF+R+IQ    Y++
Sbjct: 9   LCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKR 46

>pdb|1FBY|A Chain A, Crystal Structure Of The Human Rxr Alpha Ligand Binding Domain Bound To 9-Cis Retinoic Acid Length = 239

Iteration: 1
 Score = 59.3 bits (142), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 35/117 (29%), Positives = 63/117 (53%), Gaps = 3/117 (2%)
Query: 76  KMLEALLLCEPEMLTVRSETPQSDPTLQT--INSLSDLYDRELVCIIGWAKQIPGFTDLS 133
           ++LEA L  EP+  T        +P+     + ++    D++L  ++ WAK+IP F++L 
Sbjct: 11  RILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELP 70
Query: 134 LNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQV 190
           L+DQ+ LL++ W E+L  + ++RS+    G I  A+ L +    A   G   I+ +V
Sbjct: 71  LDDQVILLRAGWNELLIASFSHRSIAVKDG-ILLATGLHVHRNSAHSAGVGAIFDRV 126

>pdb|1XV9|A Chain A, Crystal Structure Of CarRXR HETERODIMER BOUND WITH SRC1 Peptide, Fatty Acid, And 5b-Pregnane-3,20-Dione. Length = 236

Iteration: 1
 Score = 59.3 bits (142), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 35/117 (29%), Positives = 63/117 (53%), Gaps = 3/117 (2%)
Query: 76  KMLEALLLCEPEMLTVRSETPQSDPTLQT--INSLSDLYDRELVCIIGWAKQIPGFTDLS 133
           ++LEA L  EP+  T        +P+     + ++    D++L  ++ WAK+IP F++L 
Sbjct: 8   RILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELP 67
Query: 134 LNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQV 190
           L+DQ+ LL++ W E+L  + ++RS+    G I  A+ L +    A   G   I+ +V
Sbjct: 68  LDDQVILLRAGWNELLIASFSHRSIAVKDG-ILLATGLHVHRNSAHSAGVGAIFDRV 123

>pdb|1FM6|A Chain A, The 2.1 Angstrom Resolution Crystal Structure Of The Heterodimer Of The Human Rxralpha And Ppargamma Ligand Binding Domains Respectively Bound With 9-Cis Retinoic Acid And Rosiglitazone And Co-Activator Peptides. Length = 238

Iteration: 1
 Score = 59.3 bits (142), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 35/117 (29%), Positives = 63/117 (53%), Gaps = 3/117 (2%)
Query: 76  KMLEALLLCEPEMLTVRSETPQSDPTLQT--INSLSDLYDRELVCIIGWAKQIPGFTDLS 133
           ++LEA L  EP+  T        +P+     + ++    D++L  ++ WAK+IP F++L 
Sbjct: 10  RILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELP 69
Query: 134 LNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQV 190
           L+DQ+ LL++ W E+L  + ++RS+    G I  A+ L +    A   G   I+ +V
Sbjct: 70  LDDQVILLRAGWNELLIASFSHRSIAVKDG-ILLATGLHVHRNSAHSAGVGAIFDRV 125

>pdb|3PCU|A Chain A, Crystal Structure Of Human Retinoic X Receptor Alpha Ligand-Binding Domain Complexed With Lx0278 And Src1 Peptide Length = 230

Iteration: 1
 Score = 59.3 bits (142), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 35/117 (29%), Positives = 63/117 (53%), Gaps = 3/117 (2%)
Query: 76  KMLEALLLCEPEMLTVRSETPQSDPTLQT--INSLSDLYDRELVCIIGWAKQIPGFTDLS 133
           ++LEA L  EP+  T        +P+     + ++    D++L  ++ WAK+IP F++L 
Sbjct: 6   RILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELP 65
Query: 134 LNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQV 190
           L+DQ+ LL++ W E+L  + ++RS+    G I  A+ L +    A   G   I+ +V
Sbjct: 66  LDDQVILLRAGWNELLIASFSHRSIAVKDG-ILLATGLHVHRNSAHSAGVGAIFDRV 121

>pdb|1MV9|A Chain A, Crystal Structure Of The Human Rxr Alpha Ligand Binding Domain Bound To The Eicosanoid Dha (Docosa Hexaenoic Acid) And A Coactivator Peptide Length = 240

Iteration: 1
 Score = 59.3 bits (142), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 35/117 (29%), Positives = 63/117 (53%), Gaps = 3/117 (2%)
Query: 76  KMLEALLLCEPEMLTVRSETPQSDPTLQT--INSLSDLYDRELVCIIGWAKQIPGFTDLS 133
           ++LEA L  EP+  T        +P+     + ++    D++L  ++ WAK+IP F++L 
Sbjct: 12  RILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELP 71
Query: 134 LNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQV 190
           L+DQ+ LL++ W E+L  + ++RS+    G I  A+ L +    A   G   I+ +V
Sbjct: 72  LDDQVILLRAGWNELLIASFSHRSIAVKDG-ILLATGLHVHRNSAHSAGVGAIFDRV 127

>pdb|3H0A|A Chain A, Crystal Structure Of Peroxisome Proliferator-Activated Receptor Gamma (Pparg) And Retinoic Acid Receptor Alpha (Rxra) In Complex With 9-Cis Retinoic Acid, Co-Activator Peptide, And A Partial Agonist Length = 228

Iteration: 1
 Score = 59.3 bits (142), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 35/117 (29%), Positives = 63/117 (53%), Gaps = 3/117 (2%)
Query: 76  KMLEALLLCEPEMLTVRSETPQSDPTLQT--INSLSDLYDRELVCIIGWAKQIPGFTDLS 133
           ++LEA L  EP+  T        +P+     + ++    D++L  ++ WAK+IP F++L 
Sbjct: 7   RILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELP 66
Query: 134 LNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQV 190
           L+DQ+ LL++ W E+L  + ++RS+    G I  A+ L +    A   G   I+ +V
Sbjct: 67  LDDQVILLRAGWNELLIASFSHRSIAVKDG-ILLATGLHVHRNSAHSAGVGAIFDRV 122

>pdb|1XLS|A Chain A, Crystal Structure Of The Mouse CarRXR LBD HETERODIMER Bound To Tcpobop And 9cra And A Tif2 Peptide Containg The Third Lxxll Motifs Length = 232

Iteration: 1
 Score = 59.3 bits (142), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 35/117 (29%), Positives = 63/117 (53%), Gaps = 3/117 (2%)
Query: 76  KMLEALLLCEPEMLTVRSETPQSDPTLQT--INSLSDLYDRELVCIIGWAKQIPGFTDLS 133
           ++LEA L  EP+  T        +P+     + ++    D++L  ++ WAK+IP F++L 
Sbjct: 8   RILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELP 67
Query: 134 LNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQV 190
           L+DQ+ LL++ W E+L  + ++RS+    G I  A+ L +    A   G   I+ +V
Sbjct: 68  LDDQVILLRAGWNELLIASFSHRSIAVKDG-ILLATGLHVHRNSAHSAGVGAIFDRV 123

>pdb|3OAP|A Chain A, Crystal Structure Of Human Retinoid X Receptor Alpha-Ligand Binding Domain Complex With 9-Cis Retinoic Acid And The Coactivator Peptide Grip-1 Length = 231

Iteration: 1
 Score = 59.3 bits (142), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 35/117 (29%), Positives = 63/117 (53%), Gaps = 3/117 (2%)
Query: 76  KMLEALLLCEPEMLTVRSETPQSDPTLQT--INSLSDLYDRELVCIIGWAKQIPGFTDLS 133
           ++LEA L  EP+  T        +P+     + ++    D++L  ++ WAK+IP F++L 
Sbjct: 7   RILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELP 66
Query: 134 LNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQV 190
           L+DQ+ LL++ W E+L  + ++RS+    G I  A+ L +    A   G   I+ +V
Sbjct: 67  LDDQVILLRAGWNELLIASFSHRSIAVKDG-ILLATGLHVHRNSAHSAGVGAIFDRV 122

>pdb|1HCP|A Chain A, Dna Recognition By The Oestrogen Receptor: From Solution To The Crystal Length = 76

Iteration: 1
 Score = 57.4 bits (137), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 25/37 (67%), Positives = 29/37 (78%)
Query: 207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY 243
           R C VC D ASG+HYGV SCE CKAFFKR+IQ ++ Y
Sbjct: 5   RYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDY 41

>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 = 57.0 bits (136), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 25/37 (67%), Positives = 29/37 (78%)
Query: 207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY 243
           R C VC D ASG+HYGV SCE CKAFFKR+IQ ++ Y
Sbjct: 2   RYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDY 38

>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 = 57.0 bits (136), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 25/37 (67%), Positives = 29/37 (78%)
Query: 207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY 243
           R C VC D ASG+HYGV SCE CKAFFKR+IQ ++ Y
Sbjct: 2   RYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDY 38

>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 = 57.0 bits (136), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 22/31 (70%), Positives = 26/31 (83%)
Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQV 239
           C VCGD ASGFHYGV +CE CK FF+RTI++
Sbjct: 53  CRVCGDKASGFHYGVHACEGCKGFFRRTIRL 83

>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 = 56.6 bits (135), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 37/114 (32%), Positives = 60/114 (52%), Gaps = 6/114 (5%)
Query: 106 NSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKI 165
           +  S+L  + ++ I+ +AK++PGFT LS+ DQ+ LL++   +IL L I  R  P     +
Sbjct: 47  DKFSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPE-QDTM 105
Query: 166 RFASDLVLDERQARECGFSEIYQQV-KHSGSLDGIK----EEELPRRLCLVCGD 214
            F+  L L+  Q    GF  +   V   +G L  ++    E  L   +CL+CGD
Sbjct: 106 TFSDGLTLNRTQMHNAGFGPLTDLVFAFAGQLLPLEMDDTETGLLSAICLICGD 159

>pdb|1CIT|A Chain A, Dna-Binding Mechanism Of The Monomeric Orphan Nuclear Receptor Ngfi-B Length = 89

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 28/56 (50%), Positives = 37/56 (66%)
Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNP 56
          + +Y C A+ DC ++KRRR  CQ CRFQKCL  GM+KE VR D ++G R +    P
Sbjct: 34 SAKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTDSLKGRRGRLPSKP 89

>pdb|1CIT|A Chain A, Dna-Binding Mechanism Of The Monomeric Orphan Nuclear Receptor Ngfi-B Length = 89

Iteration: 1
 Score = 55.1 bits (131), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 27/55 (49%), Positives = 33/55 (60%), Gaps = 8/55 (14%)
Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVKLDE 263
           C VCGD AS  HYGV +CE CK FFKRT+Q  + Y        + LAN D  +D+
Sbjct: 3   CAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKY--------ICLANKDCPVDK 49

>pdb|1OVL|A Chain A, Crystal Structure Of Nurr1 Lbd Length = 271

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 53/158 (33%), Positives = 74/158 (46%), Gaps = 11/158 (6%)
Query: 35  MLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEENKMLEALLLCEPEMLTVRSE 94
           M+KE VR D ++G R   R      S Q P   S P    + ++ A +   P M ++   
Sbjct: 1   MVKEVVRTDSLKGRRG--RLPSKPKSPQEPSPPSPPVSLISALVRAHVDSNPAMTSLDYS 58
Query: 95  TPQSDPTLQT-------INSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAE 147
             Q++P  Q        I    DL    +  I GWA++IPGF DL   DQ  L +S + E
Sbjct: 59  RFQANPDYQMSGDDTQHIQQFYDLLTGSMEIIRGWAEKIPGFADLPKADQDLLFESAFLE 118
Query: 148 ILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSE 185
           +  L +AYRS P   GK+ F + +VL   Q    GF E
Sbjct: 119 LFVLRLAYRSNP-VEGKLIFCNGVVLHRLQCVR-GFGE 154

>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 = 56.6 bits (135), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 37/114 (32%), Positives = 60/114 (52%), Gaps = 6/114 (5%)
Query: 106 NSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKI 165
           +  S+L  + ++ I+ +AK++PGFT LS+ DQ+ LL++   +IL L I  R  P     +
Sbjct: 46  DKFSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPE-QDTM 104
Query: 166 RFASDLVLDERQARECGFSEIYQQV-KHSGSLDGIK----EEELPRRLCLVCGD 214
            F+  L L+  Q    GF  +   V   +G L  ++    E  L   +CL+CGD
Sbjct: 105 TFSDGLTLNRTQMHNAGFGPLTDLVFAFAGQLLPLEMDDTETGLLSAICLICGD 158

>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 = 56.6 bits (135), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 37/114 (32%), Positives = 60/114 (52%), Gaps = 6/114 (5%)
Query: 106 NSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKI 165
           +  S+L  + ++ I+ +AK++PGFT LS+ DQ+ LL++   +IL L I  R  P     +
Sbjct: 51  DKFSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPE-QDTM 109
Query: 166 RFASDLVLDERQARECGFSEIYQQV-KHSGSLDGIK----EEELPRRLCLVCGD 214
            F+  L L+  Q    GF  +   V   +G L  ++    E  L   +CL+CGD
Sbjct: 110 TFSDGLTLNRTQMHNAGFGPLTDLVFAFAGQLLPLEMDDTETGLLSAICLICGD 163

>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 = 56.2 bits (134), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 37/114 (32%), Positives = 60/114 (52%), Gaps = 6/114 (5%)
Query: 106 NSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKI 165
           +  S+L  + ++ I+ +AK++PGFT LS+ DQ+ LL++   +IL L I  R  P     +
Sbjct: 72  DKFSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPE-QDTM 130
Query: 166 RFASDLVLDERQARECGFSEIYQQV-KHSGSLDGIK----EEELPRRLCLVCGD 214
            F+  L L+  Q    GF  +   V   +G L  ++    E  L   +CL+CGD
Sbjct: 131 TFSDGLTLNRTQMHNAGFGPLTDLVFAFAGQLLPLEMDDTETGLLSAICLICGD 184

>pdb|2NXX|A Chain A, Crystal Structure Of The Ligand-Binding Domains Of The T.Castaneum (Coleoptera) Heterodimer Ecrusp Bound To Ponasterone A Length = 235

Iteration: 1
 Score = 55.5 bits (132), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 53/204 (25%), Positives = 92/204 (45%), Gaps = 28/204 (13%)
Query: 114 RELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVL 173
           ++L  ++ WAK +P FT L L DQ++LL++ W E+L    ++RS+      I  A+ L +
Sbjct: 48  KQLFQLVQWAKLVPHFTSLPLTDQVQLLRAGWNELLIAAFSHRSM-QAQDAIVLATGLTV 106
Query: 174 DERQARECGFSEIYQQVKHSGSLDGIKEEELP-------RRLCLVCGDVASGFHYGVASC 226
           ++  A   G   IY +V  S  ++ +KE ++        R + L   DV      G+ S 
Sbjct: 107 NKSTAHAVGVGNIYDRVL-SELVNKMKEMKMDKTELGCLRAIILYNPDV-----RGIKSV 160
Query: 227 EACKAFFKRTIQVYSGYRQTGACGTLVLANSDVKLDEFSSLKKFRNSILSSLG-DCIYVL 285
           +  +   ++   V   Y +T             +   F+ L   R   L S+G  C+  L
Sbjct: 161 QEVEMLREKIYGVLEEYTRTTHPN---------EPGRFAKL-LLRLPALRSIGLKCLEHL 210
Query: 286 RFWSTVHKDGKVLMNKLFVEMLEA 309
            F+  +   G V ++   +EMLE 
Sbjct: 211 FFFKLI---GDVPIDTFLMEMLEG 231

>pdb|1OVL|B Chain B, Crystal Structure Of Nurr1 Lbd Length = 271

Iteration: 1
 Score = 55.5 bits (132), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 53/158 (33%), Positives = 73/158 (46%), Gaps = 11/158 (6%)
Query: 35  MLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEENKMLEALLLCEPEMLTVRSE 94
           M+KE VR D ++G R   R      S Q P   S P    + ++ A +   P M ++   
Sbjct: 1   MVKEVVRTDSLKGRRG--RLPSKPKSPQEPSPPSPPVSLISALVRAHVDSNPAMTSLDYS 58
Query: 95  TPQSDPTLQT-------INSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAE 147
             Q++P  Q        I    DL       I GWA++IPGF DL   DQ  L +S + E
Sbjct: 59  RFQANPDYQMSGDDTQHIQQFYDLLTGSXEIIRGWAEKIPGFADLPKADQDLLFESAFLE 118
Query: 148 ILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSE 185
           +  L +AYRS P   GK+ F + +VL   Q    GF E
Sbjct: 119 LFVLRLAYRSNP-VEGKLIFCNGVVLHRLQCVR-GFGE 154

>pdb|1LAT|A Chain A, Glucocorticoid Receptor MutantDNA COMPLEX Length = 82

Iteration: 1
 Score = 54.7 bits (130), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 24/39 (61%), Positives = 27/39 (69%)
Query: 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY 243
           P R CLVC D ASG HYGV +CE CKAFFKR ++    Y
Sbjct: 3   PARPCLVCSDEASGCHYGVLTCEGCKAFFKRAVEGQHNY 41

>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 = 54.7 bits (130), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 22/31 (70%), Positives = 26/31 (83%)
Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQV 239
           C VCGD ASGFHYGV +CE CK FF+RTI++
Sbjct: 10  CRVCGDKASGFHYGVHACEGCKGFFRRTIRM 40

>pdb|2QW4|A Chain A, Human Nr4a1 Ligand-Binding Domain Length = 273

Iteration: 1
 Score = 54.3 bits (129), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 35/79 (44%), Positives = 44/79 (55%), Gaps = 2/79 (2%)
Query: 105 INSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGK 164
           +    DL    L  I  WA++IPGF +LS  DQ  LL+S + E+  L +AYRS P   GK
Sbjct: 78  VQQFYDLLSGSLEVIRKWAEKIPGFAELSPADQDLLLESAFLELFILRLAYRSKP-GEGK 136
Query: 165 IRFASDLVLDERQ-ARECG 182
           + F S LVL   Q AR  G
Sbjct: 137 LIFCSGLVLHRLQCARGFG 155

>pdb|1H9U|A Chain A, The Structure Of The Human Retinoid-X-Receptor Beta Ligand Binding Domain In Complex With The Specific Synthetic Agonist Lg100268 Length = 224

Iteration: 1
 Score = 54.3 bits (129), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 46/78 (58%), Gaps = 1/78 (1%)
Query: 113 DRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLV 172
           D++L  ++ WAK+IP F+ L L+DQ+ LL++ W E+L  + ++RS+    G I  A+ L 
Sbjct: 46  DKQLFTLVEWAKRIPHFSSLPLDDQVILLRAGWNELLIASFSHRSIDVRDG-ILLATGLH 104
Query: 173 LDERQARECGFSEIYQQV 190
           +    A   G   I+ +V
Sbjct: 105 VHRNSAHSAGVGAIFDRV 122

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

Iteration: 1
 Score = 54.3 bits (129), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 46/78 (58%), Gaps = 1/78 (1%)
Query: 113 DRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLV 172
           D++L  ++ WAK+IP F+ L L+DQ+ LL++ W E+L  + ++RS+    G I  A+ L 
Sbjct: 47  DKQLFTLVEWAKRIPHFSSLPLDDQVILLRAGWNELLIASFSHRSIDVRDG-ILLATGLH 105
Query: 173 LDERQARECGFSEIYQQV 190
           +    A   G   I+ +V
Sbjct: 106 VHRNSAHSAGVGAIFDRV 123

>pdb|3V3E|B Chain B, Crystal Structure Of The Human Nur77 Ligand-Binding Domain Length = 257

Iteration: 1
 Score = 54.3 bits (129), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 35/79 (44%), Positives = 44/79 (55%), Gaps = 2/79 (2%)
Query: 105 INSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGK 164
           +    DL    L  I  WA++IPGF +LS  DQ  LL+S + E+  L +AYRS P   GK
Sbjct: 54  VQQFYDLLSGSLEVIRKWAEKIPGFAELSPADQDLLLESAFLELFILRLAYRSKPG-EGK 112
Query: 165 IRFASDLVLDERQ-ARECG 182
           + F S LVL   Q AR  G
Sbjct: 113 LIFCSGLVLHRLQCARGFG 131

>pdb|1YJE|A Chain A, Crystal Structure Of The Rngfi-B Ligand-Binding Domain Length = 264

Iteration: 1
 Score = 53.9 bits (128), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 35/79 (44%), Positives = 44/79 (55%), Gaps = 2/79 (2%)
Query: 105 INSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGK 164
           +    DL    L  I  WA++IPGF +LS  DQ  LL+S + E+  L +AYRS P   GK
Sbjct: 69  VQQFYDLLSGSLDVIRKWAEKIPGFIELSPGDQDLLLESAFLELFILRLAYRSKPG-EGK 127
Query: 165 IRFASDLVLDERQ-ARECG 182
           + F S LVL   Q AR  G
Sbjct: 128 LIFCSGLVLHRLQCARGFG 146

>pdb|2HAN|A Chain A, Structural Basis Of Heterodimeric Ecdysteroid Receptor Interaction With Natural Response Element Hsp27 Gene Promoter Length = 93

Iteration: 1
 Score = 53.5 bits (127), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 22/34 (64%), Positives = 26/34 (76%)
Query: 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
            + LC +CGD ASG HYGV SCE CK FFKRT++
Sbjct: 9   SKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVR 42

>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 = 53.5 bits (127), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 20/35 (57%), Positives = 26/35 (74%)
Query: 204 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
             + +C +CGD +SG HYGV SCE CK FFKRT++
Sbjct: 1   FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVR 35

>pdb|1R0O|A Chain A, Crystal Structure Of The Heterodimeric Ecdysone Receptor Dna-Binding Complex Length = 86

Iteration: 1
 Score = 53.5 bits (127), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 22/34 (64%), Positives = 26/34 (76%)
Query: 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
            + LC +CGD ASG HYGV SCE CK FFKRT++
Sbjct: 7   SKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVR 40

>pdb|3A9E|B Chain B, Crystal Structure Of A Mixed Agonist-Bound Rar-Alpha And Antagonist- Bound Rxr-Alpha Heterodimer Ligand Binding Domains Length = 269

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 35/114 (30%), Positives = 58/114 (50%), Gaps = 6/114 (5%)
Query: 106 NSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKI 165
           +  S+L  + ++  + +AKQ+PGFT L++ DQ+ LL++   +IL L I  R  P     +
Sbjct: 74  DKFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPE-QDTM 132
Query: 166 RFASDLVLDERQARECGFSEIYQQV-KHSGSLDGIK----EEELPRRLCLVCGD 214
            F+  L L+  Q    GF  +   V   +  L  ++    E  L   +CL+CGD
Sbjct: 133 TFSDGLTLNRTQMHNAGFGPLTDLVFAFANQLLPLEMDDAETGLLSAICLICGD 186

>pdb|4DQM|A Chain A, Revealing A Marine Natural Product As A Novel Agonist For Retinoic Acid Receptors With A Unique Binding Mode And Antitumor Activity Length = 234

Iteration: 1
 Score = 52.8 bits (125), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 35/114 (30%), Positives = 58/114 (50%), Gaps = 6/114 (5%)
Query: 106 NSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKI 165
           +  S+L  + ++  + +AKQ+PGFT L++ DQ+ LL++   +IL L I  R  P     +
Sbjct: 45  DKFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPE-QDTM 103
Query: 166 RFASDLVLDERQARECGFSEIYQQV-KHSGSLDGIK----EEELPRRLCLVCGD 214
            F+  L L+  Q    GF  +   V   +  L  ++    E  L   +CL+CGD
Sbjct: 104 TFSDGLTLNRTQMHNAGFGPLTDLVFAFANQLLPLEMDDAETGLLSAICLICGD 157

>pdb|1DKF|B Chain B, Crystal Structure Of A Heterodimeric Complex Of Rar And Rxr Ligand-Binding Domains Length = 235

Iteration: 1
 Score = 52.8 bits (125), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 35/114 (30%), Positives = 58/114 (50%), Gaps = 6/114 (5%)
Query: 106 NSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKI 165
           +  S+L  + ++  + +AKQ+PGFT L++ DQ+ LL++   +IL L I  R  P     +
Sbjct: 45  DKFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPE-QDTM 103
Query: 166 RFASDLVLDERQARECGFSEIYQQV-KHSGSLDGIK----EEELPRRLCLVCGD 214
            F+  L L+  Q    GF  +   V   +  L  ++    E  L   +CL+CGD
Sbjct: 104 TFSDGLTLNRTQMHNAGFGPLTDLVFAFANQLLPLEMDDAETGLLSAICLICGD 157

>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 = 52.8 bits (125), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 35/114 (30%), Positives = 58/114 (50%), Gaps = 6/114 (5%)
Query: 106 NSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKI 165
           +  S+L  + ++  + +AKQ+PGFT L++ DQ+ LL++   +IL L I  R  P     +
Sbjct: 71  DKFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPE-QDTM 129
Query: 166 RFASDLVLDERQARECGFSEIYQQV-KHSGSLDGIK----EEELPRRLCLVCGD 214
            F+  L L+  Q    GF  +   V   +  L  ++    E  L   +CL+CGD
Sbjct: 130 TFSDGLTLNRTQMHNAGFGPLTDLVFAFANQLLPLEMDDAETGLLSAICLICGD 183

>pdb|1XAP|A Chain A, Structure Of The Ligand Binding Domain Of The Retinoic Acid Receptor Beta Length = 267

Iteration: 1
 Score = 52.8 bits (125), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 35/114 (30%), Positives = 59/114 (51%), Gaps = 6/114 (5%)
Query: 106 NSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKI 165
           +  S+L  + ++ I+ +AK++PGFT L++ DQ+ LL++   +IL L I  R  P     +
Sbjct: 72  DKFSELATKCIIKIVEFAKRLPGFTGLTIADQITLLKAACLDILILRICTRYTPE-QDTM 130
Query: 166 RFASDLVLDERQARECGFSEIYQQV-KHSGSLDGIK----EEELPRRLCLVCGD 214
            F+  L L+  Q    GF  +   V   +  L  ++    E  L   +CL+CGD
Sbjct: 131 TFSDGLTLNRTQMHNAGFGPLTDLVFTFANQLLPLEMDDTETGLLSAICLICGD 184

>pdb|4HN6|A Chain A, Gr Dna Binding Domain R460d/d462r - Tslp Ngre Complex Length = 114

Iteration: 1
 Score = 52.8 bits (125), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 29/47 (61%)
Query: 201 EEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTG 247
           +   P +LCLVC D ASG HYGV +C +CK FFKR ++    Y   G
Sbjct: 21  QSNAPPKLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAG 67

>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 = 52.8 bits (125), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 35/114 (30%), Positives = 59/114 (51%), Gaps = 6/114 (5%)
Query: 106 NSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKI 165
           +  S+L  + ++ I+ +AK++PGFT L++ DQ+ LL++   +IL L I  R  P     +
Sbjct: 74  DKFSELATKCIIKIVEFAKRLPGFTGLTIADQITLLKAACLDILILRICTRYTPE-QDTM 132
Query: 166 RFASDLVLDERQARECGFSEIYQQV-KHSGSLDGIK----EEELPRRLCLVCGD 214
            F+  L L+  Q    GF  +   V   +  L  ++    E  L   +CL+CGD
Sbjct: 133 TFSDGLTLNRTQMHNAGFGPLTDLVFTFANQLLPLEMDDTETGLLSAICLICGD 186

>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 = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 22/39 (56%), Positives = 30/39 (76%), Gaps = 3/39 (7%)
Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQ---VYSGYR 244
           C VC D +SG+HYGV++CE CK FF+R+IQ   VY+ +R
Sbjct: 7   CFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHR 45

>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 = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 20/35 (57%), Positives = 26/35 (74%)
Query: 204 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
             + +C +CGD +SG HYGV SCE CK FFKRT++
Sbjct: 3   FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVR 37

>pdb|2C7A|A Chain A, Structure Of The Progesterone Receptor-Dna Complex Length = 78

Iteration: 1
 Score = 52.4 bits (124), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 22/43 (51%), Positives = 30/43 (69%)
Query: 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTG 247
           P+++CL+CGD ASG HYGV +C +CK FFKR ++    Y   G
Sbjct: 1   PQKICLICGDEASGCHYGVLTCGSCKVFFKRAMEGQHNYLCAG 43

>pdb|1BY4|A Chain A, Structure And Mechanism Of The Homodimeric Assembly Of The Rxr On Dna Length = 82

Iteration: 1
 Score = 52.4 bits (124), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 20/35 (57%), Positives = 26/35 (74%)
Query: 204 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
             + +C +CGD +SG HYGV SCE CK FFKRT++
Sbjct: 3   FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVR 37

>pdb|4HN5|A Chain A, Gr Dna Binding Domain - Tslp Ngre Complex Length = 117

Iteration: 1
 Score = 52.4 bits (124), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 23/43 (53%), Positives = 28/43 (65%)
Query: 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTG 247
           P +LCLVC D ASG HYGV +C +CK FFKR ++    Y   G
Sbjct: 28  PPKLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAG 70

>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 = 52.4 bits (124), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 20/34 (58%), Positives = 26/34 (76%)
Query: 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
            + +C +CGD +SG HYGV SCE CK FFKRT++
Sbjct: 2   TKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVR 35

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 23/46 (50%), Positives = 34/46 (73%), Gaps = 5/46 (10%)
Query: 204 LPR--RLCLVCGDVASGFHYGVASCEACKAFFKRTIQ---VYSGYR 244
           +PR  + C VC D +SG+HYGV++CE CK FF+R+IQ   +Y+ +R
Sbjct: 1   MPRVYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMIYTCHR 46

>pdb|2HAN|B Chain B, Structural Basis Of Heterodimeric Ecdysteroid Receptor Interaction With Natural Response Element Hsp27 Gene Promoter Length = 119

Iteration: 1
 Score = 52.4 bits (124), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 24/50 (48%), Positives = 32/50 (64%), Gaps = 5/50 (10%)
Query: 194 GSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY 243
           GS   ++EE     LCLVCGD ASG+HY   +CE CK FF+R++   + Y
Sbjct: 1   GSAPRVQEE-----LCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVY 45

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 36/106 (33%), Positives = 57/106 (53%), Gaps = 15/106 (14%)
Query: 65  PNKSIPSLEENKMLEALLLCEPEMLTVRS------ETPQSDPT----LQTINSLSDLYDR 114
           P  SIP L    +LE LL CEP+   V++      +  Q++ +    L T   +  + D+
Sbjct: 13  PRGSIPHL----ILE-LLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQ 67
Query: 115 ELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPH 160
            L  I+ WA+    F +L ++DQM+LLQ+ W+E+L L   YR + H
Sbjct: 68  TLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVH 113

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 36/106 (33%), Positives = 57/106 (53%), Gaps = 15/106 (14%)
Query: 65  PNKSIPSLEENKMLEALLLCEPEMLTVRS------ETPQSDPT----LQTINSLSDLYDR 114
           P  SIP L    +LE LL CEP+   V++      +  Q++ +    L T   +  + D+
Sbjct: 12  PRGSIPHL----ILE-LLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQ 66
Query: 115 ELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPH 160
            L  I+ WA+    F +L ++DQM+LLQ+ W+E+L L   YR + H
Sbjct: 67  TLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVH 112

>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 = 52.4 bits (124), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 24/60 (40%), Positives = 34/60 (56%), Gaps = 8/60 (13%)
Query: 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVKLDEF 264
           P++ CL+CGD ASG HYG  +C +CK FFKR  +    Y        L  + +D  +D+F
Sbjct: 6   PQKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKY--------LCASRNDCTIDKF 57

>pdb|1R0N|A Chain A, Crystal Structure Of Heterodimeric Ecdsyone Receptor Dna Binding Complex Length = 81

Iteration: 1
 Score = 52.0 bits (123), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 20/35 (57%), Positives = 26/35 (74%)
Query: 204 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
             + +C +CGD +SG HYGV SCE CK FFKRT++
Sbjct: 1   FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVR 35

>pdb|3M9E|A Chain A, Thyroid Hormone Beta Dna Binding Domain Homodimer With Inverted Palindrome Tre Length = 105

Iteration: 1
 Score = 51.6 bits (122), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 20/31 (64%), Positives = 25/31 (80%)
Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
           LC+VCGD A+G+HY   +CE CK FF+RTIQ
Sbjct: 5   LCVVCGDKATGYHYRCITCEGCKGFFRRTIQ 35

>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 = 51.6 bits (122), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 20/31 (64%), Positives = 25/31 (80%)
Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
           LC+VCGD A+G+HY   +CE CK FF+RTIQ
Sbjct: 3   LCVVCGDKATGYHYRCITCEGCKGFFRRTIQ 33

>pdb|1R0N|B Chain B, Crystal Structure Of Heterodimeric Ecdsyone Receptor Dna Binding Complex Length = 109

Iteration: 1
 Score = 51.2 bits (121), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 20/36 (55%), Positives = 26/36 (72%)
Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY 243
           LCLVCGD ASG+HY   +CE CK FF+R++   + Y
Sbjct: 8   LCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVY 43

>pdb|1GLU|A Chain A, Crystallographic Analysis Of The Interaction Of The Glucocorticoid Receptor With Dna Length = 81

Iteration: 1
 Score = 50.8 bits (120), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 23/43 (53%), Positives = 27/43 (62%)
Query: 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTG 247
           P R CLVC D ASG HYGV +C +CK FFKR ++    Y   G
Sbjct: 3   PARPCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAG 45

>pdb|1R4R|B Chain B, Crystallographic Analysis Of The Interaction Of The Glucocorticoid Receptor With Dna Length = 92

Iteration: 1
 Score = 50.8 bits (120), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 23/43 (53%), Positives = 27/43 (62%)
Query: 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTG 247
           P R CLVC D ASG HYGV +C +CK FFKR ++    Y   G
Sbjct: 3   PARPCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAG 45

>pdb|1YUC|A Chain A, Human Nuclear Receptor Liver Receptor Homologue-1, Lrh-1, Bound To Phospholipid And A Fragment Of Human Shp Length = 255

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 37/111 (33%), Positives = 58/111 (52%), Gaps = 15/111 (13%)
Query: 60  SQQWPPNKSIPSLEENKMLEALLLCEPEMLTVRS------ETPQSDPT----LQTINSLS 109
           S Q     SIP L    +LE LL CEP+   V++      +  Q++ +    L T   + 
Sbjct: 6   SYQTSSPASIPHL----ILE-LLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMC 60
Query: 110 DLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPH 160
            + D+ L  I+ WA+    F +L ++DQM+LLQ+ W+E+L L   YR + H
Sbjct: 61  KMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVH 111

>pdb|1R4O|A Chain A, Crystallographic Analysis Of The Interaction Of The Glucocorticoid Receptor With Dna Length = 92

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 23/43 (53%), Positives = 27/43 (62%)
Query: 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTG 247
           P R CLVC D ASG HYGV +C +CK FFKR ++    Y   G
Sbjct: 3   PARPCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAG 45

>pdb|1G2N|A Chain A, Crystal Structure Of The Ligand Binding Domain Of The Ultraspiracle Protein Usp, The Ortholog Of Rxrs In Insects Length = 264

Iteration: 1
 Score = 50.1 bits (118), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 18/54 (33%), Positives = 37/54 (68%)
Query: 105 INSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSL 158
           ++SL  + ++++  ++ WA+ IP F+ L + DQ+ L++ +W E+L   IA+RS+
Sbjct: 44  VSSLCQIGNKQIAALVVWARDIPHFSQLEMEDQILLIKGSWNELLLFAIAWRSM 97

>pdb|1ZH7|A Chain A, Structural And Biochemical Basis For Selective Repression Of The Orphan Nuclear Receptor Lrh-1 By Shp Length = 243

Iteration: 1
 Score = 50.1 bits (118), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 36/103 (34%), Positives = 54/103 (52%), Gaps = 15/103 (14%)
Query: 68  SIPSLEENKMLEALLLCEPEMLTVRS------ETPQSD----PTLQTINSLSDLYDRELV 117
           SIP L    +LE LL CEP+   V++      +  QS+      L     L  + D+ L 
Sbjct: 2   SIPHL----ILE-LLKCEPDEPQVQAKIMAYLQQEQSNRNRQEKLSAFGLLCKMADQTLF 56
Query: 118 CIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPH 160
            I+ WA+    F +L ++DQM+LLQ+ W+E+L L   YR + H
Sbjct: 57  SIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVAH 99

>pdb|1R1K|A Chain A, Crystal Structure Of The Ligand-Binding Domains Of The Heterodimer EcrUSP BOUND TO PONASTERONE A Length = 263

Iteration: 1
 Score = 50.1 bits (118), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 18/54 (33%), Positives = 37/54 (68%)
Query: 105 INSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSL 158
           ++SL  + ++++  ++ WA+ IP F+ L + DQ+ L++ +W E+L   IA+RS+
Sbjct: 43  VSSLCQIGNKQIAALVVWARDIPHFSQLEMEDQILLIKGSWNELLLFAIAWRSM 96

>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 = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 20/30 (66%), Positives = 24/30 (80%)
Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
           C +CGD +SG HYGV SCE CK FFKRT++
Sbjct: 1   CAICGDRSSGKHYGVYSCEGCKGFFKRTVR 30

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

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 36/103 (34%), Positives = 54/103 (52%), Gaps = 15/103 (14%)
Query: 68  SIPSLEENKMLEALLLCEPEMLTVRS------ETPQSD----PTLQTINSLSDLYDRELV 117
           SIP L    +LE LL CEP+   V++      +  QS+      L     L  + D+ L 
Sbjct: 7   SIPHL----ILE-LLKCEPDEPQVQAKIMAYLQQEQSNRNRQEKLSAFGLLCKMADQTLF 61
Query: 118 CIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPH 160
            I+ WA+    F +L ++DQM+LLQ+ W+E+L L   YR + H
Sbjct: 62  SIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVAH 104

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

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 35/103 (33%), Positives = 56/103 (54%), Gaps = 15/103 (14%)
Query: 68  SIPSLEENKMLEALLLCEPEMLTVRS------ETPQSDPT----LQTINSLSDLYDRELV 117
           SIP L    +LE LL CEP+   V++      +  Q++ +    L T   +  + D+ L 
Sbjct: 4   SIPHL----ILE-LLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLF 58
Query: 118 CIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPH 160
            I+ WA+    F +L ++DQM+LLQ+ W+E+L L   YR + H
Sbjct: 59  SIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVH 101

>pdb|4DOS|A Chain A, Human Nuclear Receptor Liver Receptor Homologue-1, Lrh-1, Bound To Dlpc And A Fragment Of Tif-2 Length = 242

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 35/103 (33%), Positives = 56/103 (54%), Gaps = 15/103 (14%)
Query: 68  SIPSLEENKMLEALLLCEPEMLTVRS------ETPQSDPT----LQTINSLSDLYDRELV 117
           SIP L    +LE LL CEP+   V++      +  Q++ +    L T   +  + D+ L 
Sbjct: 4   SIPHL----ILE-LLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLF 58
Query: 118 CIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPH 160
            I+ WA+    F +L ++DQM+LLQ+ W+E+L L   YR + H
Sbjct: 59  SIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVH 101

>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 = 48.9 bits (115), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 17/32 (53%), Positives = 25/32 (78%)
Query: 207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
           R+C VCGD A+GFH+   +CE CK FF+R+++
Sbjct: 7   RICGVCGDRATGFHFNAMTCEGCKGFFRRSMK 38

>pdb|2GDA|A Chain A, Refined Solution Structure Of The Glucocorticoid Receptor Dna-Binding Domain Length = 72

Iteration: 1
 Score = 48.5 bits (114), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 22/40 (55%), Positives = 26/40 (65%)
Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTG 247
           LCLVC D ASG HYGV +C +CK FFKR ++    Y   G
Sbjct: 1   LCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAG 40

>pdb|1GDC|A Chain A, Refined Solution Structure Of The Glucocorticoid Receptor Dna-Binding Domain Length = 72

Iteration: 1
 Score = 48.5 bits (114), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 22/40 (55%), Positives = 26/40 (65%)
Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTG 247
           LCLVC D ASG HYGV +C +CK FFKR ++    Y   G
Sbjct: 1   LCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAG 40

>pdb|1KB2|A Chain A, Crystal Structure Of Vdr Dna-Binding Domain Bound To Mouse Osteopontin (Spp) Response Element Length = 110

Iteration: 1
 Score = 48.5 bits (114), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 17/32 (53%), Positives = 25/32 (78%)
Query: 207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
           R+C VCGD A+GFH+   +CE CK FF+R+++
Sbjct: 7   RICGVCGDRATGFHFNAMTCEGCKGFFRRSMK 38

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 24/67 (35%), Positives = 37/67 (55%)
Query: 105 INSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGK 164
           I ++ +L  R L   + WA+ IP F DL + DQ+ LL+ TW+E+  L  A  S+P     
Sbjct: 39  IENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHVAP 98
Query: 165 IRFASDL 171
           +  A+ L
Sbjct: 99  LLAAAGL 105

>pdb|3CBB|A Chain A, Crystal Structure Of Hepatocyte Nuclear Factor 4alpha In Complex With Dna: Diabetes Gene Product Length = 78

Iteration: 1
 Score = 48.1 bits (113), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 17/31 (54%), Positives = 25/31 (80%)
Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
           LC +CGD A+G HYG +SC+ CK FF+R+++
Sbjct: 2   LCAICGDRATGKHYGASSCDGCKGFFRRSVR 32

>pdb|3G9P|B Chain B, Gr Dna Binding Domain:sgk 16bp Complex-7 Length = 90

Iteration: 1
 Score = 47.8 bits (112), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 21/40 (52%), Positives = 26/40 (65%)
Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTG 247
           +CLVC D ASG HYGV +C +CK FFKR ++    Y   G
Sbjct: 4   MCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAG 43

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 35/103 (33%), Positives = 56/103 (54%), Gaps = 15/103 (14%)
Query: 68  SIPSLEENKMLEALLLCEPEMLTVRS------ETPQSDPT----LQTINSLSDLYDRELV 117
           SIP L    +LE LL CEP+   V++      +  Q++ +    L T   +  + D+ L 
Sbjct: 111 SIPHL----ILE-LLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLF 165
Query: 118 CIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPH 160
            I+ WA+    F +L ++DQM+LLQ+ W+E+L L   YR + H
Sbjct: 166 SIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVH 208

>pdb|3G6T|A Chain A, Gr Gamma Dna-Binding Domain:fkbp5 16bp Complex-34 Length = 91

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 19/31 (61%), Positives = 24/31 (77%)
Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
           +CLVC D ASG HYGV +C +CK FFKR ++
Sbjct: 4   MCLVCSDEASGCHYGVLTCGSCKVFFKRAVE 34

>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 = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 18/30 (60%), Positives = 25/30 (83%)
Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
           C+VCGD +SG HYG  +CE CK+FFKR+++
Sbjct: 10  CVVCGDKSSGKHYGQFTCEGCKSFFKRSVR 39

>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 = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 25/39 (64%)
Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTG 247
           CLVC D ASG HYGV +C +CK FFKR ++    Y   G
Sbjct: 1   CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAG 39

>pdb|2HBH|A Chain A, Crystal Structure Of Vitamin D Nuclear Receptor Ligand Binding Domain Bound To A Locked Side-Chain Analog Of Calcitriol And Src-1 Peptide Length = 302

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/50 (44%), Positives = 32/50 (64%)
Query: 102 LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTL 151
           L  +  L+DL    +  +IG+AK IPGF DL+  DQ+ LL+S+  EI+ L
Sbjct: 101 LSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIML 150

>pdb|4FHH|A Chain A, Development Of Synthetically Accessible Non-Secosteroidal Hybrid Molecules Combining Vitamin D Receptor Agonism And Histone Deacetylase Inhibition Length = 300

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 22/50 (44%), Positives = 32/50 (64%)
Query: 102 LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTL 151
           L  +  L+DL    +  +IG+AK IPGF DL+  DQ+ LL+S+  EI+ L
Sbjct: 99  LSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIML 148

>pdb|3F7D|A Chain A, Sf-1 Lbd Bound By Phosphatidylcholine Length = 244

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 26/88 (29%), Positives = 47/88 (53%), Gaps = 6/88 (6%)
Query: 73  EENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDL 132
           EE+++   ++ C  E    RS+ P         + L  + D+  + I+ WA++   F +L
Sbjct: 19  EEDQVRARIVGCLQEPAKSRSDQPAP------FSLLXRMADQTFISIVDWARRCMVFKEL 72
Query: 133 SLNDQMRLLQSTWAEILTLTIAYRSLPH 160
            + DQM LLQ++W+E+L L   YR + +
Sbjct: 73  EVADQMTLLQNSWSELLVLDHIYRQVQY 100

>pdb|1RJK|A Chain A, Crystal Structure Of The Rat Vitamin D Receptor Ligand Binding Domain Complexed With 2md And A Synthetic Peptide Containing The Nr2 Box Of Drip 205 Length = 292

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 21/50 (42%), Positives = 33/50 (66%)
Query: 102 LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTL 151
           L  +  L+DL    +  +IG+AK IPGF DL+ +DQ+ LL+S+  E++ L
Sbjct: 58  LSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIML 107

>pdb|1YMT|A Chain A, Mouse Sf-1 Lbd Length = 246

Iteration: 1
 Score = 45.1 bits (105), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 26/88 (29%), Positives = 47/88 (53%), Gaps = 6/88 (6%)
Query: 73  EENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDL 132
           EE+++   ++ C  E    RS+ P         + L  + D+  + I+ WA++   F +L
Sbjct: 21  EEDQVRARIVGCLQEPAKSRSDQPAP------FSLLCRMADQTFISIVDWARRCMVFKEL 74
Query: 133 SLNDQMRLLQSTWAEILTLTIAYRSLPH 160
            + DQM LLQ++W+E+L L   YR + +
Sbjct: 75  EVADQMTLLQNSWSELLVLDHIYRQVQY 102

>pdb|2ZL9|A Chain A, 2-Substituted-16-Ene-22-Thia-1alpha,25-Dihydroxy-26,27- Dimethyl-19-Norvitamin D3 Analogs: Synthesis, Biological Evaluation And Crystal Structure Length = 271

Iteration: 1
 Score = 45.1 bits (105), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 21/50 (42%), Positives = 33/50 (66%)
Query: 102 LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTL 151
           L  +  L+DL    +  +IG+AK IPGF DL+ +DQ+ LL+S+  E++ L
Sbjct: 68  LSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIML 117

>pdb|2ZFX|A Chain A, Crystal Structure Of The Rat Vitamin D Receptor Ligand Binding Domain Complexed With Yr301 And A Synthetic Peptide Containing The Nr2 Box Of Drip 205 Length = 265

Iteration: 1
 Score = 45.1 bits (105), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 21/50 (42%), Positives = 33/50 (66%)
Query: 102 LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTL 151
           L  +  L+DL    +  +IG+AK IPGF DL+ +DQ+ LL+S+  E++ L
Sbjct: 62  LSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIML 111

>pdb|1YOW|A Chain A, Human Steroidogenic Factor 1 Lbd With Bound Co-Factor Peptide Length = 242

Iteration: 1
 Score = 44.7 bits (104), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 18/50 (36%), Positives = 30/50 (60%)
Query: 111 LYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPH 160
           + D+  + I+ WA++   F +L + DQM LLQ+ W+E+L     YR + H
Sbjct: 49  MADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQH 98

>pdb|3P8X|A Chain A, Synthesis, Structure, And Biological Activity Of Des-Side Chain Analogues Of 1alpha,25-Dihydroxyvitamin D3 With Substituents At C-18 Length = 280

Iteration: 1
 Score = 44.3 bits (103), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 21/50 (42%), Positives = 32/50 (64%)
Query: 102 LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTL 151
           L  +  L+DL    +  +IG+AK IPGF DL+  DQ+ LL+S+  E++ L
Sbjct: 77  LSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIML 126

>pdb|1YP0|A Chain A, Structure Of The Steroidogenic Factor-1 Ligand Binding Domain Bound To Phospholipid And A Shp Peptide Motif Length = 239

Iteration: 1
 Score = 44.3 bits (103), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 26/88 (29%), Positives = 46/88 (52%), Gaps = 6/88 (6%)
Query: 73  EENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDL 132
           EE+++   ++ C  E    RS+ P         + L  + D+  + I+ WA++   F +L
Sbjct: 15  EEDQVRARIVGCLQEPAKSRSDQPAP------FSLLCRMADQTFISIVDWARRCMVFKEL 68
Query: 133 SLNDQMRLLQSTWAEILTLTIAYRSLPH 160
            + DQM LLQ+ W+E+L L   YR + +
Sbjct: 69  EVADQMTLLQNCWSELLVLDHIYRQVQY 96

>pdb|1ZDT|A Chain A, The Crystal Structure Of Human Steroidogenic Factor-1 Length = 241

Iteration: 1
 Score = 44.3 bits (103), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 18/50 (36%), Positives = 30/50 (60%)
Query: 111 LYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPH 160
           + D+  + I+ WA++   F +L + DQM LLQ+ W+E+L     YR + H
Sbjct: 48  MADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQH 97

>pdb|1S0Z|A Chain A, Crystal Structure Of The Vdr Lbd Complexed To Seocalcitol. Length = 263

Iteration: 1
 Score = 44.3 bits (103), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 21/50 (42%), Positives = 32/50 (64%)
Query: 102 LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTL 151
           L  +  L+DL    +  +IG+AK IPGF DL+  DQ+ LL+S+  E++ L
Sbjct: 60  LSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIML 109

>pdb|3B0T|A Chain A, Human Vdr Ligand Binding Domain In Complex With Maxacalcitol Length = 254

Iteration: 1
 Score = 44.3 bits (103), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 21/50 (42%), Positives = 32/50 (64%)
Query: 102 LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTL 151
           L  +  L+DL    +  +IG+AK IPGF DL+  DQ+ LL+S+  E++ L
Sbjct: 55  LSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIML 104

>pdb|3AZ1|A Chain A, Crystal Structure Analysis Of Vitamin D Receptor Length = 253

Iteration: 1
 Score = 44.3 bits (103), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 21/50 (42%), Positives = 32/50 (64%)
Query: 102 LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTL 151
           L  +  L+DL    +  +IG+AK IPGF DL+  DQ+ LL+S+  E++ L
Sbjct: 54  LSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIML 103

>pdb|3A2I|A Chain A, Crystal Structure Of The Human Vitamin D Receptor (H305f) Ligand Binding Domain Complexed With Tei-9647 Length = 263

Iteration: 1
 Score = 44.3 bits (103), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 21/50 (42%), Positives = 32/50 (64%)
Query: 102 LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTL 151
           L  +  L+DL    +  +IG+AK IPGF DL+  DQ+ LL+S+  E++ L
Sbjct: 60  LSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIML 109

>pdb|3A2J|A Chain A, Crystal Structure Of The Human Vitamin D Receptor (H305fH397F) LIGAND Binding Domain Complexed With Tei-9647 Length = 263

Iteration: 1
 Score = 44.3 bits (103), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 21/50 (42%), Positives = 32/50 (64%)
Query: 102 LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTL 151
           L  +  L+DL    +  +IG+AK IPGF DL+  DQ+ LL+S+  E++ L
Sbjct: 60  LSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIML 109

>pdb|3M7R|A Chain A, Crystal Structure Of Vdr H305q Mutant Length = 253

Iteration: 1
 Score = 44.3 bits (103), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 21/50 (42%), Positives = 32/50 (64%)
Query: 102 LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTL 151
           L  +  L+DL    +  +IG+AK IPGF DL+  DQ+ LL+S+  E++ L
Sbjct: 54  LSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIML 103

>pdb|1DB1|A Chain A, Crystal Structure Of The Nuclear Receptor For Vitamin D Complexed To Vitamin D Length = 259

Iteration: 1
 Score = 44.3 bits (103), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 21/50 (42%), Positives = 32/50 (64%)
Query: 102 LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTL 151
           L  +  L+DL    +  +IG+AK IPGF DL+  DQ+ LL+S+  E++ L
Sbjct: 56  LSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIML 105

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 43/75 (57%), Gaps = 3/75 (4%)
Query: 89  LTVRSETPQSDPTLQTINSLSDL---YDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTW 145
           ++V S    +D  ++ I S+ D+     ++L+ ++ WAK IP F +L L+DQ+ LL++  
Sbjct: 18  ISVSSPGSSTDINVKKIASIGDVCESMKQQLLVLVEWAKYIPAFCELPLDDQVALLRAHA 77
Query: 146 AEILTLTIAYRSLPH 160
            E L L    RS+ +
Sbjct: 78  GEHLLLGATKRSMMY 92

>pdb|3FS1|A Chain A, Crystal Structure Of Hnf4a Lbd In Complex With The Ligand And The Coactivator Pgc-1a Fragment Length = 230

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 32/98 (32%), Positives = 54/98 (55%), Gaps = 15/98 (15%)
Query: 68  SIPSLEENKMLEALLLCEPEMLTVRSETPQS----DPTLQTINSLSDL---YDRELVCII 120
           S+PS+  N +L+A      E+L+ +  +P S    D   + I S++D+      +L+ ++
Sbjct: 1   SLPSI--NALLQA------EVLSRQITSPVSGINGDIRAKKIASIADVCESMKEQLLVLV 52
Query: 121 GWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSL 158
            WAK IP F +L L+DQ+ LL++   E L L    RS+
Sbjct: 53  EWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSM 90

>pdb|1PZL|A Chain A, Crystal Structure Of Hnf4a Lbd In Complex With The Ligand And The Coactivator Src-1 Peptide Length = 237

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 32/98 (32%), Positives = 54/98 (55%), Gaps = 15/98 (15%)
Query: 68  SIPSLEENKMLEALLLCEPEMLTVRSETPQS----DPTLQTINSLSDL---YDRELVCII 120
           S+PS+  N +L+A      E+L+ +  +P S    D   + I S++D+      +L+ ++
Sbjct: 7   SLPSI--NALLQA------EVLSRQITSPVSGINGDIRAKKIASIADVCESMKEQLLVLV 58
Query: 121 GWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSL 158
            WAK IP F +L L+DQ+ LL++   E L L    RS+
Sbjct: 59  EWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSM 96

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

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 32/100 (32%), Positives = 55/100 (55%), Gaps = 15/100 (15%)
Query: 66  NKSIPSLEENKMLEALLLCEPEMLTVRSETPQS----DPTLQTINSLSDL---YDRELVC 118
           + S+PS+  N +L+A      E+L+ +  +P S    D   + I S++D+      +L+ 
Sbjct: 5   DSSLPSI--NALLQA------EVLSQQITSPISGINGDIRAKRIASITDVCESMKEQLLV 56
Query: 119 IIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSL 158
           ++ WAK IP F +L L+DQ+ LL++   E L L    RS+
Sbjct: 57  LVEWAKYIPAFCELLLDDQVALLRAHAGEHLLLGATKRSM 96

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	312
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	2e-52
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	8e-17
3k6p_A	248	Steroid hormone receptor ERR1; estrogen related re	2e-45
1lbd_A	282	RXR_LBD, retinoid X receptor; transcription factor	6e-45
2e2r_A	244	Estrogen-related receptor gamma; ERR gamma, BPA, n	4e-44
3ltx_A	243	Estrogen receptor; constitutive, nuclear receptor,	5e-43
2ocf_A	298	Estrogen receptor; estrogen receptor, LBD, monobod	4e-41
1xpc_A	248	Estrogen receptor; nuclear receptor, transcription	5e-41
1ovl_A	271	Orphan nuclear receptor NURR1 (MSe 414, 496, 511);	1e-40
3oll_A	240	Estrogen receptor beta; steroid binding, phosphory	3e-38
3plz_A	257	FTZ-F1 related protein; alpha helical sandwhich, f	9e-37
2p1t_A	240	Retinoic acid receptor RXR-alpha; protein-ligand c	2e-36
3mnp_A	261	Glucocorticoid receptor; protein-ligand complex, s	4e-36
1l2j_A	271	Estrogen receptor beta; nuclear receptor, transcri	4e-36
2iz2_A	243	FTZ-F1 alpha, nuclear hormone receptor FTZ-F1; nuc	5e-36
2nxx_A	235	Ultraspiracle (USP, NR2B4); hormone receptor, APO	2e-35
3vhu_A	294	Mineralocorticoid receptor; nuclear receptor, tran	3e-35
1yye_A	268	ER-beta, estrogen receptor beta; ER-beta, nuclear	4e-34
1pzl_A	237	Hepatocyte nuclear factor 4-alpha; transcription;	4e-34
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	4e-34
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	2e-12
3vhv_A	260	Mineralocorticoid receptor; nuclear receptor, tran	7e-34
1sqn_A	261	PR, progesterone receptor; nuclear receptor, stero	2e-33
1z5x_E	310	Ecdysone receptor ligand binding domain; ponastero	2e-32
3cjw_A	244	COUP transcription factor 2; COUP-TFII, nuclear re	2e-32
3tx7_B	352	Nuclear receptor subfamily 5 group A member 2; LRH	5e-32
1g2n_A	264	Ultraspiracle protein; antiparallel alpha-helical	6e-32
1xdk_B	303	RAR-beta, retinoic acid receptor, beta; nuclear re	8e-32
1t7r_A	269	Androgen receptor; nuclear receptor, transcription	6e-31
1ymt_A	246	Steroidogenic factor 1; SF-1, ligand-binding domai	9e-29
1yje_A	264	Orphan nuclear receptor NR4A1; NGFI-B, NUR77, liga	2e-27
2hc4_A	302	Vitamin D receptor; alpha helical sandwich, gene r	2e-26
1hg4_A	279	Ultraspiracle; nuclear hormone receptor, transcrip	3e-26
1lo1_A	98	Steroid hormone receptor ERR2; estrogen related re	7e-26
1lo1_A	98	Steroid hormone receptor ERR2; estrogen related re	1e-18
1fcy_A	236	RAR-gamma-1, retinoic acid receptor gamma-1; isoty	2e-25
1cit_A	89	NGFI-B, protein (orphan nuclear receptor NGFI-B);	1e-24
1cit_A	89	NGFI-B, protein (orphan nuclear receptor NGFI-B);	9e-16
2a66_A	113	Orphan nuclear receptor NR5A2; protein-DNA complex	2e-24
2a66_A	113	Orphan nuclear receptor NR5A2; protein-DNA complex	2e-16
3kmr_A	266	Retinoic acid receptor alpha; nuclear receptor tra	3e-24
1pdu_A	244	DHR38, nuclear hormone receptor HR38; nuclear rece	3e-24
2nxx_E	248	Ecdysone receptor (ECR, NRH1); hormone receptor, A	7e-23
2r40_D	266	Ecdysone receptor, 20-hydroxy-ecdysone receptor; n	9e-23
3g9m_A	90	Glucocorticoid receptor; glucocorticoid, DNA-bindi	2e-22
3g9m_A	90	Glucocorticoid receptor; glucocorticoid, DNA-bindi	5e-16
1r4i_A	105	Androgen receptor; AR, steroid receptor, protein-D	5e-22
1r4i_A	105	Androgen receptor; AR, steroid receptor, protein-D	3e-17
3n00_A	245	REV-ERBA-alpha; reverba ncorid1, anti-parallel B-s	2e-21
3ipq_A	283	Oxysterols receptor LXR-alpha; LXR homodimer, LXR	4e-21
3ilz_A	267	Thyroid hormone receptor, alpha isoform 1 variant;	4e-21
1kb2_A	110	Vitamin D3 receptor; VDR, nuclear receptor, protei	6e-21
1kb2_A	110	Vitamin D3 receptor; VDR, nuclear receptor, protei	3e-16
1hcq_A	84	Protein (estrogen receptor); protein-DNA complex,	9e-21
1hcq_A	84	Protein (estrogen receptor); protein-DNA complex,	2e-17
1ynw_B	99	Retinoic acid receptor RXR-alpha, retinoid X recep	2e-20
1ynw_B	99	Retinoic acid receptor RXR-alpha, retinoid X recep	5e-17
3cqv_A	199	Nuclear receptor subfamily 1 group D member 2; rev	2e-20
2han_A	93	Protein ultraspiracle; transcription regulation, t	3e-20
2han_A	93	Protein ultraspiracle; transcription regulation, t	4e-16
3p0u_A	249	Nuclear receptor subfamily 2 group C member 2; lig	3e-20
1dsz_B	85	RXR-alpha, retinoic acid receptor RXR-alpha; RAR,	4e-20
1dsz_B	85	RXR-alpha, retinoic acid receptor RXR-alpha; RAR,	1e-16
1dsz_A	86	RAR-alpha, retinoic acid receptor alpha; RAR, nucl	5e-20
1dsz_A	86	RAR-alpha, retinoic acid receptor alpha; RAR, nucl	4e-16
2han_B	119	Ecdysone receptor; transcription regulation, trans	2e-19
2han_B	119	Ecdysone receptor; transcription regulation, trans	6e-15
1osh_A	232	BIle acid receptor; nuclear receptor, ligand bindi	4e-19
3f5c_B	268	Nuclear receptor subfamily 0 group B member 1; tra	5e-19
2o4j_A	292	Vitamin D3 receptor; nuclear receptor-ligand compl	1e-18
1a6y_A	94	Orphan nuclear receptor NR1D1; orphan receptor, DN	2e-17
1a6y_A	94	Orphan nuclear receptor NR1D1; orphan receptor, DN	4e-17
1xvp_B	246	Orphan nuclear receptor NR1I3; CAR, RXR, citco, SR	2e-17
2nll_B	103	Protein (thyroid hormone receptor); complex (trans	3e-17
2nll_B	103	Protein (thyroid hormone receptor); complex (trans	3e-14
2ebl_A	89	COUP transcription factor 1; DNA-binding, metal-bi	1e-16
2ebl_A	89	COUP transcription factor 1; DNA-binding, metal-bi	7e-15
1nq7_A	244	Nuclear receptor ROR-beta; ligand-binding domain,	3e-16
3cbb_A	78	HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DN	3e-16
3cbb_A	78	HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DN	9e-15
1n83_A	270	Nuclear receptor ROR-alpha; three-layered alpha he	7e-16
3l0l_A	248	Nuclear receptor ROR-gamma; nuclear receptor, rorg	8e-15
3b0t_A	254	Vitamin D3 receptor; nuclear receptor, transcripti	1e-14
3u9q_A	269	Peroxisome proliferator-activated receptor gamma;	1e-14
1nrl_A	316	Orphan nuclear receptor PXR; PXR, xenobiotic, SRC-	1e-13
2p54_A	267	PPAR-alpha, peroxisome proliferator-activated rece	7e-13
3up3_A	243	Acedaf-12; ligand binding domain, nematode, steroi	3e-11
3gyt_A	244	Nuclear hormone receptor of the steroid/thyroid ho	2e-10

>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 =  177 bits (451), Expect = 2e-52
 Identities = 77/338 (22%), Positives = 130/338 (38%), Gaps = 75/338 (22%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
           ++ YTC  + DC I+KR+R  CQ CR+QKCL  GM +E V+ +R RG  +          
Sbjct: 171 DLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRGKDRNENEVE---- 226

Query: 61  QQWPPNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPT--LQTINSLSDLYDRELVC 118
                + +   +   ++LEA L  EP+  T        +P+     + ++    D++L  
Sbjct: 227 ---STSSANEDMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFT 283

Query: 119 IIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQA 178
           ++ WAK+IP F++L L+DQ+ LL++ W E+L  + ++RS+      I  A+ L +    A
Sbjct: 284 LVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAV-KDGILLATGLHVHRNSA 342

Query: 179 RECGFSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
              G   I+ +V            EL  ++                         +    
Sbjct: 343 HSAGVGAIFDRVLT----------ELVSKM----------------------RDMQMDKT 370

Query: 239 VYSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCI--------------- 282
                R       +VL N D K L   + ++  R  + +SL                   
Sbjct: 371 ELGCLR------AIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLL 424

Query: 283 -----------YVLRFWSTVHKDGKVLMNKLFVEMLEA 309
                        L         G   ++   +EMLEA
Sbjct: 425 LRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEA 462

>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 = 79.8 bits (196), Expect = 8e-17
 Identities = 21/40 (52%), Positives = 27/40 (67%)

Query: 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244
            + +C +CGD +SG HYGV SCE CK FFKRT++    Y 
Sbjct: 136 TKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYT 175

>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 =  153 bits (388), Expect = 2e-45
 Identities = 83/291 (28%), Positives = 122/291 (41%), Gaps = 80/291 (27%)

Query: 54  RNPDLLSQQWPPNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYD 113
            +      +      +       ++  LL+ EPE L    +    D  L  + +L DL+D
Sbjct: 4   SHHHHHHLEVLFQGPVN-----ALVSHLLVVEPEKLYAMPDPAGPDGHLPAVATLCDLFD 58

Query: 114 RELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVL 173
           RE+V  I WAK IPGF+ LSL+DQM +LQS W E+L L +A RSLP    ++ FA DLVL
Sbjct: 59  REIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPL-QDELAFAEDLVL 117

Query: 174 DERQARECGFSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCE-AC-KA 231
           DE  AR  G  E+   +            +L RRL  +  +            E    KA
Sbjct: 118 DEEGARAAGLGELGAALL-----------QLVRRLQALRLERE----------EYVLLKA 156

Query: 232 FFKRTIQVYSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIY------- 283
                               L LANSD   +++  ++++ R ++  +L +          
Sbjct: 157 --------------------LALANSDSVHIEDAEAVEQLREALHEALLEYEAGRAGPGG 196

Query: 284 -----------------------VLRFWSTVHKDGKVLMNKLFVEMLEAYL 311
                                  VL  +  V  +GKV M+KLF+EMLEA +
Sbjct: 197 GAERRRAGRLLLTLPLLRQTAGKVLAHFYGVKLEGKVPMHKLFLEMLEAMM 247

>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 =  153 bits (388), Expect = 6e-45
 Identities = 59/320 (18%), Positives = 108/320 (33%), Gaps = 78/320 (24%)

Query: 19  RKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEENKML 78
                +    +       +E V+ +R RG  +               + +   +   ++L
Sbjct: 7   HHHHSSGLVPRG---SHKREAVQEERQRGKDRNENEVE-------STSSANEDMPVERIL 56

Query: 79  EALLLCEPEMLTVRSETPQSDPT--LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
           EA L  EP+  T        +P+     + ++    D++L  ++ WAK+IP F++L L+D
Sbjct: 57  EAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDD 116

Query: 137 QMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKHSGSL 196
           Q+ LL++ W E+L  + ++RS+      I  A+ L +    A   G   I+ +V      
Sbjct: 117 QVILLRAGWNELLIASFSHRSIAV-KDGILLATGLHVHRNSAHSAGVGAIFDRVLT---- 171

Query: 197 DGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLAN 256
                 EL  ++  +  D       G                             +VL N
Sbjct: 172 ------ELVSKMRDMQMDKTE---LGCLRA-------------------------IVLFN 197

Query: 257 SDVK-LDEFSSLKKFRNSILSSLGDCI--------------------------YVLRFWS 289
            D K L   + ++  R  + +SL                                L    
Sbjct: 198 PDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLF 257

Query: 290 TVHKDGKVLMNKLFVEMLEA 309
                G   ++   +EMLEA
Sbjct: 258 FFKLIGDTPIDTFLMEMLEA 277

>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 =  150 bits (380), Expect = 4e-44
 Identities = 78/284 (27%), Positives = 125/284 (44%), Gaps = 72/284 (25%)

Query: 56  PDLLSQQWPPNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRE 115
           P+ L+ Q       P    NK++  LL+ EPE +    +    D  ++ + +L DL DRE
Sbjct: 4   PEFLNPQLVQPAKKPY---NKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRE 60

Query: 116 LVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDE 175
           LV IIGWAK IPGF+ LSL DQM LLQS W EIL L + YRSL     ++ +A D ++DE
Sbjct: 61  LVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSF-EDELVYADDYIMDE 119

Query: 176 RQARECGFSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEAC-KAFFK 234
            Q++  G  ++   +            +L ++   +  +                KA   
Sbjct: 120 DQSKLAGLLDLNNAIL-----------QLVKKYKSMKLEKEE---------FVTLKA--- 156

Query: 235 RTIQVYSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCI----------- 282
                            + LANSD   +++  +++K ++ +  +L D             
Sbjct: 157 -----------------IALANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRA 199

Query: 283 ---------------YVLRFWSTVHKDGKVLMNKLFVEMLEAYL 311
                            ++ +  +  +GKV M+KLF+EMLEA +
Sbjct: 200 GKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPMHKLFLEMLEAKV 243

>3ltx_A Estrogen receptor; constitutive, nuclear receptor, DNA-binding, metal-binding, nucleus, transcription, transcription regulation, zinc-finger; 2.60A {Crassostrea gigas} Length = 243

 Score =  147 bits (372), Expect = 5e-43
 Identities = 65/271 (23%), Positives = 106/271 (39%), Gaps = 70/271 (25%)

Query: 68  SIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIP 127
           S    +   +L+AL      +L       Q    +  +NSL  L +RELV +I WAK +P
Sbjct: 1   SNAKSQTVTILQALNKAALPVLESHHNHGQPPTKVHLLNSLVKLAERELVHLINWAKNVP 60

Query: 128 GFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIY 187
           G+TDLSL+DQ+ L++  W E+L L  A+RS+ H    + FA DLVLD         +EI+
Sbjct: 61  GYTDLSLSDQVHLIECCWMELLLLNCAFRSIEHGGKSLAFAPDLVLDRSSWSTVEMTEIF 120

Query: 188 QQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCE-AC-KAFFKRTIQVYSGYRQ 245
           +QV             +  ++                  E    +A              
Sbjct: 121 EQVA-----------AVSEQMMQNHLHKD----------ELLLLQA-------------- 145

Query: 246 TGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCI---------------------- 282
                 +VL N++V+ L  ++ +   + S+L ++ D                        
Sbjct: 146 ------MVLVNAEVRRLASYNQIFNMQQSLLDAIVDTAQKYHPDNVRHVPAVLLLLTHIR 199

Query: 283 ----YVLRFWSTVHKDGKVLMNKLFVEMLEA 309
                 + F+  +  +G V    L  EML+A
Sbjct: 200 QAGERGIAFFQRLKSEGVVTFCDLLKEMLDA 230

>2ocf_A Estrogen receptor; estrogen receptor, LBD, monobody, estradiol, hormone-growth complex; HET: CME EST; 2.95A {Homo sapiens} Length = 298

 Score =  143 bits (363), Expect = 4e-41
 Identities = 68/255 (26%), Positives = 115/255 (45%), Gaps = 19/255 (7%)

Query: 64  PPNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWA 123
             N    SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WA
Sbjct: 5   KKNSLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWA 64

Query: 124 KQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC-G 182
           K++PGF DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q +   G
Sbjct: 65  KRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGKCVEG 123

Query: 183 FSEIYQQVKH-SGSLDGIK--EEE--LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTI 237
             EI+  +   S     +    EE    + + L+   V +     + S E      +   
Sbjct: 124 MVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLD 183

Query: 238 QVYSGYRQTGACGTLVLANSDVKLDEFSSLKKFRN--SILSSL-GDCIYVLRFWSTVHKD 294
           ++           TL+   +   L      ++      ILS +       +    ++   
Sbjct: 184 KITD---------TLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCK 234

Query: 295 GKVLMNKLFVEMLEA 309
             V ++ L +EML+A
Sbjct: 235 NVVPLSDLLLEMLDA 249

>1xpc_A Estrogen receptor; nuclear receptor, transcription factor, ER-alpha, antagonist hormone-growth factor receptor complex; HET: AIT; 1.60A {Homo sapiens} SCOP: a.123.1.1 PDB: 1sj0_A* 1xp1_A* 1xp9_A* 1xp6_A* 1yim_A* 1yin_A* 3ert_A* 1r5k_A* 3erd_A* 1l2i_A* 2iok_A* 1a52_A* 2ouz_A* 1ere_A* 1err_A* 2qxs_A* 3q95_A* 3q97_A* 2b1z_A* 1zky_A* ... Length = 248

 Score =  142 bits (359), Expect = 5e-41
 Identities = 67/248 (27%), Positives = 114/248 (45%), Gaps = 19/248 (7%)

Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 3   SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 62

Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC-GFSEIYQQ 189
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q +   G  EI+  
Sbjct: 63  DLTLHDQVHLLECAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQGKCVEGMVEIFDM 121

Query: 190 VKH-SGSLD--GIKEEE--LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244
           +   S       ++ EE    + + L+   V +     + S E      +   ++     
Sbjct: 122 LLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITD--- 178

Query: 245 QTGACGTLVLANSDVKLDEFSSLKKFRN--SILSSLGD-CIYVLRFWSTVHKDGKVLMNK 301
                 TL+   +   L      ++      ILS +       +    ++     V +  
Sbjct: 179 ------TLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYD 232

Query: 302 LFVEMLEA 309
           L +EML+A
Sbjct: 233 LLLEMLDA 240

>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 =  141 bits (358), Expect = 1e-40
 Identities = 53/163 (32%), Positives = 76/163 (46%), Gaps = 11/163 (6%)

Query: 35  MLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEENKMLEALLLCEPEMLTVRSE 94
           M+KE VR D ++G R +    P   S Q P   S P    + ++ A +   P M ++   
Sbjct: 1   MVKEVVRTDSLKGRRGRLPSKPK--SPQEPSPPSPPVSLISALVRAHVDSNPAMTSLDYS 58

Query: 95  TPQSDPT-------LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAE 147
             Q++P         Q I    DL    +  I GWA++IPGF DL   DQ  L +S + E
Sbjct: 59  RFQANPDYQMSGDDTQHIQQFYDLLTGSMEIIRGWAEKIPGFADLPKADQDLLFESAFLE 118

Query: 148 ILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQV 190
           +  L +AYRS P   GK+ F + +VL   Q    GF E    +
Sbjct: 119 LFVLRLAYRSNPV-EGKLIFCNGVVLHRLQCVR-GFGEWIDSI 159

>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 =  134 bits (339), Expect = 3e-38
 Identities = 66/279 (23%), Positives = 102/279 (36%), Gaps = 83/279 (29%)

Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           +L   +++  LL  EP  + +   +         + SL+ L D+ELV +I WAK+IPGF 
Sbjct: 2   ALSPEQLVLTLLEAEPPHVLISRPSAPFTEA-SMMMSLTKLADKELVHMISWAKKIPGFV 60

Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC-GFSEIYQQ 189
           +LSL DQ+RLL+S W E+L + + +RS+ H  GK+ FA DLVLD  + +   G  EI+  
Sbjct: 61  ELSLFDQVRLLESCWMEVLMMGLMWRSIDH-PGKLIFAPDLVLDRDEGKCVEGILEIFDM 119

Query: 190 VKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCE-AC-KAFFKRTIQVYSGYRQTG 247
           +                R   +               E  C KA                
Sbjct: 120 L-----------LATTSRFRELKLQHK----------EYLCVKA---------------- 142

Query: 248 ACGTLVLANSDVK--------LDEFSSLKKFRNSILSSLGDCI----------------- 282
               ++L NS +          D    L    N++  +L   I                 
Sbjct: 143 ----MILLNSSMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANL 198

Query: 283 ------------YVLRFWSTVHKDGKVLMNKLFVEMLEA 309
                         +     +     V +  L +EML A
Sbjct: 199 LMLLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEMLNA 237

>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 =  131 bits (331), Expect = 9e-37
 Identities = 59/308 (19%), Positives = 96/308 (31%), Gaps = 97/308 (31%)

Query: 45  VRGGRQKYRRNPDLLSQQWPPNKSIPSLEENKMLEALLLCEPE----------MLTVRSE 94
           ++ G   +                 P      ++  LL CEP+           L     
Sbjct: 1   MKKGHHHHHHLV-------------PRGSIPHLILELLKCEPDEPQVQAKIMAYLQQEQA 47

Query: 95  TPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIA 154
                  L T   +  + D+ L  I+ WA+    F +L ++DQM+LLQ+ W+E+L L   
Sbjct: 48  NRSKHEKLSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHI 107

Query: 155 YRSLPHC-AGKIRFASDLVLDERQARE---CGFSEIYQQVKHSGSLDGIKEEELPRRLCL 210
           YR + H   G I   +   +D            + +    +           EL  +L  
Sbjct: 108 YRQVVHGKEGSIFLVTGQQVDYSIIASQAGATLNNLMSHAQ-----------ELVAKLRS 156

Query: 211 VCGDVASGFHYGVASCE-AC-KAFFKRTIQVYSGYRQTGACGTLVLANSDVK-LDEFSSL 267
           +  D            E  C K                     LVL + DVK L+ F  +
Sbjct: 157 LQFDQR----------EFVCLKF--------------------LVLFSLDVKNLENFQLV 186

Query: 268 KKFRNSILSSLGDCI--------------------------YVLRFWSTVHKDGKVLMNK 301
           +  +  + ++L D                                +    H +G V  N 
Sbjct: 187 EGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNN 246

Query: 302 LFVEMLEA 309
           L +EML A
Sbjct: 247 LLIEMLHA 254

>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 =  130 bits (328), Expect = 2e-36
 Identities = 54/271 (19%), Positives = 96/271 (35%), Gaps = 68/271 (25%)

Query: 68  SIPSLEENKMLEALLLCEPEMLTVRSETPQSDPT--LQTINSLSDLYDRELVCIIGWAKQ 125
           +   +   ++LEA L  EP+  T        +P+     + ++    D++L  ++ WAK+
Sbjct: 4   ANEDMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKR 63

Query: 126 IPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSE 185
           IP F++L L+DQ+ LL++ W E+L  + ++RS+      I  A+ L +    A   G   
Sbjct: 64  IPHFSELPLDDQVILLRAGWNELLIASFSHRSIAV-KDGILLATGLHVHRNSAHSAGVGA 122

Query: 186 IYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ 245
           I+ +V            EL  ++  +  D       G                       
Sbjct: 123 IFDRVLT----------ELVSKMRDMQMDKT---ELGCLRA------------------- 150

Query: 246 TGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCI---------------------- 282
                 +VL N D K L   + ++  R  + +SL                          
Sbjct: 151 ------IVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALR 204

Query: 283 ----YVLRFWSTVHKDGKVLMNKLFVEMLEA 309
                 L         G   ++   +EMLEA
Sbjct: 205 SIGLKCLEHLFFFKLIGDTPIDTFLMEMLEA 235

>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 =  129 bits (326), Expect = 4e-36
 Identities = 50/283 (17%), Positives = 97/283 (34%), Gaps = 78/283 (27%)

Query: 64  PPNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWA 123
           P      +     ++  L + EPE+L    ++   D   + + +L+ L  R+++  + WA
Sbjct: 6   PAALPQLTPT---LVSLLEVIEPEVLYAGYDSSVPDSAWRIMTTLNMLGGRQVIAAVKWA 62

Query: 124 KQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAG-KIRFASDLVLDERQARECG 182
           K IPGF +L L+DQM LLQ +W  ++   + +RS    +G  + FA DL+++E++     
Sbjct: 63  KAIPGFRNLHLDDQMTLLQYSWMFLMVFALGWRSYRQASGNLLCFAPDLIINEQRMTLPC 122

Query: 183 FSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEAC-KAFFKRTIQVYS 241
             +  + +             +   L  +         Y       C K           
Sbjct: 123 MYDQCKHML-----------FISTELQRLQVSYE---EY------LCMKT---------- 152

Query: 242 GYRQTGACGTLVLANSDVK--LDEFSSLKKFRNSILSSLGDCIYVLR------------- 286
                     L+L +S  K  L       + R + +  LG  I                 
Sbjct: 153 ----------LLLLSSVPKEGLKSQELFDEIRMTYIKELGKAIAKRGGNSSQNWQRFYQL 202

Query: 287 ------------------FWSTVHKDGKVLMNKLFVEMLEAYL 311
                             F + + K   +   ++  E++   +
Sbjct: 203 TKLLDSMHDVVENLLSYCFQTFLDKSMSIEFPEMLAEIITNQI 245

>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 =  130 bits (327), Expect = 4e-36
 Identities = 62/270 (22%), Positives = 114/270 (42%), Gaps = 15/270 (5%)

Query: 47  GGRQKYRRNPDLLSQQWPPNK--SIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQT 104
           G    +  +   L  +    +   + +L   +++  LL  EP  + +   +         
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMRELLLDALSPEQLVLTLLEAEPPHVLISRPSAPFTEA-SM 60

Query: 105 INSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGK 164
           + SL+ L D+ELV +I WAK+IPGF +LSL DQ+RLL+S W E+L + + +RS+ H  GK
Sbjct: 61  MMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDH-PGK 119

Query: 165 IRFASDLVLDERQAREC-GFSEIYQQVKH-SGSLDGIK--EEELPRRLCLVCGDVASGFH 220
           + FA DLVLD  + +   G  EI+  +   +     +K   +E    LC+    + +   
Sbjct: 120 LIFAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEY---LCVKAMILLNSSM 176

Query: 221 YGVASCEACKAFFKRTIQVYSGYRQT-GACGTLVLANSDVKLDEFSSLKKFRNSILSSLG 279
           Y + +        ++   + +               +S  +    ++L    + +     
Sbjct: 177 YPLVTATQDADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRH--- 233

Query: 280 DCIYVLRFWSTVHKDGKVLMNKLFVEMLEA 309
                +     +     V +  L +EML A
Sbjct: 234 ASNKGMEHLLNMKCKNVVPVYDLLLEMLNA 263

>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 =  127 bits (320), Expect = 2e-35
 Identities = 51/268 (19%), Positives = 93/268 (34%), Gaps = 69/268 (25%)

Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQS-DPTLQTINSLSDLYDRELVCIIGWAKQIPGF 129
           +L+ +  LE ++  E  +           +    T+N++     ++L  ++ WAK +P F
Sbjct: 4   NLQADMPLERIIEAEKRVECNDPLVALVVNENNTTVNNICQATHKQLFQLVQWAKLVPHF 63

Query: 130 TDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQ 189
           T L L DQ++LL++ W E+L    ++RS+      I  A+ L +++  A   G   IY +
Sbjct: 64  TSLPLTDQVQLLRAGWNELLIAAFSHRSMQA-QDAIVLATGLTVNKSTAHAVGVGNIYDR 122

Query: 190 VKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEAC-KAFFKRTIQVYSGYRQTGA 248
           V            EL  ++  +  D              C +A                 
Sbjct: 123 VLS----------ELVNKMKEMKMDKTE---------LGCLRA----------------- 146

Query: 249 CGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCI------------------------- 282
              ++L N DV+ +     ++  R  I   L +                           
Sbjct: 147 ---IILYNPDVRGIKSVQEVEMLREKIYGVLEEYTRTTHPNEPGRFAKLLLRLPALRSIG 203

Query: 283 -YVLRFWSTVHKDGKVLMNKLFVEMLEA 309
              L         G V ++   +EMLE 
Sbjct: 204 LKCLEHLFFFKLIGDVPIDTFLMEMLEG 231

>3vhu_A Mineralocorticoid receptor; nuclear receptor, transcription factor, activating mutation, hypertension, antagonist, spironolactone; HET: SNL; 2.11A {Homo sapiens} Length = 294

 Score =  128 bits (323), Expect = 3e-35
 Identities = 52/296 (17%), Positives = 107/296 (36%), Gaps = 80/296 (27%)

Query: 54  RNPDLLSQQWPPNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYD 113
           + P + +   P   +I        +  L   EPE++    ++ + D     +++L+ L  
Sbjct: 25  KEPSVNTALVPQLSTISRALTPSPVMVLENIEPEIVYAGYDSSKPDTAENLLSTLNRLAG 84

Query: 114 RELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAG-KIRFASDLV 172
           ++++ ++ WAK +PGF +L L DQ+ L+Q +W  +L+  +++RS  H     + FA DLV
Sbjct: 85  KQMIQVVKWAKVLPGFKNLPLEDQITLIQYSWMSLLSFALSWRSYKHTNSQFLYFAPDLV 144

Query: 173 LDERQARECGFSEIYQQVKH-SGSLDGIK--EEELPRRLCLVCGDVASGFHYGVASCEAC 229
            +E +  +    E+ Q +   S     ++   EE      +                   
Sbjct: 145 FNEEKMHQSAMYELCQGMHQISLQFVRLQLTFEEY---TIM------------------- 182

Query: 230 KAFFKRTIQVYSGYRQTGACGTLVLANSDVK--LDEFSSLKKFRNSILSSLGDCI----- 282
           K                     L+L ++  K  L   ++ ++ R + +  L   +     
Sbjct: 183 KV--------------------LLLLSTIPKDGLKSQAAFEEMRTNYIKELRKMVTKCPN 222

Query: 283 ------------------------YVLRFWSTVHKDG---KVLMNKLFVEMLEAYL 311
                                    +L F     ++    KV    + VE++   L
Sbjct: 223 NSGQSWQRFYQLTKLLDSMHDLVSDLLEFCFYTFRESHALKVEFPAMLVEIISDQL 278

>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 =  124 bits (313), Expect = 4e-34
 Identities = 65/248 (26%), Positives = 113/248 (45%), Gaps = 23/248 (9%)

Query: 72  LEENKMLEALLLCEP-EMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           L   +++  LL  EP  +L  R   P ++ ++  + SL+ L D+ELV +I WAK+IPGF 
Sbjct: 1   LSPEQLVLTLLEAEPPHVLISRPSAPFTEASM--MMSLTKLADKELVHMISWAKKIPGFV 58

Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC-GFSEIYQQ 189
           +LSL DQ+RLL+S W E+L + + +RS+ H  GK+ FA DLVLD  + +   G  EI+  
Sbjct: 59  ELSLFDQVRLLESCWMEVLMMGLMWRSIDH-PGKLIFAPDLVLDRDEGKCVEGILEIFDM 117

Query: 190 VKH-SGSLDGIK--EEELP--RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244
           +   +     +K   +E    + + L+   +     Y + +        ++   + +   
Sbjct: 118 LLATTSRFRELKLQHKEYLCVKAMILLNSSM-----YPLVTATQDADSSRKLAHLLNAVT 172

Query: 245 QTGACGTLVLANSDVKLDEFSSLKKFRN--SILSSLGD-CIYVLRFWSTVHKDGKVLMNK 301
                  LV   +   +       +  N   +LS +       +     +     V +  
Sbjct: 173 D-----ALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVYD 227

Query: 302 LFVEMLEA 309
           L +EML A
Sbjct: 228 LLLEMLNA 235

>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 =  123 bits (311), Expect = 4e-34
 Identities = 49/275 (17%), Positives = 88/275 (32%), Gaps = 73/275 (26%)

Query: 68  SIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQ-----TINSLSDLYDRELVCIIGW 122
           S   L     + ALL  E     + S     +  ++     +I  + +    +L+ ++ W
Sbjct: 1   SSYELASLPSINALLQAEVLSRQITSPVSGINGDIRAKKIASIADVCESMKEQLLVLVEW 60

Query: 123 AKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECG 182
           AK IP F +L L+DQ+ LL++   E L L    RS+      +   +D ++         
Sbjct: 61  AKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVF-KDVLLLGNDYIVPRHCPELAE 119

Query: 183 FSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEAC-KAFFKRTIQVYS 241
            S +  ++            EL      +  D      Y      A  KA          
Sbjct: 120 MSRVSIRILD----------ELVLPFQELQIDDN---EY------AYLKA---------- 150

Query: 242 GYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCI------------------ 282
                     ++  + D K L +   +K+ R+ +  SL D I                  
Sbjct: 151 ----------IIFFDPDAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLL 200

Query: 283 --------YVLRFWSTVHKDGKVLMNKLFVEMLEA 309
                    ++     +   G   ++ L  EML  
Sbjct: 201 PTLQSITWQMIEQIQFIKLFGMAKIDNLLQEMLLG 235

>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 =  127 bits (321), Expect = 4e-34
 Identities = 41/229 (17%), Positives = 70/229 (30%), Gaps = 38/229 (16%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG-RQKYRRNPDLL 59
            + Y     N C I+K+ R  CQ CRFQKCL  GM    +R  R+    ++K        
Sbjct: 84  KLIYDRCDLN-CRIHKKSRNKCQYCRFQKCLAVGMSHNAIRFGRMPQAEKEKLLAEISSD 142

Query: 60  SQQWPPNKSIPSLEENKMLEALLLCEPEMLT----------------------------- 90
             Q  P  +        + ++ +   P                                 
Sbjct: 143 IDQLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGED 202

Query: 91  -------VRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQS 143
                     +    +  ++            +  I  +AK IPGF +L LNDQ+ LL+ 
Sbjct: 203 KIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKY 262

Query: 144 TWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKH 192
              EI+   +A                +  +  ++    F +  +    
Sbjct: 263 GVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFE 311

>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 = 66.2 bits (161), Expect = 2e-12
 Identities = 24/73 (32%), Positives = 33/73 (45%)

Query: 177 QARECGFSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRT 236
           +          ++ +            L    C VCGD ASGFHYGV +CE CK FF+RT
Sbjct: 21  KVEPASPPYYSEKTQLYNKPHEEPSNSLMAIECRVCGDKASGFHYGVHACEGCKGFFRRT 80

Query: 237 IQVYSGYRQTGAC 249
           I++   Y +    
Sbjct: 81  IRLKLIYDRCDLN 93

>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 =  123 bits (311), Expect = 7e-34
 Identities = 50/283 (17%), Positives = 102/283 (36%), Gaps = 80/283 (28%)

Query: 67  KSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQI 126
            +I        +  L   EPE++    ++ + D     +++L+ L  ++++ ++ WAK +
Sbjct: 4   STISRALTPSPVMVLENIEPEIVYAGYDSSKPDTAENLLSTLNRLAGKQMIQVVKWAKVL 63

Query: 127 PGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAG-KIRFASDLVLDERQARECGFSE 185
           PGF +L L DQ+ L+Q +W  +L+  +++RS  H     + FA DLV +E +  +    E
Sbjct: 64  PGFKNLPLEDQITLIQYSWMSLLSFALSWRSYKHTNSQFLYFAPDLVFNEEKMHQSAMYE 123

Query: 186 IYQQVKH-SGSLDGIK--EEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSG 242
           + Q +   S     ++   EE      +                   K            
Sbjct: 124 LCQGMHQISLQFVRLQLTFEEY---TIM-------------------KV----------- 150

Query: 243 YRQTGACGTLVLANSDVK--LDEFSSLKKFRNSILSSLGDCI------------------ 282
                    L+L ++  K  L   ++ ++ R + +  L   +                  
Sbjct: 151 ---------LLLLSTIPKDGLKSQAAFEEMRTNYIKELRKMVTKCPNNSGQSWQRFYQLT 201

Query: 283 -----------YVLRFWSTVHKDG---KVLMNKLFVEMLEAYL 311
                       +L F     ++    KV    + VE++   L
Sbjct: 202 KLLDSMHDLVSDLLEFCFYTFRESHALKVEFPAMLVEIISDQL 244

>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 =  122 bits (308), Expect = 2e-33
 Identities = 32/119 (26%), Positives = 69/119 (57%), Gaps = 1/119 (0%)

Query: 75  NKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSL 134
             ++  L+  EP+++    +  + D +   + SL+ L +R+L+ ++ W+K +PGF +L +
Sbjct: 13  PPLINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHI 72

Query: 135 NDQMRLLQSTWAEILTLTIAYRSLPHCAG-KIRFASDLVLDERQARECGFSEIYQQVKH 192
           +DQ+ L+Q +W  ++   + +RS  H +G  + FA DL+L+E++ +E  F  +   +  
Sbjct: 73  DDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQ 131

>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 =  121 bits (304), Expect = 2e-32
 Identities = 27/186 (14%), Positives = 67/186 (36%), Gaps = 17/186 (9%)

Query: 10  NDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSI 69
             C + KR+ K  Q  + +         +G++ +          +               
Sbjct: 21  FQCAV-KRKEKKAQKDKDKPNSTTSCSPDGIKQEIDPQRLDTDSQLLS------VNGVKP 73

Query: 70  PSLEENKMLEALLLCEPE---------MLTVRSETPQSDPTLQTINSLSDLYDRELVCII 120
            + E+ +++  L+  + E            V +   + +   +    ++++    +  I+
Sbjct: 74  ITPEQEELIHRLVYFQNEYEHPSPEDIKRIVNAAPEEENVAEERFRHITEITILTVQLIV 133

Query: 121 GWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE 180
            ++K++PGF  L   DQ+ LL++  +E++   +A R        I FA++          
Sbjct: 134 EFSKRLPGFDKLIREDQIALLKACSSEVMMFRMARRYDAE-TDSILFATNQPYTRESYTV 192

Query: 181 CGFSEI 186
            G  + 
Sbjct: 193 AGMGDT 198

>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 =  119 bits (300), Expect = 2e-32
 Identities = 49/263 (18%), Positives = 84/263 (31%), Gaps = 67/263 (25%)

Query: 75  NKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSL 134
           +  +  LL  EP   +           +  I ++ +L  R L   + WA+ IP F DL +
Sbjct: 9   SGYISLLLRAEPYPTSRFGSQCMQPNNIMGIENICELAARMLFSAVEWARNIPFFPDLQI 68

Query: 135 NDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQA-RECGFSEIYQQVKHS 193
            DQ+ LL+ TW+E+  L  A  S+P     +  A+ L      A R   F +  +  +  
Sbjct: 69  TDQVALLRLTWSELFVLNAAQCSMPLHVAPLLAAAGLHASPMSADRVVAFMDHIRIFQ-- 126

Query: 194 GSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLV 253
                    E   +L  +  D A    Y                              +V
Sbjct: 127 ---------EQVEKLKALHVDSAE---YSCLKA-------------------------IV 149

Query: 254 LANSDVK-LDEFSSLKKFRNSILSSLGDCI--------------------------YVLR 286
           L  SD   L + + ++  +     +L + +                           V+ 
Sbjct: 150 LFTSDACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIE 209

Query: 287 FWSTVHKDGKVLMNKLFVEMLEA 309
               V   GK  +  L  +ML +
Sbjct: 210 QLFFVRLVGKTPIETLIRDMLLS 232

>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 =  120 bits (303), Expect = 5e-32
 Identities = 57/289 (19%), Positives = 93/289 (32%), Gaps = 84/289 (29%)

Query: 64  PPNKSIPSLEENKMLEALLLCEPE----------MLTVRSETPQSDPTLQTINSLSDLYD 113
              ++        ++  LL CEP+           L            L T   +  + D
Sbjct: 102 DSYQTSSPASIPHLILELLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMAD 161

Query: 114 RELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHC-AGKIRFASDLV 172
           + L  I+ WA+    F +L ++DQM+LLQ+ W+E+L L   YR + H   G I   +   
Sbjct: 162 QTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQ 221

Query: 173 LDERQARE---CGFSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCE-A 228
           +D            + +    +           EL  +L  +  D            E  
Sbjct: 222 VDYSIIASQAGATLNNLMSHAQ-----------ELVAKLRSLQFDQR----------EFV 260

Query: 229 C-KAFFKRTIQVYSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCI---- 282
           C K                     LVL + DVK L+ F  ++  +  + ++L D      
Sbjct: 261 CLKF--------------------LVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNY 300

Query: 283 ----------------------YVLRFWSTVHKDGKVLMNKLFVEMLEA 309
                                     +    H +G V  N L +EML A
Sbjct: 301 PQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHA 349

>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 =  118 bits (298), Expect = 6e-32
 Identities = 50/290 (17%), Positives = 90/290 (31%), Gaps = 84/290 (28%)

Query: 65  PNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAK 124
              SI  L E + L A    E + L V  ++         ++SL  + ++++  ++ WA+
Sbjct: 4   QELSIERLLEMESLVADPSEEFQFLRVGPDSNVPPKFRAPVSSLCQIGNKQIAALVVWAR 63

Query: 125 QIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCA-----------------GKIRF 167
            IP F+ L + DQ+ L++ +W E+L   IA+RS+                       +  
Sbjct: 64  DIPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLTEERDGVDGTGNRTTSPPQLMCL 123

Query: 168 ASDLVLDERQARECGFSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCE 227
              + L    A + G  +I+ +V            EL  ++  +  D A           
Sbjct: 124 MPGMTLHRNSALQAGVGQIFDRVLS----------ELSLKMRTLRVDQAE---------Y 164

Query: 228 AC-KAFFKRTIQVYSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCI--- 282
              KA                    ++L N DVK L     ++  R  +   L +     
Sbjct: 165 VALKA--------------------IILLNPDVKGLKNRQEVEVLREKMFLCLDEYCRRS 204

Query: 283 ---YVLRF--------------------WSTVHKDGKVLMNKLFVEMLEA 309
                 RF                        H      +     + L  
Sbjct: 205 RSSEEGRFAALLLRLPALRSISLKSFEHLFFFHLVADTSIAGYIRDALRN 254

>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 =  119 bits (300), Expect = 8e-32
 Identities = 42/162 (25%), Positives = 74/162 (45%), Gaps = 11/162 (6%)

Query: 35  MLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEENKMLEALLLCEPEMLTVRSE 94
           M KE VR DR +  ++  ++     ++ +     +  L E K+ +A     P +  +   
Sbjct: 1   MSKESVRNDRNKKKKEPSKQEC---TESYEMTAELDDLTE-KIRKAHQETFPSLCQLGKY 56

Query: 95  TPQSDPT------LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEI 148
           T  S         L   +  S+L  + ++ I+ +AK++PGFT L++ DQ+ LL++   +I
Sbjct: 57  TTNSSADHRVRLDLGLWDKFSELATKCIIKIVEFAKRLPGFTGLTIADQITLLKAACLDI 116

Query: 149 LTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQV 190
           L L I  R  P     + F+  L L+  Q    GF  +   V
Sbjct: 117 LILRICTRYTPE-QDTMTFSDGLTLNRTQMHNAGFGPLTDLV 157

>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 =  116 bits (291), Expect = 6e-31
 Identities = 33/120 (27%), Positives = 65/120 (54%), Gaps = 1/120 (0%)

Query: 74  ENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLS 133
           +   L  L   EP ++    +  Q D     ++SL++L +R+LV ++ WAK +PGF +L 
Sbjct: 20  QPIFLNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLH 79

Query: 134 LNDQMRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEIYQQVKH 192
           ++DQM ++Q +W  ++   + +RS  +   + + FA DLV +E +  +        +++H
Sbjct: 80  VDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHKSRMYSQCVRMRH 139

>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 =  109 bits (275), Expect = 9e-29
 Identities = 51/279 (18%), Positives = 93/279 (33%), Gaps = 74/279 (26%)

Query: 68  SIPSLEENKMLEALLLCEPE--------MLTVRSETPQSDPTLQTINSLSDLYDRELVCI 119
           S       +++  LL  EPE        +  ++             + L  + D+  + I
Sbjct: 2   SSGGPNVPELILQLLQLEPEEDQVRARIVGCLQEPAKSRSDQPAPFSLLCRMADQTFISI 61

Query: 120 IGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHC-AGKIRFASDLVLDERQA 178
           + WA++   F +L + DQM LLQ++W+E+L L   YR + +     I   +   ++    
Sbjct: 62  VDWARRCMVFKELEVADQMTLLQNSWSELLVLDHIYRQVQYGKEDSILLVTGQEVELSTV 121

Query: 179 RECGFSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEAC-KAFFKRTI 237
                S ++  V  +        +EL  +L  +  D              C K       
Sbjct: 122 AVQAGSLLHSLVLRA--------QELVLQLHALQLDRQE---------FVCLKF------ 158

Query: 238 QVYSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIY------------- 283
                         L+L + DVK L+  S +K  +    ++L D                
Sbjct: 159 --------------LILFSLDVKFLNNHSLVKDAQEKANAALLDYTLSHYPHSGDKFQQL 204

Query: 284 -------------VLRFWSTVHKDGKVLMNKLFVEMLEA 309
                           +    H   ++  N L +EML+A
Sbjct: 205 LLSLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIEMLQA 243

>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 =  107 bits (268), Expect = 2e-27
 Identities = 40/153 (26%), Positives = 58/153 (37%), Gaps = 11/153 (7%)

Query: 47  GGRQKYRRNPDLLSQQWPPNKSIPSLEE--NKMLEALLLCEPEMLTVRSETPQSDPT--- 101
                +  +  L+ +         S       ++ A L   P    +     Q       
Sbjct: 2   SSHHHHHHSSGLVPRGSHMQPPDASPTNLLTSLIRAHLDSGPNTAKLDYSKFQELVLPRF 61

Query: 102 ----LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRS 157
                  +    DL    L  I  WA++IPGF +LS  DQ  LL+S + E+  L +AYRS
Sbjct: 62  GKEDAGDVQQFYDLLSGSLDVIRKWAEKIPGFIELSPGDQDLLLESAFLELFILRLAYRS 121

Query: 158 LPHCAGKIRFASDLVLDERQARECGFSEIYQQV 190
            P   GK+ F S LVL   Q    GF +    +
Sbjct: 122 KPG-EGKLIFCSGLVLHRLQCAR-GFGDWIDNI 152

>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 =  104 bits (262), Expect = 2e-26
 Identities = 34/166 (20%), Positives = 57/166 (34%), Gaps = 8/166 (4%)

Query: 22  CQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEENKMLEAL 81
               RF+  +R+G +                  +    +     N S  S++       L
Sbjct: 29  SDFVRFRPPVREGPVTRSASRAA--------SLHSLSDASSDSFNHSPESVDTKLNFSNL 80

Query: 82  LLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLL 141
           L+   +  +  S        L  +  L+DL    +  +IG+AK IPGF DL+  DQ+ LL
Sbjct: 81  LMMYQDSGSPDSSEEDQQSRLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALL 140

Query: 142 QSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIY 187
           +S+  EI+ L                  D         + G +   
Sbjct: 141 KSSAIEIIMLRSNQSFSLEDMSWSCGGPDFKYCINDVTKAGHTLEL 186

>1hg4_A Ultraspiracle; nuclear hormone receptor, transcription factor, ligand binding; HET: LPP; 2.4A {Drosophila melanogaster} SCOP: a.123.1.1 Length = 279

 Score =  104 bits (260), Expect = 3e-26
 Identities = 36/269 (13%), Positives = 82/269 (30%), Gaps = 46/269 (17%)

Query: 75  NKMLEALLLCEPEMLTVRSETPQSDPT-------LQTINSLSDLYDRELVCIIGWAKQIP 127
            +++EA    E +         +  P           +++L  + +++L  ++ +A+ +P
Sbjct: 12  ERIIEAEQRAETQCGDRALTFLRVGPYSTVQPDYKGAVSALCQVVNKQLFQMVEYARMMP 71

Query: 128 GFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIY 187
            F  + L+DQ+ LL++ W E+L   +A+ S+                       G  E  
Sbjct: 72  HFAQVPLDDQVILLKAAWIELLIANVAWCSIVSLDDGG-----AGGGGGGLGHDGSFERR 126

Query: 188 QQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTG 247
                   L   +     R   +  G                     +  ++    R+  
Sbjct: 127 SPGLQPQQLFLNQSFSYHRNSAIKAG-------VSAIFDRILSELSVKMKRLNLDRRELS 179

Query: 248 ACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCI------------------------ 282
               ++L N D++ +   + ++  R  + + L +                          
Sbjct: 180 CLKAIILYNPDIRGIKSRAEIEMCREKVYACLDEHCRLEHPGDDGRFAQLLLRLPALRSI 239

Query: 283 --YVLRFWSTVHKDGKVLMNKLFVEMLEA 309
                             + +LF+E LEA
Sbjct: 240 SLKCQDHLFLFRITSDRPLEELFLEQLEA 268

>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 = 97.9 bits (244), Expect = 7e-26
 Identities = 45/57 (78%), Positives = 51/57 (89%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPD 57
          NIEY+CPA+N+CEI KRRRK+CQACRF K L+ GMLKEGVRLDRVRGGRQKY+R  D
Sbjct: 38 NIEYSCPATNECEITKRRRKSCQACRFMKALKVGMLKEGVRLDRVRGGRQKYKRRLD 94

>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 = 78.6 bits (194), Expect = 1e-18
 Identities = 34/48 (70%), Positives = 38/48 (79%), Gaps = 2/48 (4%)

Query: 204 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY--RQTGAC 249
           +P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQ    Y    T  C
Sbjct: 2   IPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNEC 49

>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 =  100 bits (252), Expect = 2e-25
 Identities = 38/129 (29%), Positives = 60/129 (46%), Gaps = 9/129 (6%)

Query: 70  PSLEE--NKMLEALLLCEPEMLTVRSETPQSDP------TLQTINSLSDLYDRELVCIIG 121
           P LEE   K+ +A     P +  +   T  S         L   +  S+L  + ++ I+ 
Sbjct: 3   PQLEELITKVSKAHQETFPSLCQLGKYTTNSSADHRVQLDLGLWDKFSELATKCIIKIVE 62

Query: 122 WAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC 181
           +AK++PGFT LS+ DQ+ LL++   +IL L I  R  P     + F+  L L+  Q    
Sbjct: 63  FAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPE-QDTMTFSDGLTLNRTQMHNA 121

Query: 182 GFSEIYQQV 190
           GF  +   V
Sbjct: 122 GFGPLTDLV 130

>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 = 94.3 bits (235), Expect = 1e-24
 Identities = 28/56 (50%), Positives = 37/56 (66%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNP 56
          + +Y C A+ DC ++KRRR  CQ CRFQKCL  GM+KE VR D ++G R +    P
Sbjct: 34 SAKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTDSLKGRRGRLPSKP 89

>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 = 70.4 bits (173), Expect = 9e-16
 Identities = 23/43 (53%), Positives = 26/43 (60%), Gaps = 2/43 (4%)

Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY--RQTGAC 249
           C VCGD AS  HYGV +CE CK FFKRT+Q  + Y       C
Sbjct: 3   CAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKDC 45

>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 = 94.8 bits (236), Expect = 2e-24
 Identities = 30/69 (43%), Positives = 39/69 (56%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
           N  YTC  + +C+I+K +RK C  CRFQKCL  GM  E VR DR+RGGR K+        
Sbjct: 43  NKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMRGGRNKFGPMYKRDR 102

Query: 61  QQWPPNKSI 69
                 K++
Sbjct: 103 ALKQQKKAL 111

>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 = 73.2 bits (180), Expect = 2e-16
 Identities = 25/54 (46%), Positives = 32/54 (59%), Gaps = 2/54 (3%)

Query: 198 GIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY--RQTGAC 249
           G   +E    LC VCGD  SG+HYG+ +CE+CK FFKRT+Q    Y   +   C
Sbjct: 1   GEFGDEDLEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQNC 54

>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 = 98.3 bits (245), Expect = 3e-24
 Identities = 34/154 (22%), Positives = 62/154 (40%), Gaps = 11/154 (7%)

Query: 47  GGRQKYRRNPDLLSQQWPPNKSIPSLEENKMLEALLLCEPEM----------LTVRSETP 96
           G    +  +   L  +        + E  +++E +     E            T  S   
Sbjct: 2   GSSHHHHHHSSGLVPRGSHESYTLTPEVGELIEKVRKAHQETFPALCQLGKYTTNNSSEQ 61

Query: 97  QSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYR 156
           +    +   +  S+L  + ++  + +AKQ+PGFT L++ DQ+ LL++   +IL L I  R
Sbjct: 62  RVSLDIDLWDKFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTR 121

Query: 157 SLPHCAGKIRFASDLVLDERQARECGFSEIYQQV 190
             P     + F+  L L+  Q    GF  +   V
Sbjct: 122 YTPE-QDTMTFSDGLTLNRTQMHNAGFGPLTDLV 154

>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 = 97.5 bits (243), Expect = 3e-24
 Identities = 29/126 (23%), Positives = 48/126 (38%), Gaps = 5/126 (3%)

Query: 64  PPNKSIPSLEE-NKMLEALLLCEPEM--LTVRSETPQSDPTLQTINSLSDLYDRELVCII 120
             +    ++     ++ + +   P+   L       QS      +     L    +  I 
Sbjct: 5   HHHHHHGAISLITALVRSHVDTTPDPSCLDYSHYEEQSMSEADKVQQFYQLLTSSVDVIK 64

Query: 121 GWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE 180
            +A++IPG+ DL   DQ  L QS   E+  L +AYR+      K+ F +  VL   Q   
Sbjct: 65  QFAEKIPGYFDLLPEDQELLFQSASLELFVLRLAYRARID-DTKLIFCNGTVLHRTQCLR 123

Query: 181 CGFSEI 186
             F E 
Sbjct: 124 -SFGEW 128

>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 = 94.0 bits (234), Expect = 7e-23
 Identities = 25/137 (18%), Positives = 52/137 (37%), Gaps = 11/137 (8%)

Query: 64  PPNKSIP-SLEENKMLEALLLCEPE---------MLTVRSETPQSDPTLQTINSLSDLYD 113
             N S   S E+ +++  L+  + E            +       D        ++++  
Sbjct: 3   HMNGSKGISPEQEELIHRLVYFQNEYEHPSEEDVKRIINQPMDGEDQCDVRFRHITEITI 62

Query: 114 RELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVL 173
             +  I+ +AK++PGF  L   DQ+ LL++  +E++   +A R        I F ++   
Sbjct: 63  LTVQLIVEFAKRLPGFDKLLREDQIALLKACSSEVMMFRMARRYDVQ-TDSILFVNNQPY 121

Query: 174 DERQARECGFSEIYQQV 190
                   G  E  + +
Sbjct: 122 SRDSYNLAGMGETIEDL 138

>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 = 94.0 bits (234), Expect = 9e-23
 Identities = 28/163 (17%), Positives = 65/163 (39%), Gaps = 20/163 (12%)

Query: 39  GVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEENKMLEALL-----LCEPEMLTVRS 93
           G  +  + GG+Q  R            N    +  +  ++  L+       +P    ++ 
Sbjct: 1   GSHMASMTGGQQMGRDPL--------KNVPPLTANQKSLIARLVWYQEGYEQPSEEDLKR 52

Query: 94  ETPQSDP------TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAE 147
            T           +      ++++    +  I+ +AK +PGF  +S +DQ+ LL++  +E
Sbjct: 53  VTQTWQSDEDDEDSDMPFRQITEMTILTVQLIVEFAKGLPGFAKISQSDQITLLKACSSE 112

Query: 148 ILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQV 190
           ++ L +A R        + FA++        R+ G + + + +
Sbjct: 113 VMMLRVARRYDAA-TDSVLFANNQAYTRDNYRKAGMAYVIEDL 154

>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 = 88.2 bits (219), Expect = 2e-22
 Identities = 22/53 (41%), Positives = 29/53 (54%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYR 53
             Y C   NDC I+K RRK C ACR++KCL+ GM  E  +  +   G Q+  
Sbjct: 36 QHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEARKTKKKIKGIQQAT 88

>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 = 70.9 bits (174), Expect = 5e-16
 Identities = 21/45 (46%), Positives = 26/45 (57%), Gaps = 2/45 (4%)

Query: 207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY--RQTGAC 249
            +CLVC D ASG HYGV +C +CK FFKR ++    Y       C
Sbjct: 3   HMCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDC 47

>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 = 87.9 bits (218), Expect = 5e-22
 Identities = 18/57 (31%), Positives = 28/57 (49%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPD 57
            +Y C + NDC I+K RRK C +CR +KC   GM     +L ++   + +      
Sbjct: 41 KQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLGARKLKKLGNLKLQEEGENS 97

>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 = 74.8 bits (184), Expect = 3e-17
 Identities = 21/47 (44%), Positives = 27/47 (57%), Gaps = 2/47 (4%)

Query: 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY--RQTGAC 249
           P++ CL+CGD ASG HYG  +C +CK FFKR  +    Y       C
Sbjct: 6   PQKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLCASRNDC 52

>3n00_A REV-ERBA-alpha; reverba ncorid1, anti-parallel B-sheet, transcription regula; 2.60A {Homo sapiens} Length = 245

 Score = 90.2 bits (224), Expect = 2e-21
 Identities = 20/121 (16%), Positives = 42/121 (34%), Gaps = 1/121 (0%)

Query: 70  PSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGF 129
            + ++               +            +     S  +   +  ++ +AK IPGF
Sbjct: 32  YAHDKLGSSPGNFNANHASGSPYPHGRSGRTVQEIWEDFSMSFTPAVREVVEFAKHIPGF 91

Query: 130 TDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQ 189
            DLS +DQ+ LL++   E+L +  A          + F S      ++    G  ++   
Sbjct: 92  RDLSQHDQVTLLKAGTFEVLMVRFASLFNVK-DQTVMFLSRTTYSLQELGAMGMGDLLSA 150

Query: 190 V 190
           +
Sbjct: 151 M 151

>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 = 90.2 bits (224), Expect = 4e-21
 Identities = 30/173 (17%), Positives = 62/173 (35%), Gaps = 19/173 (10%)

Query: 28  QKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEENKMLEALL----- 82
            +   +   ++ ++        Q +  +    +   P      S E+  M+E L+     
Sbjct: 5   HQHQHQHQHQQPLQ-----EEEQAHATSLPPRASSPPQILPQLSPEQLGMIEKLVAAQQQ 59

Query: 83  --------LCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSL 134
                           +  +    +   Q     ++L    +  I+ +AKQ+PGF  LS 
Sbjct: 60  CNRRSFSDRLRVTPWPMAPDPHSREARQQRFAHFTELAIVSVQEIVDFAKQLPGFLQLSR 119

Query: 135 NDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIY 187
            DQ+ LL+++  E++ L  + R  P  +  I F  D   +     + G    +
Sbjct: 120 EDQIALLKTSAIEVMLLETSRRYNPG-SESITFLKDFSYNREDFAKAGLQVEF 171

>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 = 89.5 bits (222), Expect = 4e-21
 Identities = 24/158 (15%), Positives = 59/158 (37%), Gaps = 13/158 (8%)

Query: 43  DRVRGGRQKYRRNPD--------LLSQQWPPNKSIPSLEENKMLEALLLCEPEMLTVRSE 94
           + +R  +Q+    P+          + +     +       K     L  +     + S 
Sbjct: 6   EMIRSLQQRPEPTPEEWDLIHIATEAHR----STNAQGSHWKQRRKFLPDDIGQSPIVSM 61

Query: 95  TPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIA 154
                  L+  +  + +    +  ++ +AK++P F++L   DQ+ LL+    EI++L  A
Sbjct: 62  PDGDKVDLEAFSEFTKIITPAITRVVDFAKKLPMFSELPXEDQIILLKGCCMEIMSLRAA 121

Query: 155 YRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKH 192
            R  P  +  +  + ++ +   Q +  G   +   +  
Sbjct: 122 VRYDPE-SDTLTLSGEMAVKREQLKNGGLGVVSDAIFE 158

>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 = 85.3 bits (211), Expect = 6e-21
 Identities = 23/71 (32%), Positives = 36/71 (50%), Gaps = 3/71 (4%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKY---RRNPD 57
              +TCP + DC I K  R+ CQACR ++C+  GM+KE +  D     +++    R+  +
Sbjct: 40  KALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDEEVQRKREMILKRKEEE 99

Query: 58  LLSQQWPPNKS 68
            L     P  S
Sbjct: 100 ALKDSLRPKLS 110

>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 = 72.5 bits (178), Expect = 3e-16
 Identities = 19/50 (38%), Positives = 30/50 (60%), Gaps = 2/50 (4%)

Query: 202 EELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY--RQTGAC 249
           +    R+C VCGD A+GFH+   +CE CK FF+R+++  + +     G C
Sbjct: 2   DRNVPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDC 51

>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 = 83.6 bits (207), Expect = 9e-21
 Identities = 26/47 (55%), Positives = 34/47 (72%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG 47
          + +Y CPA+N C I+K RRK+CQACR +KC   GM+K G+R DR  G
Sbjct: 38 HNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRKDRRGG 84

>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 = 74.7 bits (184), Expect = 2e-17
 Identities = 27/47 (57%), Positives = 31/47 (65%), Gaps = 2/47 (4%)

Query: 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY--RQTGAC 249
             R C VC D ASG+HYGV SCE CKAFFKR+IQ ++ Y    T  C
Sbjct: 3   ETRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQC 49

>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 = 83.6 bits (207), Expect = 2e-20
 Identities = 25/62 (40%), Positives = 35/62 (56%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
          ++ YTC  + DC I+KR+R  CQ CR+QKCL  GM +E V+ +R RG  +         S
Sbjct: 37 DLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRGKDRNENEVESTSS 96

Query: 61 QQ 62
            
Sbjct: 97 AN 98

>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 = 74.0 bits (182), Expect = 5e-17
 Identities = 23/48 (47%), Positives = 29/48 (60%), Gaps = 2/48 (4%)

Query: 204 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY--RQTGAC 249
             + +C +CGD +SG HYGV SCE CK FFKRT++    Y  R    C
Sbjct: 1   FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDC 48

>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 = 86.3 bits (214), Expect = 2e-20
 Identities = 24/101 (23%), Positives = 43/101 (42%), Gaps = 4/101 (3%)

Query: 93  SETPQSDPT---LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEIL 149
           S++P  DP     +     S  +   +  ++ +AK+IPGF DLS +DQ+ LL++   E+L
Sbjct: 7   SKSPYVDPHKSGHEIWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVL 66

Query: 150 TLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQV 190
            +  A          + F S            G  ++   +
Sbjct: 67  MVRFASLFDAK-ERTVTFLSGKKYSVDDLHSMGAGDLLNSM 106

>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 = 82.8 bits (205), Expect = 3e-20
 Identities = 21/49 (42%), Positives = 31/49 (63%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGR 49
          ++ Y C  + +C I+KR+R  CQ CR+QKCL  GM +E V+ +R    R
Sbjct: 44 DLTYACRENRNCIIDKRQRNRCQYCRYQKCLTCGMKREAVQEERQGIHR 92

>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 = 71.6 bits (176), Expect = 4e-16
 Identities = 25/47 (53%), Positives = 30/47 (63%), Gaps = 2/47 (4%)

Query: 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY--RQTGAC 249
            + LC +CGD ASG HYGV SCE CK FFKRT++    Y  R+   C
Sbjct: 9   SKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYACRENRNC 55

>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 = 86.9 bits (215), Expect = 3e-20
 Identities = 26/118 (22%), Positives = 49/118 (41%), Gaps = 6/118 (5%)

Query: 67  KSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQI 126
           +S P +E    +E  LL +   +T +   P   P    ++ + +   R L   + WA+ I
Sbjct: 3   QSTPIIE----VEGPLLSDTH-VTFKLTMPSPMPEYLNVHYICESASRLLFLSMHWARSI 57

Query: 127 PGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFS 184
           P F  L  +    L+++ W E+ TL +A  +          A+ +   +   +E   S
Sbjct: 58  PAFQALGQDCNTSLVRACWNELFTLGLAQCAQVMS-LSTILAAIVNHLQNSIQEDKLS 114

>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 = 82.0 bits (203), Expect = 4e-20
 Identities = 24/47 (51%), Positives = 33/47 (70%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG 47
          ++ YTC  + DC I+KR+R  CQ CR+QKCL  GM +E V+ +R RG
Sbjct: 39 DLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRG 85

>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 = 72.7 bits (179), Expect = 1e-16
 Identities = 23/48 (47%), Positives = 29/48 (60%), Gaps = 2/48 (4%)

Query: 204 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY--RQTGAC 249
             + +C +CGD +SG HYGV SCE CK FFKRT++    Y  R    C
Sbjct: 3   FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDC 50

>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 = 81.6 bits (202), Expect = 5e-20
 Identities = 24/49 (48%), Positives = 28/49 (57%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGR 49
          N+ YTC    +C INK  R  CQ CR QKC   GM KE VR DR +  +
Sbjct: 38 NMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNKKKK 86

>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 = 71.2 bits (175), Expect = 4e-16
 Identities = 21/47 (44%), Positives = 29/47 (61%), Gaps = 2/47 (4%)

Query: 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY--RQTGAC 249
             + C VC D +SG+HYGV++CE CK FF+R+IQ    Y   +   C
Sbjct: 3   IYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNC 49

>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 = 81.1 bits (200), Expect = 2e-19
 Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 3/78 (3%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYR---RNPD 57
           +  Y C     CE++   R+ CQ CR +KCL  GM  E V  +     +++ +   +  D
Sbjct: 42  SAVYCCKFGRACEMDMYMRRKCQECRLKKCLAVGMRPECVVPENQCAMKRREKKAQKEKD 101

Query: 58  LLSQQWPPNKSIPSLEEN 75
            ++         P +  +
Sbjct: 102 KMTTSPSSQHGSPGIHRD 119

>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 = 69.2 bits (169), Expect = 6e-15
 Identities = 22/45 (48%), Positives = 29/45 (64%), Gaps = 2/45 (4%)

Query: 207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY--RQTGAC 249
            LCLVCGD ASG+HY   +CE CK FF+R++   + Y  +   AC
Sbjct: 9   ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRAC 53

>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 = 83.5 bits (207), Expect = 4e-19
 Identities = 20/113 (17%), Positives = 43/113 (38%), Gaps = 5/113 (4%)

Query: 75  NKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSL 134
           + ++++                +     +    L+++    +  ++ + K++PGF  L  
Sbjct: 14  HFIMDSYNKQRMPQEITNKILKEEFSAEENFLILTEMATNHVQVLVEFTKKLPGFQTLDH 73

Query: 135 NDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIY 187
            DQ+ LL+ +  E + L  A         K   +    L E + R  G S+ Y
Sbjct: 74  EDQIALLKGSAVEAMFLRSAEIF-----NKKLPSGHSDLLEERIRNSGISDEY 121

>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 = 83.7 bits (206), Expect = 5e-19
 Identities = 45/287 (15%), Positives = 90/287 (31%), Gaps = 49/287 (17%)

Query: 50  QKYRRNPDLLSQQWPPNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLS 109
           ++  +   + S         P+  + +         P +        Q   TL+    + 
Sbjct: 2   EEQPQQISVASGTPVSADQTPATPQEQPRAPWWDASPGV--------QRLITLKDPQVVC 53

Query: 110 DLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFAS 169
           +     L+  + + K +P F  L L+ Q+ L++S WA +L L +A   L     +I   +
Sbjct: 54  EAASAGLLKTLRFVKYLPCFQILPLDQQLVLVRSCWAPLLMLELAQDHLHFEMMEIPETN 113

Query: 170 DLVLDERQARECGFSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEAC 229
                    R+        + + +     +  E               G     A+ +A 
Sbjct: 114 TTQEMLTTRRQETEGPEPAEPQATEQPQMVSAEA--------------GHLLPAAAVQAI 159

Query: 230 KAFFKRTIQVYSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL--- 285
           K+FF +   +    ++       VL N D+  L     ++  +      L + I ++   
Sbjct: 160 KSFFFKCWSLNIDTKEYAYLKGTVLFNPDLPGLQCVKYIEGLQWRTQQILTEHIRMMQRE 219

Query: 286 ---RFWS--------------------TVHKDGKVLMNKLFVEMLEA 309
              R                            G V M+ + +EML A
Sbjct: 220 YQIRSAELNSALFLLRFINSDVVTELFFRPIIGAVSMDDMMLEMLCA 266

>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 = 83.0 bits (205), Expect = 1e-18
 Identities = 47/247 (19%), Positives = 86/247 (34%), Gaps = 25/247 (10%)

Query: 70  PSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGF 129
           P+  + +     +  +                L  +  L+DL    +  +IG+AK IPGF
Sbjct: 30  PTYADFRDFRPPVRMDGST----GSVTLDLSPLSMLPHLADLVSYSIQKVIGFAKMIPGF 85

Query: 130 TDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSE---- 185
            DL+ +DQ+ LL+S+  E++ L                + D   D     + G +     
Sbjct: 86  RDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMSWDCGSQDYKYDVTDVSKAGHTLELIE 145

Query: 186 -IYQQVKHSGSLDGIKEEE--LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSG 242
            + +       L  + EEE  L   +C+V  D            EA +     T+Q Y  
Sbjct: 146 PLIKFQVGLKKL-NLHEEEHVLLMAICIVSPDRPG--VQDAKLVEAIQDRLSNTLQTYIR 202

Query: 243 YRQTGACGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLRFWSTVHKDGKVLMNKL 302
            R        + A    K+     ++K   + L SL +         +   +  + +  L
Sbjct: 203 CRHPPPGSHQLYA----KM-----IQKL--ADLRSLNEEHSKQYRSLSFQPENSMKLTPL 251

Query: 303 FVEMLEA 309
            +E+   
Sbjct: 252 VLEVFGN 258

>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 = 75.5 bits (186), Expect = 2e-17
 Identities = 23/54 (42%), Positives = 32/54 (59%), Gaps = 2/54 (3%)

Query: 1  NIEYT-CPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYR 53
          NI+Y  C  + +C I +  R  CQ CRF+KCL  GM ++ VR  R+   R+K R
Sbjct: 41 NIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGRIP-KREKQR 93

>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 = 74.3 bits (183), Expect = 4e-17
 Identities = 26/48 (54%), Positives = 30/48 (62%), Gaps = 3/48 (6%)

Query: 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ---VYSGYRQTGAC 249
              LC VCGDVASGFHYGV +CE CK FF+R+IQ    Y    +   C
Sbjct: 6   MVLLCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNENC 53

>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 = 78.9 bits (195), Expect = 2e-17
 Identities = 19/91 (20%), Positives = 32/91 (35%), Gaps = 1/91 (1%)

Query: 96  PQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAY 155
           P   P L  +   +D+    ++ +I + K +P F  L + DQ+ LL+    EI  + +  
Sbjct: 47  PTLAPVLPLVTHFADINTFMVLQVIKFTKDLPVFRSLPIEDQISLLKGAAVEICHIVLNT 106

Query: 156 RSLPHCAGKIRFASDLVLDERQARECGFSEI 186
                              E  AR     E 
Sbjct: 107 TFCLQ-TQNFLCGPLRYTIEDGARVGFQVEF 136

>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 = 74.8 bits (184), Expect = 3e-17
 Identities = 19/49 (38%), Positives = 26/49 (53%)

Query: 3  EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQK 51
           Y+C     C I+K  R  CQ CRF+KC+  GM  + V  D  R  ++K
Sbjct: 39 SYSCKYEGKCVIDKVTRNQCQECRFKKCIYVGMATDLVLDDSKRLAKRK 87

>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 = 66.7 bits (163), Expect = 3e-14
 Identities = 20/31 (64%), Positives = 25/31 (80%)

Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
           LC+VCGD A+G+HY   +CE CK FF+RTIQ
Sbjct: 3   LCVVCGDKATGYHYRCITCEGCKGFFRRTIQ 33

>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 = 72.7 bits (179), Expect = 1e-16
 Identities = 19/45 (42%), Positives = 28/45 (62%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV 45
          N+ YTC A+ +C I++  R  CQ CR +KCL+ GM +E V+    
Sbjct: 41 NLTYTCRANRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQRGSG 85

>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 = 68.1 bits (167), Expect = 7e-15
 Identities = 21/47 (44%), Positives = 28/47 (59%), Gaps = 2/47 (4%)

Query: 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY--RQTGAC 249
               C+VCGD +SG HYG  +CE CK+FFKR+++    Y  R    C
Sbjct: 6   SGIECVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRANRNC 52

>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 = 75.7 bits (186), Expect = 3e-16
 Identities = 18/110 (16%), Positives = 37/110 (33%), Gaps = 2/110 (1%)

Query: 83  LCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQ 142
           L          +  QS          +      +  ++ +AK+I GF +L  NDQ+ LL+
Sbjct: 30  LAWQTHTYEEIKAYQSKSREALWQQCAIQITHAIQYVVEFAKRITGFMELCQNDQILLLK 89

Query: 143 STWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKH 192
           S   E++ + +     P                +  +  G  ++  +   
Sbjct: 90  SGCLEVVLVRMCRAFNPL--NNTVLFEGKYGGMQMFKALGSDDLVNEAFD 137

>3cbb_A HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DNA binding domain, nuclear; zinc finger; 2.00A {Homo sapiens} Length = 78

 Score = 71.2 bits (175), Expect = 3e-16
 Identities = 19/44 (43%), Positives = 27/44 (61%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
          N  Y+C  S  C ++K +R  C+ CR +KC R GM KE V+ +R
Sbjct: 34 NHMYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNER 77

>3cbb_A HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DNA binding domain, nuclear; zinc finger; 2.00A {Homo sapiens} Length = 78

 Score = 67.3 bits (165), Expect = 9e-15
 Identities = 20/44 (45%), Positives = 29/44 (65%), Gaps = 2/44 (4%)

Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY--RQTGAC 249
           LC +CGD A+G HYG +SC+ CK FF+R+++    Y  R +  C
Sbjct: 2   LCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQC 45

>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 = 74.9 bits (184), Expect = 7e-16
 Identities = 17/108 (15%), Positives = 36/108 (33%), Gaps = 2/108 (1%)

Query: 83  LCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQ 142
           +     L    E  Q+          +      +  ++ +AK+I GF +L  NDQ+ LL+
Sbjct: 45  ITWQTFLQEEIENYQNKQREVMWQLCAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLLK 104

Query: 143 STWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQV 190
           +   E++ + +             +           +  G  +    V
Sbjct: 105 AGSLEVVFIRMCRAFDSQ--NNTVYFDGKYASPDVFKSLGCEDFISFV 150

>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 = 71.9 bits (176), Expect = 8e-15
 Identities = 21/118 (17%), Positives = 44/118 (37%), Gaps = 3/118 (2%)

Query: 74  ENKMLEALLLCEPEMLTVRSETPQSDPTLQTI-NSLSDLYDRELVCIIGWAKQIPGFTDL 132
               LE LL     + +    T     ++  +    +      +  ++ +AK++ GF +L
Sbjct: 26  CQLRLEDLLRQRSNIFSREEVTGYQRKSMWEMWERCAHHLTEAIQYVVEFAKRLSGFMEL 85

Query: 133 SLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQV 190
             NDQ+ LL++   E++ + +          +  F           R  G SE+   +
Sbjct: 86  CQNDQIVLLKAGAMEVVLVRMCRAYNAD--NRTVFFEGKYGGMELFRALGCSELISSI 141

>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 = 71.4 bits (175), Expect = 1e-14
 Identities = 24/95 (25%), Positives = 36/95 (37%)

Query: 93  SETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLT 152
                    L  +  L+DL    +  +IG+AK IPGF DL+  DQ+ LL+S+  E++ L 
Sbjct: 46  GSVTLELSQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLR 105

Query: 153 IAYRSLPHCAGKIRFASDLVLDERQARECGFSEIY 187
                            D         + G S   
Sbjct: 106 SNESFTMDDMSWTCGNQDYKYRVSDVTKAGHSLEL 140

>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 = 71.3 bits (175), Expect = 1e-14
 Identities = 21/127 (16%), Positives = 46/127 (36%), Gaps = 9/127 (7%)

Query: 70  PSLEENKMLEALLLCEPEMLTVR---SETPQSDPTLQTINSLSDLYDRELVCIIGWAKQI 126
            S      + +L++ E ++        +    +  ++            +  I  +AK I
Sbjct: 37  KSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSI 96

Query: 127 PGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASD---LVLDERQARECGF 183
           PGF +L LNDQ+ LL+    EI+   +A          +  +     +  +  ++    F
Sbjct: 97  PGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDG---VLISEGQGFMTREFLKSLRKPF 153

Query: 184 SEIYQQV 190
            +  +  
Sbjct: 154 GDFMEPK 160

>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 = 69.5 bits (170), Expect = 1e-13
 Identities = 25/153 (16%), Positives = 45/153 (29%), Gaps = 5/153 (3%)

Query: 41  RLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDP 100
           RL  V     +   +    S++     S    +   +  +L L   +      + P    
Sbjct: 55  RLPGVLSSGCELPESLQAPSREEAAKWSQVRKDLCSLKVSLQLRGEDGSVWNYKPPADSG 114

Query: 101 TLQTINSLSDLYD---RELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRS 157
             +  + L  + D        II +AK I  F DL + DQ+ LL+    E+  L      
Sbjct: 115 GKEIFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVF 174

Query: 158 LPHCAGKIRFASDLVLDERQARECGFSEIYQQV 190
                        L              + + +
Sbjct: 175 NAE--TGTWECGRLSYCLEDTAGGFQQLLLEPM 205

>2p54_A PPAR-alpha, peroxisome proliferator-activated receptor alpha; PPAR alpha GW735 SRC1 agonist HDLC, transcription; HET: 735; 1.79A {Homo sapiens} SCOP: a.123.1.1 PDB: 3fei_A* 1i7g_A* 3kdu_A* 3kdt_A* 2rew_A* 1kkq_A* 3g8i_A* 3et1_A* 2znn_A* 3sp6_A* 1k7l_A* 2npa_A* 2xyj_A* 2xyw_A* 2xyx_A* 2q5g_A* 3gwx_A* 3dy6_A* 1gwx_A* 3peq_A* ... Length = 267

 Score = 66.5 bits (162), Expect = 7e-13
 Identities = 23/128 (17%), Positives = 48/128 (37%), Gaps = 6/128 (4%)

Query: 64  PPNKSIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWA 123
            P   I  +E   M E  L+ +       +     +  ++  +         +  +  +A
Sbjct: 35  NPPFVIHDMETLCMAEKTLVAKLVA----NGIQNKEAEVRIFHCCQCTSVETVTELTEFA 90

Query: 124 KQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDER-QARECG 182
           K IPGF +L LNDQ+ LL+    E +   ++          + + +  +  E  ++    
Sbjct: 91  KAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKD-GMLVAYGNGFITREFLKSLRKP 149

Query: 183 FSEIYQQV 190
           F +I +  
Sbjct: 150 FCDIMEPK 157

>3up3_A Acedaf-12; ligand binding domain, nematode, steroid binding protein- transcription complex; HET: XCA; 1.25A {Ancylostoma ceylanicum} PDB: 3up0_A* Length = 243

 Score = 61.4 bits (149), Expect = 3e-11
 Identities = 17/90 (18%), Positives = 36/90 (40%), Gaps = 3/90 (3%)

Query: 73  EENKMLEALLLCEPEM---LTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGF 129
            E + L+ +      M   +    +        ++   + ++ D  +   +  AK++P F
Sbjct: 8   AELQALDLIQEAFKGMNDPMEQGRQATSFLKNEKSPADIMNIMDVTMRRFVKMAKRLPAF 67

Query: 130 TDLSLNDQMRLLQSTWAEILTLTIAYRSLP 159
            DLS + +  LL+    E+LT+    R   
Sbjct: 68  NDLSQDGKFALLKGGMIEMLTVRGVRRFDS 97

>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 = 59.2 bits (143), Expect = 2e-10
 Identities = 14/87 (16%), Positives = 35/87 (40%), Gaps = 3/87 (3%)

Query: 73  EENKMLEALLLCEPEMLTVRSETPQSDPTLQ---TINSLSDLYDRELVCIIGWAKQIPGF 129
           ++ K L+++      M        Q+    +       + ++ D  +  ++  AK++  F
Sbjct: 8   KDLKELDSIRDSFQCMNEPLDNDQQASTLAKKEHNPTDILNVMDITMRRLVKMAKRLGAF 67

Query: 130 TDLSLNDQMRLLQSTWAEILTLTIAYR 156
            ++S   +  LL+    E+LT+     
Sbjct: 68  NEISEAGKFSLLKGGMIEMLTIRGVTV 94

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	312
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	100.0
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	100.0
1lbd_A	282	RXR_LBD, retinoid X receptor; transcription factor	100.0
3ltx_A	243	Estrogen receptor; constitutive, nuclear receptor,	99.97
1xdk_B	303	RAR-beta, retinoic acid receptor, beta; nuclear re	99.97
3k6p_A	248	Steroid hormone receptor ERR1; estrogen related re	99.97
2e2r_A	244	Estrogen-related receptor gamma; ERR gamma, BPA, n	99.97
1ovl_A	271	Orphan nuclear receptor NURR1 (MSe 414, 496, 511);	99.97
3oll_A	240	Estrogen receptor beta; steroid binding, phosphory	99.97
2ocf_A	298	Estrogen receptor; estrogen receptor, LBD, monobod	99.96
1xpc_A	248	Estrogen receptor; nuclear receptor, transcription	99.96
1g2n_A	264	Ultraspiracle protein; antiparallel alpha-helical	99.96
3v3e_B	257	Nuclear receptor subfamily 4 group A member 1; orp	99.96
1fcy_A	236	RAR-gamma-1, retinoic acid receptor gamma-1; isoty	99.96
3plz_A	257	FTZ-F1 related protein; alpha helical sandwhich, f	99.96
2nxx_A	235	Ultraspiracle (USP, NR2B4); hormone receptor, APO	99.96
1yye_A	268	ER-beta, estrogen receptor beta; ER-beta, nuclear	99.96
3kmr_A	266	Retinoic acid receptor alpha; nuclear receptor tra	99.96
1l2j_A	271	Estrogen receptor beta; nuclear receptor, transcri	99.96
2iz2_A	243	FTZ-F1 alpha, nuclear hormone receptor FTZ-F1; nuc	99.96
1pdu_A	244	DHR38, nuclear hormone receptor HR38; nuclear rece	99.95
2p1t_A	240	Retinoic acid receptor RXR-alpha; protein-ligand c	99.95
3ilz_A	267	Thyroid hormone receptor, alpha isoform 1 variant;	99.95
3vhv_A	260	Mineralocorticoid receptor; nuclear receptor, tran	99.95
1ymt_A	246	Steroidogenic factor 1; SF-1, ligand-binding domai	99.95
1hg4_A	279	Ultraspiracle; nuclear hormone receptor, transcrip	99.95
3mnp_A	261	Glucocorticoid receptor; protein-ligand complex, s	99.95
3cjw_A	244	COUP transcription factor 2; COUP-TFII, nuclear re	99.95
3f5c_B	268	Nuclear receptor subfamily 0 group B member 1; tra	99.95
3p0u_A	249	Nuclear receptor subfamily 2 group C member 2; lig	99.95
1sqn_A	261	PR, progesterone receptor; nuclear receptor, stero	99.95
3tx7_B	352	Nuclear receptor subfamily 5 group A member 2; LRH	99.94
1t7r_A	269	Androgen receptor; nuclear receptor, transcription	99.94
3vhu_A	294	Mineralocorticoid receptor; nuclear receptor, tran	99.94
3ipq_A	283	Oxysterols receptor LXR-alpha; LXR homodimer, LXR	99.94
3b0t_A	254	Vitamin D3 receptor; nuclear receptor, transcripti	99.94
2r40_D	266	Ecdysone receptor, 20-hydroxy-ecdysone receptor; n	99.94
1nq7_A	244	Nuclear receptor ROR-beta; ligand-binding domain,	99.94
1xvp_B	246	Orphan nuclear receptor NR1I3; CAR, RXR, citco, SR	99.94
1n83_A	270	Nuclear receptor ROR-alpha; three-layered alpha he	99.94
3l0l_A	248	Nuclear receptor ROR-gamma; nuclear receptor, rorg	99.93
2nxx_E	248	Ecdysone receptor (ECR, NRH1); hormone receptor, A	99.93
2o4j_A	292	Vitamin D3 receptor; nuclear receptor-ligand compl	99.93
1osh_A	232	BIle acid receptor; nuclear receptor, ligand bindi	99.93
1z5x_E	310	Ecdysone receptor ligand binding domain; ponastero	99.93
3vi8_A	273	Peroxisome proliferator-activated receptor alpha;	99.93
1nrl_A	316	Orphan nuclear receptor PXR; PXR, xenobiotic, SRC-	99.93
2hc4_A	302	Vitamin D receptor; alpha helical sandwich, gene r	99.93
1pzl_A	237	Hepatocyte nuclear factor 4-alpha; transcription;	99.92
3u9q_A	269	Peroxisome proliferator-activated receptor gamma;	99.92
3cqv_A	199	Nuclear receptor subfamily 1 group D member 2; rev	99.91
3up3_A	243	Acedaf-12; ligand binding domain, nematode, steroi	99.9
3n00_A	245	REV-ERBA-alpha; reverba ncorid1, anti-parallel B-s	99.89
3gyt_A	244	Nuclear hormone receptor of the steroid/thyroid ho	99.87
1lo1_A	98	Steroid hormone receptor ERR2; estrogen related re	99.62
3cbb_A	78	HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DN	99.6
1cit_A	89	NGFI-B, protein (orphan nuclear receptor NGFI-B);	99.6
1ynw_B	99	Retinoic acid receptor RXR-alpha, retinoid X recep	99.6
1dsz_B	85	RXR-alpha, retinoic acid receptor RXR-alpha; RAR,	99.6
2ebl_A	89	COUP transcription factor 1; DNA-binding, metal-bi	99.59
2han_A	93	Protein ultraspiracle; transcription regulation, t	99.59
1dsz_A	86	RAR-alpha, retinoic acid receptor alpha; RAR, nucl	99.58
2a66_A	113	Orphan nuclear receptor NR5A2; protein-DNA complex	99.56
1hcq_A	84	Protein (estrogen receptor); protein-DNA complex,	99.54
1a6y_A	94	Orphan nuclear receptor NR1D1; orphan receptor, DN	99.53
4hn5_A	117	Glucocorticoid receptor; glucocorticoid receptor,	99.51
3g9m_A	90	Glucocorticoid receptor; glucocorticoid, DNA-bindi	99.51
1kb2_A	110	Vitamin D3 receptor; VDR, nuclear receptor, protei	99.5
2han_B	119	Ecdysone receptor; transcription regulation, trans	99.48
2lze_A	87	A primordial catalytic fold generated by in vitro	99.48
1r4i_A	105	Androgen receptor; AR, steroid receptor, protein-D	99.45
2nll_B	103	Protein (thyroid hormone receptor); complex (trans	99.45
1dsz_A	86	RAR-alpha, retinoic acid receptor alpha; RAR, nucl	98.91
1ynw_B	99	Retinoic acid receptor RXR-alpha, retinoid X recep	98.89
1dsz_B	85	RXR-alpha, retinoic acid receptor RXR-alpha; RAR,	98.89
3cbb_A	78	HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DN	98.89
1hcq_A	84	Protein (estrogen receptor); protein-DNA complex,	98.88
1cit_A	89	NGFI-B, protein (orphan nuclear receptor NGFI-B);	98.87
2ebl_A	89	COUP transcription factor 1; DNA-binding, metal-bi	98.87
2han_A	93	Protein ultraspiracle; transcription regulation, t	98.87
3g9m_A	90	Glucocorticoid receptor; glucocorticoid, DNA-bindi	98.86
1lo1_A	98	Steroid hormone receptor ERR2; estrogen related re	98.86
1kb2_A	110	Vitamin D3 receptor; VDR, nuclear receptor, protei	98.84
2nll_B	103	Protein (thyroid hormone receptor); complex (trans	98.82
1r4i_A	105	Androgen receptor; AR, steroid receptor, protein-D	98.81
2a66_A	113	Orphan nuclear receptor NR5A2; protein-DNA complex	98.81
2han_B	119	Ecdysone receptor; transcription regulation, trans	98.81
1a6y_A	94	Orphan nuclear receptor NR1D1; orphan receptor, DN	98.79
4hn5_A	117	Glucocorticoid receptor; glucocorticoid receptor,	98.76
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	98.48
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	98.44

>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=4e-44  Score=337.49  Aligned_cols=260  Identities=29%  Similarity=0.494  Sum_probs=193.5

Q ss_pred             CceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccccccccccCCCCCccCCCCCCCCCCchhHHHHHHH
Q psy11505          1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEENKMLEA   80 (312)
Q Consensus         1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~   80 (312)
                      ++.|+|+++++|.|++..|++||+|||+||++|||++++||.+|++..++....   ....    ...........+++.
T Consensus       171 ~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~~k~r~~~~---~~~~----~~~~~~~~~~~ll~a  243 (467)
T 3dzy_A          171 DLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRGKDRNENE---VEST----SSANEDMPVERILEA  243 (467)
T ss_dssp             TCCCCCSSSSCCCCCSSSSSSCHHHHHHHHHHTTCCGGGCCCCSCCCCCCSCSS---CTTS----TTCSCSSCHHHHHHH
T ss_pred             CCceeCCCCCCCCCCcccccccccchhhhhhhccccchhhhccccccccccccc---cccc----cccCCCCchhhhhhh
Confidence            457999999999999999999999999999999999999999997654322110   1000    001111223445544


Q ss_pred             HHhcCcccccccCC--CCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcc
Q psy11505         81 LLLCEPEMLTVRSE--TPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSL  158 (312)
Q Consensus        81 l~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~  158 (312)
                      ....++........  ..........+..+.++++++++.+|+|||+||+|.+|+.+||++|||++|++++++..|++++
T Consensus       244 ~~~~e~~~~~~~~~~~~~~~~~~~~~~~~l~e~a~~~L~~vVeWAK~iP~F~~L~~~DQi~LLK~~w~elliL~~a~rs~  323 (467)
T 3dzy_A          244 ELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSI  323 (467)
T ss_dssp             HHC----------------------CCTTHHHHHHHHHHHHHHHHHHSTTSTTSCHHHHHHHHHHHHHHHHHHHHHHHTS
T ss_pred             hhhhcccchhhhhhcccCCCCcccchHHHHHHHHHHHHHHHHHHHHhCcchhcCCHHHHHHHHHhHHHHHHHHHHHHHhc
Confidence            44333322111100  0001111223456788899999999999999999999999999999999999999999999998


Q ss_pred             cCCCCeeEecccchhhHHhhhhcccchhhhhh----cccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHH
Q psy11505        159 PHCAGKIRFASDLVLDERQARECGFSEIYQQV----KHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFK  234 (312)
Q Consensus       159 ~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~i----~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~  234 (312)
                      ...+ .+++++|..+.++.....+..++++++    ...+.+|++|++||                              
T Consensus       324 ~~~~-~~ll~~g~~i~~~~~~~~~~~~~~~~il~~lv~~l~~L~ld~~E~------------------------------  372 (467)
T 3dzy_A          324 AVKD-GILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTEL------------------------------  372 (467)
T ss_dssp             SSTT-BCCCSSSCCCBTHHHHTTTCHHHHHHHHHHTHHHHHHHTCCHHHH------------------------------
T ss_pred             cCCC-ceEecCCceechhhhhhhcchHHHHHHHHHHHHHHHHhcCCHHHH------------------------------
Confidence            8766 678899988887776666665555544    44555999999999                              


Q ss_pred             HHhhhcccceecCCCCceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------------------------hh
Q psy11505        235 RTIQVYSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------------------------RF  287 (312)
Q Consensus       235 ~~~~~~~~~~~~~~~~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------------------------~~  287 (312)
                                  ++|+||+|||||++ |++.++|+++|++++.+|.+|+..+                          +.
T Consensus       373 ------------~lLkAIvLfnpd~~gL~~~~~Ve~lQe~~~~aL~~Y~~~~~p~~p~Rf~kLLl~Lp~LRsi~~~~~E~  440 (467)
T 3dzy_A          373 ------------GCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEH  440 (467)
T ss_dssp             ------------HHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTHHHHHHHHHHHHHHT
T ss_pred             ------------HHHHHHHHhCcCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                        99999999999998 9999999999999999999999765                          33


Q ss_pred             hhccccCCccchhHHHHHHHhhh
Q psy11505        288 WSTVHKDGKVLMNKLFVEMLEAY  310 (312)
Q Consensus       288 ~~~~~~~~~~~~~~~~~~~~~~~  310 (312)
                      +++++++|.+||++||.|||+|-
T Consensus       441 l~~~kl~g~v~i~~Ll~EMl~a~  463 (467)
T 3dzy_A          441 LFFFKLIGDTPIDTFLMEMLEAP  463 (467)
T ss_dssp             TTTTSTTSCCCCCSHHHHCC---
T ss_pred             HHHhhccCCccHHHHHHHHHcCC
Confidence            67789999999999999999974

>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-38  Score=293.95  Aligned_cols=258  Identities=19%  Similarity=0.307  Sum_probs=171.4

Q ss_pred             ceeE-cCCCCCcccccccccccccCchhHHHHhccccccccccccccccccccCCCCCccCCCCCCCCCCchhHHHHHHH
Q psy11505          2 IEYT-CPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEENKMLEA   80 (312)
Q Consensus         2 ~~Y~-C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~   80 (312)
                      ..|. |.  ++|.|++..|++||+|||+||++|||++++||.+|++...+...... ..+....+. + .......++..
T Consensus        85 ~~~~~c~--~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~vq~~R~~~~~k~~~~~~-~~~~~~~~~-p-~~~~~~~l~~~  159 (419)
T 3dzy_D           85 LIYDRCD--LNCRIHKKSRNKCQYCRFQKCLAVGMSHNAIRFGRMPQAEKEKLLAE-ISSDIDQLN-P-ESADLRALAKH  159 (419)
T ss_dssp             CCCCCCC--SCCCCCTTGGGTCHHHHHHHHHHTTCCGGGCCCSCCTTTTGGGSTTT-TTSTTTTSC-S-TTHHHHHHHHH
T ss_pred             ccccccc--CCCCcccccCccchhhhHHHHhhcccchhheeccccccccccccccc-ccccccCCC-C-chhhHHHHHHH
Confidence            4574 64  68999999999999999999999999999999999875543221111 110000000 0 01111111111


Q ss_pred             H----HhcCccc-----------------c---------cccC-----CCC-----CCCchhHHHhhHHHHHHHHHHHHH
Q psy11505         81 L----LLCEPEM-----------------L---------TVRS-----ETP-----QSDPTLQTINSLSDLYDRELVCII  120 (312)
Q Consensus        81 l----~~~~~~~-----------------~---------~~~~-----~~~-----~~~~~~~~~~~~~~~~~~~l~~~i  120 (312)
                      +    ....+..                 .         ....     ..+     ........+..........+..+|
T Consensus       160 ~~~a~~~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~l~~ae~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~l~~~V  239 (419)
T 3dzy_D          160 LYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEIT  239 (419)
T ss_dssp             HHHHHHTTCSSCHHHHHHHHHCCSSSCCCEEECSHHHHHCCC----------------CHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhhhccCCccchhccccccCCCCCCCCcccccchhhhhcccccccccCCCcccccchhhhHHHHHHHHHHHHHHHHHH
Confidence            1    1100000                 0         0000     000     000011122223333445677899


Q ss_pred             HHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccc-hhhHHhhhh--cccchhhhhhcccC---
Q psy11505        121 GWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDL-VLDERQARE--CGFSEIYQQVKHSG---  194 (312)
Q Consensus       121 ewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~-~~~~~~~~~--~~~~~~~~~i~~~~---  194 (312)
                      +|||++|+|.+|+.+||++|||++|+++++|+.|....+   +.+++.+|. ++.++....  .++.++++.++.+.   
T Consensus       240 ewAK~iP~F~~L~~~DQi~LLk~~w~Ell~L~~a~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~f~~~l  316 (419)
T 3dzy_D          240 EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNK---DGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKF  316 (419)
T ss_dssp             HHHTTSTTTTTSCHHHHHHHHHHHHHHHHHHHHGGGBCS---SEEEEGGGTEEEEHHHHHSSSGGGSGGGHHHHHHHHHH
T ss_pred             HHhccCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcC---CCceeecCcccccHHHHHhhhhhHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999855443   256665554 344443322  34556666555554   


Q ss_pred             ccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCCCCc-ccchHHHHHHHHH
Q psy11505        195 SLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNS  273 (312)
Q Consensus       195 ~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-l~~~~~~~~~~~~  273 (312)
                      .+|++|++||                                          ++++||+||+||++ |+++++|+++|++
T Consensus       317 ~~L~ld~~E~------------------------------------------alLkAivLf~pD~~gL~~~~~Ve~lQe~  354 (419)
T 3dzy_D          317 NALELDDSDL------------------------------------------AIFIAVIILSGDRPGLLNVKPIEDIQDN  354 (419)
T ss_dssp             HHTCCCHHHH------------------------------------------HHHHHHHHSCTTSTTCSCHHHHHHHHHH
T ss_pred             HHhCCCHHHH------------------------------------------HHHHHHHHhCCCCCCCCCHHHHHHHHHH
Confidence            4999999999                                          99999999999998 9999999999999


Q ss_pred             HHHHhHhHHHHH------hh--------------------h-hccccCCccchhHHHHHHHhh
Q psy11505        274 ILSSLGDCIYVL------RF--------------------W-STVHKDGKVLMNKLFVEMLEA  309 (312)
Q Consensus       274 ~~~~l~~~~~~~------~~--------------------~-~~~~~~~~~~~~~~~~~~~~~  309 (312)
                      ++.+|.+|+..+      ||                    + .+++..|.++|++||.|||+.
T Consensus       355 ~~~aL~~yi~~~~p~~~~rf~kLLl~Lp~LR~i~~~~~~~l~~~k~~~~~~~l~~Ll~Em~~d  417 (419)
T 3dzy_D          355 LLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKD  417 (419)
T ss_dssp             HHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCCCCCHHHHHHHTT
T ss_pred             HHHHHHHHHHHhCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCccHHHHHHHHh
Confidence            999999999876      22                    2 234567899999999999975

>1lbd_A RXR_LBD, retinoid X receptor; transcription factor, nuclear receptor, structural proteomic europe, spine, structural genomics; 2.70A {Homo sapiens} SCOP: a.123.1.1 PDB: 1z5x_U* 2q60_A

Probab=100.00  E-value=7.6e-37  Score=271.72  Aligned_cols=233  Identities=25%  Similarity=0.382  Sum_probs=161.0

Q ss_pred             hHHHHhccccccccccccccccccccCCCCCccCCCCCCCCCCchhHHHHHHHHHhcCccccccc--CCCCCCCchhHHH
Q psy11505         28 QKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEENKMLEALLLCEPEMLTVR--SETPQSDPTLQTI  105 (312)
Q Consensus        28 ~KCl~vGM~~eaVq~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~~--~~~~~~~~~~~~~  105 (312)
                      -||++|||++||||.+|.+.+++....   ..+    +.+.....+.+.+++.+...++......  .....+.+....+
T Consensus        13 ~kCl~vGMkkeaVq~~R~~~~~~~~~~---~~~----~~~~~~~~~~~~i~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~   85 (282)
T 1lbd_A           13 GLVPRGSHKREAVQEERQRGKDRNENE---VES----TSSANEDMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPV   85 (282)
T ss_dssp             ---------------------------------------CCTTTSCHHHHHHHHHTTCCCHHHHHHHTTCCCSSCTTCHH
T ss_pred             CCcCccCCcHHhhcCCCCCCCCCCCCC---CCC----CCCCCCCCCHHHHHHHHHhcCCccccccccccccCCCccccHH
Confidence            489999999999999998766532110   010    0111112235677888877776542111  1112222344578


Q ss_pred             hhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhhcccch
Q psy11505        106 NSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSE  185 (312)
Q Consensus       106 ~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~~~~~~  185 (312)
                      .++++++.+.+..+|+|||++|+|.+|+.+||++|||++|++++++..||++++..+ .+++++|..+.++.....+..+
T Consensus        86 ~~~~~~a~~~l~~~vewaK~ip~F~~L~~~DQ~~LLk~~~~el~il~~a~rs~~~~~-~~~~~~g~~~~~~~~~~~~~~~  164 (282)
T 1lbd_A           86 TNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKD-GILLATGLHVHRNSAHSAGVGA  164 (282)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHGGGGSSS-EEECTTSCEEEHHHHHHTTTHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhCcChhcCCHHHHHHHHHHHHHHHHHHHHHHhcccCCC-ceEecCCcccccchhhhcccHH
Confidence            899999999999999999999999999999999999999999999999999999876 6788999888776665555555


Q ss_pred             hhh----hhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCCCCc-
Q psy11505        186 IYQ----QVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVK-  260 (312)
Q Consensus       186 ~~~----~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-  260 (312)
                      +++    ++...+.+|++|++||                                          ++++||+|||||++ 
T Consensus       165 ~~~~~~~~~~~~l~~L~ld~~E~------------------------------------------~lLkaivL~~pd~~g  202 (282)
T 1lbd_A          165 IFDRVLTELVSKMRDMQMDKTEL------------------------------------------GCLRAIVLFNPDSKG  202 (282)
T ss_dssp             HHHHHHHHHHHHTTTTCCCHHHH------------------------------------------HHHHHHHHSCTTCTT
T ss_pred             HHHHHHHHHHHHHHhhcCCHHHH------------------------------------------HHHHHHHHcCCCCCC
Confidence            554    4556677999999999                                          99999999999998 


Q ss_pred             ccchHHHHHHHHHHHHHhHhHHHHH------hh--------------------hhccccCCccchhHHHHHHHhhh
Q psy11505        261 LDEFSSLKKFRNSILSSLGDCIYVL------RF--------------------WSTVHKDGKVLMNKLFVEMLEAY  310 (312)
Q Consensus       261 l~~~~~~~~~~~~~~~~l~~~~~~~------~~--------------------~~~~~~~~~~~~~~~~~~~~~~~  310 (312)
                      |++..+|+++|++++.+|.+|+..+      ||                    +++.+++|.+|+++||.|||++.
T Consensus       203 Ls~~~~v~~lq~~~~~~L~~y~~~~~~~~~~Rf~~LL~~L~~Lr~~~~~~~e~l~~~~~~~~~~i~~ll~eml~~~  278 (282)
T 1lbd_A          203 LSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEAP  278 (282)
T ss_dssp             CSCHHHHHHHHHHHHHHHHHHHHHHSCCSTTTHHHHHTTHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHTSC
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHcCC
Confidence            9999999999999999999999765      32                    45568899999999999999874

>3ltx_A Estrogen receptor; constitutive, nuclear receptor, DNA-binding, metal-binding, nucleus, transcription, transcription regulation, zinc-finger; 2.60A {Crassostrea gigas}

Probab=99.97  E-value=5.1e-32  Score=235.42  Aligned_cols=195  Identities=33%  Similarity=0.548  Sum_probs=169.2

Q ss_pred             HHHHHHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhh
Q psy11505         74 ENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTI  153 (312)
Q Consensus        74 ~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~  153 (312)
                      ...++..+...++...........+......+..++++..+.+..+|+|||++|+|.+|+.+||+.|||++|+++++|+.
T Consensus         7 ~~~l~~~l~~ae~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~   86 (243)
T 3ltx_A            7 TVTILQALNKAALPVLESHHNHGQPPTKVHLLNSLVKLAERELVHLINWAKNVPGYTDLSLSDQVHLIECCWMELLLLNC   86 (243)
T ss_dssp             HHHHHHHHHTTCCCCCCCCCCTTSCCCHHHHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHhCCcchhccccCCCCccHHHHHHHHHHHHHHHHHHHHHHHHcCcchhcCCHHHHHHHHHHHHHHHHHHHH
Confidence            45678899999887665544444556678899999999999999999999999999999999999999999999999999


Q ss_pred             hhhcccCCCCeeEecccchhhHHhhhhcccchhhhhhcc---cCccCCCCccccCCceeeeeCCCCcccccccccchhHH
Q psy11505        154 AYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKH---SGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACK  230 (312)
Q Consensus       154 a~rs~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~i~~---~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~  230 (312)
                      ||++++.+.+.+++++|..++++.....+..++++.+..   .+.+|++|++||                          
T Consensus        87 a~~s~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~i~~~~~~l~~L~ld~~E~--------------------------  140 (243)
T 3ltx_A           87 AFRSIEHGGKSLAFAPDLVLDRSSWSTVEMTEIFEQVAAVSEQMMQNHLHKDEL--------------------------  140 (243)
T ss_dssp             HHHTTTTTTSEEEEETTEEEEHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHH--------------------------
T ss_pred             HHHhccCCCCeEEecCCcccchhhhcccCHHHHHHHHHHHHHHHHHhCCCHHHH--------------------------
Confidence            999999888789999998887766655666666665544   445999999999                          


Q ss_pred             HHHHHHhhhcccceecCCCCceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH------------------------
Q psy11505        231 AFFKRTIQVYSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL------------------------  285 (312)
Q Consensus       231 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~------------------------  285 (312)
                                      +++|||+|||||++ +++.++|+++|++++.+|.+|+..+                        
T Consensus       141 ----------------~lLkaivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL~~Lp~Lr~l~~~  204 (243)
T 3ltx_A          141 ----------------LLLQAMVLVNAEVRRLASYNQIFNMQQSLLDAIVDTAQKYHPDNVRHVPAVLLLLTHIRQAGER  204 (243)
T ss_dssp             ----------------HHHHHHHHHTSCCSCCTTHHHHHHHHHHHHHHHHHHHHHHSTTCSSHHHHHHHHHHHHHHHHHH
T ss_pred             ----------------HHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHHHHHHHHHHH
Confidence                            99999999999998 9999999999999999999999765                        


Q ss_pred             --hhhhccccCCccchhHHHHHHHhhh
Q psy11505        286 --RFWSTVHKDGKVLMNKLFVEMLEAY  310 (312)
Q Consensus       286 --~~~~~~~~~~~~~~~~~~~~~~~~~  310 (312)
                        +++++.+++|.+|+++||.|||+++
T Consensus       205 ~~e~l~~~~~~g~~~~~~Ll~Eml~~~  231 (243)
T 3ltx_A          205 GIAFFQRLKSEGVVTFCDLLKEMLDAQ  231 (243)
T ss_dssp             HHHHHHHHHHHCSSCCCHHHHHHHHHC
T ss_pred             HHHHHHHHHhcCCCChhHHHHHHHhCc
Confidence              3355678899999999999999975

>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=99.97  E-value=1.1e-31  Score=240.36  Aligned_cols=166  Identities=27%  Similarity=0.365  Sum_probs=147.2

Q ss_pred             hHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhhc
Q psy11505        102 LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC  181 (312)
Q Consensus       102 ~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~~  181 (312)
                      ...+..++++....+..+|+|||++|+|.+|+.+||++|||++|+++++|+.||++++.. +.+++++|..++++.....
T Consensus        70 ~~~~~~~~~~~~~~l~~~VewaK~iP~F~~L~~~DQi~LLk~~~~el~lL~~a~~s~~~~-~~l~~~~g~~~~~~~~~~~  148 (303)
T 1xdk_B           70 LGLWDKFSELATKCIIKIVEFAKRLPGFTGLTIADQITLLKAACLDILILRICTRYTPEQ-DTMTFSDGLTLNRTQMHNA  148 (303)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTSTTTSSSCHHHHHHHHHHHHHHHHHHHHHTTEETTT-TEEECTTCBEEEHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCcccccCCHHHHHHHHHhhHHHHHHHHHHHHhcccC-CeEEecCCceecHHHHhhc
Confidence            457899999999999999999999999999999999999999999999999999999875 4899999988887776666


Q ss_pred             ccchhhhhhccc---CccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCCC
Q psy11505        182 GFSEIYQQVKHS---GSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSD  258 (312)
Q Consensus       182 ~~~~~~~~i~~~---~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  258 (312)
                      +..++++.++.+   +.+|++|++||                                          ++++||+|||||
T Consensus       149 g~~~~~~~i~~~~~~l~~L~ld~~E~------------------------------------------~lLkAivL~~pd  186 (303)
T 1xdk_B          149 GFGPLTDLVFTFANQLLPLEMDDTET------------------------------------------GLLSAICLICGD  186 (303)
T ss_dssp             TTGGGHHHHHHHHHHHGGGCCCHHHH------------------------------------------HHHHHHHHSCSC
T ss_pred             CcHHHHHHHHHHHHHHHHHhCCHHHH------------------------------------------HHHHHHHHhCCC
Confidence            666666666554   45999999999                                          999999999999


Q ss_pred             Cc-ccchHHHHHHHHHHHHHhHhHHHHH------h--------------------hhhccccCCccchhHHHHHHHhhh
Q psy11505        259 VK-LDEFSSLKKFRNSILSSLGDCIYVL------R--------------------FWSTVHKDGKVLMNKLFVEMLEAY  310 (312)
Q Consensus       259 ~~-l~~~~~~~~~~~~~~~~l~~~~~~~------~--------------------~~~~~~~~~~~~~~~~~~~~~~~~  310 (312)
                      ++ |++...|+++|++|+.+|.+|+..+      |                    .+++.++.|.+|+++||.|||++.
T Consensus       187 ~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~Eml~~~  265 (303)
T 1xdk_B          187 RQDLEEPTKVDKLQEPLLEALKIYIRKRRPSKPHMFPKILMKITDLRSISAKGAERVITLKMEIPGSMPPLIQEMLENS  265 (303)
T ss_dssp             SSSCSSHHHHHHHTHHHHHHHHHHHHHHCTTCTTHHHHHHTHHHHHHHHHHHHHHHHHHHTTTCSSCCCHHHHHHHCCC
T ss_pred             CCCCccHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCccHHHHHHHcCC
Confidence            98 9999999999999999999999765      2                    355678899999999999999864

>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=99.97  E-value=1.1e-31  Score=233.83  Aligned_cols=195  Identities=39%  Similarity=0.600  Sum_probs=162.7

Q ss_pred             HHHHHHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhh
Q psy11505         74 ENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTI  153 (312)
Q Consensus        74 ~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~  153 (312)
                      .+.++..+...+|...........++.....+.++++++.+.+..+|+|||++|+|.+|+.+||+.|+|++|+++++++.
T Consensus        19 ~~~~~~~l~~~ep~~~~~~~~~~~~~~~~~~~~~l~e~a~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~lL~~   98 (248)
T 3k6p_A           19 VNALVSHLLVVEPEKLYAMPDPAGPDGHLPAVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGV   98 (248)
T ss_dssp             THHHHHHHHHHSCCCCCCCC-------CCCHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCcccccCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHhcCcccccCCHHHHHHHHHHHHHHHHHHHH
Confidence            57789999999987655544444455567789999999999999999999999999999999999999999999999999


Q ss_pred             hhhcccCCCCeeEecccchhhHHhhhhcccchhhhhh---cccCccCCCCccccCCceeeeeCCCCcccccccccchhHH
Q psy11505        154 AYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQV---KHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACK  230 (312)
Q Consensus       154 a~rs~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~i---~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~  230 (312)
                      ||++++.+ +.+++++|..++++.....+..++++.+   ...+.+|++|++||                          
T Consensus        99 a~~s~~~~-~~l~~~~g~~~~~~~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~--------------------------  151 (248)
T 3k6p_A           99 AQRSLPLQ-DELAFAEDLVLDEEGARAAGLGELGAALLQLVRRLQALRLEREEY--------------------------  151 (248)
T ss_dssp             HHHHTTSS-SCEEEETTEEECHHHHHHTTTTTHHHHHHHHHHHHHTTTCCHHHH--------------------------
T ss_pred             HHHccCCC-CeEEeCCCcccChhhhhhccHHHHHHHHHHHHHHHHHhCCCHHHH--------------------------
Confidence            99999988 5899999988887665555555544444   44555999999999                          


Q ss_pred             HHHHHHhhhcccceecCCCCceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH------------------------
Q psy11505        231 AFFKRTIQVYSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL------------------------  285 (312)
Q Consensus       231 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~------------------------  285 (312)
                                      ++++||+|||||++ ++++++|+++|++++.+|.+|+..+                        
T Consensus       152 ----------------~lLkAivL~npd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~~~~~Rf~~LL~~Lp~Lr~  215 (248)
T 3k6p_A          152 ----------------VLLKALALANSDSVHIEDAEAVEQLREALHEALLEYEAGRAGPGGGAERRRAGRLLLTLPLLRQ  215 (248)
T ss_dssp             ----------------HHHHHHHHHTCCCTTCSCHHHHHHHHHHHHHHHHHHHHTC----CCCCCH-HHHHHTTHHHHHH
T ss_pred             ----------------HHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCccchHHHHHHHHHHHHHHHH
Confidence                            99999999999998 9999999999999999999999632                        


Q ss_pred             ------hhhhccccCCccchhHHHHHHHhhhc
Q psy11505        286 ------RFWSTVHKDGKVLMNKLFVEMLEAYL  311 (312)
Q Consensus       286 ------~~~~~~~~~~~~~~~~~~~~~~~~~~  311 (312)
                            +.+++++++|.+|+++||.|||+|..
T Consensus       216 l~~~~~e~l~~~k~~g~~~i~~Ll~Eml~~k~  247 (248)
T 3k6p_A          216 TAGKVLAHFYGVKLEGKVPMHKLFLEMLEAMM  247 (248)
T ss_dssp             HHHHHHHHHHCC-CCCSSCHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHhhcccCCCCHHHHHHHHHhccc
Confidence                  23566799999999999999999864

>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=99.97  E-value=1.4e-31  Score=232.85  Aligned_cols=193  Identities=38%  Similarity=0.636  Sum_probs=163.1

Q ss_pred             HHHHHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhh
Q psy11505         75 NKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIA  154 (312)
Q Consensus        75 ~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a  154 (312)
                      +.++..+...+|...........+......+.++++++.+.+..+|+|||++|+|.+|+.+||+.|||++|+++++++.|
T Consensus        20 ~~~~~~l~~~ep~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~a   99 (244)
T 2e2r_A           20 NKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVV   99 (244)
T ss_dssp             CHHHHHHHHTCCCCCCCCCCTTSCCCHHHHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhCCCcccCCCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHhHHHHHHHHHH
Confidence            45788888888864433222233344667899999999999999999999999999999999999999999999999999


Q ss_pred             hhcccCCCCeeEecccchhhHHhhhhcccchhhhhhcc---cCccCCCCccccCCceeeeeCCCCcccccccccchhHHH
Q psy11505        155 YRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKH---SGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKA  231 (312)
Q Consensus       155 ~rs~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~i~~---~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~  231 (312)
                      |++++.++ .+++++|..++++.....+..++++.+..   .+.+|++|++||                           
T Consensus       100 ~rs~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~---------------------------  151 (244)
T 2e2r_A          100 YRSLSFED-ELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEF---------------------------  151 (244)
T ss_dssp             HHTTTSSS-CEEEETTEEECHHHHHHTTCHHHHHHHHHHHHHHHHHTCCHHHH---------------------------
T ss_pred             HHhcccCC-eEEecCCEeecHHHhhhccHHHHHHHHHHHHHHHHHHcCCHHHH---------------------------
Confidence            99999876 68889998887766655666666655544   445999999999                           


Q ss_pred             HHHHHhhhcccceecCCCCceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH------h------------------
Q psy11505        232 FFKRTIQVYSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL------R------------------  286 (312)
Q Consensus       232 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~------~------------------  286 (312)
                                     +++|||+|||||++ +++.++|+++|++++.+|.+|+..+      |                  
T Consensus       152 ---------------~lLkAivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~Rf~~LL~~L~~Lr~~~~~~  216 (244)
T 2e2r_A          152 ---------------VTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKA  216 (244)
T ss_dssp             ---------------HHHHHHHHHTCCCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTTHHHHHHHHHHH
T ss_pred             ---------------HHHHHHHHhccCCCCCcCHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHHHHHH
Confidence                           99999999999998 9999999999999999999999765      3                  


Q ss_pred             --hhhccccCCccchhHHHHHHHhhh
Q psy11505        287 --FWSTVHKDGKVLMNKLFVEMLEAY  310 (312)
Q Consensus       287 --~~~~~~~~~~~~~~~~~~~~~~~~  310 (312)
                        .+++.++.|.+|+++|+.|||+++
T Consensus       217 ~e~l~~~~~~~~~~~~~Ll~Eml~~~  242 (244)
T 2e2r_A          217 VQHFYNIKLEGKVPMHKLFLEMLEAK  242 (244)
T ss_dssp             HHHHHHHHHHCCSCCCHHHHHHHTSC
T ss_pred             HHHHHHhhcCCCCChHHHHHHHHhCc
Confidence              355568889999999999999986

>1ovl_A Orphan nuclear receptor NURR1 (MSe 414, 496, 511); NUUR1, LBD, transcription; 2.20A {Homo sapiens} SCOP: a.123.1.1

Probab=99.97  E-value=9.2e-31  Score=231.18  Aligned_cols=230  Identities=26%  Similarity=0.358  Sum_probs=150.7

Q ss_pred             cccccccccccccccccccCCCCCccCCCCCCCCCCchhHHHHHHHHHhcCccc--ccccCCCC-----CCCchhHHHhh
Q psy11505         35 MLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEENKMLEALLLCEPEM--LTVRSETP-----QSDPTLQTINS  107 (312)
Q Consensus        35 M~~eaVq~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~--~~~~~~~~-----~~~~~~~~~~~  107 (312)
                      |++|+||.+|.++++.+..+.........++..  +......++.......+..  .......+     ........+..
T Consensus         1 M~kE~Vr~dr~~~~r~~~~~~~~~~~~~~~~~~--~~~li~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (271)
T 1ovl_A            1 MVKEVVRTDSLKGRRGRLPSKPKSPQEPSPPSP--PVSLISALVRAHVDSNPAMTSLDYSRFQANPDYQMSGDDTQHIQQ   78 (271)
T ss_dssp             -------------------------------------CHHHHHHHHHHHTSCCTTSCBCTTCCCC--------CHHHHHH
T ss_pred             CCccccccCccccCCCCCCCCCCCcccCCCCCC--HHHHHHHHHHHHHHhCCCcchhhhhccCCCCCcccCcchHHHHHH
Confidence            899999999999887665444332211111111  1112344555555444432  11111111     11234567889


Q ss_pred             HHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhhcccchhh
Q psy11505        108 LSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIY  187 (312)
Q Consensus       108 ~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~  187 (312)
                      ++++....+..+|+|||++|+|.+|+.+||++|||++|+++++|+.||++++..+ .+++++|..++..+. ..+..+++
T Consensus        79 ~~~~~~~~l~~~v~waK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~-~l~~~~g~~~~~~~~-~~~~~~~~  156 (271)
T 1ovl_A           79 FYDLLTGSMEIIRGWAEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSNPVEG-KLIFCNGVVLHRLQC-VRGFGEWI  156 (271)
T ss_dssp             HHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHSBTTTT-EEECTTSBEEEHHHH-TTTTTTHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCCcccCChHHHHHHHHHhHHHHHHHHHHHHhcCCCC-eEEeeCCeeecHHHH-HhhHHHHH
Confidence            9999999999999999999999999999999999999999999999999999875 899999988776654 34555666


Q ss_pred             hhhccc---CccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCCCCcccch
Q psy11505        188 QQVKHS---GSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVKLDEF  264 (312)
Q Consensus       188 ~~i~~~---~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~  264 (312)
                      +.+..+   +.+|++|++||                                          ++++||+||||..+|++.
T Consensus       157 ~~l~~~~~~l~~L~ld~~E~------------------------------------------~lLkAivL~~~~~gL~~~  194 (271)
T 1ovl_A          157 DSIVEFSSNLQNMNIDISAF------------------------------------------SCIAALAMVTERHGLKEP  194 (271)
T ss_dssp             HHHHHHHHHHHTTCCCHHHH------------------------------------------HHHHHHHHSSCCTTCSCH
T ss_pred             HHHHHHHHHHHHhcCCHHHH------------------------------------------HHHHHHHHhCCCCCCCcH
Confidence            655544   44999999999                                          999999999974449999


Q ss_pred             HHHHHHHHHHHHHhHhHHHHH--------hh--------------------hhccccCCccchhHHHHHHHhhh
Q psy11505        265 SSLKKFRNSILSSLGDCIYVL--------RF--------------------WSTVHKDGKVLMNKLFVEMLEAY  310 (312)
Q Consensus       265 ~~~~~~~~~~~~~l~~~~~~~--------~~--------------------~~~~~~~~~~~~~~~~~~~~~~~  310 (312)
                      +.|+++|++++.+|.+|+..+        ||                    +++.++.|.+|+++|+.|||..-
T Consensus       195 ~~v~~lq~~~~~aL~~y~~~~~~~~~~~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~el~~~~  268 (271)
T 1ovl_A          195 KRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLGKLPELRTLCTQGLQRIFYLKLEDLVPPPAIIDKLFLDT  268 (271)
T ss_dssp             HHHHHHHHHHHHHHHHHHHGGGTTTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSSCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCcHHHHHHHHHh
Confidence            999999999999999999753        22                    44568889999999999998753

>3oll_A Estrogen receptor beta; steroid binding, phosphorylation, hormone receptor-activator; HET: PTR EST; 1.50A {Homo sapiens} SCOP: a.123.1.1 PDB: 1u3s_A* 1u3q_A* 1x78_A* 1x7b_A* 1x7j_A* 1x76_A* 2yjd_A* 3ols_A* 3omo_A* 3omp_A* 3omq_A* 1u3r_A* 1u9e_A* 1qkm_A* 2giu_A* 1nde_A* 2jj3_A* 2i0g_A* 2qtu_A* 2z4b_A* ...

Probab=99.97  E-value=2.9e-30  Score=224.03  Aligned_cols=194  Identities=32%  Similarity=0.456  Sum_probs=159.8

Q ss_pred             HHHHHHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhh
Q psy11505         74 ENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTI  153 (312)
Q Consensus        74 ~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~  153 (312)
                      .+.++..++..+|... .......+.+....+..++++..+.+..+|+|||++|+|.+|+.+||+.|+|++|+++++|+.
T Consensus         5 ~~~~i~~ll~~e~~~~-~~~~~~~~~~~~~~~~~~~~~a~~~l~~~vewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~   83 (240)
T 3oll_A            5 PEQLVLTLLEAEPPHV-LISRPSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGL   83 (240)
T ss_dssp             HHHHHHHHHHHCCCCC-CCBCCSSCCCHHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhHHHHHHHHhCCccc-ccCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHHHHHHHHHHH
Confidence            5678888888888655 333344455677889999999999999999999999999999999999999999999999999


Q ss_pred             hhhcccCCCCeeEecccchhhHHhhh-hcccchhhhhhc---ccCccCCCCccccCCceeeeeCCCCcccccccccchhH
Q psy11505        154 AYRSLPHCAGKIRFASDLVLDERQAR-ECGFSEIYQQVK---HSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEAC  229 (312)
Q Consensus       154 a~rs~~~~~~~l~~~~g~~~~~~~~~-~~~~~~~~~~i~---~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~  229 (312)
                      ||++++.++ .+++++|..+++.... ..+..++++.+.   ..+.+|++|++||                         
T Consensus        84 a~~s~~~~~-~l~~~~g~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~-------------------------  137 (240)
T 3oll_A           84 MWRSIDHPG-KLIFAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEY-------------------------  137 (240)
T ss_dssp             HHHHTTSTT-EEEEETBEEEEGGGGGGSTTHHHHHHHHHHHHHHHHHTTCCHHHH-------------------------
T ss_pred             HHHccCCCC-eeEecCCcccchhhHHHHhhHHHHHHHHHHHHHHHHHhCCCHHHH-------------------------
Confidence            999999774 8999999887765433 234455555444   4455999999999                         


Q ss_pred             HHHHHHHhhhcccceecCCCCceeecCCCCc-ccc-------hHHHHHHHHHHHHHhHhHHHHH---------h------
Q psy11505        230 KAFFKRTIQVYSGYRQTGACGTLVLANSDVK-LDE-------FSSLKKFRNSILSSLGDCIYVL---------R------  286 (312)
Q Consensus       230 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-l~~-------~~~~~~~~~~~~~~l~~~~~~~---------~------  286 (312)
                                       +++|||+|||||++ +++       +++++++|++|..+|.+|+..+         |      
T Consensus       138 -----------------~lLkAivL~~pd~~gLs~~~~~~~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~~~~Rf~~LL~  200 (240)
T 3oll_A          138 -----------------LCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLM  200 (240)
T ss_dssp             -----------------HHHHHHHHHCSCCCCCCCCC--CHHHHHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHH
T ss_pred             -----------------HHHHHHHHcCCCCCCcccccchhhHHHHHHHHHHHHHHHHHHHHhccCCCCcchhhHHHHHHH
Confidence                             99999999999986 643       5679999999999999999631         2      


Q ss_pred             --------------hhhccccCCccchhHHHHHHHhhhc
Q psy11505        287 --------------FWSTVHKDGKVLMNKLFVEMLEAYL  311 (312)
Q Consensus       287 --------------~~~~~~~~~~~~~~~~~~~~~~~~~  311 (312)
                                    .+++++++|.+|+++||.|||++|.
T Consensus       201 ~Lp~Lr~l~~~~~e~l~~~~~~g~~~~~~Ll~eml~~~~  239 (240)
T 3oll_A          201 LLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEMLNAHV  239 (240)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTSSCCCHHHHHHHHHC-
T ss_pred             HhHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHhccc
Confidence                          3566789999999999999999973

>2ocf_A Estrogen receptor; estrogen receptor, LBD, monobody, estradiol, hormone-growth complex; HET: CME EST; 2.95A {Homo sapiens}

Probab=99.96  E-value=3.7e-30  Score=229.45  Aligned_cols=196  Identities=33%  Similarity=0.531  Sum_probs=158.8

Q ss_pred             hhHHHHHHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHH
Q psy11505         72 LEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTL  151 (312)
Q Consensus        72 ~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L  151 (312)
                      ...+.++..+...+|...........+......+..+++|..+.++.+|+|||++|+|.+|+.+||+.|||++|+++++|
T Consensus        13 ~~~~~~i~~l~~~ep~~~~~~~~~~~~~~~~~~~~~l~e~a~~~L~~~VewAK~lP~F~~L~~~DQi~LLk~~w~el~lL   92 (298)
T 2ocf_A           13 LTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMI   92 (298)
T ss_dssp             CCHHHHHHHHHHSCCCCBCCCCCSSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHhcCCCcccccCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHhCcchhcCCHHHHHHHHHHhhHHHHHH
Confidence            34567888888888865443333333444566789999999999999999999999999999999999999999999999


Q ss_pred             hhhhhcccCCCCeeEecccchhhHHhh-hhcccchhhhhhcc---cCccCCCCccccCCceeeeeCCCCcccccccccch
Q psy11505        152 TIAYRSLPHCAGKIRFASDLVLDERQA-RECGFSEIYQQVKH---SGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCE  227 (312)
Q Consensus       152 ~~a~rs~~~~~~~l~~~~g~~~~~~~~-~~~~~~~~~~~i~~---~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~  227 (312)
                      +.||++++..+ .+++++|..+++... ...+..++++.+..   .+.+|++|++||                       
T Consensus        93 ~~a~rs~~~~~-~l~~~~g~~~~~~~~~~~~g~~~~~~~l~~~~~~l~~L~ld~~Ey-----------------------  148 (298)
T 2ocf_A           93 GLVWRSMEHPG-KLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEF-----------------------  148 (298)
T ss_dssp             HHHHHTTTSTT-EEEEETTEEEEHHHHTTSTTHHHHHHHHHHHHHHHHHTTCCHHHH-----------------------
T ss_pred             HHHHHhcccCC-ceeecCCceechhhhhhhhhHHHHHHHHHHHHHhHhhhCcCHHHH-----------------------
Confidence            99999999874 899999988876553 23445555555544   455999999999                       


Q ss_pred             hHHHHHHHHhhhcccceecCCCCceeecCCCC--------c-ccchHHHHHHHHHHHHHhHhHHHHH---------hh--
Q psy11505        228 ACKAFFKRTIQVYSGYRQTGACGTLVLANSDV--------K-LDEFSSLKKFRNSILSSLGDCIYVL---------RF--  287 (312)
Q Consensus       228 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~--------~-l~~~~~~~~~~~~~~~~l~~~~~~~---------~~--  287 (312)
                                         +++|||+|||||+        + |+++..|+++|++++.+|.+|+..+         ||  
T Consensus       149 -------------------~lLkAIvLfnpd~~~LS~~~~~gL~~~~~ve~lqe~~~~aL~~y~~~~~~~~~~~~~RF~~  209 (298)
T 2ocf_A          149 -------------------VCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQ  209 (298)
T ss_dssp             -------------------HHHHHHHHHHCSCCC-----------CHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             -------------------HHHHHHHHcCCCccccccccccccccHHHHHHHHHHHHHHHHHHHHhcCCCCCcHHHHHHH
Confidence                               9999999999998        5 7888999999999999999998642         33  


Q ss_pred             ------------------hhccccCCccchhHHHHHHHhhh
Q psy11505        288 ------------------WSTVHKDGKVLMNKLFVEMLEAY  310 (312)
Q Consensus       288 ------------------~~~~~~~~~~~~~~~~~~~~~~~  310 (312)
                                        +++++++|.+|+++||.|||+++
T Consensus       210 LLl~Lp~Lr~i~~~~~e~l~~~kl~g~~~i~~Ll~Eml~~~  250 (298)
T 2ocf_A          210 LLLILSHIRHMSNKGMEHLYSMKCKNVVPLSDLLLEMLDAH  250 (298)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTSSCCCHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHcCC
Confidence                              55678899999999999999875

>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=99.96  E-value=4.5e-30  Score=223.89  Aligned_cols=195  Identities=32%  Similarity=0.532  Sum_probs=160.0

Q ss_pred             hHHHHHHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHh
Q psy11505         73 EENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLT  152 (312)
Q Consensus        73 ~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~  152 (312)
                      +.+.++..+...+|...........+......+..+++...+.+..+|+|||++|+|.+|+.+||+.|||++|+++++|+
T Consensus         5 ~~~~~~~~l~~~ep~~~~~~~~~~~~~~~~~~~~~l~~~a~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~   84 (248)
T 1xpc_A            5 TADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIG   84 (248)
T ss_dssp             CHHHHHHHHHHTCCCCCCCCSCTTSCSTTSCHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCCccccCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHcCCccccCCHHHHHHHHHHHhHHHHHHH
Confidence            35667888888888654443333334445567899999999999999999999999999999999999999999999999


Q ss_pred             hhhhcccCCCCeeEecccchhhHHhhh-hcccchhhhhhcc---cCccCCCCccccCCceeeeeCCCCcccccccccchh
Q psy11505        153 IAYRSLPHCAGKIRFASDLVLDERQAR-ECGFSEIYQQVKH---SGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEA  228 (312)
Q Consensus       153 ~a~rs~~~~~~~l~~~~g~~~~~~~~~-~~~~~~~~~~i~~---~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~  228 (312)
                      .||++++..+ .+.+++|..+++.... ..+..++++.+..   .+.+|++|++||                        
T Consensus        85 ~a~~s~~~~~-~l~~~~g~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~------------------------  139 (248)
T 1xpc_A           85 LVWRSMEHPG-KLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEF------------------------  139 (248)
T ss_dssp             HHHHHTTSTT-EEEEETTEEEEHHHHTTSTTHHHHHHHHHHHHHHHHHHTCCHHHH------------------------
T ss_pred             HHHHhccccC-ceeecCCceeCccchhhhccHHHHHHHHHHHHHHHHHhCCCHHHH------------------------
Confidence            9999998874 8999999887766532 3344555555544   445999999999                        


Q ss_pred             HHHHHHHHhhhcccceecCCCCceeecCCCC--------c-ccchHHHHHHHHHHHHHhHhHHHHH---------hh---
Q psy11505        229 CKAFFKRTIQVYSGYRQTGACGTLVLANSDV--------K-LDEFSSLKKFRNSILSSLGDCIYVL---------RF---  287 (312)
Q Consensus       229 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~--------~-l~~~~~~~~~~~~~~~~l~~~~~~~---------~~---  287 (312)
                                        +++|||+|||||+        + ++++..|+++|++++.+|.+|+..+         ||   
T Consensus       140 ------------------~lLkAivL~~pd~~~ls~~~~~gl~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~~~Rf~~L  201 (248)
T 1xpc_A          140 ------------------VCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQL  201 (248)
T ss_dssp             ------------------HHHHHHHHHHTTTTCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             ------------------HHHHHHHHcCCcccccccccccccccHHHHHHHHHHHHHHHHHHHHccCCCCcchhhHHHHH
Confidence                              9999999999998        4 6778899999999999999999742         33   


Q ss_pred             -----------------hhccccCCccchhHHHHHHHhhh
Q psy11505        288 -----------------WSTVHKDGKVLMNKLFVEMLEAY  310 (312)
Q Consensus       288 -----------------~~~~~~~~~~~~~~~~~~~~~~~  310 (312)
                                       +++.++.|.+|+++|+.|||+++
T Consensus       202 L~~L~~Lr~~~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~  241 (248)
T 1xpc_A          202 LLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDAH  241 (248)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTSSSCCSSCHHHHHHHHHSCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHhCC
Confidence                             55678899999999999999864

>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=99.96  E-value=2e-29  Score=221.68  Aligned_cols=195  Identities=19%  Similarity=0.326  Sum_probs=158.6

Q ss_pred             HHHHHHHHHhcCcc-cccccCCCCCCCch----hHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHH
Q psy11505         74 ENKMLEALLLCEPE-MLTVRSETPQSDPT----LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEI  148 (312)
Q Consensus        74 ~~~~l~~l~~~~~~-~~~~~~~~~~~~~~----~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~  148 (312)
                      .+.+++.+...++. ..........+...    ...+.++++++.+.+..+|+|||++|+|.+|+.+||+.|||++|+++
T Consensus         8 ~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~w~el   87 (264)
T 1g2n_A            8 IERLLEMESLVADPSEEFQFLRVGPDSNVPPKFRAPVSSLCQIGNKQIAALVVWARDIPHFSQLEMEDQILLIKGSWNEL   87 (264)
T ss_dssp             HHHHHHHHHCCCCCCCCCCSBCCCTTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCCccccccccCCCcccchhhhhHHHHHHHHHHHHHHHHHHHHHcCCChhcCCHHHHHHHHHHhhHHH
Confidence            56788888888872 22222111111111    36889999999999999999999999999999999999999999999


Q ss_pred             HHHhhhhhcccC---CCCe--------------eEecccchhhHHhhhhcccchhhh----hhcccCccCCCCccccCCc
Q psy11505        149 LTLTIAYRSLPH---CAGK--------------IRFASDLVLDERQARECGFSEIYQ----QVKHSGSLDGIKEEELPRR  207 (312)
Q Consensus       149 ~~L~~a~rs~~~---~~~~--------------l~~~~g~~~~~~~~~~~~~~~~~~----~i~~~~~~L~ld~~E~~~~  207 (312)
                      ++|+.||++++.   +.+.              +++++|..++++.....+..++++    ++...+.+|++|++||   
T Consensus        88 ~lL~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~ld~~E~---  164 (264)
T 1g2n_A           88 LLFAIAWRSMEFLTEERDGVDGTGNRTTSPPQLMCLMPGMTLHRNSALQAGVGQIFDRVLSELSLKMRTLRVDQAEY---  164 (264)
T ss_dssp             HHHHHHHHHGGGSCCC----------CCCCCCEEEEETTEEEEHHHHHHHTCHHHHHHHHHHTHHHHHHTTCCHHHH---
T ss_pred             HHHHHHHHccccccccccccccccccccccccceeecCCcccCchhhhhccHHHHHHHHHHHHHHHHHHhCCCHHHH---
Confidence            999999999988   2335              889999988887766666665553    3445556999999999   


Q ss_pred             eeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH-
Q psy11505        208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL-  285 (312)
Q Consensus       208 ~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~-  285 (312)
                                                             +++|||+|||||++ |+++..|+++|++|+.+|.+|+..+ 
T Consensus       165 ---------------------------------------~lLkAivL~npd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~  205 (264)
T 1g2n_A          165 ---------------------------------------VALKAIILLNPDVKGLKNRQEVEVLREKMFLCLDEYCRRSR  205 (264)
T ss_dssp             ---------------------------------------HHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             ---------------------------------------HHHHHHHHhCCCCCCCccHHHHHHHHHHHHHHHHHHHHHhC
Confidence                                                   99999999999997 9999999999999999999999765 


Q ss_pred             -----h--------------------hhhccccCCccchhHHHHHHHhhh
Q psy11505        286 -----R--------------------FWSTVHKDGKVLMNKLFVEMLEAY  310 (312)
Q Consensus       286 -----~--------------------~~~~~~~~~~~~~~~~~~~~~~~~  310 (312)
                           |                    .+++.+++|.+|+++|+.|||++.
T Consensus       206 ~~~~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~Eml~~~  255 (264)
T 1g2n_A          206 SSEEGRFAALLLRLPALRSISLKSFEHLFFFHLVADTSIAGYIRDALRNH  255 (264)
T ss_dssp             TTCTTHHHHHHTHHHHHHHHHHHHHHHHHHTTCBCTTTHHHHHHHHHTCC
T ss_pred             CCHhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCChHHHHHHHHhCC
Confidence                 2                    356678899999999999999875

>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=99.96  E-value=1.2e-29  Score=221.72  Aligned_cols=164  Identities=27%  Similarity=0.369  Sum_probs=143.6

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhh
Q psy11505        101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE  180 (312)
Q Consensus       101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~  180 (312)
                      ....+..+++..+..+..+|+|||++|+|.+|+.+||+.|||++|+++++++.|+++.+..+ .+.+++|..+++.+.. 
T Consensus        50 ~~~~~~~~~~l~~~~i~~iV~wAK~iP~F~~L~~~DQi~LLk~~w~ElllL~~a~~~~~~~~-~l~~~~~~~~~~~~~~-  127 (257)
T 3v3e_B           50 DAGDVQQFYDLLSGSLEVIRKWAEKIPGFAELSPADQDLLLESAFLELFILRLAYRSKPGEG-KLIFCSGLVLHRLQCA-  127 (257)
T ss_dssp             CHHHHHHHHHHHHHTHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHSBGGGT-EEECTTSBEEEHHHHH-
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhccCCCC-eeEeCCCccccHHHHH-
Confidence            45678899999999999999999999999999999999999999999999999999998776 7999999988876653 


Q ss_pred             cccchhhhhhcccCc---cCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCC
Q psy11505        181 CGFSEIYQQVKHSGS---LDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANS  257 (312)
Q Consensus       181 ~~~~~~~~~i~~~~~---~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  257 (312)
                      .+.+++++.++.+..   +|++|++||                                          +|+|||+||| 
T Consensus       128 ~~~~~~~~~l~~~~~~l~~L~ld~~E~------------------------------------------a~LkAivLfs-  164 (257)
T 3v3e_B          128 RGFGDWIDSILAFSRSLHSLLVDVPAF------------------------------------------ACLSALVLIT-  164 (257)
T ss_dssp             HHHTTHHHHHHHHHHHHHHTTCCHHHH------------------------------------------HHHHHHHHSS-
T ss_pred             hhhHHHHHHHHHHHHHHHhcCCCHHHH------------------------------------------HHHHHHHHhC-
Confidence            355666766665544   899999999                                          9999999999 


Q ss_pred             CCc-ccchHHHHHHHHHHHHHhHhHHHHH----------------------------hhhhccccCCccchhHHHHHHHh
Q psy11505        258 DVK-LDEFSSLKKFRNSILSSLGDCIYVL----------------------------RFWSTVHKDGKVLMNKLFVEMLE  308 (312)
Q Consensus       258 ~~~-l~~~~~~~~~~~~~~~~l~~~~~~~----------------------------~~~~~~~~~~~~~~~~~~~~~~~  308 (312)
                      |++ |+++++|+++|++++.+|.+|+...                            +.++++++.|.+|+++|+.|||.
T Consensus       165 d~~gL~~~~~Ve~lqe~~~~aL~~yi~~~~~~p~~~~rf~kLL~~Lp~LR~l~~~~~e~l~~~k~~~~~~~~~Ll~Emf~  244 (257)
T 3v3e_B          165 DRHGLQEPRRVEELQNRIASCLKEHVAAVAGEPQPASCLSRLLGKLPELRTLCTQGLQRIFYLKLEDLVPPPPIIDKIFM  244 (257)
T ss_dssp             CCTTCSSHHHHHHHHHHHHHHHHHHHHHHHCSCC-CHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHhcCCCcHhhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCccHHHHHHHH
Confidence            555 9999999999999999999999643                            23566788999999999999996


Q ss_pred             h
Q psy11505        309 A  309 (312)
Q Consensus       309 ~  309 (312)
                      .
T Consensus       245 ~  245 (257)
T 3v3e_B          245 D  245 (257)
T ss_dssp             H
T ss_pred             h
Confidence            5

>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=99.96  E-value=9.8e-30  Score=220.13  Aligned_cols=165  Identities=27%  Similarity=0.360  Sum_probs=146.3

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhh
Q psy11505        101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE  180 (312)
Q Consensus       101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~  180 (312)
                      +...+..+++++.+.+..+|+|||++|+|.+|+.+||+.|||++|+++++++.|+++++.. +.+.+++|..++++....
T Consensus        42 ~~~~~~~~~~~~~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~l~~a~~~~~~~-~~l~~~~g~~~~~~~~~~  120 (236)
T 1fcy_A           42 DLGLWDKFSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQ-DTMTFSDGLTLNRTQMHN  120 (236)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETTT-TEEECTTCBEEEHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhccCC-CeEEeCCCceecHHHHHH
Confidence            3567899999999999999999999999999999999999999999999999999999865 489999998888776666


Q ss_pred             cccchhhhhhcc---cCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCC
Q psy11505        181 CGFSEIYQQVKH---SGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANS  257 (312)
Q Consensus       181 ~~~~~~~~~i~~---~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  257 (312)
                      .|..++++.+..   .+.+|++|++||                                          +++|||+||||
T Consensus       121 ~g~~~~~~~i~~~~~~l~~L~ld~~E~------------------------------------------~lLkaivL~~p  158 (236)
T 1fcy_A          121 AGFGPLTDLVFAFAGQLLPLEMDDTET------------------------------------------GLLSAICLICG  158 (236)
T ss_dssp             HTTGGGHHHHHHHHHHHGGGCCCHHHH------------------------------------------HHHHHHHHSCT
T ss_pred             cCcHHHHHHHHHHHHHHHHHcCCHHHH------------------------------------------HHHHHHHhcCC
Confidence            666666666554   345999999999                                          99999999999


Q ss_pred             CCc-ccchHHHHHHHHHHHHHhHhHHHHH--------------------------hhhhccccCCccchhHHHHHHHh
Q psy11505        258 DVK-LDEFSSLKKFRNSILSSLGDCIYVL--------------------------RFWSTVHKDGKVLMNKLFVEMLE  308 (312)
Q Consensus       258 ~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------------------------~~~~~~~~~~~~~~~~~~~~~~~  308 (312)
                      |++ |++++.|+++|++++.+|.+|+..+                          +.+++.++.|.+|+++|+.|||+
T Consensus       159 d~~gL~~~~~v~~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~Eml~  236 (236)
T 1fcy_A          159 DRMDLEEPEKVDKLQEPLLEALRLYARRRRPSQPYMFPRMLMKITDLRGISTKGAERAITLKMEIPGPMPPLIREMLE  236 (236)
T ss_dssp             TSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCCCHHHHHHHC
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCchhHHHHHHHHhHHHHHHHHHHHHHHHHHHccCCCCccHHHHHHhC
Confidence            998 9999999999999999999999765                          23566788999999999999985

>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=99.96  E-value=4.1e-30  Score=224.97  Aligned_cols=194  Identities=27%  Similarity=0.428  Sum_probs=154.4

Q ss_pred             HHHHHHHHhcCcccccc--------c--CCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHH
Q psy11505         75 NKMLEALLLCEPEMLTV--------R--SETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQST  144 (312)
Q Consensus        75 ~~~l~~l~~~~~~~~~~--------~--~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~  144 (312)
                      ++++..+...+|.....        .  ........+...+..+++++.+.+..+|+|||++|+|.+|+.+||+.|||++
T Consensus        18 ~~~i~~l~~~~p~e~~~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~~a~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~   97 (257)
T 3plz_A           18 PHLILELLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNC   97 (257)
T ss_dssp             CHHHHHHHHTSCCHHHHHHHHHHHHHHC--------CCCHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHH
T ss_pred             hHHHHHHHhcCCchHHHHHHHhhhhhccccccCCccccchHHHHHHHHHHHHHHHHHHHHcCcChhcCCHHHHHHHHHHH
Confidence            34677777777651111        1  1111222345678999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhhhhcccCC-CCeeEecccchhhHHhhh-hccc--chhh---hhhcccCccCCCCccccCCceeeeeCCCCc
Q psy11505        145 WAEILTLTIAYRSLPHC-AGKIRFASDLVLDERQAR-ECGF--SEIY---QQVKHSGSLDGIKEEELPRRLCLVCGDVAS  217 (312)
Q Consensus       145 ~~~~~~L~~a~rs~~~~-~~~l~~~~g~~~~~~~~~-~~~~--~~~~---~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~  217 (312)
                      |+++++|+.||+++..+ .+.+.+++|..++..... ..+.  .+++   .++...+.+|++|++||             
T Consensus        98 ~~el~lL~~a~rs~~~~~~~~l~~~~g~~~~~~~~~~~~g~~~~~~~~~l~~~~~~l~~L~ld~~E~-------------  164 (257)
T 3plz_A           98 WSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREF-------------  164 (257)
T ss_dssp             HHHHHHHHHHHHHHHHCBTTEEECTTSCEEEHHHHHTTSCHHHHHHHHHHHHHHHHHHHTTCCHHHH-------------
T ss_pred             HHHHHHHHHHHHHhhcCCCCeEEecCCCccChHHHhhhcCCcHHHHHHHHHHHHHHHHHHCCCHHHH-------------
Confidence            99999999999998876 368999999887765443 2222  3333   34445556999999999             


Q ss_pred             ccccccccchhHHHHHHHHhhhcccceecCCCCceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH-----------
Q psy11505        218 GFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL-----------  285 (312)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~-----------  285 (312)
                                                   ++++||+|||||++ +++.++|+++|++++.+|.+|+..+           
T Consensus       165 -----------------------------~lLkAivL~npd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~Rf~~L  215 (257)
T 3plz_A          165 -----------------------------VCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQL  215 (257)
T ss_dssp             -----------------------------HHHHHHHHSCTTCCSCTTHHHHHHHHHHHHHHHHHHHHHHCTTSTTHHHHH
T ss_pred             -----------------------------HHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCchhHHHHH
Confidence                                         99999999999998 9999999999999999999999865           


Q ss_pred             ---------------hhhhccccCCccchhHHHHHHHhhh
Q psy11505        286 ---------------RFWSTVHKDGKVLMNKLFVEMLEAY  310 (312)
Q Consensus       286 ---------------~~~~~~~~~~~~~~~~~~~~~~~~~  310 (312)
                                     +.+++++++|.+|+++||.|||+++
T Consensus       216 L~~Lp~Lr~l~~~~~e~l~~~~~~g~~~i~~Ll~Eml~~k  255 (257)
T 3plz_A          216 LLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHAK  255 (257)
T ss_dssp             HTHHHHHHHHHHHHHHHHHHHHHTTCSCCCSHHHHHHTC-
T ss_pred             HHHhHHHHHHHHHHHHHHhhhhhcCCCCHHHHHHHHHhcc
Confidence                           3366789999999999999999985

>2nxx_A Ultraspiracle (USP, NR2B4); hormone receptor, APO and holo ligand binding pocket, hormone/growth factor complex; HET: P1A; 2.75A {Tribolium castaneum}

Probab=99.96  E-value=2.4e-29  Score=217.61  Aligned_cols=191  Identities=26%  Similarity=0.417  Sum_probs=155.9

Q ss_pred             HHHHHHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhh
Q psy11505         74 ENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTI  153 (312)
Q Consensus        74 ~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~  153 (312)
                      .+.+++.....++........  . ......+.++++++.+.+..+|+|||++|+|.+|+.+||+.|||++|+++++++.
T Consensus        11 ~~~~~~~~~~~~~~~~~~~~~--~-~~~~~~~~~~~~~~~~~l~~~vewaK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~   87 (235)
T 2nxx_A           11 LERIIEAEKRVECNDPLVALV--V-NENNTTVNNICQATHKQLFQLVQWAKLVPHFTSLPLTDQVQLLRAGWNELLIAAF   87 (235)
T ss_dssp             HHHHHHHHHHTCCCCCCCBCC--C-SCSSSHHHHHHHHHHHHHHHHHHHHHHSTTSTTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCccccccc--c-CccccHHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHhHHHHHHHHH
Confidence            456777766666642211111  1 2234578899999999999999999999999999999999999999999999999


Q ss_pred             hhhcccCCCCeeEecccchhhHHhhhhcccchhhhh----hcccCccCCCCccccCCceeeeeCCCCcccccccccchhH
Q psy11505        154 AYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQ----VKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEAC  229 (312)
Q Consensus       154 a~rs~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~----i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~  229 (312)
                      ||++++..+ .+++++|..++++.....+..+++++    +...+.+|++|++||                         
T Consensus        88 a~rs~~~~~-~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~-------------------------  141 (235)
T 2nxx_A           88 SHRSMQAQD-AIVLATGLTVNKSTAHAVGVGNIYDRVLSELVNKMKEMKMDKTEL-------------------------  141 (235)
T ss_dssp             HHTTSSSSS-SEECSSSCEECSSSCSSSSCSSSHHHHHHHTHHHHHHHTCCHHHH-------------------------
T ss_pred             HHhcccCCC-ceEecCCcccccchhhhhchHHHHHHHHHHHHHHHHHHcCCHHHH-------------------------
Confidence            999999854 78999998887665544555555544    445556999999999                         


Q ss_pred             HHHHHHHhhhcccceecCCCCceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH------hh---------------
Q psy11505        230 KAFFKRTIQVYSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL------RF---------------  287 (312)
Q Consensus       230 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~------~~---------------  287 (312)
                                       +++|||+|||||++ ++++..|+++|++++.+|.+|+..+      ||               
T Consensus       142 -----------------~lLkaivL~~pd~~gL~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LL~~L~~Lr~~~~  204 (235)
T 2nxx_A          142 -----------------GCLRAIILYNPDVRGIKSVQEVEMLREKIYGVLEEYTRTTHPNEPGRFAKLLLRLPALRSIGL  204 (235)
T ss_dssp             -----------------HHHHHHHHCCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTHHHHHHHHHH
T ss_pred             -----------------HHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHhHHHHHHHH
Confidence                             99999999999998 9999999999999999999999765      33               


Q ss_pred             -----hhccccCCccchhHHHHHHHhhh
Q psy11505        288 -----WSTVHKDGKVLMNKLFVEMLEAY  310 (312)
Q Consensus       288 -----~~~~~~~~~~~~~~~~~~~~~~~  310 (312)
                           +++.+++|.+|+++|+.|||+++
T Consensus       205 ~~~e~l~~~~~~g~~~~~~Ll~eml~~~  232 (235)
T 2nxx_A          205 KCLEHLFFFKLIGDVPIDTFLMEMLEGT  232 (235)
T ss_dssp             TCCSCTTTTSSSSCCCHHHHHHHHTTC-
T ss_pred             HHHHHHHhhcccCCCcHHHHHHHHHhCC
Confidence                 45568899999999999999875

>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=99.96  E-value=3.4e-29  Score=220.47  Aligned_cols=192  Identities=33%  Similarity=0.469  Sum_probs=153.6

Q ss_pred             HHHHHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhh
Q psy11505         75 NKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIA  154 (312)
Q Consensus        75 ~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a  154 (312)
                      +.++..+...++... .......+......+..++++..+.+..+|+|||++|+|.+|+.+||+.|||++|+++++|+.|
T Consensus         4 ~~~~~~ll~ae~~~~-~~~~~~~~~~~~~~~~~l~e~a~~~l~~~VewAK~lp~F~~L~~~DQi~LLk~~w~el~lL~~a   82 (268)
T 1yye_A            4 EQLVLTLLEAEPPHV-LISRPSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLM   82 (268)
T ss_dssp             HHHHHHHHHHCCCCC-CCCCCSCCCCHHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHhcCCccc-ccCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHhcCcchhcCCHHHHHHHHHHHHHHHHHHHHH
Confidence            456777777777543 3333333444566789999999999999999999999999999999999999999999999999


Q ss_pred             hhcccCCCCeeEecccchhhHHhhh-hcccchhhhhhc---ccCccCCCCccccCCceeeeeCCCCcccccccccchhHH
Q psy11505        155 YRSLPHCAGKIRFASDLVLDERQAR-ECGFSEIYQQVK---HSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACK  230 (312)
Q Consensus       155 ~rs~~~~~~~l~~~~g~~~~~~~~~-~~~~~~~~~~i~---~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~  230 (312)
                      |++++.. +.+++++|..+++.... ..+..++++.+.   ..+.+|++|++||                          
T Consensus        83 ~rs~~~~-~~l~~~~g~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~--------------------------  135 (268)
T 1yye_A           83 WRSIDHP-GKLIFAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEY--------------------------  135 (268)
T ss_dssp             HHHTTST-TEEEEETTEEEEGGGGGGSTTHHHHHHHHHHHHHHHHHHTCCHHHH--------------------------
T ss_pred             HHhccCC-CceEecCCcccChhhHhhhccHHHHHHHHHHHHHHHHHhCCCHHHH--------------------------
Confidence            9999987 48999999877765432 234445555554   4455999999999                          


Q ss_pred             HHHHHHhhhcccceecCCCCceeecCCCCc-ccc-------hHHHHHHHHHHHHHhHhHHHHH---------h-------
Q psy11505        231 AFFKRTIQVYSGYRQTGACGTLVLANSDVK-LDE-------FSSLKKFRNSILSSLGDCIYVL---------R-------  286 (312)
Q Consensus       231 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-l~~-------~~~~~~~~~~~~~~l~~~~~~~---------~-------  286 (312)
                                      +++|||+|||||++ +++       +.+++++|++|..+|.+|+..+         |       
T Consensus       136 ----------------~lLkAIvLfnpd~~gLs~~~~~~~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~~~~Rf~~LLl~  199 (268)
T 1yye_A          136 ----------------LCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLML  199 (268)
T ss_dssp             ----------------HHHHHHHHHTCCC----------CCHHHHHHHHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHHH
T ss_pred             ----------------HHHHHHHHcCCCCCCcccchhhHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcchhhHHHHHHHH
Confidence                            99999999999986 754       6789999999999999998642         2       


Q ss_pred             -------------hhhccccCCccchhHHHHHHHhhh
Q psy11505        287 -------------FWSTVHKDGKVLMNKLFVEMLEAY  310 (312)
Q Consensus       287 -------------~~~~~~~~~~~~~~~~~~~~~~~~  310 (312)
                                   .+++.+++|.+|+++|+.|||+++
T Consensus       200 Lp~Lr~i~~~~~e~l~~~~~~g~~~~~~Ll~Eml~~~  236 (268)
T 1yye_A          200 LSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEMLNAH  236 (268)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTCSCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhccCCCCCHHHHHHHHHhCc
Confidence                         255568899999999999999874

>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=99.96  E-value=1e-28  Score=217.06  Aligned_cols=166  Identities=25%  Similarity=0.373  Sum_probs=146.2

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhh
Q psy11505        101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE  180 (312)
Q Consensus       101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~  180 (312)
                      ....|..+++...+.+..+|+|||++|+|.+|+.+||++|||++|+++++|+.|+++.+..+ .+.+++|..+.+.....
T Consensus        66 ~~~~~~~~~e~~~~~l~~~VewaK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~~s~~~~~-~l~~~~g~~~~~~~~~~  144 (266)
T 3kmr_A           66 DIDLWDKFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQD-TMTFSDGLTLNRTQMHN  144 (266)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETTTT-EEECTTSBEEEHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHcCcChhhCCHHHHHHHHHHHHHHHHHHHHHHHhccCCC-eEEecCCcccchHHHhh
Confidence            35678999999999999999999999999999999999999999999999999999987654 89999998888777665


Q ss_pred             cccchhhhhhcc---cCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCC
Q psy11505        181 CGFSEIYQQVKH---SGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANS  257 (312)
Q Consensus       181 ~~~~~~~~~i~~---~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  257 (312)
                      .+..++.+.+..   .+.+|++|++||                                          ++++||+||||
T Consensus       145 ~g~~~~~~~i~~~~~~l~~L~ld~~E~------------------------------------------~lLkAIvL~~p  182 (266)
T 3kmr_A          145 AGFGPLTDLVFAFANQLLPLEMDDAET------------------------------------------GLLSAICLICG  182 (266)
T ss_dssp             HTTGGGHHHHHHHHHHHGGGCCCHHHH------------------------------------------HHHHHHHHSCT
T ss_pred             cchHHHHHHHHHHHHHHHHhCCCHHHH------------------------------------------HHHHHHHHhCC
Confidence            666666665544   445999999999                                          99999999999


Q ss_pred             CCc-ccchHHHHHHHHHHHHHhHhHHHHH------hh--------------------hhccccCCccchhHHHHHHHhh
Q psy11505        258 DVK-LDEFSSLKKFRNSILSSLGDCIYVL------RF--------------------WSTVHKDGKVLMNKLFVEMLEA  309 (312)
Q Consensus       258 ~~~-l~~~~~~~~~~~~~~~~l~~~~~~~------~~--------------------~~~~~~~~~~~~~~~~~~~~~~  309 (312)
                      |++ |+++++|+++|++++.+|.+|+..+      ||                    +++.++.|.+|+++|+.|||++
T Consensus       183 d~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL~~Lp~Lr~i~~~~~e~l~~~k~~~~~~~~~Ll~Eml~~  261 (266)
T 3kmr_A          183 DRQDLEQPDRVDMLQEPLLEALKVYVRKRRPSRPHMFPKMLMKITDLRSISAKGAERVITLKMEIPGSMPPLIQEMLEN  261 (266)
T ss_dssp             TSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSSCCCHHHHHHHC-
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHhHHHHHHHHHHHHHHHHHHhcCCCCcchHHHHHhcC
Confidence            998 9999999999999999999999865      32                    4556889999999999999986

>1l2j_A Estrogen receptor beta; nuclear receptor, transcription factor, antagonist transcription receptor; HET: ETC; 2.95A {Homo sapiens} SCOP: a.123.1.1

Probab=99.96  E-value=5.4e-29  Score=219.56  Aligned_cols=193  Identities=32%  Similarity=0.459  Sum_probs=151.0

Q ss_pred             HHHHHHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhh
Q psy11505         74 ENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTI  153 (312)
Q Consensus        74 ~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~  153 (312)
                      .+.++..+...++... .......+......+..++++..+.+..+|+|||++|+|.+|+.+||+.|||++|+++++|+.
T Consensus        31 ~~~~i~~ll~ae~~~~-~~~~~~~~~~~~~~~~~l~~~a~~~l~~~VewAK~lP~F~~L~~~DQi~LLk~~w~el~iL~~  109 (271)
T 1l2j_A           31 PEQLVLTLLEAEPPHV-LISRPSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGL  109 (271)
T ss_dssp             HHHHHHHHHHHCCCCC-CCCC-----CHHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHTTHHHHHHHHH
T ss_pred             hhHHHHHHHHcCCccc-cccCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHhCcccccCCHHHHHHHHHHHHHHHHHHHH
Confidence            4557888888777543 222222333445678999999999999999999999999999999999999999999999999


Q ss_pred             hhhcccCCCCeeEecccchhhHHhhh-hcccchhhhhhc---ccCccCCCCccccCCceeeeeCCCCcccccccccchhH
Q psy11505        154 AYRSLPHCAGKIRFASDLVLDERQAR-ECGFSEIYQQVK---HSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEAC  229 (312)
Q Consensus       154 a~rs~~~~~~~l~~~~g~~~~~~~~~-~~~~~~~~~~i~---~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~  229 (312)
                      ||++++..+ .+++++|..++++... ..+..++++.+.   ..+.+|++|++||                         
T Consensus       110 a~rs~~~~~-~l~~~~g~~~~~~~~~~~~g~~~~~~~l~~~~~~l~~L~ld~~E~-------------------------  163 (271)
T 1l2j_A          110 MWRSIDHPG-KLIFAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEY-------------------------  163 (271)
T ss_dssp             HHHTSSSTT-EECSSSSCCEETGGGGGSTTHHHHHHHHHHHHHHHHHTTCCHHHH-------------------------
T ss_pred             HHHhhccCC-eeeecCCccccchhhhhhccHHHHHHHHHHHHHHHHHhCCCHHHH-------------------------
Confidence            999999874 8889999877765432 234445555554   4445999999999                         


Q ss_pred             HHHHHHHhhhcccceecCCCCceeecCCCCc-ccc-------hHHHHHHHHHHHHHhHhHHHHH---------hh-----
Q psy11505        230 KAFFKRTIQVYSGYRQTGACGTLVLANSDVK-LDE-------FSSLKKFRNSILSSLGDCIYVL---------RF-----  287 (312)
Q Consensus       230 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-l~~-------~~~~~~~~~~~~~~l~~~~~~~---------~~-----  287 (312)
                                       +++|||+|||||++ +++       +++++++|++|..+|.+|+..+         ||     
T Consensus       164 -----------------~lLkAIvLfnpd~~gLs~~~~~~~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~~~~Rf~~LLl  226 (271)
T 1l2j_A          164 -----------------LCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLM  226 (271)
T ss_dssp             -----------------HHHHHHHHHHC----CCCCGGGHHHHHHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHH
T ss_pred             -----------------HHHHHHHHcCCCcCCCccchhhHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcchhHHHHHHHH
Confidence                             99999999999986 654       4578999999999999998531         33     


Q ss_pred             ---------------hhccccCCccchhHHHHHHHhhh
Q psy11505        288 ---------------WSTVHKDGKVLMNKLFVEMLEAY  310 (312)
Q Consensus       288 ---------------~~~~~~~~~~~~~~~~~~~~~~~  310 (312)
                                     ++++++.|.+|+++|+.|||+++
T Consensus       227 ~Lp~Lr~i~~~~~e~l~~~~~~g~~~~~~Ll~Eml~~~  264 (271)
T 1l2j_A          227 LLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEMLNAH  264 (271)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCTTSSCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhccCCCCChHHHHHHHHcCC
Confidence                           55678999999999999999875

>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=99.95  E-value=1.7e-28  Score=213.05  Aligned_cols=193  Identities=22%  Similarity=0.252  Sum_probs=153.8

Q ss_pred             HHHHHHHHHhcCcccc--cccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHH
Q psy11505         74 ENKMLEALLLCEPEML--TVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTL  151 (312)
Q Consensus        74 ~~~~l~~l~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L  151 (312)
                      ...+++......|...  ....+.+........+..++++....+..+|+|||++|+|.+|+.+||+.|||++|++++++
T Consensus        16 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~VewAK~lP~F~~L~~~DQi~LLk~~~~el~lL   95 (244)
T 1pdu_A           16 ITALVRSHVDTTPDPSCLDYSHYEEQSMSEADKVQQFYQLLTSSVDVIKQFAEKIPGYFDLLPEDQELLFQSASLELFVL   95 (244)
T ss_dssp             HHHHHHHHHHTSCCGGGCBCTTTSCCCCCHHHHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhccccCcCccCCCcccccccccchHHHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHH
Confidence            3455666665555422  12222233445678899999999999999999999999999999999999999999999999


Q ss_pred             hhhhhcccCCCCeeEecccchhhHHhhhhcccchhhhhhcc---cCccCCCCccccCCceeeeeCCCCcccccccccchh
Q psy11505        152 TIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKH---SGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEA  228 (312)
Q Consensus       152 ~~a~rs~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~i~~---~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~  228 (312)
                      +.||++++.. +.+++++|..+++..... +..++++.+..   .+.+|++|++||                        
T Consensus        96 ~~a~rs~~~~-~~l~~~~g~~~~~~~~~~-~~~~~~~~l~~~~~~l~~L~ld~~E~------------------------  149 (244)
T 1pdu_A           96 RLAYRARIDD-TKLIFCNGTVLHRTQCLR-SFGEWLNDIMEFSRSLHNLEIDISAF------------------------  149 (244)
T ss_dssp             HHHHHCCSSC-SEEECTTSBEEEHHHHHH-HHTTHHHHHHHHHHHHHHHCCCHHHH------------------------
T ss_pred             HHHHHhccCC-CceEeeCCeeecHHHHHh-HHHHHHHHHHHHHHHHHHHcCCHHHH------------------------
Confidence            9999998644 489999998877655432 44455555544   445999999999                        


Q ss_pred             HHHHHHHHhhhcccceecCCCCceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------hh------------
Q psy11505        229 CKAFFKRTIQVYSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------RF------------  287 (312)
Q Consensus       229 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------~~------------  287 (312)
                                        +++|||+||| |++ |++++.|+++|++++.+|.+|+..+        ||            
T Consensus       150 ------------------~lLkAIvLfn-d~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~~~Rf~~LL~~L~~Lr~  210 (244)
T 1pdu_A          150 ------------------ACLCALTLIT-ERHGLREPKKVEQLQMKIIGSLRDHVTYNAEAQKKQHYFSRLLGKLPELRS  210 (244)
T ss_dssp             ------------------HHHHHHHHSS-CCTTCSCHHHHHHHHHHHHHHHHHHHHHCHHHHTSTTHHHHHHTHHHHHHH
T ss_pred             ------------------HHHHHHHHhC-CCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHHHHHHHH
Confidence                              9999999998 676 9999999999999999999999653        22            


Q ss_pred             --------hhccccCCccchhHHHHHHHhhhc
Q psy11505        288 --------WSTVHKDGKVLMNKLFVEMLEAYL  311 (312)
Q Consensus       288 --------~~~~~~~~~~~~~~~~~~~~~~~~  311 (312)
                              +++.++.|.+|+++|+.||+++.+
T Consensus       211 l~~~~~e~l~~~~~~g~~~~~~Ll~Eml~~~~  242 (244)
T 1pdu_A          211 LSVQGLQRIFYLKLEDLVPAPALIENMFVTTL  242 (244)
T ss_dssp             HHHHHHHHHHHHHHHCSSCCCHHHHHTTTCC-
T ss_pred             HHHHHHHHHHHHccCCCCCchHHHHHHHhCCC
Confidence                    455688899999999999998753

>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=99.95  E-value=1.8e-28  Score=212.83  Aligned_cols=194  Identities=27%  Similarity=0.421  Sum_probs=152.7

Q ss_pred             HHHHHHHHHhcCcccccccCC--CCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHH
Q psy11505         74 ENKMLEALLLCEPEMLTVRSE--TPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTL  151 (312)
Q Consensus        74 ~~~~l~~l~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L  151 (312)
                      .+.+++.+...++........  ...+......+.++++++.+.+..+|+|||++|+|.+|+.+||+.|||++|.+++++
T Consensus        10 ~~~~l~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~vewak~ip~F~~L~~~DQ~~LLk~~w~e~~il   89 (240)
T 2p1t_A           10 VERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIA   89 (240)
T ss_dssp             HHHHHHHHHHHC-------------------CHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCccccccccccccCCCCcccHHHHHHHHHHHHHHHHHHHHHhCcChhcCCHHHHHHHHHHHHHHHHHH
Confidence            456777777766643211111  111223345678999999999999999999999999999999999999999999999


Q ss_pred             hhhhhcccCCCCeeEecccchhhHHhhhhcccchhhhh----hcccCccCCCCccccCCceeeeeCCCCcccccccccch
Q psy11505        152 TIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQ----VKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCE  227 (312)
Q Consensus       152 ~~a~rs~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~----i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~  227 (312)
                      +.||++++.++ .+++++|..++++.....+...++++    +...+.+|++|++||                       
T Consensus        90 ~~a~rs~~~~~-~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~-----------------------  145 (240)
T 2p1t_A           90 SFSHRSIAVKD-GILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTEL-----------------------  145 (240)
T ss_dssp             HHHHHTTTSSS-EEECTTSCEEEHHHHHTTTCHHHHHHHHHHTHHHHHHTTCCHHHH-----------------------
T ss_pred             HHHHhhccCCC-ceEecCCcccccchhhhhchHHHHHHHHHHHHHHHHhhCCCHHHH-----------------------
Confidence            99999998866 67889998887766655555555544    444556999999999                       


Q ss_pred             hHHHHHHHHhhhcccceecCCCCceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH------hh-------------
Q psy11505        228 ACKAFFKRTIQVYSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL------RF-------------  287 (312)
Q Consensus       228 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~------~~-------------  287 (312)
                                         ++++||+|||||++ ++++++|+++|+++..+|.+|+..+      ||             
T Consensus       146 -------------------~~Lkai~l~~pd~~gl~~~~~ve~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~~Lr~~  206 (240)
T 2p1t_A          146 -------------------GCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSI  206 (240)
T ss_dssp             -------------------HHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTTHHHHHHH
T ss_pred             -------------------HHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHHH
Confidence                               99999999999987 9999999999999999999999765      32             


Q ss_pred             -------hhccccCCccchhHHHHHHHhhh
Q psy11505        288 -------WSTVHKDGKVLMNKLFVEMLEAY  310 (312)
Q Consensus       288 -------~~~~~~~~~~~~~~~~~~~~~~~  310 (312)
                             +++.+++|.+|+++|+.|||++.
T Consensus       207 ~~~~~e~l~~~~~~~~~~~~~ll~eml~~~  236 (240)
T 2p1t_A          207 GLKCLEHLFFFKLIGDTPIDTFLMEMLEAP  236 (240)
T ss_dssp             HHHHHHHHHHHHHHCCSCCCHHHHHHTSCC
T ss_pred             HHHHHHHHHHhCcCCCCchHHHHHHHHcCC
Confidence                   45568899999999999999874

>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=99.95  E-value=3.6e-28  Score=213.90  Aligned_cols=168  Identities=18%  Similarity=0.318  Sum_probs=147.7

Q ss_pred             chhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhh
Q psy11505        100 PTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAR  179 (312)
Q Consensus       100 ~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~  179 (312)
                      .+...|..+++.....+..+|+|||++|+|.+|+.+||++|||++|+++++|+.|+++.+..+ .+.+++|..++++...
T Consensus        67 ~~~~~~~~~~~~~~~~l~~~VewaK~lP~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~-~l~~~~g~~~~~~~~~  145 (267)
T 3ilz_A           67 VDLEAFSEFTKIITPAITRVVDFAKKLPMFSELPXEDQIILLKGCCMEIMSLRAAVRYDPESD-TLTLSGEMAVKREQLK  145 (267)
T ss_dssp             BCHHHHHHHHHHHHHHHHHHHHHHHTSHHHHTSCHHHHHHHHHHHHHHHHHHHHHTTCBTTTT-BEEETTTEEECHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHhcCcchhhCCHhHHHHHHHHHHHHHHHHHHHHHhcCCCC-EEEecCCeeecHHHHh
Confidence            456789999999999999999999999999999999999999999999999999999988654 8999999888877766


Q ss_pred             hcccchhhhhhcc---cCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecC
Q psy11505        180 ECGFSEIYQQVKH---SGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLAN  256 (312)
Q Consensus       180 ~~~~~~~~~~i~~---~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  256 (312)
                      ..+.+++.+.+..   .+.+|++|++||                                          ++++||+|||
T Consensus       146 ~~~~~~~~~~i~~~~~~l~~L~ld~~E~------------------------------------------~lLkAivL~~  183 (267)
T 3ilz_A          146 NGGLGVVSDAIFELGKSLSAFNLDDTEV------------------------------------------ALLQAVLLMS  183 (267)
T ss_dssp             HTTTTHHHHHHHHHHHHHGGGCCCHHHH------------------------------------------HHHHHHHHSC
T ss_pred             ccCHHHHHHHHHHHHHHHHHhcCCHHHH------------------------------------------HHHHHHHhcC
Confidence            6666666655554   445999999999                                          9999999999


Q ss_pred             CCCc-ccchHHHHHHHHHHHHHhHhHHHHH------h--------------------hhhccccCCccch-hHHHHHHHh
Q psy11505        257 SDVK-LDEFSSLKKFRNSILSSLGDCIYVL------R--------------------FWSTVHKDGKVLM-NKLFVEMLE  308 (312)
Q Consensus       257 ~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~------~--------------------~~~~~~~~~~~~~-~~~~~~~~~  308 (312)
                      ||++ |+++++|+++|++++.+|.+|+..+      |                    .+++.++.|.+|+ ++|+.|||+
T Consensus       184 pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~Rf~~LL~~Lp~Lr~l~~~~~e~l~~~k~~~~~~~~~~Ll~Em~~  263 (267)
T 3ilz_A          184 TDRSGLLXVDKIEKSQEAYLLAFEHYVNHRKHNIPHFWPKLLMKVTDLRMIGAXHASRFLHMKVEXPTELFPPLFLEVFE  263 (267)
T ss_dssp             CCSSSCSCHHHHHHHHHHHHHHHHHHHHHHTCSSTTHHHHHHHHHHHHHHHHHHHHHHHHC-CCSSCGGGSCHHHHHHTC
T ss_pred             CCCCCCchHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHhHHHHHHHHHHHHHHHHHHhcCCccCCCcHHHHHhc
Confidence            9998 9999999999999999999999865      2                    3566789999997 999999998


Q ss_pred             hh
Q psy11505        309 AY  310 (312)
Q Consensus       309 ~~  310 (312)
                      +.
T Consensus       264 ~~  265 (267)
T 3ilz_A          264 DQ  265 (267)
T ss_dssp             CS
T ss_pred             CC
Confidence            73

>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=99.95  E-value=1.2e-28  Score=216.03  Aligned_cols=193  Identities=24%  Similarity=0.414  Sum_probs=160.8

Q ss_pred             HHHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhh
Q psy11505         77 MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYR  156 (312)
Q Consensus        77 ~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~r  156 (312)
                      ++..+...+|...........++.....+.+++++..+.+..+|+|||++|+|.+|+.+||+.|||++|+++++|+.||+
T Consensus        14 ~~~~l~~~ep~~~~~~~~~~~~~~~~~~~~~l~e~a~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~r   93 (260)
T 3vhv_A           14 PVMVLENIEPEIVYAGYDSSKPDTAENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQYSWMSLLSFALSWR   93 (260)
T ss_dssp             HHHHHHHHCCCCCCCCCCTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCcccccCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHhChHHhcCCHHHHHHHHHHhHHHHHHHHHHHH
Confidence            56777888887766665555666788899999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCC-CeeEecccchhhHHhhhhcccchhhhhh---cccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHH
Q psy11505        157 SLPHCA-GKIRFASDLVLDERQARECGFSEIYQQV---KHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAF  232 (312)
Q Consensus       157 s~~~~~-~~l~~~~g~~~~~~~~~~~~~~~~~~~i---~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~  232 (312)
                      +++.+. +.+.+++|..++++.....+..++++.+   ...+.+|++|++||                            
T Consensus        94 s~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~----------------------------  145 (260)
T 3vhv_A           94 SYKHTNSQFLYFAPDLVFNEEKMHQSAMYELCQGMHQISLQFVRLQLTFEEY----------------------------  145 (260)
T ss_dssp             HHHHHTTSSEEEETTEEECHHHHHHTTCHHHHHHHHHHHHHHHHHTCCHHHH----------------------------
T ss_pred             hhccCCCCeEEecCCccccHHHhhcccHHHHHHHHHHHHHHHHHcCCCHHHH----------------------------
Confidence            998765 5789999988877766556665555444   44555999999999                            


Q ss_pred             HHHHhhhcccceecCCCCceeecCC-CCc-ccchHHHHHHHHHHHHHhHhHHHHH---------hh--------------
Q psy11505        233 FKRTIQVYSGYRQTGACGTLVLANS-DVK-LDEFSSLKKFRNSILSSLGDCIYVL---------RF--------------  287 (312)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~~~~l~~~-~~~-l~~~~~~~~~~~~~~~~l~~~~~~~---------~~--------------  287 (312)
                                    +++|||+|||| |++ |+++++|+++|++++.+|.+|+..+         ||              
T Consensus       146 --------------~lLkAIvLfnp~d~~gL~~~~~ve~lqe~~~~aL~~y~~~~~~~~~~~~~RF~~LL~~Lp~Lr~l~  211 (260)
T 3vhv_A          146 --------------TIMKVLLLLSTIPKDGLKSQAAFEEMRTNYIKELRKMVTKCPNNSGQSWQRFYQLTKLLDSMHDLV  211 (260)
T ss_dssp             --------------HHHHHHHHTSEEETTCCTTHHHHHHHHHHHHHHHHHHHHC-----CCHHHHHHHHHHHHHHHHHHH
T ss_pred             --------------HHHHHHHHcCCcCCCCCcCHHHHHHHHHHHHHHHHHHHHhcCCCCCcHhhHHHHHHHHHHHHHHHH
Confidence                          99999999999 887 9999999999999999999999632         33              


Q ss_pred             ------hhcc---ccCCccchhHHHHHHHhhhc
Q psy11505        288 ------WSTV---HKDGKVLMNKLFVEMLEAYL  311 (312)
Q Consensus       288 ------~~~~---~~~~~~~~~~~~~~~~~~~~  311 (312)
                            +++.   ...+.+++++|+.||+++++
T Consensus       212 ~~~~e~lff~~~~~~~~~~~~p~Ll~Ei~~~~~  244 (260)
T 3vhv_A          212 SDLLEFCFYTFRESHALKVEFPAMLVEIISDQL  244 (260)
T ss_dssp             HHHHHHHHHHHHTHHHHTCCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhcccCCCcHHHHHHHhccC
Confidence                  1211   13568899999999998763

>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=99.95  E-value=1.5e-28  Score=213.99  Aligned_cols=168  Identities=24%  Similarity=0.359  Sum_probs=142.2

Q ss_pred             hHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCC-CCeeEecccchhhHHhhh-
Q psy11505        102 LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHC-AGKIRFASDLVLDERQAR-  179 (312)
Q Consensus       102 ~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~-~~~l~~~~g~~~~~~~~~-  179 (312)
                      ...+..++++..+.+..+|+|||++|+|.+|+.+||+.|||++|+++++|+.||++++.. .+.+.+++|..++.+... 
T Consensus        44 ~~~~~~l~~~a~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~rs~~~~~~~~~~~~~g~~~~~~~~~~  123 (246)
T 1ymt_A           44 PAPFSLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNSWSELLVLDHIYRQVQYGKEDSILLVTGQEVELSTVAV  123 (246)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCTTEEECTTSCEEEHHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHHHHHHhChhHHhCCHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCeeEecCCCccchhhhhh
Confidence            346788999999999999999999999999999999999999999999999999999873 468889999877665432 


Q ss_pred             hccc--chhh---hhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceee
Q psy11505        180 ECGF--SEIY---QQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVL  254 (312)
Q Consensus       180 ~~~~--~~~~---~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  254 (312)
                      ..+.  .+++   .++...+.+|++|++||                                          +++|||+|
T Consensus       124 ~~~~~~~~~~~~~~~~~~~~~~L~ld~~E~------------------------------------------~lLkAivL  161 (246)
T 1ymt_A          124 QAGSLLHSLVLRAQELVLQLHALQLDRQEF------------------------------------------VCLKFLIL  161 (246)
T ss_dssp             HCCHHHHHHHHHHHHHHHHHHHTTCCHHHH------------------------------------------HHHHHHHH
T ss_pred             hcchhHHHHHHHHHHHHHHHHHHCCCHHHH------------------------------------------HHHHHHHh
Confidence            2221  2333   34455556999999999                                          99999999


Q ss_pred             cCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH------h--------------------hhhccccCCccchhHHHHHHH
Q psy11505        255 ANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL------R--------------------FWSTVHKDGKVLMNKLFVEML  307 (312)
Q Consensus       255 ~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~------~--------------------~~~~~~~~~~~~~~~~~~~~~  307 (312)
                      ||||++ +++.+.|+++|++++.+|.+|+..+      |                    ++++.++.|.+|+++|+.|||
T Consensus       162 ~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~Rf~~LL~~L~~Lr~~~~~~~e~l~~~~~~~~~~~~~Ll~Eml  241 (246)
T 1ymt_A          162 FSLDVKFLNNHSLVKDAQEKANAALLDYTLSHYPHSGDKFQQLLLSLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIEML  241 (246)
T ss_dssp             TCSCGGGSSCHHHHHHHHHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSCTTCHHHHHH
T ss_pred             cCCcccccccHHHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHHHHhHHHHHHHHHHHHHHHhhcccCCCcHHHHHHHHH
Confidence            999998 9999999999999999999999765      3                    355678899999999999999


Q ss_pred             hhhc
Q psy11505        308 EAYL  311 (312)
Q Consensus       308 ~~~~  311 (312)
                      +++.
T Consensus       242 ~~~~  245 (246)
T 1ymt_A          242 QAKQ  245 (246)
T ss_dssp             HC--
T ss_pred             hCcc
Confidence            9863

>1hg4_A Ultraspiracle; nuclear hormone receptor, transcription factor, ligand binding; HET: LPP; 2.4A {Drosophila melanogaster} SCOP: a.123.1.1

Probab=99.95  E-value=7.1e-28  Score=213.57  Aligned_cols=168  Identities=20%  Similarity=0.348  Sum_probs=136.0

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCe-------eEeccc---
Q psy11505        101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGK-------IRFASD---  170 (312)
Q Consensus       101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~-------l~~~~g---  170 (312)
                      ....+.++++++.+.+..+|+|||++|+|.+|+.+||+.|||++|+++++|+.||++++.+++.       +.+++|   
T Consensus        45 ~~~~~~~l~~~~~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~rs~~~~~~~~~~~~~~~~~~dGs~~  124 (279)
T 1hg4_A           45 YKGAVSALCQVVNKQLFQMVEYARMMPHFAQVPLDDQVILLKAAWIELLIANVAWCSIVSLDDGGAGGGGGGLGHDGSFE  124 (279)
T ss_dssp             GHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTTC-------------------
T ss_pred             hhhhHHHHHHHHHHHHHHHHHHHhcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhccCcccccccccccccCcccc
Confidence            3457899999999999999999999999999999999999999999999999999999876531       344444   


Q ss_pred             ----------------chhhHHhhhhcccchhhhh----hcccCccCCCCccccCCceeeeeCCCCcccccccccchhHH
Q psy11505        171 ----------------LVLDERQARECGFSEIYQQ----VKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACK  230 (312)
Q Consensus       171 ----------------~~~~~~~~~~~~~~~~~~~----i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~  230 (312)
                                      ..+++......+..+++++    +...+.+|++|++||                          
T Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~ld~~E~--------------------------  178 (279)
T 1hg4_A          125 RRSPGLQPQQLFLNQSFSYHRNSAIKAGVSAIFDRILSELSVKMKRLNLDRREL--------------------------  178 (279)
T ss_dssp             ------CCCEEESSSSCEEEHHHHHHHTCHHHHHHHHHHTHHHHHHHTCCHHHH--------------------------
T ss_pred             ccccccccceeeecCCcccchhhHhhcchHHHHHHHHHHHHHHHHHhcCCHHHH--------------------------
Confidence                            3333333334455555544    444556999999999                          


Q ss_pred             HHHHHHhhhcccceecCCCCceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH------h-----------------
Q psy11505        231 AFFKRTIQVYSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL------R-----------------  286 (312)
Q Consensus       231 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~------~-----------------  286 (312)
                                      +++|||+|||||++ |+++..|+++|++|+.+|.+|+..+      |                 
T Consensus       179 ----------------~lLkAivL~npd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL~~L~~Lr~~~~~  242 (279)
T 1hg4_A          179 ----------------SCLKAIILYNPDIRGIKSRAEIEMCREKVYACLDEHCRLEHPGDDGRFAQLLLRLPALRSISLK  242 (279)
T ss_dssp             ----------------HHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHH
T ss_pred             ----------------HHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHHHHH
Confidence                            99999999999998 9999999999999999999999765      3                 


Q ss_pred             ---hhhccccCCccchhHHHHHHHhhh
Q psy11505        287 ---FWSTVHKDGKVLMNKLFVEMLEAY  310 (312)
Q Consensus       287 ---~~~~~~~~~~~~~~~~~~~~~~~~  310 (312)
                         .+++.+++|.+|+++|+.|||++.
T Consensus       243 ~~e~l~~~~~~g~~~~~~Ll~Eml~~~  269 (279)
T 1hg4_A          243 CQDHLFLFRITSDRPLEELFLEQLEAP  269 (279)
T ss_dssp             HHHHHHHHTCBCSSCHHHHHHHHHTSC
T ss_pred             HHHHHHHHhhhCCCcHHHHHHHHHhCC
Confidence               355678899999999999999875

>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=99.95  E-value=1.7e-28  Score=215.05  Aligned_cols=193  Identities=24%  Similarity=0.408  Sum_probs=161.2

Q ss_pred             HHHHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhh
Q psy11505         76 KMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAY  155 (312)
Q Consensus        76 ~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~  155 (312)
                      .++..+...+|.......+...++.....+.++++++.+.+..+|+|||++|+|.+|+.+||+.|+|++|+++++|+.||
T Consensus        15 ~~~~~l~~~ep~~~~~~~~~~~~~~~~~~~~~l~~~a~~~l~~~VewaK~iP~F~~L~~~DQ~~LLk~~~~el~iL~~a~   94 (261)
T 3mnp_A           15 TLVSLLEVIEPEVLYAGYDSSVPDSAWRIMTTLNMLGGRQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMVFALGW   94 (261)
T ss_dssp             SHHHHHHHHSCCCCCCCCCTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCccccccCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHhCcChhcCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            36888888999887666666666777889999999999999999999999999999999999999999999999999999


Q ss_pred             hcccCCCC-eeEecccchhhHHhhhhcccchhhhhhc---ccCccCCCCccccCCceeeeeCCCCcccccccccchhHHH
Q psy11505        156 RSLPHCAG-KIRFASDLVLDERQARECGFSEIYQQVK---HSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKA  231 (312)
Q Consensus       156 rs~~~~~~-~l~~~~g~~~~~~~~~~~~~~~~~~~i~---~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~  231 (312)
                      +|++.+.+ .+.+++|..++++.....+..++++.+.   ..+.+|++|++||                           
T Consensus        95 rs~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~---------------------------  147 (261)
T 3mnp_A           95 RSYRQASGNLLCFAPDLIINEQRMTLPCMYDQCKHMLFISTELQRLQVSYEEY---------------------------  147 (261)
T ss_dssp             HHHHHHTTSSEEEETTEEECHHHHTSTTTHHHHHHHHHHHHHHHHHTCCHHHH---------------------------
T ss_pred             HcccCCCCCEEEecCCcccchhhhhhhhHHHHHHHHHHHHHHHHHhCCCHHHH---------------------------
Confidence            99987764 5888999888877665556655555444   4455999999999                           


Q ss_pred             HHHHHhhhcccceecCCCCceeecCC-CCc-ccchHHHHHHHHHHHHHhHhHHHHH---------hh-------------
Q psy11505        232 FFKRTIQVYSGYRQTGACGTLVLANS-DVK-LDEFSSLKKFRNSILSSLGDCIYVL---------RF-------------  287 (312)
Q Consensus       232 ~~~~~~~~~~~~~~~~~~~~~~l~~~-~~~-l~~~~~~~~~~~~~~~~l~~~~~~~---------~~-------------  287 (312)
                                     +++|||+|||| |++ |++.++|+++|++|+.+|.+|+..+         ||             
T Consensus       148 ---------------~lLkAIvL~np~d~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~~~~Rf~~LL~lL~~Lr~l  212 (261)
T 3mnp_A          148 ---------------LCMKTLLLLSSVPKEGLKSQELFDEIRMTYIKELGKAIAKRGGNSSQNWQRFYQLTKLLDSMHDV  212 (261)
T ss_dssp             ---------------HHHHHHHHTSEEETTCCTTHHHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ---------------HHHHHHHHcCCCCcCCCccHHHHHHHHHHHHHHHHHHHHhhCCCCchhhhHHHHHHHHHHHHHHH
Confidence                           99999999999 987 9999999999999999999999643         33             


Q ss_pred             -------hhcccc--CCccchhHHHHHHHhhh
Q psy11505        288 -------WSTVHK--DGKVLMNKLFVEMLEAY  310 (312)
Q Consensus       288 -------~~~~~~--~~~~~~~~~~~~~~~~~  310 (312)
                             +++.++  .+.+.+++|+.||++.+
T Consensus       213 ~~~~~e~~f~~~~~~~~~~~~p~Ll~Ei~~~~  244 (261)
T 3mnp_A          213 VENLLSYCFQTFLDKSMSIEFPEMLAEIITNQ  244 (261)
T ss_dssp             HHHHHHHHHHHHHCGGGCCCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhcccCCCcHHHHHHHhcc
Confidence                   111222  24677999999999875

>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=99.95  E-value=3.1e-28  Score=211.81  Aligned_cols=195  Identities=24%  Similarity=0.325  Sum_probs=141.0

Q ss_pred             HHHHHHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhh
Q psy11505         74 ENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTI  153 (312)
Q Consensus        74 ~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~  153 (312)
                      .+.++..+...+|..................+.++++++.+.+..+|+|||++|+|.+|+.+||+.|||++|+++++|+.
T Consensus         8 ~~~~~~~l~~~e~~~~~~~~~~~~~~~~~~~~~~l~e~a~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~   87 (244)
T 3cjw_A            8 LSGYISLLLRAEPYPTSRFGSQCMQPNNIMGIENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNA   87 (244)
T ss_dssp             HHHHHHHHHHTCSSCC-------------CCCCCHHHHHHHHHHHHHHHHHHSSSGGGSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCCCcCCCCcccCCCccccHHHHHHHHHHHHHHHHhHHHhCCChhcCCHHHHHHHHHHHHHHHHHHHH
Confidence            35567777777764321100001111223467889999999999999999999999999999999999999999999999


Q ss_pred             hhhcccCCCCeeEecccchhhHHhh-hhcccch---hhhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhH
Q psy11505        154 AYRSLPHCAGKIRFASDLVLDERQA-RECGFSE---IYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEAC  229 (312)
Q Consensus       154 a~rs~~~~~~~l~~~~g~~~~~~~~-~~~~~~~---~~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~  229 (312)
                      ||++++.+.+.+.+++|........ ...++.+   .+.++...+.+|++|++||                         
T Consensus        88 a~~s~~~~~~~~l~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~ld~~E~-------------------------  142 (244)
T 3cjw_A           88 AQCSMPLHVAPLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEY-------------------------  142 (244)
T ss_dssp             HHHTCCCSCCC-----------------CCCSHHHHHHHHHHHHHHHTTCCHHHH-------------------------
T ss_pred             HHHhccccccccccccccccCccchhhhHHHHHHHHHHHHHHHHHHHhCCCHHHH-------------------------
Confidence            9999998876677777754321111 1111222   2344455666999999999                         


Q ss_pred             HHHHHHHhhhcccceecCCCCceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH------h----------------
Q psy11505        230 KAFFKRTIQVYSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL------R----------------  286 (312)
Q Consensus       230 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~------~----------------  286 (312)
                                       +++|||+|||||++ +++.+.|+++|++++.+|.+|+..+      |                
T Consensus       143 -----------------~lLkaivL~~pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~Rf~~LLl~L~~Lr~l~~  205 (244)
T 3cjw_A          143 -----------------SCLKAIVLFTSDACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSS  205 (244)
T ss_dssp             -----------------HHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTTHHHHHHSCH
T ss_pred             -----------------HHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHhHHHHhhhH
Confidence                             99999999999998 9999999999999999999999865      2                


Q ss_pred             ----hhhccccCCccchhHHHHHHHhhh
Q psy11505        287 ----FWSTVHKDGKVLMNKLFVEMLEAY  310 (312)
Q Consensus       287 ----~~~~~~~~~~~~~~~~~~~~~~~~  310 (312)
                          .+++.++.|.+|+++|+.|||++.
T Consensus       206 ~~~e~l~~~~~~~~~~~~~Ll~eml~~~  233 (244)
T 3cjw_A          206 SVIEQLFFVRLVGKTPIETLIRDMLLSG  233 (244)
T ss_dssp             HHHHHHHTHHHHTTCCGGGTHHHHHTCC
T ss_pred             HHHHHHHhhcccCCCcHHHHHHHHHhCC
Confidence                355568889999999999999864

>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=99.95  E-value=1.7e-28  Score=215.64  Aligned_cols=168  Identities=21%  Similarity=0.216  Sum_probs=132.2

Q ss_pred             hHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeE---ecccchhhHHh-
Q psy11505        102 LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIR---FASDLVLDERQ-  177 (312)
Q Consensus       102 ~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~---~~~g~~~~~~~-  177 (312)
                      ....+.+++++.+.++.+|+|||++|+|.+|+.+||++|||++|+++++|+.|+++++.....+.   +.+|...+... 
T Consensus        46 l~~~~~l~e~a~~~L~~~V~wAK~iP~F~~L~~~DQv~LLk~~w~ElllL~~A~rs~~~~~~~~~~~~~~~~il~~~~~~  125 (268)
T 3f5c_B           46 LKDPQVVCEAASAGLLKTLRFVKYLPCFQILPLDQQLVLVRSCWAPLLMLELAQDHLHFEMMEIPETNTTQEMLTTRRQE  125 (268)
T ss_dssp             -CCHHHHHHHHHHHHHHHHHHHHTCHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTTCCCCCCCC----------------
T ss_pred             cCCHHHHHHHHHHHHHHHHHHHccCCCcccCCHHHHHHHHHHHhHHHHHHHHHHHhccccccccchhhhhhhhhcccccc
Confidence            34678899999999999999999999999999999999999999999999999999987763321   12232222211 


Q ss_pred             --------------------hhhcc-cchhh---hhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHH
Q psy11505        178 --------------------ARECG-FSEIY---QQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFF  233 (312)
Q Consensus       178 --------------------~~~~~-~~~~~---~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~  233 (312)
                                          ....+ ..+.+   .++...+.+|++|++||                             
T Consensus       126 ~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~i~~l~~~~~~l~~L~ld~~E~-----------------------------  176 (268)
T 3f5c_B          126 TEGPEPAEPQATEQPQMVSAEAGHLLPAAAVQAIKSFFFKCWSLNIDTKEY-----------------------------  176 (268)
T ss_dssp             -----------------------CCCCSSHHHHHHHHHHHHHHTTCCHHHH-----------------------------
T ss_pred             cccccccccccccccccccchhccccHHHHHHHHHHHHHHHHHhCCCHHHH-----------------------------
Confidence                                00111 12333   34445556999999999                             


Q ss_pred             HHHhhhcccceecCCCCceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------------------------h
Q psy11505        234 KRTIQVYSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------------------------R  286 (312)
Q Consensus       234 ~~~~~~~~~~~~~~~~~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------------------------~  286 (312)
                                   +++|||+|||||++ |++..+|+++|++++.+|.+|+..+                          +
T Consensus       177 -------------~lLkAivL~npd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL~~Lp~LR~i~~~~~e  243 (268)
T 3f5c_B          177 -------------AYLKGTVLFNPDLPGLQCVKYIEGLQWRTQQILTEHIRMMQREYQIRSAELNSALFLLRFINSDVVT  243 (268)
T ss_dssp             -------------HHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHSSCSSHHHHHHHHHHHHHTTSCSSHHH
T ss_pred             -------------HHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHHHHHHHHHH
Confidence                         99999999999998 9999999999999999999999865                          3


Q ss_pred             hhhccccCCccchhHHHHHHHhhhc
Q psy11505        287 FWSTVHKDGKVLMNKLFVEMLEAYL  311 (312)
Q Consensus       287 ~~~~~~~~~~~~~~~~~~~~~~~~~  311 (312)
                      .+++++++|.+||++||.|||+|++
T Consensus       244 ~l~~~k~~g~~~i~~Ll~Eml~a~~  268 (268)
T 3f5c_B          244 ELFFRPIIGAVSMDDMMLEMLCAKL  268 (268)
T ss_dssp             HHHTHHHHCSCCHHHHHHHHTTSCC
T ss_pred             HHhhhhhcCCCCchHHHHHHHhCcC
Confidence            3667899999999999999999864

>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=99.95  E-value=1.8e-28  Score=213.79  Aligned_cols=170  Identities=21%  Similarity=0.239  Sum_probs=136.6

Q ss_pred             CchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchh----h
Q psy11505         99 DPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVL----D  174 (312)
Q Consensus        99 ~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~----~  174 (312)
                      .+....+.++++|..+.++.+|+|||++|+|.+|+.+||+.|||++|+++++|+.|+++++.+.+.+.+++|...    .
T Consensus        30 ~p~~~~~~~~~e~a~~~L~~~VewaK~iP~F~~L~~~DQ~~LLk~~w~el~~L~~a~~s~~~~~~~~l~~~~~~~~~~~~  109 (249)
T 3p0u_A           30 MPEYLNVHYICESASRLLFLSMHWARSIPAFQALGQDCNTSLVRACWNELFTLGLAQCAQVMSLSTILAAIVNHLQNSIQ  109 (249)
T ss_dssp             CCCCSCSSCHHHHHHHHHHHHHHHHHTCTTTGGGCHHHHHHHHHTTHHHHHHHHHHHTTTSCCCCCCCCC-CC---CC--
T ss_pred             CCcccCHHHHHHHHHHHHHHHHHHHHcCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHcccCCcchhhcccccccccccc
Confidence            344556889999999999999999999999999999999999999999999999999999877656666554322    1


Q ss_pred             HHhhhhcccchh------hhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCC
Q psy11505        175 ERQARECGFSEI------YQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGA  248 (312)
Q Consensus       175 ~~~~~~~~~~~~------~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  248 (312)
                      ++.....+...+      +.++...+.+|++|++||                                          ++
T Consensus       110 ~~~~~~~~~~~~~~~i~~l~~~~~~l~~L~ld~~E~------------------------------------------~l  147 (249)
T 3p0u_A          110 EDKLSGDRIKQVMEHIWKLQEFCNSMAKLDIDGYEY------------------------------------------AY  147 (249)
T ss_dssp             -------CCCCHHHHHHHHHHHHHHHHHTTCCHHHH------------------------------------------HH
T ss_pred             cccchhhhhhhHHHHHHHHHHHHHHHHhhCCCHHHH------------------------------------------HH
Confidence            111111222222      234455666999999999                                          99


Q ss_pred             CCceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------------------------hhhhccccCCccchhH
Q psy11505        249 CGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------------------------RFWSTVHKDGKVLMNK  301 (312)
Q Consensus       249 ~~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------------------------~~~~~~~~~~~~~~~~  301 (312)
                      +|||+|||||++ |+++.+|+++|++++.+|.+|+..+                          +.+++++++|.+|+++
T Consensus       148 LkAivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~Rf~~LL~~L~~Lr~i~~~~~e~l~f~~~~g~~~i~~  227 (249)
T 3p0u_A          148 LKAIVLFSPDHPGLTSTSQIEKFQEAAQMELQDYVQATYSEDTYRLARILVRLPALRLMSSNITEELFFTGLIGNVSIDS  227 (249)
T ss_dssp             HHHHHHTCSCSTTCCCSHHHHHHHHHHHHHHHHHHHHHTTTCSTHHHHHHTTHHHHHTSCHHHHHHHHCCSSHHHHCHHH
T ss_pred             HHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHHHHeeeecccCCCCHHH
Confidence            999999999998 9999999999999999999999876                          3367789999999999


Q ss_pred             HHHHHHhhh
Q psy11505        302 LFVEMLEAY  310 (312)
Q Consensus       302 ~~~~~~~~~  310 (312)
                      ||.|||++.
T Consensus       228 Ll~eml~~~  236 (249)
T 3p0u_A          228 IIPYILKME  236 (249)
T ss_dssp             HHHHHTTC-
T ss_pred             HHHHHHhCC
Confidence            999999864

>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=99.95  E-value=2.4e-28  Score=214.29  Aligned_cols=193  Identities=25%  Similarity=0.489  Sum_probs=154.9

Q ss_pred             HHHHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhh
Q psy11505         76 KMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAY  155 (312)
Q Consensus        76 ~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~  155 (312)
                      .++..+...+|...........++.....+..++++..+.+..+|+|||++|+|.+|+.+||+.|||++|.++++++.||
T Consensus        14 ~~~~~l~~~ep~~~~~~~~~~~~~~~~~~~~~l~e~a~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~a~   93 (261)
T 1sqn_A           14 PLINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGW   93 (261)
T ss_dssp             HHHHHHHHHSCCCCCCCCCC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCcccccCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHhCccHhhCCHHHHHHHHHhhHHHHHHHHHHH
Confidence            57788888888654443333344556678899999999999999999999999999999999999999999999999999


Q ss_pred             hcccCCCC-eeEecccchhhHHhhhhcccchhh---hhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHH
Q psy11505        156 RSLPHCAG-KIRFASDLVLDERQARECGFSEIY---QQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKA  231 (312)
Q Consensus       156 rs~~~~~~-~l~~~~g~~~~~~~~~~~~~~~~~---~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~  231 (312)
                      ++++.+.+ .+.+++|..++++.....+..++.   .++...+++|++|++||                           
T Consensus        94 ~s~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~l~~L~ld~~E~---------------------------  146 (261)
T 1sqn_A           94 RSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEF---------------------------  146 (261)
T ss_dssp             HHHHHHTTSSEEEETTEEECGGGCCSHHHHHHHHHHHHHHHHHHHHTCCHHHH---------------------------
T ss_pred             HhhhcCCCCeEEeCCCcccchHhhhhhhHHHHHHHHHHHHHHHHHHCCCHHHH---------------------------
Confidence            99887654 578888887766543333333333   34455566999999999                           


Q ss_pred             HHHHHhhhcccceecCCCCceeecCC-CCc-ccchHHHHHHHHHHHHHhHhHHHHH---------hh-------------
Q psy11505        232 FFKRTIQVYSGYRQTGACGTLVLANS-DVK-LDEFSSLKKFRNSILSSLGDCIYVL---------RF-------------  287 (312)
Q Consensus       232 ~~~~~~~~~~~~~~~~~~~~~~l~~~-~~~-l~~~~~~~~~~~~~~~~l~~~~~~~---------~~-------------  287 (312)
                                     +++|||+|||| |++ |++.++|+++|++++.+|.+|+..+         ||             
T Consensus       147 ---------------~lLkAIvLfnp~~~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~~~~Rf~~LL~~L~~Lr~~  211 (261)
T 1sqn_A          147 ---------------LCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDL  211 (261)
T ss_dssp             ---------------HHHHHHHHTSEECTTCCTTHHHHHHHHHHHHHHHHHHHHTTC-CHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ---------------HHHHHHHHcCCCcccccccHHHHHHHHHHHHHHHHHHHHhhCCCCCchHHHHHHHHHHhHHHHHH
Confidence                           99999999999 887 9999999999999999999999631         33             


Q ss_pred             -----hhccccC-----CccchhHHHHHHHhhh
Q psy11505        288 -----WSTVHKD-----GKVLMNKLFVEMLEAY  310 (312)
Q Consensus       288 -----~~~~~~~-----~~~~~~~~~~~~~~~~  310 (312)
                           .++.+++     |.+++++|+.||+++.
T Consensus       212 ~~~~~~~~~~~~~q~~~~~~~~~~Ll~Ei~~~~  244 (261)
T 1sqn_A          212 VKQLHLYCLNTFIQSRALSVEFPEMMSEVIAAQ  244 (261)
T ss_dssp             HHHHHHHHHHHHHTHHHHTCCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcCCCCChHHHHHHHHhcC
Confidence                 1224566     8999999999999853

>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=99.94  E-value=1.6e-28  Score=222.93  Aligned_cols=194  Identities=27%  Similarity=0.427  Sum_probs=140.3

Q ss_pred             HHHHHHHHhcCcccccc--------cC--CCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHH
Q psy11505         75 NKMLEALLLCEPEMLTV--------RS--ETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQST  144 (312)
Q Consensus        75 ~~~l~~l~~~~~~~~~~--------~~--~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~  144 (312)
                      +.++..+...++.....        ..  .......+...+..+++++.+.+..+|+|||++|+|.+|+.+||+.|||++
T Consensus       113 p~~i~~l~~~epde~~~~~~i~~~l~~~~~~~~~~~r~~~~~~l~e~a~~~L~~~VewAK~iP~F~~L~~~DQi~LLk~~  192 (352)
T 3tx7_B          113 PHLILELLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNC  192 (352)
T ss_dssp             CHHHHHHHTTCCCHHHHHHHHHHHHHTTCC------CCCHHHHHHHHHHHHHHHHHHHTCCC----------CHHHHHHH
T ss_pred             CHHHHHHHHhCCcHHHHHHHhhcccccccccccccchhHHHHHHHHHHHHHHHHHHHHHHcChhhhhCCHHHHHHHHHHH
Confidence            35778888877761111        10  111222345788999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhhhhcccCCC-CeeEecccchhhHHhhh-hccc--chhh---hhhcccCccCCCCccccCCceeeeeCCCCc
Q psy11505        145 WAEILTLTIAYRSLPHCA-GKIRFASDLVLDERQAR-ECGF--SEIY---QQVKHSGSLDGIKEEELPRRLCLVCGDVAS  217 (312)
Q Consensus       145 ~~~~~~L~~a~rs~~~~~-~~l~~~~g~~~~~~~~~-~~~~--~~~~---~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~  217 (312)
                      |+++++|+.||+++..+. +.+++++|..++..... ..+.  .+++   .++...+.+|++|++||             
T Consensus       193 w~ElllL~~a~rs~~~~~~~~ll~~~G~~i~~~~~~~~~g~~~~~l~~~l~~l~~~l~~L~ld~~Ey-------------  259 (352)
T 3tx7_B          193 WSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREF-------------  259 (352)
T ss_dssp             HHHHHHHHHHHHHHHTCCSSCCBCTTCCBCCHHHHHHTSCHHHHHHHHHHHHHHHHHHHTTCCHHHH-------------
T ss_pred             HHHHHHHHHHHHHHhcCCCCeEEecCCCcccHHHHHHhccccHHHHHHHHHHHHHHHHHHcCCHHHH-------------
Confidence            999999999999988763 67888999877765443 2222  2333   44555566999999999             


Q ss_pred             ccccccccchhHHHHHHHHhhhcccceecCCCCceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH-----------
Q psy11505        218 GFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL-----------  285 (312)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~-----------  285 (312)
                                                   ++||||+|||||++ |++.++|+++|++++.+|.+|+..+           
T Consensus       260 -----------------------------alLkAIvLfnpd~~gLs~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~RF~kL  310 (352)
T 3tx7_B          260 -----------------------------VCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQL  310 (352)
T ss_dssp             -----------------------------HHHHHHHHSCSCC------CHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHH
T ss_pred             -----------------------------HHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHHHHhCCCccHHHHHH
Confidence                                         99999999999998 9999999999999999999999765           


Q ss_pred             ---------------hhhhccccCCccchhHHHHHHHhhh
Q psy11505        286 ---------------RFWSTVHKDGKVLMNKLFVEMLEAY  310 (312)
Q Consensus       286 ---------------~~~~~~~~~~~~~~~~~~~~~~~~~  310 (312)
                                     +.+++++++|.+|+++||.|||+++
T Consensus       311 LllLp~LR~ls~~~~e~L~~~kl~g~~~i~~LL~EMl~ak  350 (352)
T 3tx7_B          311 LLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHAK  350 (352)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTTCSCSSCHHHHHHHC-
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhhcCCCCccHHHHHHHhcc
Confidence                           3366789999999999999999985

>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=99.94  E-value=8.6e-28  Score=211.69  Aligned_cols=193  Identities=23%  Similarity=0.404  Sum_probs=156.4

Q ss_pred             HHHHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhh
Q psy11505         76 KMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAY  155 (312)
Q Consensus        76 ~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~  155 (312)
                      .++..+...+|.......+...++.....+.++++...+.+..+|+|||++|+|.+|+.+||+.|||++|+++++|+.||
T Consensus        22 ~~~~~l~~~ep~~~~~~~~~~~p~~~~~~~~~l~e~a~~~l~~~VewAK~ip~F~~L~~~DQv~LLk~~w~el~iL~~a~  101 (269)
T 1t7r_A           22 IFLNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGW  101 (269)
T ss_dssp             HHHHHHHHHCCCCCCCCCCTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCCcccCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHhCccHhhCCHHHHHHHHHHhHHHHHHHHHHH
Confidence            46777888888654444444455556778899999999999999999999999999999999999999999999999999


Q ss_pred             hcccCCCC-eeEecccchhhHHhhhhcccchhh---hhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHH
Q psy11505        156 RSLPHCAG-KIRFASDLVLDERQARECGFSEIY---QQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKA  231 (312)
Q Consensus       156 rs~~~~~~-~l~~~~g~~~~~~~~~~~~~~~~~---~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~  231 (312)
                      |+++.+.+ .+++++|..++++.....+..+++   .++...+++|++|++||                           
T Consensus       102 rs~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~i~~~~~~l~~L~ld~~E~---------------------------  154 (269)
T 1t7r_A          102 RSFTNVNSRMLYFAPDLVFNEYRMHKSRMYSQCVRMRHLSQEFGWLQITPQEF---------------------------  154 (269)
T ss_dssp             HHHHHHTTSSEEEETTEEECHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHH---------------------------
T ss_pred             HhcccCCCCeEEeCCCceecHHhhhhhhHHHHHHHHHHHHHHHHHhCCCHHHH---------------------------
Confidence            99987653 688899988877665544443433   34555566999999999                           


Q ss_pred             HHHHHhhhcccceecCCCCceeecCC-CCc-ccchHHHHHHHHHHHHHhHhHHHHH---------hh-------------
Q psy11505        232 FFKRTIQVYSGYRQTGACGTLVLANS-DVK-LDEFSSLKKFRNSILSSLGDCIYVL---------RF-------------  287 (312)
Q Consensus       232 ~~~~~~~~~~~~~~~~~~~~~~l~~~-~~~-l~~~~~~~~~~~~~~~~l~~~~~~~---------~~-------------  287 (312)
                                     +++|||+|||| |++ |++.+.|+++|++|+.+|.+|+..+         ||             
T Consensus       155 ---------------~lLkAIvLfnp~~~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~~~~Rf~~LL~~L~~Lr~l  219 (269)
T 1t7r_A          155 ---------------LCMKALLLFSIIPVDGLKNQKFFDELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPI  219 (269)
T ss_dssp             ---------------HHHHHHHHTSEEETTCCTTHHHHHHHHHHHHHHHHHHHHTTCCSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ---------------HHHHHHHHcCCCccCCCccHHHHHHHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHHHHHH
Confidence                           99999999999 887 9999999999999999999999532         33             


Q ss_pred             -------hhc--cc-cCCccchhHHHHHHHhhh
Q psy11505        288 -------WST--VH-KDGKVLMNKLFVEMLEAY  310 (312)
Q Consensus       288 -------~~~--~~-~~~~~~~~~~~~~~~~~~  310 (312)
                             ++.  ++ ..|.+++++|+.||+++.
T Consensus       220 ~~~~~e~lf~~~~~~~~~~~~~~~Ll~E~~~~~  252 (269)
T 1t7r_A          220 ARELHQFTFDLLIKSHMVSVDFPEMMAEIISVQ  252 (269)
T ss_dssp             HHHHHHHHHHHHHTHHHHTCCCCHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHhhcCCcChHHHHHHHHhCc
Confidence                   121  12 238899999999999864

>3vhu_A Mineralocorticoid receptor; nuclear receptor, transcription factor, activating mutation, hypertension, antagonist, spironolactone; HET: SNL; 2.11A {Homo sapiens}

Probab=99.94  E-value=7.2e-28  Score=214.16  Aligned_cols=193  Identities=24%  Similarity=0.415  Sum_probs=159.1

Q ss_pred             HHHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhh
Q psy11505         77 MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYR  156 (312)
Q Consensus        77 ~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~r  156 (312)
                      .+..+...+|...........+.+....+.+++++..+.+..+|+|||++|+|.+|+.+||+.|||++|+++++|+.||+
T Consensus        48 ~~~~l~~~eP~~~~~~~~~~~p~~~~~~~~~l~e~a~~~l~~~VewAK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~r  127 (294)
T 3vhu_A           48 PVMVLENIEPEIVYAGYDSSKPDTAENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQYSWMSLLSFALSWR  127 (294)
T ss_dssp             HHHHHHHHCCCCCCCCCCTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHTCTTTTSSCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCCCccccCCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHhCcchhhCCHHHHHHHHHHhHHHHHHHHHHHH
Confidence            56677788887766655555666778899999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCC-CeeEecccchhhHHhhhhcccchhhhh---hcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHH
Q psy11505        157 SLPHCA-GKIRFASDLVLDERQARECGFSEIYQQ---VKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAF  232 (312)
Q Consensus       157 s~~~~~-~~l~~~~g~~~~~~~~~~~~~~~~~~~---i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~  232 (312)
                      +++.+. +.+++++|..++++.....+..++.+.   +...+.+|++|++||                            
T Consensus       128 S~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~l~~~~~~l~~L~ld~~Ey----------------------------  179 (294)
T 3vhu_A          128 SYKHTNSQFLYFAPDLVFNEEKMHQSAMYELCQGMHQISLQFVRLQLTFEEY----------------------------  179 (294)
T ss_dssp             HHHHHTTSSEEEETTEEECHHHHHHTTCHHHHHHHHHHHHHHHHHTCCHHHH----------------------------
T ss_pred             hhhcCCCCeEEeCCCccccHHHhhcccHHHHHHHHHHHHHHHHHhCCCHHHH----------------------------
Confidence            988765 578999998887766655565555444   444555999999999                            


Q ss_pred             HHHHhhhcccceecCCCCceeecCC-CCc-ccchHHHHHHHHHHHHHhHhHHHHH---------hh--------------
Q psy11505        233 FKRTIQVYSGYRQTGACGTLVLANS-DVK-LDEFSSLKKFRNSILSSLGDCIYVL---------RF--------------  287 (312)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~~~~l~~~-~~~-l~~~~~~~~~~~~~~~~l~~~~~~~---------~~--------------  287 (312)
                                    ++++||+|||| |++ |++.++|+++|++++.+|.+|+..+         ||              
T Consensus       180 --------------alLkAIvLfnp~d~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~~~~~~~~~RF~~LL~lLp~Lr~l~  245 (294)
T 3vhu_A          180 --------------TIMKVLLLLSTIPKDGLKSQAAFEEMRTNYIKELRKMVTKCPNNSGQSWQRFYQLTKLLDSMHDLV  245 (294)
T ss_dssp             --------------HHHHHHHHTSEEETTCCTTHHHHHHHHHHHHHHHHHHHC------CHHHHHHHHHHHHHHHHHHHH
T ss_pred             --------------HHHHHHHHhCCCCCCCCCcHHHHHHHHHHHHHHHHHHHHhcCCCCccHhHHHHHHHHHHHHHHHHH
Confidence                          99999999999 887 9999999999999999999999642         33              


Q ss_pred             ------hhc--cc-cCCccchhHHHHHHHhhhc
Q psy11505        288 ------WST--VH-KDGKVLMNKLFVEMLEAYL  311 (312)
Q Consensus       288 ------~~~--~~-~~~~~~~~~~~~~~~~~~~  311 (312)
                            +++  ++ ..+.+++++|+.||+++++
T Consensus       246 ~~~~e~lff~~~q~~~~~~~~p~Ll~Ei~~~~~  278 (294)
T 3vhu_A          246 SDLLEFCFYTFRESHALKVEFPAMLVEIISDQL  278 (294)
T ss_dssp             HHHHHHHHHHHHTHHHHTCCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhccCcCCCCHHHHHHHcCCC
Confidence                  111  11 2467889999999998763

>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=99.94  E-value=1.8e-27  Score=211.15  Aligned_cols=167  Identities=19%  Similarity=0.304  Sum_probs=142.7

Q ss_pred             chhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhh
Q psy11505        100 PTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAR  179 (312)
Q Consensus       100 ~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~  179 (312)
                      .+...+..+++|....+..+|+|||++|+|.+|+.+||++|||++|+++++|+.|+++.+.. +.+.+++|..+++....
T Consensus        85 ~~~~~~~~l~e~~~~~l~~~VewaK~lP~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~-~~~~~~~g~~~~~~~~~  163 (283)
T 3ipq_A           85 ARQQRFAHFTELAIVSVQEIVDFAKQLPGFLQLSREDQIALLKTSAIEVMLLETSRRYNPGS-ESITFLKDFSYNREDFA  163 (283)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETTT-TEEEETTTEEECHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhcCcChhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCCC-CeEEeCCCceecHHHHH
Confidence            45677899999999999999999999999999999999999999999999999998887655 48999999888776655


Q ss_pred             hcccc-hhhhhhc---ccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeec
Q psy11505        180 ECGFS-EIYQQVK---HSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLA  255 (312)
Q Consensus       180 ~~~~~-~~~~~i~---~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  255 (312)
                      ..+.. ++++.+.   ..+.+|++|++||                                          ++++||+||
T Consensus       164 ~~g~~~~~~~~l~~~~~~l~~L~ld~~E~------------------------------------------~lLkAIvL~  201 (283)
T 3ipq_A          164 KAGLQVEFINPIFEFSRAMNELQLNDAEF------------------------------------------ALLIAISIF  201 (283)
T ss_dssp             HTTCCHHHHHHHHHHHHHHHHHTCCHHHH------------------------------------------HHHHHHHHT
T ss_pred             HcCCCHHHHHHHHHHHHHHHHHcCCHHHH------------------------------------------HHHHHHHHH
Confidence            55543 4444444   4555999999999                                          999999999


Q ss_pred             CCCCc-ccchHHHHHHHHHHHHHhHhHHHHH------hh--------------------hhccccCCccchhHHHHHHHh
Q psy11505        256 NSDVK-LDEFSSLKKFRNSILSSLGDCIYVL------RF--------------------WSTVHKDGKVLMNKLFVEMLE  308 (312)
Q Consensus       256 ~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~------~~--------------------~~~~~~~~~~~~~~~~~~~~~  308 (312)
                      |||++ |++...|+++|++|+.+|.+|+..+      ||                    +++.++.|. ++++|+.|||+
T Consensus       202 npd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL~~Lp~Lr~l~~~~~e~l~~~k~~~~-~~~~Ll~Em~~  280 (283)
T 3ipq_A          202 SADRPNVQDQLQVERLQHTYVEALHAYVSIHHPHDRLMFPRMLMKLVSLRTLSSVHSEQVFALRLQDK-KLPPLLSEIWD  280 (283)
T ss_dssp             CTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHSTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC-CCCHHHHHHHC
T ss_pred             CCCCCCCCcHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCC-CCChHHHHHhc
Confidence            99998 9999999999999999999999765      22                    455677775 99999999998


Q ss_pred             hh
Q psy11505        309 AY  310 (312)
Q Consensus       309 ~~  310 (312)
                      .|
T Consensus       281 ~~  282 (283)
T 3ipq_A          281 VH  282 (283)
T ss_dssp             C-
T ss_pred             CC
Confidence            76

>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=99.94  E-value=1.7e-27  Score=208.29  Aligned_cols=164  Identities=20%  Similarity=0.280  Sum_probs=137.7

Q ss_pred             hHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecc-cchhhHHhhhh
Q psy11505        102 LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFAS-DLVLDERQARE  180 (312)
Q Consensus       102 ~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~-g~~~~~~~~~~  180 (312)
                      ...+..+++++.+.+..+|+|||++|+|.+|+.+||+.|||++|+++++|+.|+++.+.. +.+.+++ |..+.......
T Consensus        55 ~~~~~~~~~~~~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~~l~~a~~~~~~~-~~~~~~~~~~~~~~~~~~~  133 (254)
T 3b0t_A           55 LSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDD-MSWTCGNQDYKYRVSDVTK  133 (254)
T ss_dssp             CTTHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHGGGTEETTT-TEEECSSGGGEECHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCcccCCHHHHHHHHHHhhHHHHHHHHHHHhccCC-CeEEecCCCeeeeHHHHHH
Confidence            345889999999999999999999999999999999999999999999999999876654 4788875 65555555444


Q ss_pred             cccc-hhhhhhc---ccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecC
Q psy11505        181 CGFS-EIYQQVK---HSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLAN  256 (312)
Q Consensus       181 ~~~~-~~~~~i~---~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  256 (312)
                      .+.. ++++.+.   ..+.+|++|++||                                          +++|||+|||
T Consensus       134 ~~~~~~~~~~l~~~~~~l~~L~ld~~E~------------------------------------------~lLkAivL~~  171 (254)
T 3b0t_A          134 AGHSLELIEPLIKFQVGLKKLNLHEEEH------------------------------------------VLLMAICIVS  171 (254)
T ss_dssp             TTCCHHHHHHHHHHHHHHHTTCCCHHHH------------------------------------------HHHHHHHHSC
T ss_pred             cCCcHHHHHHHHHHHHHHHHhcCCHHHH------------------------------------------HHHHHHHHhC
Confidence            4554 5555544   4455999999999                                          9999999999


Q ss_pred             CCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------hh--------------------hhcccc--CCccchhHHHHH
Q psy11505        257 SDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------RF--------------------WSTVHK--DGKVLMNKLFVE  305 (312)
Q Consensus       257 ~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------~~--------------------~~~~~~--~~~~~~~~~~~~  305 (312)
                      ||++ |++++.|+++|++|+.+|.+|+..+        ||                    +++.++  .|.+|+++|+.|
T Consensus       172 pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~~~Ll~E  251 (254)
T 3b0t_A          172 PDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNEEHSKQYRCLSFQPECSMKLTPLVLE  251 (254)
T ss_dssp             SCSTTCSCHHHHHHHHHHHHHHHHHHHHHHCCTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTTHHHHSCHHHHH
T ss_pred             CCccCCcCHHHHHHHHHHHHHHHHHHHHHhCCCCCchhHHHHHHHHhHHHHHHHHHHHHHHHHHhccccCCCCCChHHHH
Confidence            9997 9999999999999999999999764        22                    455677  778999999999


Q ss_pred             HHh
Q psy11505        306 MLE  308 (312)
Q Consensus       306 ~~~  308 (312)
                      |++
T Consensus       252 m~~  254 (254)
T 3b0t_A          252 VFG  254 (254)
T ss_dssp             HHC
T ss_pred             hcC
Confidence            985

>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=99.94  E-value=2.4e-27  Score=208.51  Aligned_cols=164  Identities=17%  Similarity=0.247  Sum_probs=142.5

Q ss_pred             hHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhhc
Q psy11505        102 LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC  181 (312)
Q Consensus       102 ~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~~  181 (312)
                      ...+..++++..+.+..+|+|||++|+|.+|+.+||+.|||++|+++++++.||++.+.. +.+++++|..++++.....
T Consensus        67 ~~~~~~l~~~~~~~l~~~VewaK~lp~F~~L~~~DQi~LLk~~~~el~~L~~a~~~~~~~-~~l~~~~g~~~~~~~~~~~  145 (266)
T 2r40_D           67 DMPFRQITEMTILTVQLIVEFAKGLPGFAKISQSDQITLLKACSSEVMMLRVARRYDAAT-DSVLFANNQAYTRDNYRKA  145 (266)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEETTT-TEEECTTSCEECHHHHHHT
T ss_pred             hccHHHHHHHHHHHHHHHHHHHhcCcccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCC-CeEEecCCceecHHHHhhc
Confidence            356889999999999999999999999999999999999999999999999999987655 4899999988887766666


Q ss_pred             ccchhhhhhccc---CccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCCC
Q psy11505        182 GFSEIYQQVKHS---GSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSD  258 (312)
Q Consensus       182 ~~~~~~~~i~~~---~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  258 (312)
                      +..++++.+..+   +.+|++|++||                                          +++|||+||| |
T Consensus       146 g~~~~~~~l~~~~~~l~~L~ld~~E~------------------------------------------~lLkAivL~n-d  182 (266)
T 2r40_D          146 GMAYVIEDLLHFCRCMYSMMMDNVHY------------------------------------------ALLTAIVIFS-D  182 (266)
T ss_dssp             TCHHHHHHHHHHHHHHHTTTCCHHHH------------------------------------------HHHHHHHHTS-C
T ss_pred             CHHHHHHHHHHHHHHHhcccCCHHHH------------------------------------------HHHhhheeec-C
Confidence            666666665544   44999999999                                          9999999999 9


Q ss_pred             Cc-ccchHHHHHHHHHHHHHhHhHHHHH---------hh--------------------hhccccCCccchhHHHHHHHh
Q psy11505        259 VK-LDEFSSLKKFRNSILSSLGDCIYVL---------RF--------------------WSTVHKDGKVLMNKLFVEMLE  308 (312)
Q Consensus       259 ~~-l~~~~~~~~~~~~~~~~l~~~~~~~---------~~--------------------~~~~~~~~~~~~~~~~~~~~~  308 (312)
                      ++ |++++.|+++|++|+.+|.+|+..+         ||                    +++.++.| +++++|+.||++
T Consensus       183 ~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~~-~~~~~Ll~Em~~  261 (266)
T 2r40_D          183 RPGLEQPLLVEEIQRYYLNTLRVYILNQNSASPRCAVIFGKILGILTEIRTLGMQNSNMCISLKLKN-RKLPPFLEEIWD  261 (266)
T ss_dssp             CTTCSCHHHHHHHHHHHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-CCCCHHHHHHTT
T ss_pred             CCCCcCHHHHHHHHHHHHHHHHHHHHHhCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCccHHHHHHhC
Confidence            87 9999999999999999999999753         22                    44557788 699999999998


Q ss_pred             hh
Q psy11505        309 AY  310 (312)
Q Consensus       309 ~~  310 (312)
                      ++
T Consensus       262 ~~  263 (266)
T 2r40_D          262 VA  263 (266)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>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=99.94  E-value=2.5e-27  Score=205.89  Aligned_cols=164  Identities=19%  Similarity=0.219  Sum_probs=141.2

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhh
Q psy11505        101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE  180 (312)
Q Consensus       101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~  180 (312)
                      ....+..+++.....+..+|+|||++|+|.+|+.+||+.|||++|+++++++.|+++.+..+ .+.+ +|..++++....
T Consensus        48 ~~~~~~~~~~~~~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~l~~a~~~~~~~~-~~~~-~g~~~~~~~~~~  125 (244)
T 1nq7_A           48 REALWQQCAIQITHAIQYVVEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPLNN-TVLF-EGKYGGMQMFKA  125 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTCHHHHTSCHHHHHHHHHHHHHHHHHHHHGGGEETTTT-EEEE-TTEEEEGGGGGG
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcCCCC-EEeE-CCEEecHHHHhh
Confidence            45678889999999999999999999999999999999999999999999999999876554 7888 888877766655


Q ss_pred             cccchhhhhhccc---CccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCC
Q psy11505        181 CGFSEIYQQVKHS---GSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANS  257 (312)
Q Consensus       181 ~~~~~~~~~i~~~---~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  257 (312)
                      .+..++++.+..+   +.+|++|++||                                          +++|||+||||
T Consensus       126 ~~~~~~~~~i~~~~~~l~~L~ld~~E~------------------------------------------~lLkAivL~~p  163 (244)
T 1nq7_A          126 LGSDDLVNEAFDFAKNLCSLQLTEEEI------------------------------------------ALFSSAVLISP  163 (244)
T ss_dssp             GSCHHHHHHHHHHHHHHHTTCCCHHHH------------------------------------------HHHHHHHHSCT
T ss_pred             cChHHHHHHHHHHHHHHHHhCCCHHHH------------------------------------------HHHHHHHHcCC
Confidence            5666666665544   44999999999                                          99999999999


Q ss_pred             CCc-ccchHHHHHHHHHHHHHhHhHHHHH-----hh--------------------hhccccCCcc----chhHHHHHHH
Q psy11505        258 DVK-LDEFSSLKKFRNSILSSLGDCIYVL-----RF--------------------WSTVHKDGKV----LMNKLFVEML  307 (312)
Q Consensus       258 ~~~-l~~~~~~~~~~~~~~~~l~~~~~~~-----~~--------------------~~~~~~~~~~----~~~~~~~~~~  307 (312)
                      |++ |++++.|+++|+++..+|.+|+..+     ||                    +++.+..|..    |+++|+.||+
T Consensus       164 d~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~~~~~Ll~Em~  243 (244)
T 1nq7_A          164 DRAWLLEPRKVQKLQEKIYFALQHVIQKNHLDDETLAKLIAKIPTITAVCNLHGEKLQVFKQSHPDIVNTLFPPLYKELF  243 (244)
T ss_dssp             TSTTCSCHHHHHHHHHHHHHHHHHHHHHHCSCTTHHHHHHHTHHHHHHHHHHHHHHHHHHHHHCHHHHHHTSCHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcccccCCCChHHHHhh
Confidence            998 9999999999999999999999764     32                    4556777765    8999999998


Q ss_pred             h
Q psy11505        308 E  308 (312)
Q Consensus       308 ~  308 (312)
                      +
T Consensus       244 ~  244 (244)
T 1nq7_A          244 N  244 (244)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.94  E-value=4.7e-27  Score=204.58  Aligned_cols=165  Identities=18%  Similarity=0.256  Sum_probs=136.1

Q ss_pred             chhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhh
Q psy11505        100 PTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAR  179 (312)
Q Consensus       100 ~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~  179 (312)
                      +....+..+++++.+.+..+|+|||++|+|.+|+.+||++|||++|+++++++.|++++...+ .+ +.++..+++....
T Consensus        51 ~~~~~~~~~~e~~~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~l~~a~~~~~~~~-~~-~~~~~~~~~~~~~  128 (246)
T 1xvp_B           51 PVLPLVTHFADINTFMVLQVIKFTKDLPVFRSLPIEDQISLLKGAAVEICHIVLNTTFCLQTQ-NF-LCGPLRYTIEDGA  128 (246)
T ss_dssp             CSHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHSCHHHHHHHHHHHHHHHHHHHHGGGEETTTT-EE-ECSSCEECHHHHH
T ss_pred             hHhHHHHHHHHHHHHHHHHHHHHHHcCcchhhCCHHHHHHHHHhhHHHHHHHHHHHHhccccC-eE-eeCCeeecHHHHH
Confidence            456789999999999999999999999999999999999999999999999999999987755 44 4555555555444


Q ss_pred             hcccc-hhhhhhc---ccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeec
Q psy11505        180 ECGFS-EIYQQVK---HSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLA  255 (312)
Q Consensus       180 ~~~~~-~~~~~i~---~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  255 (312)
                      ..+.. ++.+.+.   ..+.+|++|++||                                          +++|||+||
T Consensus       129 ~~~~~~~~~~~i~~~~~~l~~L~ld~~E~------------------------------------------~lLkAivL~  166 (246)
T 1xvp_B          129 RVGFQVEFLELLFHFHGTLRKLQLQEPEY------------------------------------------VLLAAMALF  166 (246)
T ss_dssp             HHTCCHHHHHHHHHHHHHHHHTCCCHHHH------------------------------------------HHHHHHHHS
T ss_pred             HccccHHHHHHHHHHHHHHHHHcCCHHHH------------------------------------------HHHHHHHHc
Confidence            45554 4444444   4455999999999                                          999999999


Q ss_pred             CCCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------hhhh------------------ccccCCccchhHHHHHHHh
Q psy11505        256 NSDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------RFWS------------------TVHKDGKVLMNKLFVEMLE  308 (312)
Q Consensus       256 ~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------~~~~------------------~~~~~~~~~~~~~~~~~~~  308 (312)
                      |||++ |++++.|+++|++++.+|.+|+..+        ||..                  ...+.|.+|+++||.||++
T Consensus       167 ~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~~rf~~LL~~L~~Lr~i~~~~~e~l~~~~~~~~~~~Ll~Em~~  246 (246)
T 1xvp_B          167 SPDRPGVTQRDEIDQLQEEMALTLQSYIKGQQRRPRDRFLYAKLLGLLAELRSINEAYGYQIQHIQGLSAMMPLLQEICS  246 (246)
T ss_dssp             CSSSTTCSCHHHHHHHHHHHHHHHHHHHHTCSSCCSCSSHHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHCHHHHHHTC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccHHHHHhcC
Confidence            99998 9999999999999999999999832        3311                  0125799999999999985

>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=99.94  E-value=8e-27  Score=205.46  Aligned_cols=166  Identities=16%  Similarity=0.176  Sum_probs=136.4

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhh
Q psy11505        101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE  180 (312)
Q Consensus       101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~  180 (312)
                      +...+..+++.....+..+|+|||++|+|.+|+.+||+.|||++|+++++++.|+++.+..+ .+.++ |.+++.+....
T Consensus        63 ~~~~~~~~~~~~~~~l~~~VewaK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~~~~~~~~-~~l~~-g~~~~~~~~~~  140 (270)
T 1n83_A           63 REVMWQLCAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQNN-TVYFD-GKYASPDVFKS  140 (270)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHSTTTTTSCHHHHHHHHHHHHHHHHHHHGGGGEETTTT-EEEET-TEEECGGGGGG
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHcCCChhhcCHHHHHHHHHHhHHHHHHHHHHHHhcCCCC-eEEeC-CccccHHHHHh
Confidence            35578888999999999999999999999999999999999999999999999999776544 67774 54555554444


Q ss_pred             cccchhhhhhccc---CccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCC
Q psy11505        181 CGFSEIYQQVKHS---GSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANS  257 (312)
Q Consensus       181 ~~~~~~~~~i~~~---~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  257 (312)
                      .+..++++.+..+   +.+|++|++||                                          +++|||+||||
T Consensus       141 ~~~~~~~~~i~~~~~~l~~L~ld~~E~------------------------------------------~lLkAivLfnp  178 (270)
T 1n83_A          141 LGCEDFISFVFEFGKSLCSMHLTEDEI------------------------------------------ALFSAFVLMSA  178 (270)
T ss_dssp             GSCHHHHHHHHHHHHHHHTTCCCHHHH------------------------------------------HHHHHHHHSCT
T ss_pred             cCHHHHHHHHHHHHHHHHHHCCCHHHH------------------------------------------HHHHHHHHhCC
Confidence            4555666655544   44999999999                                          99999999999


Q ss_pred             CCc-ccchHHHHHHHHHHHHHhHhHHHHH-----hh--------------------hhccccCCc----cchhHHHHHHH
Q psy11505        258 DVK-LDEFSSLKKFRNSILSSLGDCIYVL-----RF--------------------WSTVHKDGK----VLMNKLFVEML  307 (312)
Q Consensus       258 ~~~-l~~~~~~~~~~~~~~~~l~~~~~~~-----~~--------------------~~~~~~~~~----~~~~~~~~~~~  307 (312)
                      |++ |++++.|+++|++|+.+|.+|+..+     ||                    +++.++.|.    +|+++|+.|||
T Consensus       179 d~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~~~~~Ll~Em~  258 (270)
T 1n83_A          179 DRSWLQEKVKIEKLQQKIQLALQHVLQKNHREDGILTKLICKVSTLRALCGRHTEKLMAFKAIYPDIVRLHFPPLYKELF  258 (270)
T ss_dssp             TSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHSCHHHHHHC
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccccCCcCHHHHHHh
Confidence            998 9999999999999999999999765     33                    444567765    59999999999


Q ss_pred             hhh
Q psy11505        308 EAY  310 (312)
Q Consensus       308 ~~~  310 (312)
                      ++.
T Consensus       259 ~~~  261 (270)
T 1n83_A          259 TSE  261 (270)
T ss_dssp             ---
T ss_pred             CCC
Confidence            864

>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=99.93  E-value=9.6e-27  Score=202.62  Aligned_cols=165  Identities=16%  Similarity=0.206  Sum_probs=138.5

Q ss_pred             chhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhh
Q psy11505        100 PTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAR  179 (312)
Q Consensus       100 ~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~  179 (312)
                      .+...|..+++..+..+..+|+|||++|+|.+|+.+||+.|||++|+++++++.|+++.+..+ .+.+ +|..++.+...
T Consensus        53 ~~~~~~~~~~~~~~~~l~~~VewaK~iP~F~~L~~~DQi~LLk~~~~el~lL~~a~~~~~~~~-~~~~-~g~~~~~~~~~  130 (248)
T 3l0l_A           53 SMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNR-TVFF-EGKYGGMELFR  130 (248)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHGGGGEETTTT-EEEE-TTEEECGGGGG
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcCCCC-EEEe-CCCcccHHHHh
Confidence            356678999999999999999999999999999999999999999999999999998776654 6777 45455555545


Q ss_pred             hcccchhhhhhccc---CccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecC
Q psy11505        180 ECGFSEIYQQVKHS---GSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLAN  256 (312)
Q Consensus       180 ~~~~~~~~~~i~~~---~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  256 (312)
                      ..+..++++.+..+   +.+|++|++||                                          ++++||+|||
T Consensus       131 ~~~~~~~~~~l~~~~~~l~~L~ld~~E~------------------------------------------~lLkAivLfn  168 (248)
T 3l0l_A          131 ALGCSELISSIFDFSHSLSALHFSEDEI------------------------------------------ALYTALVLIN  168 (248)
T ss_dssp             GGSCHHHHHHHHHHHHHHHTTCCCHHHH------------------------------------------HHHHHHHHSC
T ss_pred             hccHHHHHHHHHHHHHHHHHhCCCHHHH------------------------------------------HHHHHHHHHC
Confidence            55666666666554   44999999999                                          9999999999


Q ss_pred             CCCc-ccchHHHHHHHHHHHHHhHhHHHHH-----------------------hhhhccccCC----ccchhHHHHHHHh
Q psy11505        257 SDVK-LDEFSSLKKFRNSILSSLGDCIYVL-----------------------RFWSTVHKDG----KVLMNKLFVEMLE  308 (312)
Q Consensus       257 ~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~-----------------------~~~~~~~~~~----~~~~~~~~~~~~~  308 (312)
                      ||++ |+++++|+++|++++.+|.+|+..+                       +.+++.+..|    .+|+++|+.||++
T Consensus       169 pd~~gL~~~~~ve~lqe~~~~aL~~y~~~~~~~~rf~~LLl~p~LR~i~~~~~e~l~~~k~~~p~~~~~~~p~Ll~Emf~  248 (248)
T 3l0l_A          169 AHRPGLQEKRKVEQLQYNLELAFHHHLCKTHRQSILAKLPPKGKLRSLCSQHVERLQIFQHLHPIVVQAAFPPLYKELFS  248 (248)
T ss_dssp             TTCTTCSCHHHHHHHHHHHHHHHHHHHHHTTCGGGGGGSCCTTHHHHHHHHHHHHHHHHHHHCHHHHHHHSCHHHHHHHC
T ss_pred             CCCCCCccHHHHHHHHHHHHHHHHHHHHhhChHHHHHHhhccHHHHHHHHHHHHHHHHHHhhCcccccCCCChHHHHhhC
Confidence            9998 9999999999999999999999754                       2244567788    4789999999984

>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=99.93  E-value=1.1e-26  Score=202.40  Aligned_cols=167  Identities=17%  Similarity=0.221  Sum_probs=142.7

Q ss_pred             chhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhh
Q psy11505        100 PTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAR  179 (312)
Q Consensus       100 ~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~  179 (312)
                      .....+..++++....+..+|+|||++|+|.+|+.+||+.|||++|+++++++.|+++.+.. +.+++++|..++++...
T Consensus        49 ~~~~~~~~l~~~~~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~~~~~~-~~~~~~~g~~~~~~~~~  127 (248)
T 2nxx_E           49 QCDVRFRHITEITILTVQLIVEFAKRLPGFDKLLREDQIALLKACSSEVMMFRMARRYDVQT-DSILFVNNQPYSRDSYN  127 (248)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEETTT-TEEECTTSCEECHHHHH
T ss_pred             chhhHHHHHHHHHHHHHHHHHHHHHcCCchhhCCHHHHHHHHHHhHHHHHHHHHHHHhcCCC-CeEEecCCceecHHHHH
Confidence            34567899999999999999999999999999999999999999999999999999987644 48999999888777665


Q ss_pred             hcccchhhhhhccc---CccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecC
Q psy11505        180 ECGFSEIYQQVKHS---GSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLAN  256 (312)
Q Consensus       180 ~~~~~~~~~~i~~~---~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  256 (312)
                      ..+..++++.+..+   +.+|++|++||                                          ++++||+|||
T Consensus       128 ~~~~~~~~~~i~~~~~~l~~L~ld~~E~------------------------------------------~lLkAivL~~  165 (248)
T 2nxx_E          128 LAGMGETIEDLLHFCRTMYSMRVDNAEY------------------------------------------ALLTAIVIFS  165 (248)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHTTCCHHHH------------------------------------------HHHHHHHHTC
T ss_pred             hcchHHHHHHHHHHHHHHHHhcCCHHHH------------------------------------------HHHHHHHHcC
Confidence            56666666666544   44999999999                                          9999999997


Q ss_pred             CCCc-ccchHHHHHHHHHHHHHhHhHHHHH-------hh--------------------hhccccCCccchhHHHHHHHh
Q psy11505        257 SDVK-LDEFSSLKKFRNSILSSLGDCIYVL-------RF--------------------WSTVHKDGKVLMNKLFVEMLE  308 (312)
Q Consensus       257 ~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~-------~~--------------------~~~~~~~~~~~~~~~~~~~~~  308 (312)
                       |++ |++++.|+++|++++.+|.+|+..+       ||                    +++.++.| +++++|+.||++
T Consensus       166 -d~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~~-~~~~~Ll~Em~~  243 (248)
T 2nxx_E          166 -ERPALIEGWKVEKIQEIYLEALRAYVDNRRKPKPGTIFAKLLSVLTELRTLGNQNSEMCFSLKLKN-KKLPPFLAEIWD  243 (248)
T ss_dssp             -CCSSCTTHHHHHHHHHHHHHHHHHHHHHSCCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-CCCCHHHHHHTT
T ss_pred             -CCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC-CCccHHHHHHhc
Confidence             776 9999999999999999999999764       32                    44456666 599999999999


Q ss_pred             hhc
Q psy11505        309 AYL  311 (312)
Q Consensus       309 ~~~  311 (312)
                      ++.
T Consensus       244 ~~~  246 (248)
T 2nxx_E          244 VDL  246 (248)
T ss_dssp             TTC
T ss_pred             CcC
Confidence            864

>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=99.93  E-value=6.6e-27  Score=208.27  Aligned_cols=167  Identities=20%  Similarity=0.285  Sum_probs=139.6

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEec-ccchhhHHhhh
Q psy11505        101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFA-SDLVLDERQAR  179 (312)
Q Consensus       101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~-~g~~~~~~~~~  179 (312)
                      ....+..+++.+.+.+..+|+|||++|+|.+|+.+||++|||++|+++++|+.|+++.+.. +.+.++ +|..+......
T Consensus        57 ~~~~~~~l~~~~~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~~~el~lL~~a~~~~~~~-~~~l~~~~~~~~~~~~~~  135 (292)
T 2o4j_A           57 PLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDD-MSWDCGSQDYKYDVTDVS  135 (292)
T ss_dssp             CCTTHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHGGGTEETTT-TEEECSSGGGEECHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHcCcchhhccHHHHHHHHHHhHHHHHHHHHHHHhcCCC-CeEEecCCCeEEcHHHHH
Confidence            3456899999999999999999999999999999999999999999999999999866544 478887 47666665554


Q ss_pred             hcccc-hhhhhhc---ccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeec
Q psy11505        180 ECGFS-EIYQQVK---HSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLA  255 (312)
Q Consensus       180 ~~~~~-~~~~~i~---~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  255 (312)
                      ..+.. ++++.+.   ..+.+|++|++||                                          +|+|||+||
T Consensus       136 ~~g~~~~~~~~l~~~~~~l~~L~ld~~E~------------------------------------------~lLkAIvLf  173 (292)
T 2o4j_A          136 KAGHTLELIEPLIKFQVGLKKLNLHEEEH------------------------------------------VLLMAICIV  173 (292)
T ss_dssp             TTTCCHHHHHHHHHHHHHHHHTCCCHHHH------------------------------------------HHHHHHHHS
T ss_pred             hcCCcHHHHHHHHHHHHHHHHHcCCHHHH------------------------------------------HHHHHHHHh
Confidence            44554 5555554   4455999999999                                          999999999


Q ss_pred             CCCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------hh--------------------hhcccc--CCccchhHHHH
Q psy11505        256 NSDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------RF--------------------WSTVHK--DGKVLMNKLFV  304 (312)
Q Consensus       256 ~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------~~--------------------~~~~~~--~~~~~~~~~~~  304 (312)
                      |||++ |++.+.|+++|++|+.+|.+|+..+        ||                    +++.++  .|.+++++|+.
T Consensus       174 npd~~gL~~~~~Ve~lq~~~~~aL~~y~~~~~p~~~~~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~~~Ll~  253 (292)
T 2o4j_A          174 SPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQKLADLRSLNEEHSKQYRSLSFQPENSMKLTPLVL  253 (292)
T ss_dssp             CTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHSCTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHTTSCHHHH
T ss_pred             CCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCCCChhHHHH
Confidence            99998 9999999999999999999999764        22                    444566  45889999999


Q ss_pred             HHHhhh
Q psy11505        305 EMLEAY  310 (312)
Q Consensus       305 ~~~~~~  310 (312)
                      |||++.
T Consensus       254 Eml~~~  259 (292)
T 2o4j_A          254 EVFGNE  259 (292)
T ss_dssp             HHHCCC
T ss_pred             HHHcCC
Confidence            999864

>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=99.93  E-value=1.5e-26  Score=199.62  Aligned_cols=162  Identities=19%  Similarity=0.264  Sum_probs=130.5

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhh
Q psy11505        101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE  180 (312)
Q Consensus       101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~  180 (312)
                      ....+..+++|....+..+|+|||++|+|.+|+.+||++|||++|+++++++.|+++.....     ++|..+..+....
T Consensus        40 ~~~~~~~~~~~~~~~l~~~vewaK~lp~F~~L~~~DQ~~LLk~~~~e~~~l~~a~~~~~~~~-----~~~~~~~~~~~~~  114 (232)
T 1osh_A           40 AEENFLILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLP-----SGHSDLLEERIRN  114 (232)
T ss_dssp             --CHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHTSC-----HHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcCCchhhCCHHHHHHHHHHhHHHHHHHHHHHHhCCccC-----CCCceecHHHHHH
Confidence            34578899999999999999999999999999999999999999999999999998754422     2344444443333


Q ss_pred             cccc-hhhhhh---cccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecC
Q psy11505        181 CGFS-EIYQQV---KHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLAN  256 (312)
Q Consensus       181 ~~~~-~~~~~i---~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  256 (312)
                      .+.. ++.+.+   ...+.+|++|++||                                          ++++||+|||
T Consensus       115 ~~~~~~~~~~i~~~~~~l~~L~ld~~E~------------------------------------------~lLkaivL~~  152 (232)
T 1osh_A          115 SGISDEYITPMFSFYKSIGELKMTQEEY------------------------------------------ALLTAIVILS  152 (232)
T ss_dssp             SSCCTTTHHHHHHHHHHHHTTCCCHHHH------------------------------------------HHHHHHHHTC
T ss_pred             cCCcHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHhC
Confidence            3432 344444   44455999999999                                          9999999999


Q ss_pred             CCCc-ccchHHHHHHHHHHHHHhHhHHHHH------hh--------------------hhccccCCccchhHHHHHHHhh
Q psy11505        257 SDVK-LDEFSSLKKFRNSILSSLGDCIYVL------RF--------------------WSTVHKDGKVLMNKLFVEMLEA  309 (312)
Q Consensus       257 ~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~------~~--------------------~~~~~~~~~~~~~~~~~~~~~~  309 (312)
                      ||++ |+++..|+++|++|+.+|.+|+..+      ||                    +++.+. |.+|+++|+.||++.
T Consensus       153 pd~~gL~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~k~-~~~~~~~Ll~Em~~~  231 (232)
T 1osh_A          153 PDRQYIKDREAVEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAEMLMSWRV-NDHKFTPLLCEIWDV  231 (232)
T ss_dssp             TTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHTHHHHHHHHHHHHHH-TTCCCCHHHHHHHTC
T ss_pred             CCCCCCCChHHHHHHHHHHHHHHHHHHHHHCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCCChHHHHHhcC
Confidence            9998 9999999999999999999999765      33                    344565 799999999999987


Q ss_pred             h
Q psy11505        310 Y  310 (312)
Q Consensus       310 ~  310 (312)
                      |
T Consensus       232 ~  232 (232)
T 1osh_A          232 Q  232 (232)
T ss_dssp             -
T ss_pred             C
Confidence            5

>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=99.93  E-value=1e-26  Score=208.16  Aligned_cols=166  Identities=15%  Similarity=0.235  Sum_probs=142.3

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhh
Q psy11505        101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE  180 (312)
Q Consensus       101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~  180 (312)
                      ....+..++++....+..+|+|||++|+|.+|+.+||++|||++|+++++|+.||++.+.. +.+++++|..++++....
T Consensus       114 ~~~~~~~l~el~~~~l~~~VewAK~lP~F~~L~~~DQi~LLk~~w~el~lL~~a~rs~~~~-~~l~~~~g~~~~~~~~~~  192 (310)
T 1z5x_E          114 AEERFRHITEITILTVQLIVEFSKRLPGFDKLIREDQIALLKACSSEVMMFRMARRYDAET-DSILFATNQPYTRESYTV  192 (310)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEETTT-TEEECTTSCEECHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHcCcchhhCCHHHHHHHHHHHHHHHHHHHHHHHhccCC-CeEEeCCCccccHHHHHh
Confidence            4567899999999999999999999999999999999999999999999999999998754 489999998887776655


Q ss_pred             cccchhhhhhccc---CccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCC
Q psy11505        181 CGFSEIYQQVKHS---GSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANS  257 (312)
Q Consensus       181 ~~~~~~~~~i~~~---~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  257 (312)
                      .+..++++.+..+   +.+|++|++||                                          ++++||+||| 
T Consensus       193 ~g~~~~~~~i~~~~~~l~~L~ld~~E~------------------------------------------alLkAIvLf~-  229 (310)
T 1z5x_E          193 AGMGDTVEDLLRFCRHMCAMKVDNAEY------------------------------------------ALLTAIVIFS-  229 (310)
T ss_dssp             TTTHHHHHHHHHHHHHHHHHTCCHHHH------------------------------------------HHHHHHHHTC-
T ss_pred             cchhHHHHHHHHHHHHHHHHcCCHHHH------------------------------------------HHHHHHHHcC-
Confidence            6666666666544   44999999999                                          9999999997 


Q ss_pred             CCc-ccchHHHHHHHHHHHHHhHhHHHHH-------hh--------------------hhccccCCccchhHHHHHHHhh
Q psy11505        258 DVK-LDEFSSLKKFRNSILSSLGDCIYVL-------RF--------------------WSTVHKDGKVLMNKLFVEMLEA  309 (312)
Q Consensus       258 ~~~-l~~~~~~~~~~~~~~~~l~~~~~~~-------~~--------------------~~~~~~~~~~~~~~~~~~~~~~  309 (312)
                      |++ |++.+.|+++|++|+.+|.+|+..+       ||                    +++.++.|. ++++|+.|||++
T Consensus       230 d~~gL~~~~~Ve~lqe~~~~aL~~y~~~~~~~~~~~RF~kLLl~Lp~LR~l~~~~~e~l~~~~~~~~-~~~~Ll~Eml~~  308 (310)
T 1z5x_E          230 ERPSLSEGWKVEKIQEIYIEALKAYVENRRKPYATTIFAKLLSVLTELRTLGNMNSETCFSLKLKNR-KVPSFLEEIWDV  308 (310)
T ss_dssp             CCTTCTTHHHHHHHHHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC-CCCHHHHHHHTC
T ss_pred             CCCCCccHHHHHHHHHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC-CchHHHHHHHcC
Confidence            887 9999999999999999999999654       32                    444566664 999999999997


Q ss_pred             hc
Q psy11505        310 YL  311 (312)
Q Consensus       310 ~~  311 (312)
                      ++
T Consensus       309 ~~  310 (310)
T 1z5x_E          309 VS  310 (310)
T ss_dssp             C-
T ss_pred             CC
Confidence            63

>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=99.93  E-value=1e-26  Score=204.81  Aligned_cols=169  Identities=15%  Similarity=0.198  Sum_probs=136.8

Q ss_pred             CCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHh
Q psy11505         98 SDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQ  177 (312)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~  177 (312)
                      .......|..+....+..+..+|+|||++|+|.+|+.+||++|||++|+++++++.|+++.+.+. .+.++++.......
T Consensus        71 ~~~~~~~~~~~~~~~~~~v~~iVewAK~iPgF~~L~~~DQi~LLk~~w~ElllL~~a~~~~~~~~-~~~~~~~~~~~~~~  149 (273)
T 3vi8_A           71 KEAEVRIFHCCQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGM-LVAYGNGFITREFL  149 (273)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHGGGSTTTTTSCHHHHHHHHHHHHHHHHHHHHGGGEETTEE-EETTTTEEEEHHHH
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHccCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCC-eeeeCCCccchHHH
Confidence            34456679999999999999999999999999999999999999999999999999998876543 44445554443322


Q ss_pred             -hhhcccchhhhhhcc---cCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCcee
Q psy11505        178 -ARECGFSEIYQQVKH---SGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLV  253 (312)
Q Consensus       178 -~~~~~~~~~~~~i~~---~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  253 (312)
                       ....+..++++.+..   .+.+|++|++||                                          +|+|||+
T Consensus       150 ~~~~~~~~~~~~~l~~~~~~~~~L~ld~~E~------------------------------------------alLkAiv  187 (273)
T 3vi8_A          150 KSLRKPFCDIMEPKFDFAMKFNALELDDSDI------------------------------------------SLFVAAI  187 (273)
T ss_dssp             HHSCTTTHHHHHHHHHHHHHHHTTCCCHHHH------------------------------------------HHHHHHH
T ss_pred             HHhhhhHHHHHHHHHHHHHHHHHhCCCHHHH------------------------------------------HHHHHHH
Confidence             222334455554444   455999999999                                          9999999


Q ss_pred             ecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH------hh--------------------hh-ccccCCccchhHHHHH
Q psy11505        254 LANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL------RF--------------------WS-TVHKDGKVLMNKLFVE  305 (312)
Q Consensus       254 l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~------~~--------------------~~-~~~~~~~~~~~~~~~~  305 (312)
                      |||||++ |.++++|+++|++|+.+|.+|+..+      ||                    ++ +++..|.+|+++|+.|
T Consensus       188 Lf~pd~~gL~~~~~Ve~lqe~~~~aL~~yi~~~~p~~~~rF~kLL~~Lp~LR~l~~~~~e~l~~~k~~~~~~~~~~Ll~E  267 (273)
T 3vi8_A          188 ICCGDRPGLLNVGHIEKMQEGIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQLVTEHAQLVQIIKKTESDAALHPLLQE  267 (273)
T ss_dssp             HSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCCCCHHHHH
T ss_pred             HhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCccHHHHH
Confidence            9999998 9999999999999999999999876      22                    22 3456899999999999


Q ss_pred             HHhh
Q psy11505        306 MLEA  309 (312)
Q Consensus       306 ~~~~  309 (312)
                      |+..
T Consensus       268 mf~d  271 (273)
T 3vi8_A          268 IYRD  271 (273)
T ss_dssp             HHTT
T ss_pred             HHHh
Confidence            9953

>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=99.93  E-value=1.2e-26  Score=208.00  Aligned_cols=163  Identities=17%  Similarity=0.183  Sum_probs=135.0

Q ss_pred             hHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhhc
Q psy11505        102 LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC  181 (312)
Q Consensus       102 ~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~~  181 (312)
                      ...+..+++...+.+..+|+|||++|+|.+|+.+||++|||++|+++++|+.|+++.+..+ .+.+++ ..+..... ..
T Consensus       119 ~~~~~~l~e~~~~~L~~~VewAK~lP~F~~L~~~DQi~LLk~~w~el~lL~~a~~~~~~~~-~~l~~~-~~~~~~~~-~~  195 (316)
T 1nrl_A          119 FSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETG-TWECGR-LSYCLEDT-AG  195 (316)
T ss_dssp             GTTHHHHHHHHHHHHHHHHHHHHHCHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTEETTTT-EEEETT-EEEEECCC-SS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCcchhhcCHHHHHHHHHHHHHHHHHHHHHHHhhcCCC-eEEECC-EeecHHHH-hc
Confidence            5578999999999999999999999999999999999999999999999999999876554 677655 44444333 23


Q ss_pred             ccc-hhhhhh---cccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCC
Q psy11505        182 GFS-EIYQQV---KHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANS  257 (312)
Q Consensus       182 ~~~-~~~~~i---~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  257 (312)
                      +.. ++++.+   ...+.+|++|++||                                          +|+|||+||||
T Consensus       196 g~~~~~~~~i~~~~~~l~~L~ld~~E~------------------------------------------alLkAIvLfnp  233 (316)
T 1nrl_A          196 GFQQLLLEPMLKFHYMLKKLQLHEEEY------------------------------------------VLMQAISLFSP  233 (316)
T ss_dssp             CHHHHTTSHHHHHHHHHHHTCCCHHHH------------------------------------------HHHHHHHHTCT
T ss_pred             cccHHHHHHHHHHHHHHHHhCCCHHHH------------------------------------------HHHHHHHHhCC
Confidence            333 444444   44455999999999                                          99999999999


Q ss_pred             CCc-ccchHHHHHHHHHHHHHhHhHHHHH--------hh--------------------hhccccCCccchhHHHHHHHh
Q psy11505        258 DVK-LDEFSSLKKFRNSILSSLGDCIYVL--------RF--------------------WSTVHKDGKVLMNKLFVEMLE  308 (312)
Q Consensus       258 ~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------~~--------------------~~~~~~~~~~~~~~~~~~~~~  308 (312)
                      |++ |++...|+++|++|+.+|.+|+..+        ||                    +++.+..|. |+++||.|||+
T Consensus       234 d~~gL~~~~~Ve~lqe~~~~aL~~y~~~~~p~~~~~~RF~kLLl~Lp~LR~l~~~~~e~l~~~k~~~~-~i~~Ll~Eml~  312 (316)
T 1nrl_A          234 DRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLKIMAMLTELRSINAQHTQRLLRIQDIHP-FATPLMQELFG  312 (316)
T ss_dssp             TSTTCSCHHHHHHHHHHHHHHHHHHHHHHCCSGGGTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSC-CCCHHHHHHTT
T ss_pred             CCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-chHHHHHHHHc
Confidence            998 9999999999999999999999764        22                    444566777 99999999998


Q ss_pred             hh
Q psy11505        309 AY  310 (312)
Q Consensus       309 ~~  310 (312)
                      ++
T Consensus       313 ~~  314 (316)
T 1nrl_A          313 IT  314 (316)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>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=99.93  E-value=4e-26  Score=203.97  Aligned_cols=167  Identities=20%  Similarity=0.298  Sum_probs=136.1

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecc-cchhhHHhhh
Q psy11505        101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFAS-DLVLDERQAR  179 (312)
Q Consensus       101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~-g~~~~~~~~~  179 (312)
                      ....+..++++..+.+..+|+|||++|+|.+|+.+||++|||++|+++++|+.|++ +....+.+.+++ |..+......
T Consensus       100 ~~~~~~~l~e~~~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w~el~lL~~a~~-~~~~~~~~l~~~~~~~~~~~~~~  178 (302)
T 2hc4_A          100 RLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLRSNQS-FSLEDMSWSCGGPDFKYCINDVT  178 (302)
T ss_dssp             CCTTHHHHHHHHHHHHHHHHHHHTTSTTTTTSCHHHHHHHHHHHHHHHHHHHGGGT-EETTTTEEECSSSTTEECHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHH-hccCCCeEEecCCCeeecHHHHH
Confidence            35668999999999999999999999999999999999999999999999999965 444555677764 4444444443


Q ss_pred             hccc-chhhhhh---cccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeec
Q psy11505        180 ECGF-SEIYQQV---KHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLA  255 (312)
Q Consensus       180 ~~~~-~~~~~~i---~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  255 (312)
                      ..+. .++++.+   ...+++|++|++||                                          +|+|||+||
T Consensus       179 ~~g~~~~~~~~l~~~~~~l~~L~ld~~E~------------------------------------------alLkAIvLf  216 (302)
T 2hc4_A          179 KAGHTLELLEPLVKFQVGLKKLKLHEEEH------------------------------------------VLLMAICLL  216 (302)
T ss_dssp             TTTCCHHHHHHHHHHHHHHHTTCCCHHHH------------------------------------------HHHHHHHHT
T ss_pred             HccCcHHHHHHHHHHHHHHHHhcCCHHHH------------------------------------------HHHHHHHHh
Confidence            4444 3444444   44455999999999                                          999999999


Q ss_pred             CCCCc-ccchHHHHHHHHHHHHHhHhHHHHH------hh--------------------hhccccCCc--cchhHHHHHH
Q psy11505        256 NSDVK-LDEFSSLKKFRNSILSSLGDCIYVL------RF--------------------WSTVHKDGK--VLMNKLFVEM  306 (312)
Q Consensus       256 ~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~------~~--------------------~~~~~~~~~--~~~~~~~~~~  306 (312)
                      |||++ |++++.|+++|++|+.+|.+||..+      ||                    +++.++.|.  +++++|+.||
T Consensus       217 npd~~gL~~~~~Ve~lqe~~~~aL~~y~~~~~p~~~~RF~~LLl~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~~~Ll~Em  296 (302)
T 2hc4_A          217 SPDRPGVQDHVRIEALQDRLCDVLQAYIRIQHPGGRLLYAKMIQKLADLRSLNEEHSKQYRSLSFQPEHSMQLTPLVLEV  296 (302)
T ss_dssp             CSCSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHTTSCHHHHHH
T ss_pred             CCCCCCCcCHHHHHHHHHHHHHHHHHHHHHHCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCccHHHHHH
Confidence            99998 9999999999999999999999775      33                    444566655  8999999999


Q ss_pred             Hhhh
Q psy11505        307 LEAY  310 (312)
Q Consensus       307 ~~~~  310 (312)
                      +++.
T Consensus       297 ~~~~  300 (302)
T 2hc4_A          297 FGSE  300 (302)
T ss_dssp             SSSC
T ss_pred             HcCC
Confidence            9875

>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=99.92  E-value=1.9e-26  Score=199.53  Aligned_cols=167  Identities=24%  Similarity=0.367  Sum_probs=141.5

Q ss_pred             chhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhh
Q psy11505        100 PTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAR  179 (312)
Q Consensus       100 ~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~  179 (312)
                      .+...+.++.+++.+++..+++|+|++|+|..|+.+||+.|||++|+++++|+.|+++.+.. +.+.+++|..++.....
T Consensus        38 ~~~~~~~~~~~~~~~~l~~~v~wak~~p~F~~L~~~DQ~~LLk~~~~~~~~L~~a~~s~~~~-~~~~~~~g~~~~~~~~~  116 (237)
T 1pzl_A           38 KKIASIADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFK-DVLLLGNDYIVPRHCPE  116 (237)
T ss_dssp             SCBCCHHHHHHHHHHHHHHHHHHHTTCHHHHTSCHHHHHHHHHHSHHHHHHHHHHHHHTTSS-SEEECTTSCEEESSCGG
T ss_pred             cccCCHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHhhccC-CceeecCCcccCccchh
Confidence            44567899999999999999999999999999999999999999999999999999998854 47888888776544332


Q ss_pred             hcccch----hhhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeec
Q psy11505        180 ECGFSE----IYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLA  255 (312)
Q Consensus       180 ~~~~~~----~~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  255 (312)
                      ..+..+    +++.+...+.+|++|++||                                          ++++||++|
T Consensus       117 ~~~~~~~~~~~~~~l~~~l~~L~ld~~E~------------------------------------------~~L~ai~l~  154 (237)
T 1pzl_A          117 LAEMSRVSIRILDELVLPFQELQIDDNEY------------------------------------------AYLKAIIFF  154 (237)
T ss_dssp             GGGGHHHHHHHHHHTHHHHHHHTCCHHHH------------------------------------------HHHHHHHHC
T ss_pred             hhhhHHHHHHHHHHHHHHHHhhCCCHHHH------------------------------------------HHHHHHHHh
Confidence            223333    3445556666999999999                                          999999999


Q ss_pred             CCCCc-ccchHHHHHHHHHHHHHhHhHHHHH------hh--------------------hhccccCCccchhHHHHHHHh
Q psy11505        256 NSDVK-LDEFSSLKKFRNSILSSLGDCIYVL------RF--------------------WSTVHKDGKVLMNKLFVEMLE  308 (312)
Q Consensus       256 ~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~------~~--------------------~~~~~~~~~~~~~~~~~~~~~  308 (312)
                      +||++ +++.+.++++|+++..+|.+|+..+      ||                    +++.+++|.+++++|+.|||+
T Consensus       155 ~~~~~~l~~~~~ve~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~~lr~~~~~~~e~l~~~~~~~~~~~~~l~~em~~  234 (237)
T 1pzl_A          155 DPDAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFIKLFGMAKIDNLLQEMLL  234 (237)
T ss_dssp             CTTCTTCSCHHHHHHHHHHHHHHHHHHHHSSSSCCTTHHHHHHTHHHHHHHHHHHHHHHHHHHHHTTCSCCCHHHHHHHT
T ss_pred             CCCCCCCCcHHHHHHHHHHHHHHHHHHHHhcCCChhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHhCCCcHHHHHHHHHc
Confidence            99998 9999999999999999999999643      32                    455688999999999999998


Q ss_pred             h
Q psy11505        309 A  309 (312)
Q Consensus       309 ~  309 (312)
                      +
T Consensus       235 ~  235 (237)
T 1pzl_A          235 G  235 (237)
T ss_dssp             T
T ss_pred             C
Confidence            6

>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=99.92  E-value=3.5e-25  Score=194.72  Aligned_cols=162  Identities=16%  Similarity=0.205  Sum_probs=128.0

Q ss_pred             HHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccch-hhHHhhhh-
Q psy11505        103 QTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLV-LDERQARE-  180 (312)
Q Consensus       103 ~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~-~~~~~~~~-  180 (312)
                      ..+..........+..+|+|||++|+|.+|+.+||+.|||++|+++++|+.|++..+   +.+++++|.. ++++.... 
T Consensus        73 ~~~~~c~~~~~~~v~~~VewAK~iP~F~~L~~~DQi~LLk~~~~el~lL~~a~~~~~---~~~~~~~g~~~~~~~~~~~~  149 (269)
T 3u9q_A           73 RIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNK---DGVLISEGQGFMTREFLKSL  149 (269)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEET---TEEEETTTTEEEEHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCCChhhcCHHHHHHHHHHhhHHHHHHHHHHhcCC---CCeEEeCCCccccHHHHHHh
Confidence            334444444445577899999999999999999999999999999999999977543   3577777654 45544332 


Q ss_pred             -cccchhhhhhc---ccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecC
Q psy11505        181 -CGFSEIYQQVK---HSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLAN  256 (312)
Q Consensus       181 -~~~~~~~~~i~---~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  256 (312)
                       .+..++++.+.   ..+.+|++|++||                                          ++++||+|||
T Consensus       150 ~~~~~~~~~~l~~~~~~l~~L~ld~~E~------------------------------------------alLkAIvLfn  187 (269)
T 3u9q_A          150 RKPFGDFMEPKFEFAVKFNALELDDSDL------------------------------------------AIFIAVIILS  187 (269)
T ss_dssp             CTTGGGSSHHHHHHHHHHHTTCCCHHHH------------------------------------------HHHHHHHHTC
T ss_pred             hhhHHHHHHHHHHHHHHHHhhcCCHHHH------------------------------------------HHHHHHHHhC
Confidence             34445555444   4455999999999                                          9999999999


Q ss_pred             CCCc-ccchHHHHHHHHHHHHHhHhHHHHH------hh--------------------hh-ccccCCccchhHHHHHHHh
Q psy11505        257 SDVK-LDEFSSLKKFRNSILSSLGDCIYVL------RF--------------------WS-TVHKDGKVLMNKLFVEMLE  308 (312)
Q Consensus       257 ~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~------~~--------------------~~-~~~~~~~~~~~~~~~~~~~  308 (312)
                      ||++ |+++++|+++|++++.+|.+|+..+      ||                    +. +++..|.+|+++||.|||+
T Consensus       188 pd~~gL~~~~~Ve~lqe~~~~aL~~y~~~~~p~~~~Rf~kLL~~Lp~LR~i~~~~~~~l~~~k~~~~~~~~~~Ll~Em~~  267 (269)
T 3u9q_A          188 GDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYK  267 (269)
T ss_dssp             TTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCSSCCCCHHHHHHHS
T ss_pred             CCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHhHHHHHHHHHHHHHHHHHhCcCCCCCcCHHHHHHHh
Confidence            9998 9999999999999999999999765      22                    32 3456889999999999997


Q ss_pred             h
Q psy11505        309 A  309 (312)
Q Consensus       309 ~  309 (312)
                      +
T Consensus       268 ~  268 (269)
T 3u9q_A          268 D  268 (269)
T ss_dssp             C
T ss_pred             h
Confidence            4

>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=99.91  E-value=1e-24  Score=183.75  Aligned_cols=143  Identities=20%  Similarity=0.293  Sum_probs=125.3

Q ss_pred             chhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhh
Q psy11505        100 PTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAR  179 (312)
Q Consensus       100 ~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~  179 (312)
                      +....|..+++.....+..+|+|||++|+|.+|+.+||++|+|++|+++++++.|+++... .+.+.+++|..++.+...
T Consensus        17 ~~~~~~~~~~~~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~e~~~l~~a~~~~~~-~~~~~~~~g~~~~~~~~~   95 (199)
T 3cqv_A           17 SGHEIWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLFDAK-ERTVTFLSGKKYSVDDLH   95 (199)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHTSGGGGGSCHHHHHHHHHHHHHHHHHHHTGGGEETT-TTEEECTTSCEEEHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHhcCCChhhCCHHHHHHHHHHhHHHHHHHHHHHHhCCC-CCeEEecCCCeecHHHHH
Confidence            4667899999999999999999999999999999999999999999999999999876444 458899999888777665


Q ss_pred             hcccchhhhhhcc---cCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecC
Q psy11505        180 ECGFSEIYQQVKH---SGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLAN  256 (312)
Q Consensus       180 ~~~~~~~~~~i~~---~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  256 (312)
                      ..+..++++.+..   .+.+|++|++||                                          +++|||+|||
T Consensus        96 ~~~~~~~~~~i~~~~~~~~~L~ld~~E~------------------------------------------~lLkaivL~~  133 (199)
T 3cqv_A           96 SMGAGDLLNSMFEFSEKLNALQLSDEEM------------------------------------------SLFTAVVLVS  133 (199)
T ss_dssp             HTTCCHHHHHHHHHHHHHHTTCCCHHHH------------------------------------------HHHHHHHHHT
T ss_pred             hcCcHHHHHHHHHHHHHHHHhCCCHHHH------------------------------------------HHHHHHHHhc
Confidence            5566666655544   444999999999                                          9999999999


Q ss_pred             CCCc-ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505        257 SDVK-LDEFSSLKKFRNSILSSLGDCIYVL  285 (312)
Q Consensus       257 ~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~  285 (312)
                      ||++ +++++.|+++|++++.+|.+|+..+
T Consensus       134 pd~~gL~~~~~v~~~q~~~~~aL~~y~~~~  163 (199)
T 3cqv_A          134 ADRSGIENVNSVEALQETLIRALRTLIMKN  163 (199)
T ss_dssp             SCCTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence            9998 9999999999999999999999765

>3up3_A Acedaf-12; ligand binding domain, nematode, steroid binding protein- transcription complex; HET: XCA; 1.25A {Ancylostoma ceylanicum} PDB: 3up0_A*

Probab=99.90  E-value=1.1e-24  Score=188.70  Aligned_cols=158  Identities=13%  Similarity=0.077  Sum_probs=125.6

Q ss_pred             hHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCee---EecccchhhHHhhhh--c
Q psy11505        107 SLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKI---RFASDLVLDERQARE--C  181 (312)
Q Consensus       107 ~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l---~~~~g~~~~~~~~~~--~  181 (312)
                      ++.++.+..+..+|+|||++|+|.+|+.+||++|||++|+++++++.|+++.+..+ .+   .+++|..++++....  .
T Consensus        45 ~l~~l~~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w~Ell~L~~a~r~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~  123 (243)
T 3up3_A           45 DIMNIMDVTMRRFVKMAKRLPAFNDLSQDGKFALLKGGMIEMLTVRGVRRFDSSSG-SWTTPTLGESSEVSINMFDQLNA  123 (243)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHEETTTT-EECCTTSCTTCCEEGGGGGGSCT
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcccCC-eeeecccCCCccccHHHHhhhcc
Confidence            67899999999999999999999999999999999999999999999999888766 44   235665555443322  3


Q ss_pred             ccch-hhhhh---cccCcc-CCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecC
Q psy11505        182 GFSE-IYQQV---KHSGSL-DGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLAN  256 (312)
Q Consensus       182 ~~~~-~~~~i---~~~~~~-L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  256 (312)
                      +..+ +++.+   ...+.+ |++|++||                                          ++++||+|||
T Consensus       124 g~~~~~~~~l~~~~~~~~~~L~ld~~E~------------------------------------------alLkAivLfs  161 (243)
T 3up3_A          124 DVRSEQKMRFLQFFKIFHEDIRSNDLVI------------------------------------------SMIMLIVLFS  161 (243)
T ss_dssp             TTHHHHHHHHHHHHHTSCHHHHTCHHHH------------------------------------------HHHHHHHHSC
T ss_pred             cccHHHHHHHHHHHHHHHHHHCCCHHHH------------------------------------------HHHHHHhhcC
Confidence            4443 33333   344555 99999999                                          9999999999


Q ss_pred             CCCcccch---HHHHHHHHHHHHHhHhHHHHH-------hh-------------------hhccccCCccchhHHHHHHH
Q psy11505        257 SDVKLDEF---SSLKKFRNSILSSLGDCIYVL-------RF-------------------WSTVHKDGKVLMNKLFVEML  307 (312)
Q Consensus       257 ~~~~l~~~---~~~~~~~~~~~~~l~~~~~~~-------~~-------------------~~~~~~~~~~~~~~~~~~~~  307 (312)
                      ||.+|+++   .+|+++|++++.+|.+|+..+       ||                   +++.+ .+..++++|+.||+
T Consensus       162 p~~gL~~~~~~~~Ve~lQe~~~~aL~~y~~~~~~p~~~~rf~kLL~~Lp~LR~i~~~~e~lf~~k-~~~~~~~pLl~E~f  240 (243)
T 3up3_A          162 PRDSITDPEDRRIIARHHEQFSALLNRYLESLYGDDAHQLNEQLPTALRMLREISASSGMLFLGT-VNTSEAEPLPREFF  240 (243)
T ss_dssp             CCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHGGGHHHHHHHHHHHHHHHHHHHHTCTTTTTTS-CCGGGSCHHHHTTS
T ss_pred             CCCCCCCcchHHHHHHHHHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHHHHHHHHHHHHHHhcc-cCCCCCCcHHHHHh
Confidence            99559876   789999999999999999743       22                   22223 56679999999998


Q ss_pred             h
Q psy11505        308 E  308 (312)
Q Consensus       308 ~  308 (312)
                      +
T Consensus       241 ~  241 (243)
T 3up3_A          241 K  241 (243)
T ss_dssp             C
T ss_pred             C
Confidence            6

>3n00_A REV-ERBA-alpha; reverba ncorid1, anti-parallel B-sheet, transcription regula; 2.60A {Homo sapiens}

Probab=99.89  E-value=6.5e-24  Score=184.19  Aligned_cols=141  Identities=22%  Similarity=0.307  Sum_probs=111.4

Q ss_pred             hHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhhc
Q psy11505        102 LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC  181 (312)
Q Consensus       102 ~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~~  181 (312)
                      ...|+.+.+.....+..+|+|||++|+|.+|+.+||+.|||++|+++++|+.|+++.. ..+.+.+++|..+..+.....
T Consensus        64 ~~~~~~~~~~~~~~l~~~VewAK~lP~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~-~~~~l~~~~g~~~~~~~~~~~  142 (245)
T 3n00_A           64 QEIWEDFSMSFTPAVREVVEFAKHIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFNV-KDQTVMFLSRTTYSLQELGAM  142 (245)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTCCS-CC--------------CCGGG
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhcC-CCCeEEecCCCeecHHHHhhc
Confidence            3678899999999999999999999999999999999999999999999999987444 445788899988776655555


Q ss_pred             ccchhhhhhccc---CccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCCC
Q psy11505        182 GFSEIYQQVKHS---GSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSD  258 (312)
Q Consensus       182 ~~~~~~~~i~~~---~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  258 (312)
                      +..++++.+..+   +.+|++|++||                                          ++++||+|||||
T Consensus       143 ~~~~~~~~i~~~~~~l~~L~ld~~E~------------------------------------------~lLkAIvL~npd  180 (245)
T 3n00_A          143 GMGDLLSAMFDFSEKLNSLALTEEEL------------------------------------------GLFTAVVLVSAD  180 (245)
T ss_dssp             TTHHHHHHHHHHHHHHHHTCCCHHHH------------------------------------------HHHHHHHHHTSC
T ss_pred             cHHHHHHHHHHHHHHHHHHcCCHHHH------------------------------------------HHHHHHHHhCCC
Confidence            566666655544   44999999999                                          999999999999


Q ss_pred             Cc-ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505        259 VK-LDEFSSLKKFRNSILSSLGDCIYVL  285 (312)
Q Consensus       259 ~~-l~~~~~~~~~~~~~~~~l~~~~~~~  285 (312)
                      ++ |++.++|+++|++++.+|.+|+..+
T Consensus       181 ~~gL~~~~~ve~lq~~~~~aL~~y~~~~  208 (245)
T 3n00_A          181 RSGMENSASVEQLQETLLRALRALVLKN  208 (245)
T ss_dssp             CTTCSSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCccHHHHHHHHHHHHHHHHHHHHHh
Confidence            98 9999999999999999999999765

>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=99.87  E-value=3.8e-23  Score=178.57  Aligned_cols=160  Identities=15%  Similarity=0.113  Sum_probs=122.4

Q ss_pred             hHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhh--HH--hhhhcc
Q psy11505        107 SLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLD--ER--QARECG  182 (312)
Q Consensus       107 ~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~--~~--~~~~~~  182 (312)
                      ++.++.+..+..+|+|||++|+|.+|+.+||++|||++|+|+++++.|+++.+... .+.+++|..+.  ..  .....+
T Consensus        45 ~i~~l~~~~l~~iVefAK~iPgF~~L~~~DQi~LLK~~~~ElliLr~a~~~~~~~~-~~~~~~~~~~~~~~~~l~~l~~~  123 (244)
T 3gyt_A           45 DILNVMDITMRRLVKMAKRLGAFNEISEAGKFSLLKGGMIEMLTIRGVTVFNADKG-VWQTPVDGHSQISFNMFDKLRPD  123 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCGGGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETTTT-EECCTTSTTCCEEGGGGGGSCTT
T ss_pred             HHHHHHHHHHHHHHHHHccCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcccCC-eEeecCCcccchhHHHHHHhhhc
Confidence            56788888899999999999999999999999999999999999999999776655 67776653111  10  000011


Q ss_pred             -----cchhhhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCC
Q psy11505        183 -----FSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANS  257 (312)
Q Consensus       183 -----~~~~~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  257 (312)
                           ..++.+.++.+...++.++.||                                          ++++||+||||
T Consensus       124 ~~~~~~~~~~~~~~~f~~~l~~~~~E~------------------------------------------alLkAivLfsp  161 (244)
T 3gyt_A          124 IKDTQKKGFLHFFNLLHSDVRKNDLAI------------------------------------------DIIVLMVLFDS  161 (244)
T ss_dssp             THHHHHHHHHHHHHHSCHHHHTCHHHH------------------------------------------HHHHHHHHSCT
T ss_pred             chhhHHHHHHHHHHHHHHHHHHhHHHH------------------------------------------HHHHHHHHHhc
Confidence                 1234455666666666778899                                          99999999999


Q ss_pred             CCc-cc---chHHHHHHHHHHHHHhHhHHHHH-------hh------------hhc------cccCCccchhHHHHHHHh
Q psy11505        258 DVK-LD---EFSSLKKFRNSILSSLGDCIYVL-------RF------------WST------VHKDGKVLMNKLFVEMLE  308 (312)
Q Consensus       258 ~~~-l~---~~~~~~~~~~~~~~~l~~~~~~~-------~~------------~~~------~~~~~~~~~~~~~~~~~~  308 (312)
                      |++ |.   ++.+|+++|++++.+|.+|+..+       ||            +..      .+..+..++++|+.||++
T Consensus       162 Dr~gL~~~~d~~~Ve~lQe~~~~aL~~y~~~~~~p~~~~rf~kLL~~Lp~LR~i~~~~~~lf~~~~~~~~~~pLl~Eif~  241 (244)
T 3gyt_A          162 KREGLVSQQDKETVEKLHRNYESLLHRYLYSIHKEEAEQRFASIPKALVALRKVAENAVTLFLGAGNTTEAASLPKEFFA  241 (244)
T ss_dssp             TSTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHHHHHTTTTTTTTSCCCTTSCTTGGGTSC
T ss_pred             cCCCCCccccHHHHHHHHHHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHhccCCccCCcHHHHHhC
Confidence            998 98   68899999999999999999754       22            111      123445679999999987


Q ss_pred             h
Q psy11505        309 A  309 (312)
Q Consensus       309 ~  309 (312)
                      .
T Consensus       242 ~  242 (244)
T 3gyt_A          242 T  242 (244)
T ss_dssp             C
T ss_pred             c
Confidence            4

>1lo1_A Steroid hormone receptor ERR2; estrogen related receptor 2, DNA binding domain, HERR2, hormone nuclear receptor; NMR {Homo sapiens} SCOP: g.39.1.2

Probab=99.62  E-value=4.1e-17  Score=119.37  Aligned_cols=55  Identities=80%  Similarity=1.429  Sum_probs=48.8

Q ss_pred             CceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccccccccccCC
Q psy11505          1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRN   55 (312)
Q Consensus         1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~~~~~~~~   55 (312)
                      +..|+|..+++|.|++..|+.||+|||+|||+|||++++||.+|+++++.+....
T Consensus        38 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~~~r~k~~~~   92 (98)
T 1lo1_A           38 NIEYSCPATNECEITKRRRKSCQACRFMKALKVGMLKEGVRLDRVRGGRQKYKRR   92 (98)
T ss_dssp             TCCCCCSSCSCCCCCHHHHHHCHHHHHHHHHHHTCCGGGSCSSCCTTCCCCCC--
T ss_pred             cCccccCccccccccccccccccchhHHHHhHcCCCHHHeecccccCcccccCCC
Confidence            3579999999999999999999999999999999999999999998887765443

>3cbb_A HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DNA binding domain, nuclear; zinc finger; 2.00A {Homo sapiens}

Probab=99.60  E-value=1.2e-16  Score=112.06  Aligned_cols=45  Identities=42%  Similarity=0.891  Sum_probs=40.9

Q ss_pred             CceeEcCCCCCcccccccccccccCchhHHHHhcccccccccccc
Q psy11505          1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV   45 (312)
Q Consensus         1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~   45 (312)
                      +..|+|+.+++|.|++..|+.||+|||+|||+|||++++||.+|+
T Consensus        34 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~Rd   78 (78)
T 3cbb_A           34 NHMYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNERD   78 (78)
T ss_dssp             TCCCCCSSCSCCCCSTTTTTTCHHHHHHHHHHHTCCGGGCCCC--
T ss_pred             ccCcccccccccCcCccccccChhhhhHHHhHcCCCHHHccccCC
Confidence            357999999999999999999999999999999999999999874

>1cit_A NGFI-B, protein (orphan nuclear receptor NGFI-B); early immediate response gene product, transcription factor, monomeric protein-DNA complex; HET: DNA; 2.70A {Rattus norvegicus} SCOP: g.39.1.2

Probab=99.60  E-value=2.3e-16  Score=113.42  Aligned_cols=50  Identities=54%  Similarity=1.038  Sum_probs=45.0

Q ss_pred             CceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccccccc
Q psy11505          1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQ   50 (312)
Q Consensus         1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~~~   50 (312)
                      ++.|+|..+++|.|++..|+.||+|||+|||+|||++++||.++...++.
T Consensus        34 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~~~~~~r~   83 (89)
T 1cit_A           34 SAKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTDSLKGRRG   83 (89)
T ss_dssp             TCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHTTCCGGGSCCGGGTTCCS
T ss_pred             cceeeeccCCccccCCCCcccChhhhhHHHhHcCCCHHHeecccccCccc
Confidence            35799999999999999999999999999999999999999988665543

>1ynw_B Retinoic acid receptor RXR-alpha, retinoid X receptor; VDR, nuclear receptor, protein-DNA complex, transcripti complex; 3.00A {Homo sapiens} SCOP: g.39.1.2

Probab=99.60  E-value=1.3e-16  Score=116.89  Aligned_cols=50  Identities=48%  Similarity=0.991  Sum_probs=39.2

Q ss_pred             CceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccccccc
Q psy11505          1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQ   50 (312)
Q Consensus         1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~~~   50 (312)
                      ++.|+|+.+++|.|++..|+.||+|||+|||+|||++++||.+|++.+.+
T Consensus        37 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~~~~~   86 (99)
T 1ynw_B           37 DLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRGKDR   86 (99)
T ss_dssp             TCCCCCSSSSCCCCCSTTSSSCHHHHHHHHHHTTCCSTTCC---------
T ss_pred             ccccccCCCCcccccccCCccCccccHHHHhHcCCCHHHhhhcccccccc
Confidence            45799999999999999999999999999999999999999999876543

>1dsz_B RXR-alpha, retinoic acid receptor RXR-alpha; RAR, nuclear receptor, protein-DNA, transcription/DNA complex; HET: DNA; 1.70A {Homo sapiens} SCOP: g.39.1.2 PDB: 1by4_A* 1rxr_A 1r0n_A 1r0o_A 2nll_A*

Probab=99.60  E-value=1.6e-16  Score=113.24  Aligned_cols=46  Identities=50%  Similarity=1.029  Sum_probs=43.2

Q ss_pred             CceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccc
Q psy11505          1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR   46 (312)
Q Consensus         1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~   46 (312)
                      ++.|+|+.+++|.|++..|+.||+|||+|||+|||++++||.+|++
T Consensus        39 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~   84 (85)
T 1dsz_B           39 DLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQR   84 (85)
T ss_dssp             TCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCCCCC
T ss_pred             ccceeecccccccccccccccCcchhHHHHhHcCCCHHHhhcccCC
Confidence            4579999999999999999999999999999999999999999875

>2ebl_A COUP transcription factor 1; DNA-binding, metal-binding, nuclear protein, receptor, transcription regulation, zinc, EAR3, erbal3 tfcoup1; NMR {Homo sapiens}

Probab=99.59  E-value=2e-16  Score=113.66  Aligned_cols=47  Identities=40%  Similarity=0.880  Sum_probs=43.7

Q ss_pred             CceeEcCCCCCcccccccccccccCchhHHHHhcccccccccccccc
Q psy11505          1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG   47 (312)
Q Consensus         1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~   47 (312)
                      ++.|+|+.+++|.|++..|+.||+|||+|||+|||++++||.+|++.
T Consensus        41 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~~   87 (89)
T 2ebl_A           41 NLTYTCRANRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQRGSGPS   87 (89)
T ss_dssp             TCCCCCSSCSCCCCCSSSSSCCSHHHHHHHHHHTCCHHHHSCSCCCC
T ss_pred             ccceecccCccCCcCccCccccccchHHHhhhccCCHHHcccCCCCC
Confidence            45799999999999999999999999999999999999999998753

>2han_A Protein ultraspiracle; transcription regulation, transcription factor, DNA-binding, nuclear protein, nuclear receptor, zinc finger; 1.95A {Drosophila melanogaster} SCOP: g.39.1.2

Probab=99.59  E-value=2.2e-16  Score=114.49  Aligned_cols=48  Identities=42%  Similarity=0.868  Sum_probs=42.0

Q ss_pred             CceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccccc
Q psy11505          1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG   48 (312)
Q Consensus         1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~   48 (312)
                      ++.|+|+.+++|.|++..|+.||+|||+|||+|||++++||.+|++.+
T Consensus        44 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~~~   91 (93)
T 2han_A           44 DLTYACRENRNCIIDKRQRNRCQYCRYQKCLTCGMKREAVQEERQGIH   91 (93)
T ss_dssp             TCCCCCSSCSCCCCSTTTGGGCHHHHHHHHHHHTCCGGGSCCCC----
T ss_pred             ccCcCcCCCCcCCcCCCCCccCccccHHHHhHhCCCHHHhhhccCccc
Confidence            457999999999999999999999999999999999999999998654

>1dsz_A RAR-alpha, retinoic acid receptor alpha; RAR, nuclear receptor, protein-DNA, transcription/DNA complex; HET: DNA; 1.70A {Homo sapiens} SCOP: g.39.1.2 PDB: 1hra_A

Probab=99.58  E-value=2.8e-16  Score=112.38  Aligned_cols=47  Identities=51%  Similarity=0.912  Sum_probs=41.0

Q ss_pred             CceeEcCCCCCcccccccccccccCchhHHHHhcccccccccccccc
Q psy11505          1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG   47 (312)
Q Consensus         1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~   47 (312)
                      +..|+|..+++|.|++..|+.||+|||+|||+|||++++||.+|++.
T Consensus        38 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~~   84 (86)
T 1dsz_A           38 NMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNKK   84 (86)
T ss_dssp             TCCCCCSSCSCCCCSTTTGGGCHHHHHHHHHHTTCCGGGSCCC----
T ss_pred             ccceeeccCCccccCccccccchhhhHHHHHHhCCCHHHhhhccccc
Confidence            35799999999999999999999999999999999999999998764

>2a66_A Orphan nuclear receptor NR5A2; protein-DNA complex, zinc finger, DNA- binding domain, transcription factor, FTZ-F1, C-terminal extension; 2.20A {Homo sapiens} PDB: 2ff0_A

Probab=99.56  E-value=6.7e-16  Score=115.68  Aligned_cols=51  Identities=57%  Similarity=1.066  Sum_probs=46.9

Q ss_pred             CceeEcCCCCCcccccccccccccCchhHHHHhcccccccccccccccccc
Q psy11505          1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQK   51 (312)
Q Consensus         1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~~~~   51 (312)
                      ++.|.|+.+++|.|++..|+.||+|||+|||+|||++++||.+|+++++.+
T Consensus        43 ~~~y~C~~~~~C~i~~~~R~~Cr~CR~~KCl~vGM~~~~vq~~R~~~~r~~   93 (113)
T 2a66_A           43 NKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMRGGRNK   93 (113)
T ss_dssp             TCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCTTCCCSSCCT
T ss_pred             cccccccccccCCcCCCccccccchhHHHHhHhCCCHHHhccccccCCCCC
Confidence            357999999999999999999999999999999999999999998877654

>1hcq_A Protein (estrogen receptor); protein-DNA complex, complexed with drug, transcription/DNA complex; HET: DNA; 2.40A {Homo sapiens} SCOP: g.39.1.2 PDB: 1hcp_A 4aa6_A

Probab=99.54  E-value=8.6e-16  Score=109.21  Aligned_cols=45  Identities=56%  Similarity=1.156  Sum_probs=35.2

Q ss_pred             CceeEcCCCCCcccccccccccccCchhHHHHhcccccccccccc
Q psy11505          1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV   45 (312)
Q Consensus         1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~   45 (312)
                      +..|+|+.+++|.|++..|+.||+|||+|||+|||++++||.+|.
T Consensus        38 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~   82 (84)
T 1hcq_A           38 HNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRKDRR   82 (84)
T ss_dssp             CCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHHTCCC--------
T ss_pred             ccccccccCccCCcCCcCcccChhhhhHHHhHcCCCHHHhcccCC
Confidence            357999999999999999999999999999999999999999874

>1a6y_A Orphan nuclear receptor NR1D1; orphan receptor, DNA-binding, reverb, REV- ERB, transcription regulation, transcription/DNA complex; HET: DNA 5IU; 2.30A {Homo sapiens} SCOP: g.39.1.2 PDB: 1ga5_A* 1hlz_A

Probab=99.53  E-value=1.2e-15  Score=110.91  Aligned_cols=47  Identities=40%  Similarity=0.923  Sum_probs=40.9

Q ss_pred             cee-EcCCCCCcccccccccccccCchhHHHHhccccccccccccccc
Q psy11505          2 IEY-TCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG   48 (312)
Q Consensus         2 ~~Y-~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~   48 (312)
                      ..| .|..+++|.|++..|+.||+|||+|||+|||++++||.+|++..
T Consensus        42 ~~y~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~~~   89 (94)
T 1a6y_A           42 IQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGRIPKR   89 (94)
T ss_dssp             CCCCCCSSTTCCCCCTTTTTSCHHHHHHHHTTTTCCSTTCCCCC----
T ss_pred             cceEEccCCCCCccCccccccccchhHHHhhHccCCHHHhccCcCcCc
Confidence            468 59999999999999999999999999999999999999997654

>4hn5_A Glucocorticoid receptor; glucocorticoid receptor, steroid receptors, NGRE, repre transcription; HET: DNA; 1.90A {Homo sapiens} PDB: 4hn6_A*

Probab=99.51  E-value=2.6e-15  Score=113.10  Aligned_cols=48  Identities=44%  Similarity=0.866  Sum_probs=37.1

Q ss_pred             CceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccccc
Q psy11505          1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG   48 (312)
Q Consensus         1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~   48 (312)
                      +..|.|+++++|.|++..|+.||+|||+|||+|||++++||.+|+..+
T Consensus        63 ~~~y~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~avq~kR~~k~  110 (117)
T 4hn5_A           63 QHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEARKTKKKIKG  110 (117)
T ss_dssp             CCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHHTCCTTC---------
T ss_pred             CCceecCCCCccccCcccccCCcccchHHHhHcCCCHHHhcccccccc
Confidence            357999999999999999999999999999999999999999886544

>3g9m_A Glucocorticoid receptor; glucocorticoid, DNA-binding, allostery, lever ARM, transcription, hormone; HET: DNA; 1.61A {Rattus norvegicus} SCOP: g.39.1.2 PDB: 3g6p_A* 3g6q_B* 3g6r_B* 3g6u_A* 3g8u_A* 3g8x_A* 3g97_B* 3g99_A* 3g9i_A* 3g9j_A* 3fyl_A* 3g9o_B* 3g9p_B* 3g6t_A* 1r4o_A 1r4r_A 1glu_A* 1gdc_A 2gda_A 1rgd_A ...

Probab=99.51  E-value=2.1e-15  Score=109.04  Aligned_cols=49  Identities=43%  Similarity=0.832  Sum_probs=41.8

Q ss_pred             CceeEcCCCCCcccccccccccccCchhHHHHhcccccccccccccccc
Q psy11505          1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGR   49 (312)
Q Consensus         1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~~   49 (312)
                      +..|.|..+++|.|++..|+.||+|||+|||+|||++++||.+|+..+.
T Consensus        36 ~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~avq~~r~~~~~   84 (90)
T 3g9m_A           36 QHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEARKTKKKIKGI   84 (90)
T ss_dssp             CCCCCCSSSSCCCCCTTGGGTCHHHHHHHHHHHTCCTTHHHHHC-----
T ss_pred             CCceeCCCCCccccCcccccCCcchhhHHHHHcCCCHHHhccccccccc
Confidence            3579999999999999999999999999999999999999999865543

>1kb2_A Vitamin D3 receptor; VDR, nuclear receptor, protein-DNA complex, transcription/DNA complex; 2.70A {Homo sapiens} SCOP: g.39.1.2 PDB: 1kb4_A 1kb6_A 1ynw_A

Probab=99.50  E-value=1.4e-15  Score=113.72  Aligned_cols=47  Identities=40%  Similarity=0.842  Sum_probs=42.7

Q ss_pred             CceeEcCCCCCcccccccccccccCchhHHHHhcccccccccccccc
Q psy11505          1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG   47 (312)
Q Consensus         1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~   47 (312)
                      +..|+|+.+++|.|++..|+.||+|||+|||+|||++++|+.+|+..
T Consensus        40 ~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~q   86 (110)
T 1kb2_A           40 KALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDEEVQ   86 (110)
T ss_dssp             TCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCHHHHH
T ss_pred             ccceeeCCCCCccCCcccceecccccHhhhhhcCCcHHhcccHHHHh
Confidence            35799999999999999999999999999999999999998887543

>2han_B Ecdysone receptor; transcription regulation, transcription factor, DNA-binding, nuclear protein, nuclear receptor, zinc finger; 1.95A {Drosophila melanogaster} SCOP: g.39.1.2 PDB: 1r0o_B 1r0n_B

Probab=99.48  E-value=4e-15  Score=112.89  Aligned_cols=46  Identities=35%  Similarity=0.687  Sum_probs=42.7

Q ss_pred             CceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccc
Q psy11505          1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR   46 (312)
Q Consensus         1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~   46 (312)
                      +..|.|+.+++|.|++..|+.||+|||+|||+|||++++||.+|+.
T Consensus        42 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~   87 (119)
T 2han_B           42 SAVYCCKFGRACEMDMYMRRKCQECRLKKCLAVGMRPECVVPENQC   87 (119)
T ss_dssp             TCCCCCSSCSCCCCSTTGGGTCHHHHHHHHHHTTCCGGGSSCSSHH
T ss_pred             ccccccccccccccCccccccchhhHHHHHHHhCCCHHHccchhhh
Confidence            3579999999999999999999999999999999999999998764

>2lze_A A primordial catalytic fold generated by in vitro evolution; ligase, de novo protein; NMR {Synthetic construct}

Probab=99.48  E-value=6.9e-15  Score=104.57  Aligned_cols=43  Identities=26%  Similarity=0.367  Sum_probs=38.8

Q ss_pred             CceeEcCCCCCcccccccccccccCchhHHHHhcccccccccc
Q psy11505          1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLD   43 (312)
Q Consensus         1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~   43 (312)
                      ++.|+|+.+++|.|++..|++||+|||+|||+|||+...+...
T Consensus        36 ~~~y~C~~~~~C~i~~~~R~~C~~CR~qKCl~VgM~~~~~~~~   78 (87)
T 2lze_A           36 DLTYTDRDYKNCESYHKCSDLCQYCRYQKDLAIHHQHHHGGSM   78 (87)
T ss_dssp             SCTTTSCCCCCCCCSSCCSSSCSGGGTSCCHHHHCSSCCCCCC
T ss_pred             CCeeEcCCCCccccCCCccCcCCcccChhhccCcCEeccCccc
Confidence            4679999999999999999999999999999999998866544

>1r4i_A Androgen receptor; AR, steroid receptor, protein-DNA complex, transcription/DNA complex; 3.10A {Rattus norvegicus} SCOP: g.39.1.2

Probab=99.45  E-value=1.3e-14  Score=107.37  Aligned_cols=45  Identities=40%  Similarity=0.899  Sum_probs=37.1

Q ss_pred             CceeEcCCCCCcccccccccccccCchhHHHHhcccccccccccc
Q psy11505          1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV   45 (312)
Q Consensus         1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~   45 (312)
                      +..|+|+.+++|.|++..|+.||+|||+|||+|||++++++..+.
T Consensus        41 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~~k~~k~   85 (105)
T 1r4i_A           41 KQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLGARKLKKL   85 (105)
T ss_dssp             CCCCCCSSSSCCCCCTTTTTTCHHHHHHHHHHHTCCSCC------
T ss_pred             cCceeeccCCccccCccccccchhchHHHHHhhhcccchhhhccc
Confidence            357999999999999999999999999999999999999988764

>2nll_B Protein (thyroid hormone receptor); complex (transcription regulation/DNA), DNA-binding, nuclear protein, zinc- finger, multigene family; HET: DNA 5IU; 1.90A {Homo sapiens} SCOP: g.39.1.2 PDB: 3m9e_A*

Probab=99.45  E-value=6.1e-15  Score=108.97  Aligned_cols=47  Identities=38%  Similarity=0.751  Sum_probs=43.2

Q ss_pred             eeEcCCCCCcccccccccccccCchhHHHHhcccccccccccccccc
Q psy11505          3 EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGR   49 (312)
Q Consensus         3 ~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~~   49 (312)
                      .|.|..+++|.|++..|+.||+|||+|||+|||++++||.++.+..+
T Consensus        39 ~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~~~~~~k   85 (103)
T 2nll_B           39 SYSCKYEGKCVIDKVTRNQCQECRFKKCIYVGMATDLVLDDSKRLAK   85 (103)
T ss_dssp             GCCCSSCTTCCCSTTTTTSCHHHHHHHHHHTTCCGGGSCCHHHHHHH
T ss_pred             hhhhhccCCcCcCccCccccchhhhHhhhHhCCCHHHhhhhhhhHHh
Confidence            69999999999999999999999999999999999999998865443

>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=98.91  E-value=3.2e-10  Score=80.84  Aligned_cols=39  Identities=51%  Similarity=1.111  Sum_probs=34.5

Q ss_pred             CceeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505        206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR  244 (312)
Q Consensus       206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (312)
                      ...|.||++.++|+||||.+|+||++||+|+|+....|.
T Consensus         4 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~   42 (86)
T 1dsz_A            4 YKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYT   42 (86)
T ss_dssp             --CCTTTCSCCCSEETTEECCHHHHHHHHHHHHTTCCCC
T ss_pred             CCCCcEECCCccceeeCchhHHHHHHHHHHHhhccccee
Confidence            457999999999999999999999999999998877664

>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=98.89  E-value=5.1e-10  Score=81.85  Aligned_cols=40  Identities=53%  Similarity=1.066  Sum_probs=35.2

Q ss_pred             CceeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505        206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ  245 (312)
Q Consensus       206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (312)
                      ...|.|||+.++|+||||.+|+||++||+|+|+....|.+
T Consensus         3 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C   42 (99)
T 1ynw_B            3 KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTC   42 (99)
T ss_dssp             --CBTTTBSCCCBCCTTSCBCSHHHHHHHHHHHTTCCCCC
T ss_pred             CCCCceeCCCCcceeeCccchHHHHHHHHhhhcccccccc
Confidence            4579999999999999999999999999999988777743

>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=98.89  E-value=4.1e-10  Score=80.05  Aligned_cols=40  Identities=53%  Similarity=1.066  Sum_probs=36.2

Q ss_pred             CceeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505        206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ  245 (312)
Q Consensus       206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (312)
                      ...|.||++.++|+||||.+|++|++||+|+|+....|.+
T Consensus         5 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C   44 (85)
T 1dsz_B            5 KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTC   44 (85)
T ss_dssp             CEECTTTCCEESSEETTEECCHHHHHHHHHHHHHTCCCCC
T ss_pred             CCCCCEeCCCCCceeeCccchHHHHHHHHHhhccccceee
Confidence            4579999999999999999999999999999988777743

>3cbb_A HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DNA binding domain, nuclear; zinc finger; 2.00A {Homo sapiens}

Probab=98.89  E-value=4.9e-10  Score=78.36  Aligned_cols=38  Identities=47%  Similarity=1.095  Sum_probs=34.7

Q ss_pred             eeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505        208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ  245 (312)
Q Consensus       208 ~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (312)
                      .|.||++.++|+||||.+|++|++||+|+|+....|.+
T Consensus         2 ~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C   39 (78)
T 3cbb_A            2 LCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSC   39 (78)
T ss_dssp             BCTTTSSBCCSEETTEECCHHHHHHHHHHHHTTCCCCC
T ss_pred             CCeEeCCCCCceEeCCcchhhhceeeeEEEecccCccc
Confidence            59999999999999999999999999999988776643

>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=98.88  E-value=4.3e-10  Score=79.76  Aligned_cols=38  Identities=66%  Similarity=1.200  Sum_probs=35.2

Q ss_pred             ceeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505        207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR  244 (312)
Q Consensus       207 ~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (312)
                      ..|.||++.++|+||||.+|++|++||+|+|+....|.
T Consensus         5 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~   42 (84)
T 1hcq_A            5 RYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYM   42 (84)
T ss_dssp             CBCTTTCSBCCEEETTEEECHHHHHHHHHHHSSCCCCC
T ss_pred             CcCcEECCCCCCeeeCccchHHhhhhhhhccccccccc
Confidence            57999999999999999999999999999998877774

>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=98.87  E-value=5.6e-10  Score=80.03  Aligned_cols=38  Identities=58%  Similarity=1.039  Sum_probs=34.8

Q ss_pred             ceeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505        207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR  244 (312)
Q Consensus       207 ~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (312)
                      ..|.||++.++|+||||.+|++|++||+|+|+....|.
T Consensus         1 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~   38 (89)
T 1cit_A            1 GRCAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYI   38 (89)
T ss_dssp             CCCSSSCCCCCEEETTEEECHHHHHHHHHHHHHTCCCC
T ss_pred             CCCeEeCCCCcceEeCccchhhhhhhceeeEEecceee
Confidence            36999999999999999999999999999998877664

>2ebl_A COUP transcription factor 1; DNA-binding, metal-binding, nuclear protein, receptor, transcription regulation, zinc, EAR3, erbal3 tfcoup1; NMR {Homo sapiens}

Probab=98.87  E-value=6.4e-10  Score=79.68  Aligned_cols=40  Identities=48%  Similarity=0.952  Sum_probs=36.0

Q ss_pred             CceeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505        206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ  245 (312)
Q Consensus       206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (312)
                      ...|.||++.++|+||||.+|++|++||+|+|+....|++
T Consensus         7 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C   46 (89)
T 2ebl_A            7 GIECVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTC   46 (89)
T ss_dssp             SCBCTTTCSBCCSEETTEECCHHHHHHHHHHHTTTCCCCC
T ss_pred             CCCCcEeCCCCcceEeCchhhHHhhhhhheeeeeccceec
Confidence            4579999999999999999999999999999987776643

>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=98.87  E-value=5.3e-10  Score=80.84  Aligned_cols=40  Identities=58%  Similarity=1.075  Sum_probs=36.0

Q ss_pred             CceeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505        206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ  245 (312)
Q Consensus       206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (312)
                      ...|.||++.++|+||||.+|++|++||+|+|+....|.+
T Consensus        10 ~~~C~VCgd~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C   49 (93)
T 2han_A           10 KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYAC   49 (93)
T ss_dssp             CCBCTTTCSBCCEEETTEEECHHHHHHHHHHHHHTCCCCC
T ss_pred             CCCCcEeCCCCcCeecCcchhHHHHHHHHhhhccccCcCc
Confidence            3579999999999999999999999999999988777743

>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=98.86  E-value=5.8e-10  Score=80.37  Aligned_cols=40  Identities=50%  Similarity=1.029  Sum_probs=36.5

Q ss_pred             CceeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505        206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ  245 (312)
Q Consensus       206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (312)
                      +..|.||++.++|+||||.+|++|++||+|+|+....|++
T Consensus         2 ~~~C~VCg~~a~g~hyGv~sC~~Ck~FFRR~v~~~~~~~C   41 (90)
T 3g9m_A            2 SHMCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLC   41 (90)
T ss_dssp             CCBCTTTCSBCCEEETTEEECHHHHHHHHHHHHSCCCCCC
T ss_pred             CCcCccCCCcCcccccCCccchhHhHHhhhhhhcCCceeC
Confidence            3579999999999999999999999999999998887743

>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=98.86  E-value=6.6e-10  Score=81.10  Aligned_cols=39  Identities=79%  Similarity=1.424  Sum_probs=35.7

Q ss_pred             CceeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505        206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR  244 (312)
Q Consensus       206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (312)
                      ...|.|||+.++|+||||.+|+||++||+|+|+....|.
T Consensus         4 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~   42 (98)
T 1lo1_A            4 KRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYS   42 (98)
T ss_dssp             CCEETTTTEECSEESSSSEECHHHHHHHHHHHHTTCCCC
T ss_pred             CCCCcEeCCCCcCeeeCccchhhhhhhheeeecccCccc
Confidence            468999999999999999999999999999998877663

>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=98.84  E-value=8.5e-10  Score=82.25  Aligned_cols=40  Identities=43%  Similarity=1.004  Sum_probs=35.9

Q ss_pred             CceeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505        206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ  245 (312)
Q Consensus       206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (312)
                      ...|.|||+.++|+||||.+|+||++||+|+|.....|++
T Consensus         6 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C   45 (110)
T 1kb2_A            6 PRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTC   45 (110)
T ss_dssp             -CBCTTTCSBCCSEETTEECCHHHHHHHHHHHHTTCCCCC
T ss_pred             CCCCcEeCCCCCceEeCchhHhhhhhhheeeeecccceee
Confidence            4679999999999999999999999999999998777744

>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=98.82  E-value=1.2e-09  Score=80.62  Aligned_cols=38  Identities=55%  Similarity=1.187  Sum_probs=33.9

Q ss_pred             ceeeeeCCCCcccccccccchhHHHHHHHHhhhcc--cce
Q psy11505        207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYS--GYR  244 (312)
Q Consensus       207 ~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~  244 (312)
                      ..|.|||+.++|+||||.+|+||++||+|+|....  .|.
T Consensus         2 ~~C~VCgd~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~y~   41 (103)
T 2nll_B            2 ELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYS   41 (103)
T ss_dssp             CBCTTTCSBCCSEETTEECCHHHHHHHHHHHHTTCGGGCC
T ss_pred             CCCeEeCCcCcCeecCcccHHHhhhhheecccccccchhh
Confidence            57999999999999999999999999999998653  553

>1r4i_A Androgen receptor; AR, steroid receptor, protein-DNA complex, transcription/DNA complex; 3.10A {Rattus norvegicus} SCOP: g.39.1.2

Probab=98.81  E-value=9.3e-10  Score=81.27  Aligned_cols=40  Identities=48%  Similarity=0.991  Sum_probs=36.0

Q ss_pred             CceeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505        206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ  245 (312)
Q Consensus       206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (312)
                      ...|.||++.++|+||||.+|++|++||||+|.....|.+
T Consensus         7 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C   46 (105)
T 1r4i_A            7 QKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLC   46 (105)
T ss_dssp             CCBCSSSCSBEEEEETTEEEEHHHHHHHHHHHTSCCCCCC
T ss_pred             CCCCcEeCCCCCceEeCCcchhhhhhhhceeEEecCceee
Confidence            4679999999999999999999999999999988776643

>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=98.81  E-value=8.3e-10  Score=82.58  Aligned_cols=40  Identities=55%  Similarity=1.143  Sum_probs=35.8

Q ss_pred             CceeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505        206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ  245 (312)
Q Consensus       206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (312)
                      ...|.||++.++|+||||.+|+||++||+|+|.....|.+
T Consensus         9 ~~~C~VCgd~a~G~HyGv~sC~aCk~FFRR~v~~~~~y~C   48 (113)
T 2a66_A            9 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTC   48 (113)
T ss_dssp             -CBCTTTCCBEEEEETTEEEEHHHHHHHHHHHHTTCCCCC
T ss_pred             CCCCcEeCCCCcceeeCcccHHHHHHHHhhhhhccccccc
Confidence            5679999999999999999999999999999988777743

>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=98.81  E-value=1.2e-09  Score=82.78  Aligned_cols=40  Identities=50%  Similarity=1.079  Sum_probs=36.2

Q ss_pred             CceeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505        206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ  245 (312)
Q Consensus       206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (312)
                      ...|.|||+.++|+||||.+|+||++||+|+|.....|.+
T Consensus         8 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C   47 (119)
T 2han_B            8 EELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCC   47 (119)
T ss_dssp             SCBCTTTCSBCCEEETTEEECHHHHHHHHHHHHTTCCCCC
T ss_pred             CCcCeEeCCcCCcceECchhHHhhHHhhhhheEecccccc
Confidence            5679999999999999999999999999999987776643

>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=98.79  E-value=1.1e-09  Score=79.36  Aligned_cols=38  Identities=66%  Similarity=1.254  Sum_probs=34.2

Q ss_pred             CceeeeeCCCCcccccccccchhHHHHHHHHhhhcccc
Q psy11505        206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY  243 (312)
Q Consensus       206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  243 (312)
                      ...|.||++.++|+||||.+|+||++||+|+|+....|
T Consensus         7 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y   44 (94)
T 1a6y_A            7 VLLCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQY   44 (94)
T ss_dssp             -CBCTTTSSBCCEEETTEEECHHHHHHHHHHHSSCCCC
T ss_pred             CCcCcEeCCCCcceEeCccchhhhhhehheeeecccce
Confidence            35799999999999999999999999999999876655

>4hn5_A Glucocorticoid receptor; glucocorticoid receptor, steroid receptors, NGRE, repre transcription; HET: DNA; 1.90A {Homo sapiens} PDB: 4hn6_A*

Probab=98.76  E-value=1.7e-09  Score=81.27  Aligned_cols=40  Identities=53%  Similarity=1.051  Sum_probs=35.9

Q ss_pred             CceeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505        206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ  245 (312)
Q Consensus       206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (312)
                      ...|.||++.++|+||||.+|++|++||||+|+....|.+
T Consensus        29 ~~~C~VCgd~a~G~HyGv~sC~aCk~FFRRsv~~~~~y~C   68 (117)
T 4hn5_A           29 PKLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLC   68 (117)
T ss_dssp             -CBCTTTCSBCCEEETTEEECHHHHHHHHHHHSSCCCCCC
T ss_pred             CCcCCcCCCcCcccccCCcccchhhhhhhcceecCCceec
Confidence            3569999999999999999999999999999988887743

>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=98.48  E-value=3.3e-08  Score=92.94  Aligned_cols=41  Identities=51%  Similarity=1.038  Sum_probs=37.0

Q ss_pred             CceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceec
Q psy11505        206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQT  246 (312)
Q Consensus       206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  246 (312)
                      ...|.||||.++|+||||.+|+||++||||+|++...|+|.
T Consensus       137 ~~~C~VCg~~a~g~hygv~sC~~Ck~FFrR~~~~~~~~~C~  177 (467)
T 3dzy_A          137 KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCR  177 (467)
T ss_dssp             CEECTTTSSEECSEETTEECCHHHHHHHHHHHHTTCCCCCS
T ss_pred             CCcceeCCCCCCCCcCCCcchhhhhHhccccccCCCceeCC
Confidence            45699999999999999999999999999999988777543

>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=98.44  E-value=6.9e-08  Score=89.64  Aligned_cols=38  Identities=61%  Similarity=1.151  Sum_probs=34.8

Q ss_pred             CceeeeeCCCCcccccccccchhHHHHHHHHhhhcccc
Q psy11505        206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY  243 (312)
Q Consensus       206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  243 (312)
                      ...|.|||+.++|+||||.+|+||++||||+|+....|
T Consensus        50 ~~~C~vC~~~~~g~hygv~~C~~C~~FFrR~~~~~~~~   87 (419)
T 3dzy_D           50 AIECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLIY   87 (419)
T ss_dssp             CCCCSSSCSCCCSBCSSSBCCHHHHHHHHHHHTTTCCC
T ss_pred             CCcCeECCCcCCCCccCcccchhhhHHHccchhccccc
Confidence            45799999999999999999999999999999876665

---

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	312
d3d24a1	227	a.123.1.1 (A:194-420) Steroid hormone receptor ERR	9e-28
d2e2ra1	223	a.123.1.1 (A:234-456) Orphan nuclear receptor ERR3	6e-26
d1xpca_	245	a.123.1.1 (A:) Estrogen receptor alpha {Human (Hom	5e-25
d1nhza_	247	a.123.1.1 (A:) Glucocorticoid receptor {Human (Hom	1e-23
d2p1ta1	230	a.123.1.1 (A:229-458) Retinoid-X receptor alpha (R	9e-23
d1sqna_	251	a.123.1.1 (A:) Progesterone receptor {Human (Homo	4e-22
d2j7ya1	236	a.123.1.1 (A:217-452) Estrogen receptor beta {Rat	5e-22
d1t7ra_	250	a.123.1.1 (A:) Androgen receptor {Chimpanzee (Pan	2e-21
d1fcya_	236	a.123.1.1 (A:) Retinoic acid receptor gamma (RAR-g	1e-20
d1hg4a_	265	a.123.1.1 (A:) Ultraspiracle protein, usp {Drosoph	1e-20
d1pk5a_	242	a.123.1.1 (A:) Orphan nuclear receptor NR5a2 (LRH-	3e-20
d1pdua_	230	a.123.1.1 (A:) Nuclear hormone receptor HR38 {Frui	7e-20
d1pzla_	233	a.123.1.1 (A:) Hepatocyte nuclear factor 4-alpha {	3e-19
d1g2na_	256	a.123.1.1 (A:) Ultraspiracle protein, usp {Helioth	7e-19
d1ovla_	236	a.123.1.1 (A:) Orphan nuclear receptor NURR1 {Huma	5e-18
d1n46a_	251	a.123.1.1 (A:) Thyroid hormone receptor beta (TR-b	1e-17
d2qw4a1	233	a.123.1.1 (A:32-264) Orphan nuclear receptor NR4A1	2e-16
d2r40d1	243	a.123.1.1 (D:287-529) Ecdysone receptor {Noctuid m	6e-16
d1lo1a_	90	g.39.1.2 (A:) Steroid hormone receptor Err2 DNA-bi	7e-16
d1lo1a_	90	g.39.1.2 (A:) Steroid hormone receptor Err2 DNA-bi	2e-11
d1pq9a_	239	a.123.1.1 (A:) Oxysterols receptor LXR-beta {Human	1e-15
d2b50b1	265	a.123.1.1 (B:211-475) Peroxisome proliferator-acti	1e-14
d1cita_	89	g.39.1.2 (A:) Orphan nuclear receptor NGFI-B DNA-b	3e-14
d1cita_	89	g.39.1.2 (A:) Orphan nuclear receptor NGFI-B DNA-b	4e-10
d1nrla_	292	a.123.1.1 (A:) Pregnane x receptor, PXR {Human (Ho	3e-14
d1n83a_	251	a.123.1.1 (A:) Orphan nuclear receptor ROR-alpha {	3e-14
d1osha_	231	a.123.1.1 (A:) Bile acid receptor FXR {Human (Homo	1e-13
d2fvja1	271	a.123.1.1 (A:207-477) Peroxisome proliferator acti	9e-13
d1dszb_	84	g.39.1.2 (B:) Retinoid X receptor (RXR-alpha) DNA-	1e-12
d1dszb_	84	g.39.1.2 (B:) Retinoid X receptor (RXR-alpha) DNA-	4e-12
d1nq7a_	244	a.123.1.1 (A:) Orphan nuclear receptor ROR-beta {R	8e-12
d2hanb1	83	g.39.1.2 (B:5-87) Ecdysone receptor DNA-binding do	9e-12
d2hanb1	83	g.39.1.2 (B:5-87) Ecdysone receptor DNA-binding do	1e-09
d1kb2a_	89	g.39.1.2 (A:) Vitamin D3 receptor, VDR, DNA-bindin	1e-11
d1kb2a_	89	g.39.1.2 (A:) Vitamin D3 receptor, VDR, DNA-bindin	7e-11
d1xvpb_	246	a.123.1.1 (B:) Orphan nuclear receptor NR1I3 (CAR)	3e-11
d1r4ia_	74	g.39.1.2 (A:) Androgen receptor {Rat (Rattus norve	3e-11
d1r4ia_	74	g.39.1.2 (A:) Androgen receptor {Rat (Rattus norve	5e-09
d1ie9a_	255	a.123.1.1 (A:) Vitamin D nuclear receptor {Human (	3e-11
d1xnxa_	232	a.123.1.1 (A:) Orphan nuclear receptor NR1I3 (CAR)	3e-11
d1a6ya_	78	g.39.1.2 (A:) Orphan nuclear receptor reverb DNA-b	6e-11
d1a6ya_	78	g.39.1.2 (A:) Orphan nuclear receptor reverb DNA-b	2e-10
d1dsza_	75	g.39.1.2 (A:) Retinoic acid receptor DNA-binding d	1e-10
d1dsza_	75	g.39.1.2 (A:) Retinoic acid receptor DNA-binding d	2e-09
d1hcqa_	74	g.39.1.2 (A:) Estrogen receptor DNA-binding domain	2e-10
d1hcqa_	74	g.39.1.2 (A:) Estrogen receptor DNA-binding domain	6e-08
d1lata_	71	g.39.1.2 (A:) Glucocorticoid receptor DNA-binding	6e-10
d1lata_	71	g.39.1.2 (A:) Glucocorticoid receptor DNA-binding	4e-08
d2p54a1	267	a.123.1.1 (A:202-468) Peroxisome proliferator acti	9e-10
d2nllb_	103	g.39.1.2 (B:) Thyroid hormone receptor (TR-beta) D	1e-08
d2nllb_	103	g.39.1.2 (B:) Thyroid hormone receptor (TR-beta) D	4e-08

>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 =  105 bits (263), Expect = 9e-28
 Identities = 78/243 (32%), Positives = 109/243 (44%), Gaps = 25/243 (10%)

Query: 75  NKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSL 134
           N ++  LL+ EPE L    +    D  L  + +L DL+DRE+V  I WAK IPGF+ LSL
Sbjct: 2   NALVSHLLVVEPEKLYAMPDPAGPDGHLPAVATLCDLFDREIVVTISWAKSIPGFSSLSL 61

Query: 135 NDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKH-S 193
           +DQM +LQS W E+L L +A RSLP    ++ FA DLVLDE  AR  G  E+   +    
Sbjct: 62  SDQMSVLQSVWMEVLVLGVAQRSLPLQ-DELAFAEDLVLDEEGARAAGLGELGAALLQLV 120

Query: 194 GSLD--GIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ-----VYSGYRQT 246
             L    ++ EE    + L    +A+     +   EA +   +   +             
Sbjct: 121 RRLQALRLEREEY---VLLKALALANSDSVHIEDAEAVEQLREALHEALLEYEAGRAGPG 177

Query: 247 GACGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLRFWSTVHKDGKVLMNKLFVEM 306
           G           + L                      VL  +  V  +GKV M+KLF+EM
Sbjct: 178 GGAERRRAGRLLLTLPLLRQT-------------AGKVLAHFYGVKLEGKVPMHKLFLEM 224

Query: 307 LEA 309
           LEA
Sbjct: 225 LEA 227

>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 =  100 bits (250), Expect = 6e-26
 Identities = 73/239 (30%), Positives = 110/239 (46%), Gaps = 21/239 (8%)

Query: 75  NKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSL 134
           NK++  LL+ EPE +    +    D  ++ + +L DL DRELV IIGWAK IPGF+ LSL
Sbjct: 2   NKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSL 61

Query: 135 NDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKH-S 193
            DQM LLQS W EIL L + YRSL     ++ +A D ++DE Q++  G  ++   +    
Sbjct: 62  ADQMSLLQSAWMEILILGVVYRSLSFE-DELVYADDYIMDEDQSKLAGLLDLNNAILQLV 120

Query: 194 GSLDGIK--EEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGT 251
                +K  +EE    + L    +A+     +   EA +       +         A   
Sbjct: 121 KKYKSMKLEKEEF---VTLKAIALANSDSMHIEDVEAVQKLQDVLHE---------ALQD 168

Query: 252 LVLANSDVKLDEFSSLKKFRNSILSSLGD-CIYVLRFWSTVHKDGKVLMNKLFVEMLEA 309
                          +       L  L       ++ +  +  +GKV M+KLF+EMLEA
Sbjct: 169 YEAGQHMEDPRRAGKM----LMTLPLLRQTSTKAVQHFYNIKLEGKVPMHKLFLEMLEA 223

>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 = 98.6 bits (245), Expect = 5e-25
 Identities = 68/246 (27%), Positives = 115/246 (46%), Gaps = 15/246 (6%)

Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           SL  ++M+ ALL  EP +L    +  +       +  L++L DRELV +I WAK++PGF 
Sbjct: 3   SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 62

Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC-GFSEIYQQ 189
           DL+L+DQ+ LL+  W EIL + + +RS+ H  GK+ FA +L+LD  Q +   G  EI+  
Sbjct: 63  DLTLHDQVHLLECAWLEILMIGLVWRSMEHP-GKLLFAPNLLLDRNQGKCVEGMVEIFDM 121

Query: 190 VKHSGS---LDGIKEEE--LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244
           +  + S   +  ++ EE    + + L+   V +     + S E      +   ++     
Sbjct: 122 LLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLI 181

Query: 245 QTGACGTLVLANSDVKLDEFSSLKKFRNSILSSLGD-CIYVLRFWSTVHKDGKVLMNKLF 303
              A   L L     +    + L      ILS +       +    ++     V +  L 
Sbjct: 182 HLMAKAGLTLQQQHQR---LAQL----LLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLL 234

Query: 304 VEMLEA 309
           +EML+A
Sbjct: 235 LEMLDA 240

>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 = 95.2 bits (236), Expect = 1e-23
 Identities = 50/241 (20%), Positives = 102/241 (42%), Gaps = 17/241 (7%)

Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
           ++  L + EPE+L    ++   D T + + +L+ L  R+++  + WAK IPGF +L L+D
Sbjct: 3   LVSLLEVIEPEVLYAGYDSSVPDSTWRIMTTLNMLGGRQVIAAVKWAKAIPGFRNLHLDD 62

Query: 137 QMRLLQSTWAEILTLTIAYRSLPH-CAGKIRFASDLVLDERQARECGFSEIYQQV-KHSG 194
           QM LLQ +W  ++   + +RS     A  + FA DL+++E++       +  + +   S 
Sbjct: 63  QMTLLQYSWMSLMAFALGWRSYRQSSANLLCFAPDLIINEQRMTLPDMYDQCKHMLYVSS 122

Query: 195 SLDGIK--EEE--LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACG 250
            L  ++   EE    + L L+      G        +  +  + + +      R+     
Sbjct: 123 ELHRLQVSYEEYLCMKTLLLLSSVPKDGLK-SQELFDEIRMTYIKELGKAIVKRE----- 176

Query: 251 TLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLRFWSTVHKDGKVLMNKLFVEMLEAY 310
                NS      F  L K     +  + + +    F + + K   +   ++  E++   
Sbjct: 177 ----GNSSQNWQRFYQLTK-LLDSMHEVVENLLNYCFQTFLDKTMSIEFPEMLAEIITNQ 231

Query: 311 L 311
           +
Sbjct: 232 I 232

>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 = 92.1 bits (228), Expect = 9e-23
 Identities = 54/243 (22%), Positives = 97/243 (39%), Gaps = 28/243 (11%)

Query: 76  KMLEALLLCEP--EMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLS 133
           ++LEA L  EP  E     +           + ++    D++L  ++ WAK+IP F++L 
Sbjct: 6   RILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELP 65

Query: 134 LNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKHS 193
           L+DQ+ LL++ W E+L  + ++RS+      I  A+ L +    A   G   I+ +V   
Sbjct: 66  LDDQVILLRAGWNELLIASFSHRSIAVK-DGILLATGLHVHRNSAHSAGVGAIFDRVLTE 124

Query: 194 GSLD----GIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR---QT 246
                    + + EL     +V  +  S      A  EA +     +++ Y  ++   Q 
Sbjct: 125 LVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQP 184

Query: 247 GACGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLRFWSTVHKDGKVLMNKLFVEM 306
           G    L+L     +L    S+              +  L         G   ++   +EM
Sbjct: 185 GRFAKLLL-----RLPALRSI-------------GLKCLEHLFFFKLIGDTPIDTFLMEM 226

Query: 307 LEA 309
           LEA
Sbjct: 227 LEA 229

>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 = 90.9 bits (225), Expect = 4e-22
 Identities = 31/117 (26%), Positives = 67/117 (57%), Gaps = 1/117 (0%)

Query: 77  MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLND 136
           ++  L+  EP+++    +  + D +   + SL+ L +R+L+ ++ W+K +PGF +L ++D
Sbjct: 6   LINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDD 65

Query: 137 QMRLLQSTWAEILTLTIAYRSLPH-CAGKIRFASDLVLDERQARECGFSEIYQQVKH 192
           Q+ L+Q +W  ++   + +RS  H     + FA DL+L+E++ +E  F  +   +  
Sbjct: 66  QITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQ 122

>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 = 90.5 bits (224), Expect = 5e-22
 Identities = 66/247 (26%), Positives = 109/247 (44%), Gaps = 19/247 (7%)

Query: 71  SLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFT 130
           +L   +++  LL  EP  + V S           + SL+ L D+ELV +IGWAK+IPGF 
Sbjct: 1   TLSPEQLVLTLLEAEPPNVLV-SRPSMPFTEASMMMSLTKLADKELVHMIGWAKKIPGFV 59

Query: 131 DLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECG-----FSE 185
           +LSL DQ+RLL+S W E+L + + +RS+ H  GK+ FA DLVLD  + +        F  
Sbjct: 60  ELSLLDQVRLLESCWMEVLMVGLMWRSIDHP-GKLIFAPDLVLDRDEGKCVEGILEIFDM 118

Query: 186 IYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ 245
           +         L  ++ +E    LC+    + +   Y +AS        ++   + +    
Sbjct: 119 LLATTSRFRELK-LQHKEY---LCVKAMILLNSSMYPLASANQEAESSRKLTHLLNAVTD 174

Query: 246 TGACGTLVLANSDVKLDEFSSLKKFRN--SILSSLGD-CIYVLRFWSTVHKDGKVLMNKL 302
                 LV   +   +       +  N   +LS +       +    ++     V +  L
Sbjct: 175 A-----LVWVIAKSGISSQQQSVRLANLLMLLSHVRHISNKGMEHLLSMKCKNVVPVYDL 229

Query: 303 FVEMLEA 309
            +EML A
Sbjct: 230 LLEMLNA 236

>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 = 89.0 bits (220), Expect = 2e-21
 Identities = 45/242 (18%), Positives = 91/242 (37%), Gaps = 16/242 (6%)

Query: 74  ENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLS 133
           +   L  L   EP ++    +  Q D     ++SL++L +R+LV ++ WAK +PGF +L 
Sbjct: 2   QPIFLNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLH 61

Query: 134 LNDQMRLLQSTWAEILTLTIAYRSLPHCAGK-IRFASDLVLDERQARECGFSEI----YQ 188
           ++DQM ++Q +W  ++   + +RS  +   + + FA DLV +E +  +            
Sbjct: 62  VDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHKSRMYSQCVRMRH 121

Query: 189 QVKHSGSLDGIKEE-ELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTG 247
             +  G L    +E    + L L       G        +  +  + + +      ++  
Sbjct: 122 LSQEFGWLQITPQEFLCMKALLLFSIIPVDGLK-NQKFFDELRMNYIKELDRIIACKR-- 178

Query: 248 ACGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLRFWSTVHKDGKVLMNKLFVEML 307
                   N       F  L K  +S+     +                V   ++  E++
Sbjct: 179 -------KNPTSCSRRFYQLTKLLDSVQPIARELHQFTFDLLIKSHMVSVDFPEMMAEII 231

Query: 308 EA 309
             
Sbjct: 232 SV 233

>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 = 86.2 bits (213), Expect = 1e-20
 Identities = 33/111 (29%), Positives = 52/111 (46%), Gaps = 2/111 (1%)

Query: 83  LCEPEMLTVRSETPQSDPT-LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLL 141
           LC+    T  S         L   +  S+L  + ++ I+ +AK++PGFT LS+ DQ+ LL
Sbjct: 23  LCQLGKYTTNSSADHRVQLDLGLWDKFSELATKCIIKIVEFAKRLPGFTGLSIADQITLL 82

Query: 142 QSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKH 192
           ++   +IL L I  R  P     + F+  L L+  Q    GF  +   V  
Sbjct: 83  KAACLDILMLRICTRYTPEQ-DTMTFSDGLTLNRTQMHNAGFGPLTDLVFA 132

>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 = 87.1 bits (215), Expect = 1e-20
 Identities = 38/274 (13%), Positives = 87/274 (31%), Gaps = 56/274 (20%)

Query: 75  NKMLEALLLCEPEM-------LTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIP 127
            +++EA    E +        L V   +         +++L  + +++L  ++ +A+ +P
Sbjct: 4   ERIIEAEQRAETQCGDRALTFLRVGPYSTVQPDYKGAVSALCQVVNKQLFQMVEYARMMP 63

Query: 128 GFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHC-------------------------- 161
            F  + L+DQ+ LL++ W E+L   +A+ S+                             
Sbjct: 64  HFAQVPLDDQVILLKAAWIELLIANVAWCSIVSLDDGGAGGGGGGLGHDGSFERRSPGLQ 123

Query: 162 AGKIRFASDLVLDERQARECGFSEIYQQ-----VKHSGSLDGIKEEELPRRLCLVCGDVA 216
             ++            A + G S I+ +           L+  + E    +  ++     
Sbjct: 124 PQQLFLNQSFSYHRNSAIKAGVSAIFDRILSELSVKMKRLNLDRRELSCLKAIILY---- 179

Query: 217 SGFHYGVASCEACKAFFKRTIQVYSGY-RQTGACGTLVLANSDVKLDEFSSLKKFRNSIL 275
           +    G+ S    +   ++       + R          A   ++L    S+        
Sbjct: 180 NPDIRGIKSRAEIEMCREKVYACLDEHCRLEHPGDDGRFAQLLLRLPALRSI-------- 231

Query: 276 SSLGDCIYVLRFWSTVHKDGKVLMNKLFVEMLEA 309
                 +                + +LF+E LEA
Sbjct: 232 -----SLKCQDHLFLFRITSDRPLEELFLEQLEA 260

>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 = 85.5 bits (211), Expect = 3e-20
 Identities = 54/252 (21%), Positives = 95/252 (37%), Gaps = 34/252 (13%)

Query: 76  KMLEALLLCEPE--------MLTVRSETPQSDPT--LQTINSLSDLYDRELVCIIGWAKQ 125
            ++  LL CEP+        M  ++ E    +    L     L  + D+ L  I+ WA+ 
Sbjct: 5   HLILELLKCEPDEPQVQAKIMAYLQQEQSNRNRQEKLSAFGLLCKMADQTLFSIVEWARS 64

Query: 126 IPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHC-AGKIRFASDLVLDERQA---REC 181
              F +L ++DQM+LLQ+ W+E+L L   YR + H   G I   +   +D        E 
Sbjct: 65  SIFFRELKVDDQMKLLQNCWSELLILDHIYRQVAHGKEGTIFLVTGEHVDYSTIISHTEV 124

Query: 182 GFSEIYQQVKH-SGSLDGIK--EEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
            F+ +    +     L  ++  + E    +CL    + S     + + +  +   ++   
Sbjct: 125 AFNNLLSLAQELVVRLRSLQFDQREF---VCLKFLVLFSSDVKNLENLQLVEGVQEQVNA 181

Query: 239 VYSGYRQTGACGTLVLANSDVKLDEFSSLKKFRNSILSSLGD-CIYVLRFWSTVHKDGKV 297
               Y          + N   + ++F  L       L  L         +    H +G V
Sbjct: 182 ALLDY---------TVCNYPQQTEKFGQL----LLRLPELRAISKQAEDYLYYKHVNGDV 228

Query: 298 LMNKLFVEMLEA 309
             N L +EML A
Sbjct: 229 PYNNLLIEMLHA 240

>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 = 84.3 bits (208), Expect = 7e-20
 Identities = 46/243 (18%), Positives = 73/243 (30%), Gaps = 29/243 (11%)

Query: 75  NKMLEALLLCEPEM--LTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDL 132
             ++ + +   P+   L       QS      +     L    +  I  +A++IPG+ DL
Sbjct: 6   TALVRSHVDTTPDPSCLDYSHYEEQSMSEADKVQQFYQLLTSSVDVIKQFAEKIPGYFDL 65

Query: 133 SLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKH 192
              DQ  L QS   E+  L +AYR+      K+ F +  VL   Q     F E    +  
Sbjct: 66  LPEDQELLFQSASLELFVLRLAYRARIDD-TKLIFCNGTVLHRTQCL-RSFGEWLNDIME 123

Query: 193 -SGSLD--GIKEEELP--RRLCLVCGDVASGFHYGVASC--EACKAFFKRTIQVYSGYRQ 245
            S SL    I          L L+           V     +   +            ++
Sbjct: 124 FSRSLHNLEIDISAFACLCALTLITERHGLREPKKVEQLQMKIIGSLRDHVTYNAEAQKK 183

Query: 246 TGACGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLRFWSTVHKDGKVLMNKLFVE 305
                 L+      KL E  SL              +  L+    +  +  V    L   
Sbjct: 184 QHYFSRLLG-----KLPELRSL-------------SVQGLQRIFYLKLEDLVPAPALIEN 225

Query: 306 MLE 308
           M  
Sbjct: 226 MFV 228

>d1pzla_ a.123.1.1 (A:) Hepatocyte nuclear factor 4-alpha {Human (Homo sapiens) [TaxId: 9606]} Length = 233

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Hepatocyte nuclear factor 4-alpha
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 82.8 bits (204), Expect = 3e-19
 Identities = 29/128 (22%), Positives = 55/128 (42%), Gaps = 12/128 (9%)

Query: 68  SIPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQ-----TINSLSDLYDRELVCIIGW 122
           S+PS+       ALL  E     + S     +  ++     +I  + +    +L+ ++ W
Sbjct: 3   SLPSIN------ALLQAEVLSRQITSPVSGINGDIRAKKIASIADVCESMKEQLLVLVEW 56

Query: 123 AKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECG 182
           AK IP F +L L+DQ+ LL++   E L L    RS+      +   +D ++         
Sbjct: 57  AKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFK-DVLLLGNDYIVPRHCPELAE 115

Query: 183 FSEIYQQV 190
            S +  ++
Sbjct: 116 MSRVSIRI 123

>d1g2na_ a.123.1.1 (A:) Ultraspiracle protein, usp {Heliothis virescens [TaxId: 7102]} Length = 256

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Ultraspiracle protein, usp
species: Heliothis virescens [TaxId: 7102]

 Score = 82.1 bits (202), Expect = 7e-19
 Identities = 30/147 (20%), Positives = 64/147 (43%), Gaps = 22/147 (14%)

Query: 68  SIPSLEENKMLEA-LLLCEP----EMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGW 122
           ++  L   ++LE   L+ +P    + L V  ++         ++SL  + ++++  ++ W
Sbjct: 2   AVQELSIERLLEMESLVADPSEEFQFLRVGPDSNVPPKFRAPVSSLCQIGNKQIAALVVW 61

Query: 123 AKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHC-----------------AGKI 165
           A+ IP F+ L + DQ+ L++ +W E+L   IA+RS+                       +
Sbjct: 62  ARDIPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLTEERDGVDGTGNRTTSPPQLM 121

Query: 166 RFASDLVLDERQARECGFSEIYQQVKH 192
                + L    A + G  +I+ +V  
Sbjct: 122 CLMPGMTLHRNSALQAGVGQIFDRVLS 148

>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 = 79.3 bits (195), Expect = 5e-18
 Identities = 50/255 (19%), Positives = 83/255 (32%), Gaps = 42/255 (16%)

Query: 75  NKMLEALLLCEPEM--LTVRSETPQSDPTLQTINS-----LSDLYDRELVCIIGWAKQIP 127
           + ++ A +   P M  L         D  +   ++       DL    +  I GWA++IP
Sbjct: 4   SALVRAHVDSNPAMTSLDYSRFQANPDYQMSGDDTQHIQQFYDLLTGSMEIIRGWAEKIP 63

Query: 128 GFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIY 187
           GF DL   DQ  L +S + E+  L +AYRS P   GK+ F + +VL   Q    GF E  
Sbjct: 64  GFADLPKADQDLLFESAFLELFVLRLAYRSNPVE-GKLIFCNGVVLHRLQC-VRGFGEWI 121

Query: 188 QQVKH-SGSLDGIK--EEELPRRLCLVCGDVASGFHYGVASCE--------ACKAFFKRT 236
             +   S +L  +             +         +G+   +                 
Sbjct: 122 DSIVEFSSNLQNMNIDISA----FSCIAALAMVTERHGLKEPKRVEELQNKIVNCLKDHV 177

Query: 237 IQVYSGYRQTGACGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLRFWSTVHKDGK 296
                G  +      L+      KL E  +L             C   L+    +  +  
Sbjct: 178 TFNNGGLNRPNYLSKLLG-----KLPELRTL-------------CTQGLQRIFYLKLEDL 219

Query: 297 VLMNKLFVEMLEAYL 311
           V    +  ++    L
Sbjct: 220 VPPPAIIDKLFLDTL 234

>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 = 78.5 bits (193), Expect = 1e-17
 Identities = 20/112 (17%), Positives = 44/112 (39%), Gaps = 4/112 (3%)

Query: 84  CEPEMLTVRSETPQSDPT---LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRL 140
             PE +         +     L+  +  + +    +  ++ +AK++P F +L   DQ+ L
Sbjct: 35  FLPEDIGQAPIVNAPEGGKVDLEAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIIL 94

Query: 141 LQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKH 192
           L+    EI++L  A R  P     +    ++ +   Q +  G   +   +  
Sbjct: 95  LKGCCMEIMSLRAAVRYDPES-ETLTLNGEMAVTRGQLKNGGLGVVSDAIFD 145

>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 = 75.1 bits (184), Expect = 2e-16
 Identities = 38/125 (30%), Positives = 52/125 (41%), Gaps = 9/125 (7%)

Query: 75  NKMLEALLLCEPEMLTVRSETPQ-------SDPTLQTINSLSDLYDRELVCIIGWAKQIP 127
             ++ A L   P    +     Q              +    DL    L  I  WA++IP
Sbjct: 4   TSLVRAHLDSGPSTAKLDYSKFQELVLPHFGKEDAGDVQQFYDLLSGSLEVIRKWAEKIP 63

Query: 128 GFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIY 187
           GF +LS  DQ  LL+S + E+  L +AYRS P   GK+ F S LVL   Q    GF +  
Sbjct: 64  GFAELSPADQDLLLESAFLELFILRLAYRSKPGE-GKLIFCSGLVLHRLQC-ARGFGDWI 121

Query: 188 QQVKH 192
             +  
Sbjct: 122 DSILA 126

>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 = 73.5 bits (180), Expect = 6e-16
 Identities = 29/137 (21%), Positives = 64/137 (46%), Gaps = 14/137 (10%)

Query: 69  IPSL--EENKMLEALLLCE-------PEMLTVRSETPQSDPTLQTINS----LSDLYDRE 115
           +P L   +  ++  L+  +        E L   ++T QSD   +  +     ++++    
Sbjct: 1   VPPLTANQKSLIARLVWYQEGYEQPSEEDLKRVTQTWQSDEDDEDSDMPFRQITEMTILT 60

Query: 116 LVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDE 175
           +  I+ +AK +PGF  +S +DQ+ LL++  +E++ L +A R        + FA++     
Sbjct: 61  VQLIVEFAKGLPGFAKISQSDQITLLKACSSEVMMLRVARRYDAAT-DSVLFANNQAYTR 119

Query: 176 RQARECGFSEIYQQVKH 192
              R+ G + + + + H
Sbjct: 120 DNYRKAGMAYVIEDLLH 136

>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 = 69.7 bits (170), Expect = 7e-16
 Identities = 43/53 (81%), Positives = 49/53 (92%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYR 53
          NIEY+CPA+N+CEI KRRRK+CQACRF K L+ GMLKEGVRLDRVRGGRQKY+
Sbjct: 38 NIEYSCPATNECEITKRRRKSCQACRFMKALKVGMLKEGVRLDRVRGGRQKYK 90

>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 = 57.3 bits (138), Expect = 2e-11
 Identities = 31/35 (88%), Positives = 35/35 (100%)

Query: 204 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
           +P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQ
Sbjct: 2   IPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQ 36

>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 = 72.8 bits (178), Expect = 1e-15
 Identities = 27/122 (22%), Positives = 47/122 (38%), Gaps = 10/122 (8%)

Query: 75  NKMLEALLLCEPEMLTVR---------SETPQSDPTLQTINSLSDLYDRELVCIIGWAKQ 125
            +++ A L C     + +         ++    D   Q     ++L    +  I+ +AKQ
Sbjct: 10  QQLVAAQLQCNKRSFSDQPKVTPWPLGADPQSRDARQQRFAHFTELAIISVQEIVDFAKQ 69

Query: 126 IPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSE 185
           +PGF  L   DQ+ LL+++  EI+ L  A R        I F  D    +      G   
Sbjct: 70  VPGFLQLGREDQIALLKASTIEIMLLETARRYNHET-ECITFLKDFTYSKDDFHRAGLQV 128

Query: 186 IY 187
            +
Sbjct: 129 EF 130

>d2b50b1 a.123.1.1 (B:211-475) Peroxisome proliferator-activated receptor delta, PPAR-DELTA {Human (Homo sapiens) [TaxId: 9606]} Length = 265

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Peroxisome proliferator-activated receptor delta, PPAR-DELTA
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 70.4 bits (172), Expect = 1e-14
 Identities = 32/236 (13%), Positives = 74/236 (31%), Gaps = 26/236 (11%)

Query: 83  LCEPEMLTVRSETPQSDPT-----LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQ 137
           L + E   V  +     P      +             +  +  +AK IP F+ L LNDQ
Sbjct: 45  LWQAEKGLVWKQLVNGLPPYKEISVHVFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQ 104

Query: 138 MRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDER-QARECGFSEIYQQVKH-SGS 195
           + LL+    E +   +A          +   S  V  E  ++    FS+I +     +  
Sbjct: 105 VTLLKYGVHEAIFAMLASIVNKDG-LLVANGSGFVTREFLRSLRKPFSDIIEPKFEFAVK 163

Query: 196 LD--GIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY-RQTGACGTL 252
            +   + + +L      +   +  G   G+ +    +A     ++    + +        
Sbjct: 164 FNALELDDSDL---ALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQQ 220

Query: 253 VLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLRFWSTVHKDGKVLMNKLFVEMLE 308
           +      K+ +   L              +  ++       + +  ++ L  E+ +
Sbjct: 221 LFPKLLQKMADLRQLVTEHA-------QMMQRIK-----KTETETSLHPLLQEIYK 264

>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 = 65.1 bits (158), Expect = 3e-14
 Identities = 28/56 (50%), Positives = 37/56 (66%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNP 56
          + +Y C A+ DC ++KRRR  CQ CRFQKCL  GM+KE VR D ++G R +    P
Sbjct: 34 SAKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTDSLKGRRGRLPSKP 89

>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 = 53.5 bits (128), Expect = 4e-10
 Identities = 22/36 (61%), Positives = 25/36 (69%)

Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244
           C VCGD AS  HYGV +CE CK FFKRT+Q  + Y 
Sbjct: 3   CAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYI 38

>d1nrla_ a.123.1.1 (A:) Pregnane x receptor, PXR {Human (Homo sapiens) [TaxId: 9606]} Length = 292

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Pregnane x receptor, PXR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.7 bits (170), Expect = 3e-14
 Identities = 24/115 (20%), Positives = 38/115 (33%), Gaps = 6/115 (5%)

Query: 82  LLCEPEMLTVRSETPQSDPTLQTINSL----SDLYDRELVCIIGWAKQIPGFTDLSLNDQ 137
           L    E  +V +  P +D   + I SL    +D+       II +AK I  F DL + DQ
Sbjct: 72  LQLRGEDGSVWNYKPPADSGGKEIFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQ 131

Query: 138 MRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKH 192
           + LL+    E+  L                   L              + + +  
Sbjct: 132 ISLLKGAAFELCQLRFNTVFNAE--TGTWECGRLSYCLEDTAGGFQQLLLEPMLK 184

>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 = 69.0 bits (168), Expect = 3e-14
 Identities = 17/110 (15%), Positives = 36/110 (32%), Gaps = 2/110 (1%)

Query: 83  LCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQ 142
           +     L    E  Q+          +      +  ++ +AK+I GF +L  NDQ+ LL+
Sbjct: 38  ITWQTFLQEEIENYQNKQREVMWQLCAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLLK 97

Query: 143 STWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKH 192
           +   E++ + +             +           +  G  +    V  
Sbjct: 98  AGSLEVVFIRMCRAFDSQ--NNTVYFDGKYASPDVFKSLGCEDFISFVFE 145

>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 = 67.0 bits (163), Expect = 1e-13
 Identities = 18/118 (15%), Positives = 42/118 (35%), Gaps = 4/118 (3%)

Query: 75  NKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSL 134
           + ++++                +     +    L+++    +  ++ + K++PGF  L  
Sbjct: 14  HFIMDSYNKQRMPQEITNKILKEEFSAEENFLILTEMATNHVQVLVEFTKKLPGFQTLDH 73

Query: 135 NDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKH 192
            DQ+ LL+ +  E + L  A         K+      +L+ER        E    +  
Sbjct: 74  EDQIALLKGSAVEAMFLRSAEI----FNKKLPSGHSDLLEERIRNSGISDEYITPMFS 127

>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 = 65.0 bits (158), Expect = 9e-13
 Identities = 22/119 (18%), Positives = 44/119 (36%), Gaps = 5/119 (4%)

Query: 78  LEALLLCEPEM---LTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSL 134
           + +L++ E ++        +    +  ++            +  I  +AK IPGF +L L
Sbjct: 46  MNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDL 105

Query: 135 NDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDER-QARECGFSEIYQQVKH 192
           NDQ+ LL+    EI+   +A          I      +  E  ++    F +  +    
Sbjct: 106 NDQVTLLKYGVHEIIYTMLASLMNKDG-VLISEGQGFMTREFLKSLRKPFGDFMEPKFE 163

>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 = 60.7 bits (147), Expect = 1e-12
 Identities = 21/41 (51%), Positives = 27/41 (65%)

Query: 204 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244
             + +C +CGD +SG HYGV SCE CK FFKRT++    Y 
Sbjct: 3   FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYT 43

>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 = 59.2 bits (143), Expect = 4e-12
 Identities = 23/46 (50%), Positives = 32/46 (69%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR 46
          ++ YTC  + DC I+KR+R  CQ CR+QKCL  GM +E V+ +R R
Sbjct: 39 DLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQR 84

>d1nq7a_ a.123.1.1 (A:) Orphan nuclear receptor ROR-beta {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 244

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor ROR-beta
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 61.7 bits (149), Expect = 8e-12
 Identities = 17/97 (17%), Positives = 35/97 (36%), Gaps = 2/97 (2%)

Query: 96  PQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAY 155
            QS          +      +  ++ +AK+I GF +L  NDQ+ LL+S   E++ + +  
Sbjct: 43  YQSKSREALWQQCAIQITHAIQYVVEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCR 102

Query: 156 RSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKH 192
              P                +  +  G  ++  +   
Sbjct: 103 AFNPL--NNTVLFEGKYGGMQMFKALGSDDLVNEAFD 137

>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 = 58.1 bits (140), Expect = 9e-12
 Identities = 16/49 (32%), Positives = 23/49 (46%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGR 49
          +  Y C     CE++   R+ CQ CR +KCL  GM  E V  +     +
Sbjct: 34 SAVYCCKFGRACEMDMYMRRKCQECRLKKCLAVGMRPECVVPENQCAMK 82

>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 = 52.3 bits (125), Expect = 1e-09
 Identities = 19/31 (61%), Positives = 24/31 (77%)

Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
           LCLVCGD ASG+HY   +CE CK FF+R++ 
Sbjct: 2   LCLVCGDRASGYHYNALTCEGCKGFFRRSVT 32

>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 = 58.1 bits (140), Expect = 1e-11
 Identities = 19/51 (37%), Positives = 30/51 (58%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQK 51
             +TCP + DC I K  R+ CQACR ++C+  GM+KE +  D     +++
Sbjct: 34 KALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDEEVQRKRE 84

>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 = 55.8 bits (134), Expect = 7e-11
 Identities = 17/32 (53%), Positives = 25/32 (78%)

Query: 207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
           R+C VCGD A+GFH+   +CE CK FF+R+++
Sbjct: 1   RICGVCGDRATGFHFNAMTCEGCKGFFRRSMK 32

>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 = 60.5 bits (146), Expect = 3e-11
 Identities = 20/100 (20%), Positives = 35/100 (35%), Gaps = 1/100 (1%)

Query: 93  SETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLT 152
              P   P L  +   +D+    ++ +I + K +P F  L + DQ+ LL+    EI  + 
Sbjct: 44  QPLPTLAPVLPLVTHFADINTFMVLQVIKFTKDLPVFRSLPIEDQISLLKGAAVEICHIV 103

Query: 153 IAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKH 192
           +                     E  AR     E  + + H
Sbjct: 104 LNTTFCLQT-QNFLCGPLRYTIEDGARVGFQVEFLELLFH 142

>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 = 56.3 bits (135), Expect = 3e-11
 Identities = 20/41 (48%), Positives = 26/41 (63%)

Query: 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ 245
           P++ CL+CGD ASG HYG  +C +CK FFKR  +    Y  
Sbjct: 1   PQKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLC 41

>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 = 50.1 bits (119), Expect = 5e-09
 Identities = 17/38 (44%), Positives = 22/38 (57%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE 38
            +Y C + NDC I+K RRK C +CR +KC   GM   
Sbjct: 36 KQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLG 73

>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 = 60.1 bits (145), Expect = 3e-11
 Identities = 28/118 (23%), Positives = 44/118 (37%), Gaps = 4/118 (3%)

Query: 69  IPSLEENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPG 128
            P+  +       +       +V  E  Q    L  +  L+DL    +  +IG+AK IPG
Sbjct: 27  DPTYSDFCQFRPPVRVNDGGGSVTLELSQ----LSMLPHLADLVSYSIQKVIGFAKMIPG 82

Query: 129 FTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEI 186
           F DL+  DQ+ LL+S+  E++ L                  D         + G S  
Sbjct: 83  FRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVSDVTKAGHSLE 140

>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 = 59.7 bits (144), Expect = 3e-11
 Identities = 21/95 (22%), Positives = 37/95 (38%), Gaps = 2/95 (2%)

Query: 95  TPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIA 154
                P L  +   +D+    +  II + K +P F  L++ DQ+ LL+    EIL +++ 
Sbjct: 45  FQPRGPVLPLLTHFADINTFMVQQIIKFTKDLPLFRSLTMEDQISLLKGAAVEILHISLN 104

Query: 155 YRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQ 189
                    +  F   L      A   GF   + +
Sbjct: 105 TTFCLQT--ENFFCGPLCYKMEDAVHAGFQYEFLE 137

>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 = 55.4 bits (133), Expect = 6e-11
 Identities = 17/41 (41%), Positives = 23/41 (56%)

Query: 4  YTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
            C  + +C I +  R  CQ CRF+KCL  GM ++ VR  R
Sbjct: 38 KRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGR 78

>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 = 54.2 bits (130), Expect = 2e-10
 Identities = 24/31 (77%), Positives = 27/31 (87%)

Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
           LC VCGDVASGFHYGV +CE CK FF+R+IQ
Sbjct: 2   LCKVCGDVASGFHYGVLACEGCKGFFRRSIQ 32

>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 = 54.3 bits (130), Expect = 1e-10
 Identities = 20/36 (55%), Positives = 26/36 (72%)

Query: 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244
           C VC D +SG+HYGV++CE CK FF+R+IQ    Y 
Sbjct: 2   CFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYT 37

>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 = 51.2 bits (122), Expect = 2e-09
 Identities = 23/43 (53%), Positives = 25/43 (58%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLD 43
          N+ YTC    +C INK  R  CQ CR QKC   GM KE VR D
Sbjct: 33 NMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRND 75

>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 = 54.0 bits (129), Expect = 2e-10
 Identities = 24/34 (70%), Positives = 26/34 (76%)

Query: 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 238
             R C VC D ASG+HYGV SCE CKAFFKR+IQ
Sbjct: 3   ETRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQ 36

>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 = 47.0 bits (111), Expect = 6e-08
 Identities = 21/37 (56%), Positives = 28/37 (75%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLK 37
          + +Y CPA+N C I+K RRK+CQACR +KC   GM+K
Sbjct: 38 HNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMK 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 = 52.4 bits (125), Expect = 6e-10
 Identities = 23/41 (56%), Positives = 26/41 (63%)

Query: 207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTG 247
           R CLVC D ASG HYGV +CE CKAFFKR ++    Y    
Sbjct: 1   RPCLVCSDEASGCHYGVLTCEGCKAFFKRAVEGQHNYLCKY 41

>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 = 47.4 bits (112), Expect = 4e-08
 Identities = 18/38 (47%), Positives = 22/38 (57%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE 38
             Y C     C I+K RRK C ACR++KCL+ GM  E
Sbjct: 34 QHNYLCKYEGKCIIDKIRRKNCPACRYRKCLQAGMNLE 71

>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 = 56.2 bits (135), Expect = 9e-10
 Identities = 21/118 (17%), Positives = 47/118 (39%), Gaps = 4/118 (3%)

Query: 78  LEALLLCEPEML--TVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLN 135
           +E L + E  ++   V +     +  ++  +         +  +  +AK IPGF +L LN
Sbjct: 43  METLCMAEKTLVAKLVANGIQNKEAEVRIFHCCQCTSVETVTELTEFAKAIPGFANLDLN 102

Query: 136 DQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDER-QARECGFSEIYQQVKH 192
           DQ+ LL+    E +   ++          + + +  +  E  ++    F +I +    
Sbjct: 103 DQVTLLKYGVYEAIFAMLSSVMNKDG-MLVAYGNGFITREFLKSLRKPFCDIMEPKFD 159

>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 = 49.8 bits (118), Expect = 1e-08
 Identities = 19/54 (35%), Positives = 27/54 (50%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRR 54
          +  Y+C     C I+K  R  CQ CRF+KC+  GM  + V  D  R  ++K   
Sbjct: 37 HPSYSCKYEGKCVIDKVTRNQCQECRFKKCIYVGMATDLVLDDSKRLAKRKLIE 90

>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 = 48.2 bits (114), Expect = 4e-08
 Identities = 20/38 (52%), Positives = 25/38 (65%)

Query: 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ 245
           LC+VCGD A+G+HY   +CE CK FF+RTIQ       
Sbjct: 3   LCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSY 40

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	312
d2e2ra1	223	Orphan nuclear receptor ERR3 {Human (Homo sapiens)	99.97
d3d24a1	227	Steroid hormone receptor ERR1 {Human (Homo sapiens	99.97
d1g2na_	256	Ultraspiracle protein, usp {Heliothis virescens [T	99.96
d1xpca_	245	Estrogen receptor alpha {Human (Homo sapiens) [Tax	99.96
d1pk5a_	242	Orphan nuclear receptor NR5a2 (LRH-1) {Mouse (Mus	99.96
d1hg4a_	265	Ultraspiracle protein, usp {Drosophila melanogaste	99.96
d2p1ta1	230	Retinoid-X receptor alpha (RXR-alpha) {Human (Homo	99.96
d1fcya_	236	Retinoic acid receptor gamma (RAR-gamma) {Human (H	99.96
d1t7ra_	250	Androgen receptor {Chimpanzee (Pan troglodytes) [T	99.95
d2j7ya1	236	Estrogen receptor beta {Rat (Rattus norvegicus) [T	99.95
d1sqna_	251	Progesterone receptor {Human (Homo sapiens) [TaxId	99.95
d1ovla_	236	Orphan nuclear receptor NURR1 {Human (Homo sapiens	99.95
d1pdua_	230	Nuclear hormone receptor HR38 {Fruit fly (Drosophi	99.95
d1pzla_	233	Hepatocyte nuclear factor 4-alpha {Human (Homo sap	99.95
d1nhza_	247	Glucocorticoid receptor {Human (Homo sapiens) [Tax	99.94
d2qw4a1	233	Orphan nuclear receptor NR4A1 {Human (Homo sapiens	99.94
d1n46a_	251	Thyroid hormone receptor beta (TR-beta) {Human (Ho	99.94
d1pq9a_	239	Oxysterols receptor LXR-beta {Human (Homo sapiens)	99.94
d1xvpb_	246	Orphan nuclear receptor NR1I3 (CAR) {Human (Homo s	99.93
d2r40d1	243	Ecdysone receptor {Noctuid moth (Heliothis viresce	99.93
d1osha_	231	Bile acid receptor FXR {Human (Homo sapiens) [TaxI	99.92
d1ie9a_	255	Vitamin D nuclear receptor {Human (Homo sapiens) [	99.92
d1nq7a_	244	Orphan nuclear receptor ROR-beta {Rat (Rattus norv	99.91
d1xnxa_	232	Orphan nuclear receptor NR1I3 (CAR) {Mouse (Mus mu	99.91
d1n83a_	251	Orphan nuclear receptor ROR-alpha {Human (Homo sap	99.91
d2fvja1	271	Peroxisome proliferator activated receptor gamma,	99.91
d2p54a1	267	Peroxisome proliferator activated receptor alpha,	99.91
d1nrla_	292	Pregnane x receptor, PXR {Human (Homo sapiens) [Ta	99.9
d2b50b1	265	Peroxisome proliferator-activated receptor delta,	99.89
d1lo1a_	90	Steroid hormone receptor Err2 DNA-binding domain {	99.59
d2hanb1	83	Ecdysone receptor DNA-binding domain {Fruit fly (D	99.52
d1dszb_	84	Retinoid X receptor (RXR-alpha) DNA-binding domain	99.52
d1cita_	89	Orphan nuclear receptor NGFI-B DNA-binding domain	99.51
d1dsza_	75	Retinoic acid receptor DNA-binding domain {Human (	99.49
d1kb2a_	89	Vitamin D3 receptor, VDR, DNA-binding domain {Huma	99.48
d1a6ya_	78	Orphan nuclear receptor reverb DNA-binding domain	99.46
d1r4ia_	74	Androgen receptor {Rat (Rattus norvegicus) [TaxId:	99.41
d2nllb_	103	Thyroid hormone receptor (TR-beta) DNA-binding dom	99.38
d1lata_	71	Glucocorticoid receptor DNA-binding domain {Rat (R	99.33
d1hcqa_	74	Estrogen receptor DNA-binding domain {Human and ch	99.31
d1dszb_	84	Retinoid X receptor (RXR-alpha) DNA-binding domain	98.88
d2nllb_	103	Thyroid hormone receptor (TR-beta) DNA-binding dom	98.83
d2hanb1	83	Ecdysone receptor DNA-binding domain {Fruit fly (D	98.82
d1r4ia_	74	Androgen receptor {Rat (Rattus norvegicus) [TaxId:	98.81
d1kb2a_	89	Vitamin D3 receptor, VDR, DNA-binding domain {Huma	98.81
d1a6ya_	78	Orphan nuclear receptor reverb DNA-binding domain	98.75
d1hcqa_	74	Estrogen receptor DNA-binding domain {Human and ch	98.74
d1lata_	71	Glucocorticoid receptor DNA-binding domain {Rat (R	98.73
d1dsza_	75	Retinoic acid receptor DNA-binding domain {Human (	98.69
d1lo1a_	90	Steroid hormone receptor Err2 DNA-binding domain {	98.66
d1cita_	89	Orphan nuclear receptor NGFI-B DNA-binding domain	98.66

>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=99.97  E-value=3.1e-32  Score=231.64  Aligned_cols=191  Identities=38%  Similarity=0.631  Sum_probs=167.4

Q ss_pred             HHHHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhh
Q psy11505         76 KMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAY  155 (312)
Q Consensus        76 ~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~  155 (312)
                      +++.++...+|...........+++....+..++++.++.+..+|+|||++|+|.+|+.+||+.|+|++|+++++++.|+
T Consensus         3 ~~v~~l~~~ep~~~~~~~~~~~~~~~~~~~~~l~~~a~~~l~~~V~waK~lp~F~~L~~~DQi~LLk~~~~el~~L~~a~   82 (223)
T d2e2ra1           3 KIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVY   82 (223)
T ss_dssp             HHHHHHHHTCCCCCCCCCCTTSCCCHHHHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCcccCCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHhCcchhhcCHHHHHHHHHHHHHHHHHHHHHH
Confidence            57788888888766555545555667788999999999999999999999999999999999999999999999999999


Q ss_pred             hcccCCCCeeEecccchhhHHhhhhcccchhhhhhccc---CccCCCCccccCCceeeeeCCCCcccccccccchhHHHH
Q psy11505        156 RSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKHS---GSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAF  232 (312)
Q Consensus       156 rs~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~i~~~---~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~  232 (312)
                      ++.+..+ .+.+++|..+++......+..++.+.+..+   +++|++|++||                            
T Consensus        83 ~s~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~l~~L~ld~~E~----------------------------  133 (223)
T d2e2ra1          83 RSLSFED-ELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEF----------------------------  133 (223)
T ss_dssp             HTTTSSS-CEEEETTEEECHHHHHHTTCHHHHHHHHHHHHHHHHHTCCHHHH----------------------------
T ss_pred             HhcCCCC-eeeecCCcccchHHhhhccHHHHHHHHHHHHHHHHHcCCCHHHH----------------------------
Confidence            9998876 688899988888877777777766655544   45999999999                            


Q ss_pred             HHHHhhhcccceecCCCCceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------------------------
Q psy11505        233 FKRTIQVYSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------------------------  285 (312)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------------------------  285 (312)
                                    ++++||+|||||++ +++.++|+++|+++..||.+|+..+                          
T Consensus       134 --------------~lLkaivL~~pd~~~L~~~~~I~~~q~~~~~aL~~y~~~~~~~~~~rf~~LL~~Lp~Lr~l~~~~~  199 (223)
T d2e2ra1         134 --------------VTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAV  199 (223)
T ss_dssp             --------------HHHHHHHHHTCCCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTTHHHHHHHHHHHH
T ss_pred             --------------HHHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHHHHH
Confidence                          99999999999998 9999999999999999999999877                          


Q ss_pred             hhhhccccCCccchhHHHHHHHhh
Q psy11505        286 RFWSTVHKDGKVLMNKLFVEMLEA  309 (312)
Q Consensus       286 ~~~~~~~~~~~~~~~~~~~~~~~~  309 (312)
                      .++++++..|.+|+++|+.|||+|
T Consensus       200 e~l~~~~~~~~~~~~~Ll~E~l~a  223 (223)
T d2e2ra1         200 QHFYNIKLEGKVPMHKLFLEMLEA  223 (223)
T ss_dssp             HHHHHHHHHCCSCCCHHHHHHHTS
T ss_pred             HHHHHhhcCCCCCchHHHHHHHcC
Confidence            235667899999999999999986

>d3d24a1 a.123.1.1 (A:194-420) Steroid hormone receptor ERR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Steroid hormone receptor ERR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=3.5e-32  Score=232.02  Aligned_cols=191  Identities=40%  Similarity=0.603  Sum_probs=158.7

Q ss_pred             HHHHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhh
Q psy11505         76 KMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAY  155 (312)
Q Consensus        76 ~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~  155 (312)
                      .+++.+...+|...........+......+..+++..++.+..+|+|||++|+|..|+.+||++|+|++|+++++++.|+
T Consensus         3 ~li~~l~~~ep~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~   82 (227)
T d3d24a1           3 ALVSHLLVVEPEKLYAMPDPAGPDGHLPAVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQ   82 (227)
T ss_dssp             HHHHHHHHTCCCCCCCCC----------CHHHHHHHHHHHHHHHHHHHHHSTTTTTSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCccccCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHhCcchhcCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            46888888888776544444444455667899999999999999999999999999999999999999999999999999


Q ss_pred             hcccCCCCeeEecccchhhHHhhhhcccchhhhhhc---ccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHH
Q psy11505        156 RSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVK---HSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAF  232 (312)
Q Consensus       156 rs~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~i~---~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~  232 (312)
                      ++++..+ .+.+++|..++.......+..++.+.+.   ..+++|++|++||                            
T Consensus        83 ~s~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~L~ld~~E~----------------------------  133 (227)
T d3d24a1          83 RSLPLQD-ELAFAEDLVLDEEGARAAGLGELGAALLQLVRRLQALRLEREEY----------------------------  133 (227)
T ss_dssp             HHTTSSS-EEEEETTEEEEHHHHHHTTCTTHHHHHHHHHHHHHTTTCCHHHH----------------------------
T ss_pred             hhccCCC-eeeecCCcccchhhhccccHHHHHHHHHHHHHHHHHcCCCHHHH----------------------------
Confidence            9998876 7889999888887777767666555444   4455999999999                            


Q ss_pred             HHHHhhhcccceecCCCCceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------------------------
Q psy11505        233 FKRTIQVYSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------------------------  285 (312)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------------------------  285 (312)
                                    +++|||+|||||++ |++.++|+++|++++.+|.+|+..+                          
T Consensus       134 --------------~lLkaivLf~pd~~gL~~~~~I~~~q~~~~~aL~~y~~~~~~~~~~~~~~Rf~~LL~~Lp~Lr~l~  199 (227)
T d3d24a1         134 --------------VLLKALALANSDSVHIEDAEAVEQLREALHEALLEYEAGRAGPGGGAERRRAGRLLLTLPLLRQTA  199 (227)
T ss_dssp             --------------HHHHHHHHHTCCCTTCSCHHHHHHHHHHHHHHHHHHHTC--------CHHHHHHHHTTHHHHHHHH
T ss_pred             --------------HHHHHHHHhCCcCCCcccHHHHHHHHHHHHHHHHHHHHHhcCCCchhHHhHHHHHHHHHHHHHHHH
Confidence                          99999999999998 9999999999999999999998542                          


Q ss_pred             ----hhhhccccCCccchhHHHHHHHhh
Q psy11505        286 ----RFWSTVHKDGKVLMNKLFVEMLEA  309 (312)
Q Consensus       286 ----~~~~~~~~~~~~~~~~~~~~~~~~  309 (312)
                          ..+++++++|.+|+++|+.|||||
T Consensus       200 ~~~~e~l~~~~~~g~~~~~~Ll~Eml~~  227 (227)
T d3d24a1         200 GKVLAHFYGVKLEGKVPMHKLFLEMLEA  227 (227)
T ss_dssp             HHHHHHHHHHHHSCCSCCCHHHHHHHHC
T ss_pred             HHHHHHHHhhccCCCCCchHHHHHHHcC
Confidence                235667999999999999999996

>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=99.96  E-value=2.7e-30  Score=224.18  Aligned_cols=170  Identities=21%  Similarity=0.379  Sum_probs=148.1

Q ss_pred             chhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCC-----------------
Q psy11505        100 PTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCA-----------------  162 (312)
Q Consensus       100 ~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~-----------------  162 (312)
                      .....+.+++++..+.++.+|+|||++|+|.+|+.+||+.|||++|.++++++.||||++...                 
T Consensus        39 ~~~~~~~~lc~~~~~~L~~~VewAK~lP~F~~L~~~DQi~LLk~~w~el~iL~~a~rs~~~~~~~~~~~~~~~~~~~~~~  118 (256)
T d1g2na_          39 KFRAPVSSLCQIGNKQIAALVVWARDIPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLTEERDGVDGTGNRTTSPP  118 (256)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHGGGSCCC----------CCCCC
T ss_pred             ccccHHHHHHHHHHHHHHHHHHHHhcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccCcc
Confidence            345568899999999999999999999999999999999999999999999999999887643                 


Q ss_pred             CeeEecccchhhHHhhhhcccchhhhh----hcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhh
Q psy11505        163 GKIRFASDLVLDERQARECGFSEIYQQ----VKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ  238 (312)
Q Consensus       163 ~~l~~~~g~~~~~~~~~~~~~~~~~~~----i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  238 (312)
                      +.+.+.+|..+++.+....+..+++++    +...+++|++|++||                                  
T Consensus       119 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~L~ld~~E~----------------------------------  164 (256)
T d1g2na_         119 QLMCLMPGMTLHRNSALQAGVGQIFDRVLSELSLKMRTLRVDQAEY----------------------------------  164 (256)
T ss_dssp             CEEEEETTEEEEHHHHHHHTCHHHHHHHHHHTHHHHHHTTCCHHHH----------------------------------
T ss_pred             hhhccCCCcccCHHHHHhcchHHHHHHHHHHHHHHHHHcCCCHHHH----------------------------------
Confidence            245667788788877777777665544    444566999999999                                  


Q ss_pred             hcccceecCCCCceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH------h--------------------hhhcc
Q psy11505        239 VYSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL------R--------------------FWSTV  291 (312)
Q Consensus       239 ~~~~~~~~~~~~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~------~--------------------~~~~~  291 (312)
                              +++|||+|||||++ ++++++|+++|++|+.+|.+|+..+      |                    .+++.
T Consensus       165 --------~~LkaIvLfnpd~~gL~~~~~Ie~lqe~~~~aL~~y~~~~~p~~~~Rf~~LLl~Lp~LR~l~~~~~e~lff~  236 (256)
T d1g2na_         165 --------VALKAIILLNPDVKGLKNRQEVEVLREKMFLCLDEYCRRSRSSEEGRFAALLLRLPALRSISLKSFEHLFFF  236 (256)
T ss_dssp             --------HHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHSTTCTTHHHHHHTHHHHHHHHHHHHHHHHHHT
T ss_pred             --------HHHHHHHHhcCccCCcccHHHHHHHHHHHHHHHHHHHHhcCCChhhHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence                    99999999999998 9999999999999999999999876      2                    36778


Q ss_pred             ccCCccchhHHHHHHHhhhc
Q psy11505        292 HKDGKVLMNKLFVEMLEAYL  311 (312)
Q Consensus       292 ~~~~~~~~~~~~~~~~~~~~  311 (312)
                      +++|.+|+++||.|||++|.
T Consensus       237 ~l~g~~~i~~ll~eml~~~~  256 (256)
T d1g2na_         237 HLVADTSIAGYIRDALRNHA  256 (256)
T ss_dssp             TCBCTTTHHHHHHHHHTCCC
T ss_pred             cccCCCChHHHHHHHHhccC
Confidence            99999999999999999863

>d1xpca_ a.123.1.1 (A:) Estrogen receptor alpha {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Estrogen receptor alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=1.1e-30  Score=225.01  Aligned_cols=195  Identities=32%  Similarity=0.514  Sum_probs=162.1

Q ss_pred             HHHHHHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhh
Q psy11505         74 ENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTI  153 (312)
Q Consensus        74 ~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~  153 (312)
                      .+++++.+...+|...........+......+..+++++++.+..+|+|||++|+|..|+.+||+.|+|++|+++++|+.
T Consensus         6 ~~~lv~~l~~aep~~~~~~~~~~~~~~~~~~~~~l~~la~~~l~~~V~waK~ip~F~~L~~~DQi~LLk~~~~el~iL~~   85 (245)
T d1xpca_           6 ADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGL   85 (245)
T ss_dssp             HHHHHHHHHHTCCCCCCCCSCTTSCSTTSCHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhHHHHHHHHcCCCcccCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhCccHHhcCHHHHHHHHHHHHHHHHHHHH
Confidence            45688999999987655444444444555678999999999999999999999999999999999999999999999999


Q ss_pred             hhhcccCCCCeeEecccchhhHHhhhh-cccchhhhhhcc---cCccCCCCccccCCceeeeeCCCCcccccccccchhH
Q psy11505        154 AYRSLPHCAGKIRFASDLVLDERQARE-CGFSEIYQQVKH---SGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEAC  229 (312)
Q Consensus       154 a~rs~~~~~~~l~~~~g~~~~~~~~~~-~~~~~~~~~i~~---~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~  229 (312)
                      ||+++...+ .+.+++|..+++..... .+..++.+.+..   .+++|++|++||                         
T Consensus        86 a~~s~~~~~-~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~ld~~E~-------------------------  139 (245)
T d1xpca_          86 VWRSMEHPG-KLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEF-------------------------  139 (245)
T ss_dssp             HHHHTTSTT-EEEEETTEEEEHHHHTTSTTHHHHHHHHHHHHHHHHHHTCCHHHH-------------------------
T ss_pred             HHHhhccCC-ceeecCCcccchhHHhhhccHHHHHHHHHHHHHHHHHcCCCHHHH-------------------------
Confidence            999998765 78999999888766654 344555555444   455999999999                         


Q ss_pred             HHHHHHHhhhcccceecCCCCceeecCCCCc---------ccchHHHHHHHHHHHHHhHhHHHHH---------h-----
Q psy11505        230 KAFFKRTIQVYSGYRQTGACGTLVLANSDVK---------LDEFSSLKKFRNSILSSLGDCIYVL---------R-----  286 (312)
Q Consensus       230 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~---------l~~~~~~~~~~~~~~~~l~~~~~~~---------~-----  286 (312)
                                       +++|||+|||||++         ++++++|+++|++++.+|.+|+...         |     
T Consensus       140 -----------------~lLkaI~L~~pd~~~l~~~~r~~l~~~~~v~~~q~~~~~aL~~~~~~~~~~~~~~~~Rf~~LL  202 (245)
T d1xpca_         140 -----------------VCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLL  202 (245)
T ss_dssp             -----------------HHHHHHHHHHTTTTCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             -----------------HHHHHHHHcCCccccccccchhhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcccHHHHHH
Confidence                             99999999999963         5567889999999999999998542         2     


Q ss_pred             ---------------hhhccccCCccchhHHHHHHHhhhc
Q psy11505        287 ---------------FWSTVHKDGKVLMNKLFVEMLEAYL  311 (312)
Q Consensus       287 ---------------~~~~~~~~~~~~~~~~~~~~~~~~~  311 (312)
                                     +++++++.|.+|+++|+.|||+||.
T Consensus       203 ~~Lp~Lr~~~~~~~e~l~~~~~~~~~~~~~Ll~Eml~~~~  242 (245)
T d1xpca_         203 LILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDAHR  242 (245)
T ss_dssp             HHHHHHHHHHHHHHHHHTTSSSCCSSCHHHHHHHHHSCCS
T ss_pred             HHHHHHHHHHHHHHHHHHHhhcCCCCCccHHHHHHHHccc
Confidence                           3566799999999999999999873

>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=99.96  E-value=5.2e-31  Score=226.91  Aligned_cols=168  Identities=28%  Similarity=0.414  Sum_probs=143.8

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCC-CeeEecccchhhHHhhh
Q psy11505        101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCA-GKIRFASDLVLDERQAR  179 (312)
Q Consensus       101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~-~~l~~~~g~~~~~~~~~  179 (312)
                      ....+..+++.+.+.+..+|+|||++|+|.+|+.+||+.|||++|+++++|+.||+++..+. +.+.+++|..++.....
T Consensus        40 ~~~~~~~l~~~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~iL~~a~~s~~~~~~~~~~~~~g~~~~~~~~~  119 (242)
T d1pk5a_          40 KLSAFGLLCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVAHGKEGTIFLVTGEHVDYSTII  119 (242)
T ss_dssp             CCCSHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCSSEEECTTSCEEEHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHHHHHHHhCCCHhhcCHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCeeEecCCCcccchHHh
Confidence            34567888999999999999999999999999999999999999999999999999998765 46778888877654432


Q ss_pred             hc---ccchh---hhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCcee
Q psy11505        180 EC---GFSEI---YQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLV  253 (312)
Q Consensus       180 ~~---~~~~~---~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  253 (312)
                      ..   +...+   +.++...+++|++|++||                                          +++|||+
T Consensus       120 ~~~~~~~~~~~~~~~~l~~~l~~L~ld~~E~------------------------------------------~lLkai~  157 (242)
T d1pk5a_         120 SHTEVAFNNLLSLAQELVVRLRSLQFDQREF------------------------------------------VCLKFLV  157 (242)
T ss_dssp             HTSCHHHHHHHHHHHHHHHHHHHTTCCHHHH------------------------------------------HHHHHHH
T ss_pred             hhcccchHHHHHHHHHHHHHHHHhCCCHHHH------------------------------------------HHHHHHH
Confidence            21   22223   344555566999999999                                          9999999


Q ss_pred             ecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------------------------hhhhccccCCccchhHHHHHH
Q psy11505        254 LANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------------------------RFWSTVHKDGKVLMNKLFVEM  306 (312)
Q Consensus       254 l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------------------------~~~~~~~~~~~~~~~~~~~~~  306 (312)
                      |||||++ +++.+.|+.+|++++.+|.+|+..+                          .++++++++|.+|+++||.||
T Consensus       158 Lf~pd~~gL~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LLl~Lp~Lr~~~~~~~e~L~~~~~~g~~~~~~Ll~Em  237 (242)
T d1pk5a_         158 LFSSDVKNLENLQLVEGVQEQVNAALLDYTVCNYPQQTEKFGQLLLRLPELRAISKQAEDYLYYKHVNGDVPYNNLLIEM  237 (242)
T ss_dssp             HSCSCCSSCTTHHHHHHHHHHHHHHHHHHHHHHCTTSTTHHHHHHTTHHHHHHHHHHHHHHHHHHHHTTCSCCCHHHHHH
T ss_pred             hcCCCCCCchhHHHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHH
Confidence            9999998 9999999999999999999999776                          346778999999999999999


Q ss_pred             Hhhh
Q psy11505        307 LEAY  310 (312)
Q Consensus       307 ~~~~  310 (312)
                      |+|+
T Consensus       238 l~~~  241 (242)
T d1pk5a_         238 LHAK  241 (242)
T ss_dssp             HTTT
T ss_pred             HhCC
Confidence            9996

>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=99.96  E-value=1.5e-29  Score=220.62  Aligned_cols=170  Identities=19%  Similarity=0.368  Sum_probs=146.0

Q ss_pred             chhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCC-----------------
Q psy11505        100 PTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCA-----------------  162 (312)
Q Consensus       100 ~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~-----------------  162 (312)
                      .....+..++++..+.+..+|+|||++|+|..|+.+||+.|||++|+++++|+.||++.....                 
T Consensus        36 ~~~~~~~~l~~~~~~~L~~~VewaK~lP~F~~L~~~DQ~~LLk~~~~el~iL~~a~~s~~~~~~~~~~~~~~~~~~~~~~  115 (265)
T d1hg4a_          36 DYKGAVSALCQVVNKQLFQMVEYARMMPHFAQVPLDDQVILLKAAWIELLIANVAWCSIVSLDDGGAGGGGGGLGHDGSF  115 (265)
T ss_dssp             GGHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTTC------------------
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHcCCchhcCCHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccccchhh
Confidence            345678999999999999999999999999999999999999999999999999999987643                 


Q ss_pred             ---------CeeEecccchhhHHhhhhcccchhhh----hhcccCccCCCCccccCCceeeeeCCCCcccccccccchhH
Q psy11505        163 ---------GKIRFASDLVLDERQARECGFSEIYQ----QVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEAC  229 (312)
Q Consensus       163 ---------~~l~~~~g~~~~~~~~~~~~~~~~~~----~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~  229 (312)
                               +.+.+.+|..++++.....+..+.+.    .+...+++|++|++||                         
T Consensus       116 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~L~ld~~E~-------------------------  170 (265)
T d1hg4a_         116 ERRSPGLQPQQLFLNQSFSYHRNSAIKAGVSAIFDRILSELSVKMKRLNLDRREL-------------------------  170 (265)
T ss_dssp             -------CCCEEESSSSCEEEHHHHHHHTCHHHHHHHHHHTHHHHHHHTCCHHHH-------------------------
T ss_pred             hccCcccCcceeeccCCcccchHHHHHhccHHHHHHHHHHHHHHHHHcCCCHHHH-------------------------
Confidence                     23555667677777666666655443    4455566999999999                         


Q ss_pred             HHHHHHHhhhcccceecCCCCceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH------h----------------
Q psy11505        230 KAFFKRTIQVYSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL------R----------------  286 (312)
Q Consensus       230 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~------~----------------  286 (312)
                                       +++|||+|||||++ +++.++|+++|++++.||.+|+..+      |                
T Consensus       171 -----------------~lLkaivLf~pd~~~l~~~~~Ie~lqe~~~~aL~~y~~~~~p~~~~Rf~~LLl~Lp~Lr~l~~  233 (265)
T d1hg4a_         171 -----------------SCLKAIILYNPDIRGIKSRAEIEMCREKVYACLDEHCRLEHPGDDGRFAQLLLRLPALRSISL  233 (265)
T ss_dssp             -----------------HHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHH
T ss_pred             -----------------HHHHHHHHccccCCCCcCHHHHHHHHHHHHHHHHHHHHhhCCChhhHHHHHHHHHHHHHHHHH
Confidence                             99999999999998 9999999999999999999999887      2                


Q ss_pred             ----hhhccccCCccchhHHHHHHHhhhc
Q psy11505        287 ----FWSTVHKDGKVLMNKLFVEMLEAYL  311 (312)
Q Consensus       287 ----~~~~~~~~~~~~~~~~~~~~~~~~~  311 (312)
                          .+++.++.|.+||++||.|||+|+.
T Consensus       234 ~~~e~l~~~~~~g~~~i~~Ll~Eml~~~~  262 (265)
T d1hg4a_         234 KCQDHLFLFRITSDRPLEELFLEQLEAPP  262 (265)
T ss_dssp             HHHHHHHHHTCBCSSCHHHHHHHHHTSCC
T ss_pred             HHHHHHhhcccCCCCChhHHHHHHhcCCC
Confidence                3566799999999999999999863

>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=99.96  E-value=1.8e-29  Score=215.65  Aligned_cols=193  Identities=26%  Similarity=0.405  Sum_probs=154.6

Q ss_pred             HHHHHHHHHhcCcccccccC--CCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHH
Q psy11505         74 ENKMLEALLLCEPEMLTVRS--ETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTL  151 (312)
Q Consensus        74 ~~~~l~~l~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L  151 (312)
                      ..++++.+...+|.......  ....+......+.++++++.+.+..+|+|||++|+|..|+.+||+.|+|++|+++++|
T Consensus         4 ~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~l~~~a~~~l~~~v~wak~lp~F~~L~~~DQ~~LLk~~~~el~~L   83 (230)
T d2p1ta1           4 VERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIA   83 (230)
T ss_dssp             HHHHHHHHHHHC-------------------CHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCCcccccccCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHcCCccccCCHHHHHHHHHHHHHHHHHH
Confidence            45567777766664322211  1122233445678899999999999999999999999999999999999999999999


Q ss_pred             hhhhhcccCCCCeeEecccchhhHHhhhhcccchhhh----hhcccCccCCCCccccCCceeeeeCCCCcccccccccch
Q psy11505        152 TIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQ----QVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCE  227 (312)
Q Consensus       152 ~~a~rs~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~----~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~  227 (312)
                      +.||++.+.++ .+.+.+|..++.......+..+++.    .+...+.+|++|++||                       
T Consensus        84 ~~a~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~ld~~E~-----------------------  139 (230)
T d2p1ta1          84 SFSHRSIAVKD-GILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTEL-----------------------  139 (230)
T ss_dssp             HHHHHTTTSSS-EEECTTSCEEEHHHHHTTTCHHHHHHHHHHTHHHHHHTTCCHHHH-----------------------
T ss_pred             HHHHHhhcCCC-eEEecCCeeecHhHHHhccchHHHHHHHHHHHHHHHHcCCCHHHH-----------------------
Confidence            99999998876 7889999888887777766665543    3444556999999999                       


Q ss_pred             hHHHHHHHHhhhcccceecCCCCceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH---------------------
Q psy11505        228 ACKAFFKRTIQVYSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL---------------------  285 (312)
Q Consensus       228 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~---------------------  285 (312)
                                         +++|||+|||||+. +++.++|+++|++++.+|.+|+..+                     
T Consensus       140 -------------------~lLkaivL~~pd~~~l~~~~~i~~~q~~~~~aL~~y~~~~~~~~~~R~~~Ll~~L~~Lr~l  200 (230)
T d2p1ta1         140 -------------------GCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSI  200 (230)
T ss_dssp             -------------------HHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTTHHHHHHH
T ss_pred             -------------------HHHHHHHHhccccCCcccHHHHHHHHHHHHHHHHHHHHhhCCCchhHHHHHHHHHHHHHHH
Confidence                               99999999999998 9999999999999999999999876                     


Q ss_pred             -----hhhhccccCCccchhHHHHHHHhh
Q psy11505        286 -----RFWSTVHKDGKVLMNKLFVEMLEA  309 (312)
Q Consensus       286 -----~~~~~~~~~~~~~~~~~~~~~~~~  309 (312)
                           +.+++++++|.+|+++|+.|||+|
T Consensus       201 ~~~~~e~l~~~~~~~~~~~~~Ll~Eml~~  229 (230)
T d2p1ta1         201 GLKCLEHLFFFKLIGDTPIDTFLMEMLEA  229 (230)
T ss_dssp             HHHHHHHHHHHHHHCCSCCCHHHHHHTSC
T ss_pred             HHHHHHHHHhcCcCCCCChhHHHHHHHcC
Confidence                 235667999999999999999986

>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=99.96  E-value=4.8e-29  Score=213.53  Aligned_cols=165  Identities=27%  Similarity=0.349  Sum_probs=148.4

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhh
Q psy11505        101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE  180 (312)
Q Consensus       101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~  180 (312)
                      ....|+.+.+..+..+..+|+|||++|+|.+|+.+||++|||++|+++++++.|+++.+..+ .+.+++|..+.++....
T Consensus        42 ~~~~~~~~~~~~~~~i~~iV~faK~ip~F~~L~~~DQi~LLk~~~~el~~l~~a~~~~~~~~-~~~~~~g~~~~~~~~~~  120 (236)
T d1fcya_          42 DLGLWDKFSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQD-TMTFSDGLTLNRTQMHN  120 (236)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETTTT-EEECTTCBEEEHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcccCC-eeeccCCceecHHHHhh
Confidence            44578999999999999999999999999999999999999999999999999999887765 89999999999888888


Q ss_pred             cccchhhhhhccc---CccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCC
Q psy11505        181 CGFSEIYQQVKHS---GSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANS  257 (312)
Q Consensus       181 ~~~~~~~~~i~~~---~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  257 (312)
                      .+.+++.+.+..+   +.+|++|++||                                          ++++||+||||
T Consensus       121 ~~~~~l~~~~~~~~~~l~~L~ld~~E~------------------------------------------alL~Ai~L~~p  158 (236)
T d1fcya_         121 AGFGPLTDLVFAFAGQLLPLEMDDTET------------------------------------------GLLSAICLICG  158 (236)
T ss_dssp             HTTGGGHHHHHHHHHHHGGGCCCHHHH------------------------------------------HHHHHHHHSCT
T ss_pred             cccHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHhhccC
Confidence            7877777766655   44999999999                                          99999999999


Q ss_pred             CCc-ccchHHHHHHHHHHHHHhHhHHHHH------h--------------------hhhccccCCccchhHHHHHHHh
Q psy11505        258 DVK-LDEFSSLKKFRNSILSSLGDCIYVL------R--------------------FWSTVHKDGKVLMNKLFVEMLE  308 (312)
Q Consensus       258 ~~~-l~~~~~~~~~~~~~~~~l~~~~~~~------~--------------------~~~~~~~~~~~~~~~~~~~~~~  308 (312)
                      |++ |+++.+|+++|++++.||.+|+..+      |                    .++..+..|.+|+++|+.||||
T Consensus       159 d~~gL~~~~~Ve~lq~~~~~aL~~y~~~~~~~~~~rf~~LL~~Lp~LR~l~~~~~e~l~~~k~~~~~~~~~L~~E~~d  236 (236)
T d1fcya_         159 DRMDLEEPEKVDKLQEPLLEALRLYARRRRPSQPYMFPRMLMKITDLRGISTKGAERAITLKMEIPGPMPPLIREMLE  236 (236)
T ss_dssp             TSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCCCHHHHHHHC
T ss_pred             CCCCcccccHHHHHHHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCccHHHHHHcC
Confidence            998 9999999999999999999999876      2                    2445688999999999999996

>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=99.95  E-value=3.7e-29  Score=216.01  Aligned_cols=193  Identities=23%  Similarity=0.390  Sum_probs=161.0

Q ss_pred             HHHHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhh
Q psy11505         76 KMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAY  155 (312)
Q Consensus        76 ~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~  155 (312)
                      .+++.+...||.......+...++.....+..+++++++.++.+|+|||++|+|.+|+.+||+.|+|++|+++++++.||
T Consensus         4 ~~~~~l~~~ep~~~~~~~~~~~p~~~~~~l~~l~~~a~~~L~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~   83 (250)
T d1t7ra_           4 IFLNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGW   83 (250)
T ss_dssp             HHHHHHHHHCCCCCCCCCCTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHhCCCCcccCCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHhCccHHHhhHHHHHHHHHHHHHHHHHHHHHH
Confidence            46777778888877776666566667788899999999999999999999999999999999999999999999999999


Q ss_pred             hcccCCC-CeeEecccchhhHHhhhhcccchhhhhhcc---cCccCCCCccccCCceeeeeCCCCcccccccccchhHHH
Q psy11505        156 RSLPHCA-GKIRFASDLVLDERQARECGFSEIYQQVKH---SGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKA  231 (312)
Q Consensus       156 rs~~~~~-~~l~~~~g~~~~~~~~~~~~~~~~~~~i~~---~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~  231 (312)
                      ++.+... ..+.++++...+.......+..+++.++..   .+++|++|++||                           
T Consensus        84 rs~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~ld~~E~---------------------------  136 (250)
T d1t7ra_          84 RSFTNVNSRMLYFAPDLVFNEYRMHKSRMYSQCVRMRHLSQEFGWLQITPQEF---------------------------  136 (250)
T ss_dssp             HHHHHHTTSSEEEETTEEECHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHH---------------------------
T ss_pred             HhhccCCCceEecCCCcccCHHHHhhchhHHHHHHHHHHHHHHHHcCCCHHHH---------------------------
Confidence            9988765 346678887777666655555555554444   456999999999                           


Q ss_pred             HHHHHhhhcccceecCCCCceeecCCCC-c-ccchHHHHHHHHHHHHHhHhHHHHH---------hh-------------
Q psy11505        232 FFKRTIQVYSGYRQTGACGTLVLANSDV-K-LDEFSSLKKFRNSILSSLGDCIYVL---------RF-------------  287 (312)
Q Consensus       232 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~-~-l~~~~~~~~~~~~~~~~l~~~~~~~---------~~-------------  287 (312)
                                     +++|||+|||||. + +.+.+.|+.+|++++.||.+|+...         ||             
T Consensus       137 ---------------~lLkaIvL~npd~~~~l~~~~~i~~lq~~~~~aL~~y~~~~~~~~~~~p~Rf~~LL~~Lp~lr~l  201 (250)
T d1t7ra_         137 ---------------LCMKALLLFSIIPVDGLKNQKFFDELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPI  201 (250)
T ss_dssp             ---------------HHHHHHHHTSEEETTCCTTHHHHHHHHHHHHHHHHHHHHTTCCSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ---------------HHHHHHHhcCCccccCCccHHHHHHHHHHHHHHHHHHHHHhCCCCcchhhHHHHHHHHHHHHHHH
Confidence                           9999999999985 5 9999999999999999999999743         33             


Q ss_pred             ----------hhccccCCccchhHHHHHHHhhh
Q psy11505        288 ----------WSTVHKDGKVLMNKLFVEMLEAY  310 (312)
Q Consensus       288 ----------~~~~~~~~~~~~~~~~~~~~~~~  310 (312)
                                +.+.+..|.+++++|+.||++++
T Consensus       202 ~~~~~~~~~~l~~~~~~~~~~i~~Ll~Eml~~~  234 (250)
T d1t7ra_         202 ARELHQFTFDLLIKSHMVSVDFPEMMAEIISVQ  234 (250)
T ss_dssp             HHHHHHHHHHHHHTHHHHTCCCCHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhccccCCCChHHHHHHHHhcc
Confidence                      22456788899999999999986

>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=99.95  E-value=1.6e-28  Score=210.54  Aligned_cols=191  Identities=32%  Similarity=0.467  Sum_probs=151.1

Q ss_pred             HHHHHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhh
Q psy11505         75 NKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIA  154 (312)
Q Consensus        75 ~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a  154 (312)
                      +++++.+...+|.......+ ..+......+..++++.++.+..+|+|||++|+|.+|+.+||+.|+|++|+++++++.|
T Consensus         5 ~~l~~~l~~~epp~~~~~~~-~~~~~~~~~~~~l~~~a~~~l~~~V~waK~lp~F~~L~~~DQi~LLk~~~~el~~L~~a   83 (236)
T d2j7ya1           5 EQLVLTLLEAEPPNVLVSRP-SMPFTEASMMMSLTKLADKELVHMIGWAKKIPGFVELSLLDQVRLLESCWMEVLMVGLM   83 (236)
T ss_dssp             HHHHHHHHHTCCCCCCCC------CCHHHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCccccCCC-CCCCChHHHHHHHHHHHHHHHHHHHHHHHcCchHHHhhHHHHHHHHHHHHHHHHHHHHH
Confidence            46788888888754433322 22334566788899999999999999999999999999999999999999999999999


Q ss_pred             hhcccCCCCeeEecccchhhHHhhhh-cccchhhhhhcc---cCccCCCCccccCCceeeeeCCCCcccccccccchhHH
Q psy11505        155 YRSLPHCAGKIRFASDLVLDERQARE-CGFSEIYQQVKH---SGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACK  230 (312)
Q Consensus       155 ~rs~~~~~~~l~~~~g~~~~~~~~~~-~~~~~~~~~i~~---~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~  230 (312)
                      |+++..++ .+++.+|....+..... .+..++++.+..   .+++|++|++||                          
T Consensus        84 ~~s~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~l~~L~ld~~E~--------------------------  136 (236)
T d2j7ya1          84 WRSIDHPG-KLIFAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEY--------------------------  136 (236)
T ss_dssp             HHHTTSTT-EEEEETTEEEEGGGGGGSTTHHHHHHHHHHHHHHHHHHTCCHHHH--------------------------
T ss_pred             HHhhcCCC-cEEecCCcccCHHHHHHHhhHHHHHHHHHHHHHHHHHcCCCHHHH--------------------------
Confidence            99999876 78888898877766543 344555554444   455999999999                          


Q ss_pred             HHHHHHhhhcccceecCCCCceeecCCCCc-ccc-------hHHHHHHHHHHHHHhHhHHHHH-----------------
Q psy11505        231 AFFKRTIQVYSGYRQTGACGTLVLANSDVK-LDE-------FSSLKKFRNSILSSLGDCIYVL-----------------  285 (312)
Q Consensus       231 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-l~~-------~~~~~~~~~~~~~~l~~~~~~~-----------------  285 (312)
                                      +++|||+|||||++ +.+       ++++..+++++..+|.+|+...                 
T Consensus       137 ----------------~lLkaIvLf~pd~~~l~~~~~~~~~~~~v~~~~~~~~~~l~~~~~~~~~~~p~~~~Rf~~LL~~  200 (236)
T d2j7ya1         137 ----------------LCVKAMILLNSSMYPLASANQEAESSRKLTHLLNAVTDALVWVIAKSGISSQQQSVRLANLLML  200 (236)
T ss_dssp             ----------------HHHHHHHHTTTTCCCCC------HHHHHHHHHHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHHH
T ss_pred             ----------------HHHHHHHHhCCcCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcchhHHHHHHHHH
Confidence                            99999999999986 554       3457778888888888887532                 


Q ss_pred             ------------hhhhccccCCccchhHHHHHHHhh
Q psy11505        286 ------------RFWSTVHKDGKVLMNKLFVEMLEA  309 (312)
Q Consensus       286 ------------~~~~~~~~~~~~~~~~~~~~~~~~  309 (312)
                                  .+++++++.|.+||++|+.|||+|
T Consensus       201 Lp~Lr~l~~~~~e~l~~~~~~g~~~i~~Ll~Eml~a  236 (236)
T d2j7ya1         201 LSHVRHISNKGMEHLLSMKCKNVVPVYDLLLEMLNA  236 (236)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTSSCCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCCccHHHHHHhCc
Confidence                        336678999999999999999997

>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=99.95  E-value=3e-29  Score=216.72  Aligned_cols=194  Identities=25%  Similarity=0.474  Sum_probs=156.5

Q ss_pred             HHHHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhh
Q psy11505         76 KMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAY  155 (312)
Q Consensus        76 ~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~  155 (312)
                      +++..+...||...........+......+..++++.++.++.+|+|||++|+|.+|+.+||+.|+|++|+++++++.||
T Consensus         5 ~~~~~l~~~eP~~~~~~~~~~~~~~~~~~~~~l~~la~r~L~~~VewaK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~   84 (251)
T d1sqna_           5 PLINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGW   84 (251)
T ss_dssp             HHHHHHHHHSCCCCCCCCCC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCCcccCCCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHhccchhhcCHHHHHHHHHHHHHHHHHHHHHH
Confidence            46777888888776666555566677888999999999999999999999999999999999999999999999999999


Q ss_pred             hcccCCC-CeeEecccchhhHHhhhhcccchhhh---hhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHH
Q psy11505        156 RSLPHCA-GKIRFASDLVLDERQARECGFSEIYQ---QVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKA  231 (312)
Q Consensus       156 rs~~~~~-~~l~~~~g~~~~~~~~~~~~~~~~~~---~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~  231 (312)
                      ++.+.+. +.+.+.+|...+.......+..++.+   ++...+++|++|++||                           
T Consensus        85 rs~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~---------------------------  137 (251)
T d1sqna_          85 RSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEF---------------------------  137 (251)
T ss_dssp             HHHHHHTTSSEEEETTEEECGGGCCSHHHHHHHHHHHHHHHHHHHHTCCHHHH---------------------------
T ss_pred             HhhhccCcceeeccCCceecHHhhccccHHHHHHHHHHHHHHHHHcCCCHHHH---------------------------
Confidence            9988765 45666777666655444433344333   4445566999999999                           


Q ss_pred             HHHHHhhhcccceecCCCCceeecCCC-Cc-ccchHHHHHHHHHHHHHhHhHHHHH---------hh-------------
Q psy11505        232 FFKRTIQVYSGYRQTGACGTLVLANSD-VK-LDEFSSLKKFRNSILSSLGDCIYVL---------RF-------------  287 (312)
Q Consensus       232 ~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~-l~~~~~~~~~~~~~~~~l~~~~~~~---------~~-------------  287 (312)
                                     +++|||++|||| ++ +++.++|+++|++|++||.+|+..+         ||             
T Consensus       138 ---------------~lLkAIiL~npd~~~~l~~~~~V~~lq~~~~~aL~~~~~~~~~~~~~~~~Rf~~LL~lLp~lR~l  202 (251)
T d1sqna_         138 ---------------LCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDL  202 (251)
T ss_dssp             ---------------HHHHHHHHTSEECTTCCTTHHHHHHHHHHHHHHHHHHHHTTC-CHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ---------------HHHHHHHHcCCccccCCcCHHHHHHHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHHHHHH
Confidence                           999999999997 56 9999999999999999999999643         33             


Q ss_pred             ----------hhccccCCccchhHHHHHHHhhhc
Q psy11505        288 ----------WSTVHKDGKVLMNKLFVEMLEAYL  311 (312)
Q Consensus       288 ----------~~~~~~~~~~~~~~~~~~~~~~~~  311 (312)
                                ++.+...|.+++++|+.|||++++
T Consensus       203 ~~~~~~~~~~~~~~~~~~~v~~p~Ll~E~l~~~~  236 (251)
T d1sqna_         203 VKQLHLYCLNTFIQSRALSVEFPEMMSEVIAAQL  236 (251)
T ss_dssp             HHHHHHHHHHHHHTHHHHTCCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCCCCcChhHHHHHHHHccC
Confidence                      122345678999999999999874

>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=99.95  E-value=3.1e-28  Score=208.13  Aligned_cols=166  Identities=26%  Similarity=0.377  Sum_probs=145.2

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhh
Q psy11505        101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE  180 (312)
Q Consensus       101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~  180 (312)
                      +...++.+.+.....+..+|+|||++|+|.+|+.+||+.|||++|+++++++.|+++.+..+ .+++++|..+++.+. .
T Consensus        37 ~~~~~~~f~~~~~~~i~~iv~fAK~iPgF~~L~~~DQi~LLk~~~~ElllL~~a~~~~~~~~-~l~~~~~~~~~~~~~-~  114 (236)
T d1ovla_          37 DTQHIQQFYDLLTGSMEIIRGWAEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSNPVEG-KLIFCNGVVLHRLQC-V  114 (236)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHSBTTTT-EEECTTSBEEEHHHH-T
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCC-eEEecCCceechHhh-c
Confidence            44567888999999999999999999999999999999999999999999999999988775 899999999988775 4


Q ss_pred             cccchhhhhhcccC---ccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCC
Q psy11505        181 CGFSEIYQQVKHSG---SLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANS  257 (312)
Q Consensus       181 ~~~~~~~~~i~~~~---~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  257 (312)
                      .+.+++++.+..+.   ++|++|++||                                          ++++||+||+ 
T Consensus       115 ~~~~~~~~~i~~~~~~l~~L~ld~~E~------------------------------------------alLkAI~L~~-  151 (236)
T d1ovla_         115 RGFGEWIDSIVEFSSNLQNMNIDISAF------------------------------------------SCIAALAMVT-  151 (236)
T ss_dssp             TTTTTHHHHHHHHHHHHHTTCCCHHHH------------------------------------------HHHHHHHHSS-
T ss_pred             ccHHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHcC-
Confidence            45667777666654   4999999999                                          9999999998 


Q ss_pred             CCc-ccchHHHHHHHHHHHHHhHhHHHHH----------------------------hhhhccccCCccchhHHHHHHHh
Q psy11505        258 DVK-LDEFSSLKKFRNSILSSLGDCIYVL----------------------------RFWSTVHKDGKVLMNKLFVEMLE  308 (312)
Q Consensus       258 ~~~-l~~~~~~~~~~~~~~~~l~~~~~~~----------------------------~~~~~~~~~~~~~~~~~~~~~~~  308 (312)
                      |++ |+++++|+++|++++.||.+|+..+                            +.+++.++.|.+|+++|+.|||.
T Consensus       152 dr~gL~~~~~Ve~lQ~~~~~aL~~~~~~~~~~~~~~~rf~~LL~~Lp~LR~l~~~~~e~l~~~kl~~~~~~~~L~~elf~  231 (236)
T d1ovla_         152 ERHGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLGKLPELRTLCTQGLQRIFYLKLEDLVPPPAIIDKLFL  231 (236)
T ss_dssp             CCTTCSCHHHHHHHHHHHHHHHHHHHHGGGTTTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSSCCCHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCccHHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcCCCCCcHHHHHHHHH
Confidence            666 9999999999999999999999754                            22555788999999999999997


Q ss_pred             hhc
Q psy11505        309 AYL  311 (312)
Q Consensus       309 ~~~  311 (312)
                      +.+
T Consensus       232 ~~l  234 (236)
T d1ovla_         232 DTL  234 (236)
T ss_dssp             HHC
T ss_pred             hhC
Confidence            643

>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=99.95  E-value=4.1e-28  Score=206.72  Aligned_cols=167  Identities=22%  Similarity=0.251  Sum_probs=143.6

Q ss_pred             CchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhh
Q psy11505         99 DPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQA  178 (312)
Q Consensus        99 ~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~  178 (312)
                      ......+..+.+.....+..+|+|||++|+|.+|+.+||+.|||++|+++++++.|+++.+..+ .+++++|..+++.+.
T Consensus        32 ~~~~~~~~~~~~~~~~~i~~ivefAK~iPgF~~L~~~DQi~LLk~~~~El~~L~~a~~~~~~~~-~l~~~~g~~~~~~~~  110 (230)
T d1pdua_          32 MSEADKVQQFYQLLTSSVDVIKQFAEKIPGYFDLLPEDQELLFQSASLELFVLRLAYRARIDDT-KLIFCNGTVLHRTQC  110 (230)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHCCSSCS-EEECTTSBEEEHHHH
T ss_pred             CChHHHHHHHHHHHHHHHHHHHHHHHcCCChhcCCHHHHHHHHHHHHHHHHHHHHHHhccCCCC-eEEecCCccccHHHH
Confidence            3456678888999999999999999999999999999999999999999999999999998876 899999998887765


Q ss_pred             hhcccchhhhhhcccCc---cCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeec
Q psy11505        179 RECGFSEIYQQVKHSGS---LDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLA  255 (312)
Q Consensus       179 ~~~~~~~~~~~i~~~~~---~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  255 (312)
                      .. +++++++.++.+..   +|++|++||                                          ++++||+||
T Consensus       111 ~~-~~~~~~~~i~~~~~~~~~L~ld~~E~------------------------------------------alL~AivL~  147 (230)
T d1pdua_         111 LR-SFGEWLNDIMEFSRSLHNLEIDISAF------------------------------------------ACLCALTLI  147 (230)
T ss_dssp             HH-HHTTHHHHHHHHHHHHHHHCCCHHHH------------------------------------------HHHHHHHHS
T ss_pred             HH-hHHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHhhheee
Confidence            44 45667766665544   899999999                                          999999999


Q ss_pred             CCCCcccchHHHHHHHHHHHHHhHhHHHHH--------h--------------------hhhccccCCccchhHHHHHHH
Q psy11505        256 NSDVKLDEFSSLKKFRNSILSSLGDCIYVL--------R--------------------FWSTVHKDGKVLMNKLFVEML  307 (312)
Q Consensus       256 ~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~--------~--------------------~~~~~~~~~~~~~~~~~~~~~  307 (312)
                      ++..+|+++++|+++|++++.||.+|+..+        |                    .++..++.|.+|+++|+.|||
T Consensus       148 ~d~~~L~~~~~Ve~lq~~~~~aL~~~i~~~~~~~~~~~rf~~LL~~Lp~LR~l~~~~~e~l~~~k~~~~~~~~~L~~Em~  227 (230)
T d1pdua_         148 TERHGLREPKKVEQLQMKIIGSLRDHVTYNAEAQKKQHYFSRLLGKLPELRSLSVQGLQRIFYLKLEDLVPAPALIENMF  227 (230)
T ss_dssp             SCCTTCSCHHHHHHHHHHHHHHHHHHHHHCHHHHTSTTHHHHHHTHHHHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHTT
T ss_pred             cCcccccCHHHHHHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHHhHHHHHHHHHHHHHHHHHHcCCCCCccHHHHHHh
Confidence            643349999999999999999999999654        2                    244568889999999999998


Q ss_pred             hh
Q psy11505        308 EA  309 (312)
Q Consensus       308 ~~  309 (312)
                      ..
T Consensus       228 ~~  229 (230)
T d1pdua_         228 VT  229 (230)
T ss_dssp             TC
T ss_pred             hc
Confidence            63

>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=99.95  E-value=6.4e-29  Score=212.52  Aligned_cols=166  Identities=23%  Similarity=0.341  Sum_probs=145.0

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhh
Q psy11505        101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE  180 (312)
Q Consensus       101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~  180 (312)
                      ...++.++++++.+.++.+|+|||++|+|.+|+.+||+.|+|++|.++++|..||++.+..+ .+++++|...++.....
T Consensus        35 ~~~~~~~l~~~a~~~l~~~vewaK~ip~F~~L~~~DQ~~LLk~~~~el~lL~~a~~s~~~~~-~~~l~~~~~~~~~~~~~  113 (233)
T d1pzla_          35 KIASIADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKD-VLLLGNDYIVPRHCPEL  113 (233)
T ss_dssp             CBCCHHHHHHHHHHHHHHHHHHHTTCHHHHTSCHHHHHHHHHHSHHHHHHHHHHHHHTTSSS-EEECTTSCEEESSCGGG
T ss_pred             ccccHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhccCC-ceeecCCccccchhhhh
Confidence            34568889999999999999999999999999999999999999999999999999998876 78888888776655444


Q ss_pred             cccc----hhhhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecC
Q psy11505        181 CGFS----EIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLAN  256 (312)
Q Consensus       181 ~~~~----~~~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  256 (312)
                      .+..    +.++++...+++|++|++||                                          +++|||+||+
T Consensus       114 ~~~~~~~~~~l~~~~~~~~~L~ld~~E~------------------------------------------~lLkaiiL~~  151 (233)
T d1pzla_         114 AEMSRVSIRILDELVLPFQELQIDDNEY------------------------------------------AYLKAIIFFD  151 (233)
T ss_dssp             GGGHHHHHHHHHHTHHHHHHHTCCHHHH------------------------------------------HHHHHHHHCC
T ss_pred             hhhHHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHhcc
Confidence            3332    34556666677999999999                                          9999999999


Q ss_pred             CCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------------------------hhhhccccCCccchhHHHHHHHhh
Q psy11505        257 SDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------------------------RFWSTVHKDGKVLMNKLFVEMLEA  309 (312)
Q Consensus       257 ~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------------------------~~~~~~~~~~~~~~~~~~~~~~~~  309 (312)
                      ||++ +++.++|+.+|++++.+|.+|+..+                          +.+++++++|.+|+++|+.|||.+
T Consensus       152 pd~~~l~~~~~i~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LLl~Lp~Lr~i~~~~~e~l~~~~~~~~~~~~~Ll~emL~~  231 (233)
T d1pzla_         152 PDAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFIKLFGMAKIDNLLQEMLLG  231 (233)
T ss_dssp             TTCTTCSCHHHHHHHHHHHHHHHHHHHHSSSSCCTTHHHHHHTHHHHHHHHHHHHHHHHHHHHHTTCSCCCHHHHHHHTT
T ss_pred             cccCCcccHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCCChHHHHHHHhcc
Confidence            9998 9999999999999999999999865                          235677999999999999999964

>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=99.94  E-value=2.5e-28  Score=210.44  Aligned_cols=192  Identities=26%  Similarity=0.437  Sum_probs=153.6

Q ss_pred             HHHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhh
Q psy11505         77 MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYR  156 (312)
Q Consensus        77 ~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~r  156 (312)
                      +++.+...+|.......+...+......+..++++.+++++.+|+|||++|+|..|+.+||+.|+|++|+++++|+.||+
T Consensus         3 ~~~~l~~~eP~~~~~~~~~~~p~~~~~~~~~l~~la~r~L~~~IewaK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~   82 (247)
T d1nhza_           3 LVSLLEVIEPEVLYAGYDSSVPDSTWRIMTTLNMLGGRQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMSLMAFALGWR   82 (247)
T ss_dssp             HHHHHHHHCCCCCCCCCCTTSCCCHHHHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCCCCCcCCCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHhcccHhhcCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45667777887666555555555666788999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCC-CeeEecccchhhHHhhhhcccchhhhh---hcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHH
Q psy11505        157 SLPHCA-GKIRFASDLVLDERQARECGFSEIYQQ---VKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAF  232 (312)
Q Consensus       157 s~~~~~-~~l~~~~g~~~~~~~~~~~~~~~~~~~---i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~  232 (312)
                      ++..+. +.+.+++|..++.......+..++.+.   +...+++|++|++||                            
T Consensus        83 s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~l~~~E~----------------------------  134 (247)
T d1nhza_          83 SYRQSSANLLCFAPDLIINEQRMTLPDMYDQCKHMLYVSSELHRLQVSYEEY----------------------------  134 (247)
T ss_dssp             HHHHHTTSSEEEETTEEECTTGGGSTTHHHHHHHHHHHHHHHHHTTCCHHHH----------------------------
T ss_pred             HHhCCCCCeEeccccceecHHhhccccHHHHHHHHHHHHHHHHHcCCCHHHH----------------------------
Confidence            987765 345667777776655555554444443   444555999999999                            


Q ss_pred             HHHHhhhcccceecCCCCceeecCCC-Cc-ccchHHHHHHHHHHHHHhHhHHHHH---------hhh-------------
Q psy11505        233 FKRTIQVYSGYRQTGACGTLVLANSD-VK-LDEFSSLKKFRNSILSSLGDCIYVL---------RFW-------------  288 (312)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~~~~l~~~~-~~-l~~~~~~~~~~~~~~~~l~~~~~~~---------~~~-------------  288 (312)
                                    +++|||+||||| +. +++++.|+++|+++++||.+|+..+         ||.             
T Consensus       135 --------------~lLkaIvLfnpd~~~~l~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~~~~Rf~~LL~~Lp~lR~~~  200 (247)
T d1nhza_         135 --------------LCMKTLLLLSSVPKDGLKSQELFDEIRMTYIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEVV  200 (247)
T ss_dssp             --------------HHHHHHHHTSEEETTCCTTHHHHHHHHHHHHHHHHHHHHHHCCSTHHHHHHHHHHHHHHHHHHHHH
T ss_pred             --------------HHHHHHHHcCCCCCcccccHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHHHHHH
Confidence                          999999999999 55 9999999999999999999999654         331             


Q ss_pred             -------hc--cccCCccchhHHHHHHHhhh
Q psy11505        289 -------ST--VHKDGKVLMNKLFVEMLEAY  310 (312)
Q Consensus       289 -------~~--~~~~~~~~~~~~~~~~~~~~  310 (312)
                             +.  ..-.+.+++++|+.|||.++
T Consensus       201 ~~~~~~l~~~~~~~~~~v~~~~Ll~Eml~~~  231 (247)
T d1nhza_         201 ENLLNYCFQTFLDKTMSIEFPEMLAEIITNQ  231 (247)
T ss_dssp             HHHTTSCCCCHHHHHHHSCHHHHHHHHHTC-
T ss_pred             HHHHHHHHHHHhcCcCCCChhHHHHHHHhcc
Confidence                   11  12346789999999999865

>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=99.94  E-value=9e-28  Score=205.07  Aligned_cols=163  Identities=27%  Similarity=0.372  Sum_probs=142.2

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhh
Q psy11505        101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE  180 (312)
Q Consensus       101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~  180 (312)
                      ....++.+.+..+..+..+|+|||++|+|.+|+.+||+.|||++|+++++++.|+++.+..+ .+++++|...++.+.. 
T Consensus        37 ~~~~~~~~~~~~~~~i~~iv~wAK~iPgF~~L~~~DQi~LLk~~~~el~lL~~a~~~~~~~~-~l~~~~~~~~~~~~~~-  114 (233)
T d2qw4a1          37 DAGDVQQFYDLLSGSLEVIRKWAEKIPGFAELSPADQDLLLESAFLELFILRLAYRSKPGEG-KLIFCSGLVLHRLQCA-  114 (233)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHTSTTTTTSCHHHHHHHHHHHHHHHHHHHHHHHSBGGGT-EEECTTSCEEEHHHHH-
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhCCCCCC-ceeecCCeeecHHhhh-
Confidence            45678899999999999999999999999999999999999999999999999999998776 8999999888877654 


Q ss_pred             cccchhhhhhcccCc---cCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCC
Q psy11505        181 CGFSEIYQQVKHSGS---LDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANS  257 (312)
Q Consensus       181 ~~~~~~~~~i~~~~~---~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  257 (312)
                      .+++++++.+..+..   +|++|++||                                          ++++||+||+ 
T Consensus       115 ~~~~~~~~~i~~~~~~l~~L~ld~~E~------------------------------------------alLkAivL~~-  151 (233)
T d2qw4a1         115 RGFGDWIDSILAFSRSLHSLLVDVPAF------------------------------------------ACLSALVLIT-  151 (233)
T ss_dssp             HHHTTHHHHHHHHHHHHHHHTCCHHHH------------------------------------------HHHHHHHHSS-
T ss_pred             hhhHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHhcC-
Confidence            345667776666544   899999999                                          9999999999 


Q ss_pred             CCc-ccchHHHHHHHHHHHHHhHhHHHHH----------------------------hhhhccccCCccchhHHHHHHHh
Q psy11505        258 DVK-LDEFSSLKKFRNSILSSLGDCIYVL----------------------------RFWSTVHKDGKVLMNKLFVEMLE  308 (312)
Q Consensus       258 ~~~-l~~~~~~~~~~~~~~~~l~~~~~~~----------------------------~~~~~~~~~~~~~~~~~~~~~~~  308 (312)
                      |++ |+++++|+++|++++.+|.+|+..+                            ..+++.++.|.+|+++|+.|||.
T Consensus       152 d~~gL~~~~~Ve~lq~~~~~aL~~yi~~~~~~~~~~~rf~kLL~~Lp~LR~l~~~~~e~l~~~k~~~~~~~p~L~~Emf~  231 (233)
T d2qw4a1         152 DRHGLQEPRRVEELQNRIASCLKEHVAAVAGEPQPASCLSRLLGKLPELRTLCTQGLQRIFYLKLEDLVPPPPIIDKIFM  231 (233)
T ss_dssp             CCTTCSCHHHHHHHHHHHHHHHHHHHHHSCC---CCTTHHHHHTHHHHHHHHHHHHHHHHHHHHHHCCSCCCHHHHHHHH
T ss_pred             cccCccCHHHHHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCchHHHHHHcc
Confidence            555 9999999999999999999999753                            22455688999999999999984

>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=99.94  E-value=1.8e-27  Score=205.14  Aligned_cols=166  Identities=20%  Similarity=0.356  Sum_probs=143.9

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhh
Q psy11505        101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE  180 (312)
Q Consensus       101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~  180 (312)
                      ....+..+++..+..+..+|+|||++|+|.+|+.+||++|||++|+++++++.|+++.+.++ .+.+.+|..++++....
T Consensus        55 ~~~~~~~~~~~~~~~i~~vV~fAK~iPgF~~L~~~DQi~LLk~~~~El~lL~~a~~~~~~~~-~~~~~~~~~~~~~~~~~  133 (251)
T d1n46a_          55 DLEAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESE-TLTLNGEMAVTRGQLKN  133 (251)
T ss_dssp             CHHHHHHHHTTHHHHHHHHHHHHHTCTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTCBTTTT-BEEETTTEEECHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCC-eEEeCCCccccHHHHhh
Confidence            35668999999999999999999999999999999999999999999999999999987776 78899999999888877


Q ss_pred             cccchhhhhhcccCc---cCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCC
Q psy11505        181 CGFSEIYQQVKHSGS---LDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANS  257 (312)
Q Consensus       181 ~~~~~~~~~i~~~~~---~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  257 (312)
                      .+..++.+.+..+..   +|++|++||                                          ++++||+||+|
T Consensus       134 ~~~~~~~~~i~~f~~~l~~L~ld~~E~------------------------------------------alL~AivL~~p  171 (251)
T d1n46a_         134 GGLGVVSDAIFDLGMSLSSFNLDDTEV------------------------------------------ALLQAVLLMSS  171 (251)
T ss_dssp             TTTTTHHHHHHHHHHHHGGGTCCHHHH------------------------------------------HHHHHHHHTCT
T ss_pred             cccHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHhcC
Confidence            777777777666544   999999999                                          99999999999


Q ss_pred             CCc-ccchHHHHHHHHHHHHHhHhHHHHH------hh--------------------hhcccc-CCccchhHHHHHHHhh
Q psy11505        258 DVK-LDEFSSLKKFRNSILSSLGDCIYVL------RF--------------------WSTVHK-DGKVLMNKLFVEMLEA  309 (312)
Q Consensus       258 ~~~-l~~~~~~~~~~~~~~~~l~~~~~~~------~~--------------------~~~~~~-~~~~~~~~~~~~~~~~  309 (312)
                      |++ |+++++|+++|++++.||.+|+..+      ||                    +...+. .+...+++|+.|||+.
T Consensus       172 dr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~rf~kLL~~Lp~LR~l~~~~~e~l~~~k~~~~~~~~ppLl~E~fd~  251 (251)
T d1n46a_         172 DRPGLACVERIEKYQDSFLLAFEHYINYRKHHVTHFWPKLLMKVTDLRMIGACHASRFLHMKVECPTELFPPLFLEVFED  251 (251)
T ss_dssp             TSTTCSCHHHHHHHHHHHHHHHHHHHHHHCCSSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCGGGSCHHHHHHHC-
T ss_pred             CCCCCcCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHhHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHhcC
Confidence            998 9999999999999999999999876      22                    222343 3455679999999973

>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=99.94  E-value=1.5e-27  Score=204.61  Aligned_cols=165  Identities=20%  Similarity=0.273  Sum_probs=141.9

Q ss_pred             chhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhh
Q psy11505        100 PTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAR  179 (312)
Q Consensus       100 ~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~  179 (312)
                      .....+..+.++....+..+|+|||++|+|.+|+.+||+.|||++|+++++++.++++...++ .+.+.+|..+.+....
T Consensus        44 ~~~~~~~~~~~~~~~~i~~iVefAK~lP~F~~L~~~DQi~LLk~~~~el~ll~~a~~~~~~~~-~~~~~~~~~~~~~~~~  122 (239)
T d1pq9a_          44 ARQQRFAHFTELAIISVQEIVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETARRYNHETE-CITFLKDFTYSKDDFH  122 (239)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTSTTSTTSCHHHHHHHHHHHHHHHHHHHHHHTEETTTT-EEEEETTEEECHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHhHhhhcCcCHHhcCHHHHHHHHHHHHHHHHHHHHHHHhcCCCC-eEeecCCCcccHHHHh
Confidence            345668889999999999999999999999999999999999999999999999999887765 7889999888888777


Q ss_pred             hcccc-hhhhhhccc---CccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeec
Q psy11505        180 ECGFS-EIYQQVKHS---GSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLA  255 (312)
Q Consensus       180 ~~~~~-~~~~~i~~~---~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  255 (312)
                      ..+.. ++++.+..+   +++|++|++||                                          ++++||+||
T Consensus       123 ~~~~~~~~~~~i~~~~~~l~~L~ld~~E~------------------------------------------alLkAivL~  160 (239)
T d1pq9a_         123 RAGLQVEFINPIFEFSRAMRRLGLDDAEY------------------------------------------ALLIAINIF  160 (239)
T ss_dssp             HTTCCHHHHHHHHHHHHHHHHHTCCHHHH------------------------------------------HHHHHHHHT
T ss_pred             hhhhhHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHh
Confidence            76654 455555554   44999999999                                          999999999


Q ss_pred             CCCCc-ccchHHHHHHHHHHHHHhHhHHHHH------hh--------------------hhccccCCccchhHHHHHHHh
Q psy11505        256 NSDVK-LDEFSSLKKFRNSILSSLGDCIYVL------RF--------------------WSTVHKDGKVLMNKLFVEMLE  308 (312)
Q Consensus       256 ~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~------~~--------------------~~~~~~~~~~~~~~~~~~~~~  308 (312)
                      +||++ ++++++|+++|++++.||.+|+..+      ||                    ++..++ +..++++|+.||||
T Consensus       161 ~pd~~gl~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~rf~~LL~~L~~LR~l~~~~~e~l~~~k~-~~~~~~~L~~Em~d  239 (239)
T d1pq9a_         161 SADRPNVQEPGRVEALQQPYVEALLSYTRIKRPQDQLRFPRMLMKLVSLRTLSSVHSEQVFALRL-QDKKLPPLLSEIWD  239 (239)
T ss_dssp             CTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TTCCCCHHHHHHHC
T ss_pred             CCCcCccccHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCCCcHHHHHhcC
Confidence            99998 9999999999999999999999877      22                    233454 45688999999986

>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=99.93  E-value=9.4e-27  Score=200.37  Aligned_cols=165  Identities=18%  Similarity=0.197  Sum_probs=135.9

Q ss_pred             chhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhh
Q psy11505        100 PTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAR  179 (312)
Q Consensus       100 ~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~  179 (312)
                      +....+..++++.+..+..+|+|||++|+|..|+.+||+.|||++|+++++++.++++..... .+.++++.........
T Consensus        51 ~~~~~~~~~~~~~~~~i~~iV~waK~lP~F~~L~~~DQi~LLk~~~~El~~l~~~~~~~~~~~-~~~~~~~~~~~~~~~~  129 (246)
T d1xvpb_          51 PVLPLVTHFADINTFMVLQVIKFTKDLPVFRSLPIEDQISLLKGAAVEICHIVLNTTFCLQTQ-NFLCGPLRYTIEDGAR  129 (246)
T ss_dssp             CSHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHSCHHHHHHHHHHHHHHHHHHHHGGGEETTTT-EEECSSCEECHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHhcccCC-eeecCCCccchHHHhc
Confidence            345668889999999999999999999999999999999999999999999999988876655 6666666555544444


Q ss_pred             hcccchhhhhhccc---CccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecC
Q psy11505        180 ECGFSEIYQQVKHS---GSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLAN  256 (312)
Q Consensus       180 ~~~~~~~~~~i~~~---~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  256 (312)
                      ..+..++.+.+..+   +++|++|++||                                          ++++||+|||
T Consensus       130 ~~~~~~~~~~~~~f~~~l~~L~ld~~E~------------------------------------------alLkAivL~~  167 (246)
T d1xvpb_         130 VGFQVEFLELLFHFHGTLRKLQLQEPEY------------------------------------------VLLAAMALFS  167 (246)
T ss_dssp             HTCCHHHHHHHHHHHHHHHHTCCCHHHH------------------------------------------HHHHHHHHSC
T ss_pred             cccchHHHHHHHHHHHHHHHhCCCHHHH------------------------------------------HHHhhhhhcc
Confidence            44444555555554   44999999999                                          9999999999


Q ss_pred             CCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------hh------------hh------ccccCCccchhHHHHHHH
Q psy11505        257 SDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------RF------------WS------TVHKDGKVLMNKLFVEML  307 (312)
Q Consensus       257 ~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------~~------------~~------~~~~~~~~~~~~~~~~~~  307 (312)
                      ||++ |++.++|+++|++++.||.+|+..+        ||            +.      .....+..++++|+.||+
T Consensus       168 pD~~gL~~~~~Ve~lQ~~~~~aL~~y~~~~~~~p~~~~rf~~LL~~L~~LR~l~~~~~e~l~~~k~~~~~~pLl~E~f  245 (246)
T d1xvpb_         168 PDRPGVTQRDEIDQLQEEMALTLQSYIKGQQRRPRDRFLYAKLLGLLAELRSINEAYGYQIQHIQGLSAMMPLLQEIC  245 (246)
T ss_dssp             SSSTTCSCHHHHHHHHHHHHHHHHHHHHTCSSCCSCSSHHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHCHHHHHHT
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHHHHHHcCCCCCcccHHHHHHHHhHHHHHHHHHHHHHHHHhcCCCCCChHHHHhc
Confidence            9999 9999999999999999999999754        22            11      125568889999999997

>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=99.93  E-value=2.6e-26  Score=197.16  Aligned_cols=162  Identities=17%  Similarity=0.261  Sum_probs=140.6

Q ss_pred             hHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhhc
Q psy11505        102 LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC  181 (312)
Q Consensus       102 ~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~~  181 (312)
                      ...+..+.++....+..+|+|||++|+|.+|+.+||+.|||++|+++++++.|+++.+..+ .+.+++|..+.++.....
T Consensus        47 ~~~~~~~~~~~~~~i~~iV~faK~lP~F~~L~~~DQi~LLk~~~~El~lL~~a~~~~~~~~-~~~~~~~~~~~~~~~~~~  125 (243)
T d2r40d1          47 DMPFRQITEMTILTVQLIVEFAKGLPGFAKISQSDQITLLKACSSEVMMLRVARRYDAATD-SVLFANNQAYTRDNYRKA  125 (243)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEETTTT-EEECTTSCEECHHHHHHT
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHcCcChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhccCC-eEEecCCeeecHHHHhhc
Confidence            3457888999999999999999999999999999999999999999999999999988776 899999999998888888


Q ss_pred             ccchhhhhhcccCc---cCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCCC
Q psy11505        182 GFSEIYQQVKHSGS---LDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSD  258 (312)
Q Consensus       182 ~~~~~~~~i~~~~~---~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  258 (312)
                      +.+++++.+..+..   +|++|++||                                          ++++||+||+ |
T Consensus       126 ~~~~~~~~l~~f~~~l~~L~ld~~E~------------------------------------------alL~AivL~s-d  162 (243)
T d2r40d1         126 GMAYVIEDLLHFCRCMYSMMMDNVHY------------------------------------------ALLTAIVIFS-D  162 (243)
T ss_dssp             TCHHHHHHHHHHHHHHHTTTCCHHHH------------------------------------------HHHHHHHHTS-C
T ss_pred             ccHHHHHHHHHHHHHHHHhCCCHHHH------------------------------------------HHHHHHHhcC-C
Confidence            88888777766554   999999999                                          9999999999 6


Q ss_pred             Cc-ccchHHHHHHHHHHHHHhHhHHHHH---------hh--------------------hhccccCCccchhHHHHHHHh
Q psy11505        259 VK-LDEFSSLKKFRNSILSSLGDCIYVL---------RF--------------------WSTVHKDGKVLMNKLFVEMLE  308 (312)
Q Consensus       259 ~~-l~~~~~~~~~~~~~~~~l~~~~~~~---------~~--------------------~~~~~~~~~~~~~~~~~~~~~  308 (312)
                      ++ |.++.+|+++|++|+.+|.+|+..+         ||                    +...+.. ..++++|+.||+|
T Consensus       163 ~~~L~~~~~ve~lq~~~~~aL~~y~~~~~~~~p~~~~rf~~LL~~L~~LR~l~~~~~e~l~~~k~~-~~~~~pLl~E~~d  241 (243)
T d2r40d1         163 RPGLEQPLLVEEIQRYYLNTLRVYILNQNSASPRCAVIFGKILGILTEIRTLGMQNSNMCISLKLK-NRKLPPFLEEIWD  241 (243)
T ss_dssp             CTTCSCHHHHHHHHHHHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TCCCCHHHHHHTT
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHHHHHhhCCCCccHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCCCChHHHHHhC
Confidence            76 9999999999999999999999654         22                    1112333 3578899999987

>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=99.92  E-value=1.2e-25  Score=191.46  Aligned_cols=159  Identities=18%  Similarity=0.249  Sum_probs=128.2

Q ss_pred             hHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhhc
Q psy11505        102 LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC  181 (312)
Q Consensus       102 ~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~~  181 (312)
                      ...+..++++.+..+..+|+|||++|+|.+|+.+||+.|||++|+++++++.++++.+..     +.++..+........
T Consensus        41 ~~~~~~l~~~~~~~i~~iVe~AK~iP~F~~L~~~DQi~LLk~~~~El~~L~~~~~~~~~~-----~~~~~~~~~~~~~~~  115 (231)
T d1osha_          41 EENFLILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKL-----PSGHSDLLEERIRNS  115 (231)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHTS-----CHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhcCccc-----cCCCccccHHHHHhc
Confidence            345778899999999999999999999999999999999999999999999998765442     234444444444444


Q ss_pred             ccc-hhhhhhcccC---ccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCC
Q psy11505        182 GFS-EIYQQVKHSG---SLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANS  257 (312)
Q Consensus       182 ~~~-~~~~~i~~~~---~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  257 (312)
                      +.. ++.+.+..+.   .+|++|++||                                          ++++||+||||
T Consensus       116 ~~~~~~~~~i~~~~~~l~~L~ld~~E~------------------------------------------~lLkAivL~~p  153 (231)
T d1osha_         116 GISDEYITPMFSFYKSIGELKMTQEEY------------------------------------------ALLTAIVILSP  153 (231)
T ss_dssp             SCCTTTHHHHHHHHHHHHTTCCCHHHH------------------------------------------HHHHHHHHTCT
T ss_pred             cchHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHhcc
Confidence            443 4555555544   4999999999                                          99999999999


Q ss_pred             CCc-ccchHHHHHHHHHHHHHhHhHHHHH------hh--------------------hhccccCCccchhHHHHHHHh
Q psy11505        258 DVK-LDEFSSLKKFRNSILSSLGDCIYVL------RF--------------------WSTVHKDGKVLMNKLFVEMLE  308 (312)
Q Consensus       258 ~~~-l~~~~~~~~~~~~~~~~l~~~~~~~------~~--------------------~~~~~~~~~~~~~~~~~~~~~  308 (312)
                      |++ |++.++|+++|++|+.||.+|+..+      ||                    ++..+. +..++++|+.||+|
T Consensus       154 d~~gL~~~~~Ve~lq~~~~~aL~~y~~~~~p~~~~rf~~LL~~L~~LR~l~~~~~e~l~~~k~-~~~~~~pLl~E~fd  230 (231)
T d1osha_         154 DRQYIKDREAVEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAEMLMSWRV-NDHKFTPLLCEIWD  230 (231)
T ss_dssp             TCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHTHHHHHHHHHHHHHH-TTCCCCHHHHHHHT
T ss_pred             CCCCCccHHHHHHHHHHHHHHHHHHHHHHCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCCCChHHHHHhC
Confidence            998 9999999999999999999999877      32                    222233 56688999999997

>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=99.92  E-value=1.3e-25  Score=194.03  Aligned_cols=161  Identities=19%  Similarity=0.243  Sum_probs=130.2

Q ss_pred             HHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhh-HHhhhhcc
Q psy11505        104 TINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLD-ERQARECG  182 (312)
Q Consensus       104 ~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~-~~~~~~~~  182 (312)
                      .+..++++.+..+..+|+|||++|+|..|+.+||+.|||++|+++++++.|+++..... .+.++++.... .......+
T Consensus        58 ~~~~~~~l~~~~i~~iVefAK~iPgF~~L~~~DQi~LLK~~~~El~ll~~a~~~~~~~~-~~~~~~~~~~~~~~~~~~~~  136 (255)
T d1ie9a_          58 MLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDM-SWTCGNQDYKYRVSDVTKAG  136 (255)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHGGGTEETTTT-EEECSSGGGEECHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCcccccCCHHHHHHHHHHHHHHHHHHHHHHheeCCCC-eEEeCCCCeeecHHHHHhcc
Confidence            57788999999999999999999999999999999999999999999999987666554 67777665433 33333333


Q ss_pred             -cchhhhhhccc---CccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCCC
Q psy11505        183 -FSEIYQQVKHS---GSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSD  258 (312)
Q Consensus       183 -~~~~~~~i~~~---~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  258 (312)
                       ..++++.+..+   +.+|++|++||                                          ++++||+|||||
T Consensus       137 ~~~~~~~~i~~f~~~l~~L~ld~~E~------------------------------------------~lLkAiiL~~pd  174 (255)
T d1ie9a_         137 HSLELIEPLIKFQVGLKKLNLHEEEH------------------------------------------VLLMAICIVSPD  174 (255)
T ss_dssp             CCHHHHHHHHHHHHHHHTTCCCHHHH------------------------------------------HHHHHHHHSCSC
T ss_pred             chHHHHHHHHHHHHHHHHhCCCHHHH------------------------------------------HHHHHHHhcCCC
Confidence             34566666554   44999999999                                          999999999999


Q ss_pred             Cc-ccchHHHHHHHHHHHHHhHhHHHHH--------hh--------------------hhccccCCc--cchhHHHHHHH
Q psy11505        259 VK-LDEFSSLKKFRNSILSSLGDCIYVL--------RF--------------------WSTVHKDGK--VLMNKLFVEML  307 (312)
Q Consensus       259 ~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------~~--------------------~~~~~~~~~--~~~~~~~~~~~  307 (312)
                      ++ |+++++|+++|++++.||.+|+..+        ||                    ++..++.+.  +.+++|+.||+
T Consensus       175 r~gL~~~~~Ve~lq~~~~~aL~~y~~~~~~~~~~~~~f~kLL~~L~~LR~l~~~~~e~l~~~~~~~~~~~~lppLl~E~f  254 (255)
T d1ie9a_         175 RPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNEEHSKQYRCLSFQPECSMKLTPLVLEVF  254 (255)
T ss_dssp             STTCSCHHHHHHHHHHHHHHHHHHHHHHCCTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTTHHHHSCHHHHHHH
T ss_pred             cccccCHHHHHHHHHHHHHHHHHHHHHhCCCCCcccHHHHHHHHhHHHHHHHHHHHHHHHHHhhCCCCCCCccHHHHHhc
Confidence            98 9999999999999999999999765        12                    222355554  45789999997

>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=99.91  E-value=2.6e-25  Score=191.17  Aligned_cols=142  Identities=20%  Similarity=0.219  Sum_probs=123.7

Q ss_pred             chhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhh
Q psy11505        100 PTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAR  179 (312)
Q Consensus       100 ~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~  179 (312)
                      .....|..+.+.....+..+|+|||++|+|.+|+.+||+.|||++|+++++++.|+++.+..+ .+++.+ ...+.....
T Consensus        47 ~~~~~~~~~~~~~~~~i~~vV~faK~lP~F~~L~~~DQi~LLk~~~~el~~l~~a~~~~~~~~-~~~~~~-~~~~~~~~~  124 (244)
T d1nq7a_          47 SREALWQQCAIQITHAIQYVVEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPLNN-TVLFEG-KYGGMQMFK  124 (244)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHTSCHHHHHHHHHHHHHHHHHHHHGGGEETTTT-EEEETT-EEEEGGGGG
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHccCCCC-eEeeCC-ccccHHHHh
Confidence            356678999999999999999999999999999999999999999999999999999877665 666654 445556666


Q ss_pred             hcccchhhhhhcccCc---cCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecC
Q psy11505        180 ECGFSEIYQQVKHSGS---LDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLAN  256 (312)
Q Consensus       180 ~~~~~~~~~~i~~~~~---~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  256 (312)
                      ..+..++.+.+..+..   +|++|++||                                          ++++||+||+
T Consensus       125 ~~~~~~~~~~~~~~~~~~~~L~l~~~E~------------------------------------------all~AivL~~  162 (244)
T d1nq7a_         125 ALGSDDLVNEAFDFAKNLCSLQLTEEEI------------------------------------------ALFSSAVLIS  162 (244)
T ss_dssp             GGSCHHHHHHHHHHHHHHHTTCCCHHHH------------------------------------------HHHHHHHHSC
T ss_pred             hcccHHHHHHHHHHHHHHHHhCCCHHHH------------------------------------------HHHHHHHHHc
Confidence            6666677666665544   999999999                                          9999999999


Q ss_pred             CCCc-ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505        257 SDVK-LDEFSSLKKFRNSILSSLGDCIYVL  285 (312)
Q Consensus       257 ~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~  285 (312)
                      ||++ ++++++|+++|+++..||.+|+..+
T Consensus       163 pd~~~l~~~~~Ve~lq~~~~~aL~~~~~~~  192 (244)
T d1nq7a_         163 PDRAWLLEPRKVQKLQEKIYFALQHVIQKN  192 (244)
T ss_dssp             TTSTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcccHHHHHHHHHHHHHHHHHHHHhc
Confidence            9998 9999999999999999999999877

>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=99.91  E-value=3.5e-25  Score=188.57  Aligned_cols=143  Identities=17%  Similarity=0.193  Sum_probs=124.5

Q ss_pred             chhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhh
Q psy11505        100 PTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAR  179 (312)
Q Consensus       100 ~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~  179 (312)
                      +....+..++++....+..+|+|||++|+|..|+.+||+.|||++|+++++++.|+++..... .+.++++.....+...
T Consensus        50 ~~~~~~~~~~~~~~~~i~~iV~faK~lP~F~~L~~eDQi~LLk~~~~El~~L~~a~~~~~~~~-~~~~~~~~~~~~~~~~  128 (232)
T d1xnxa_          50 PVLPLLTHFADINTFMVQQIIKFTKDLPLFRSLTMEDQISLLKGAAVEILHISLNTTFCLQTE-NFFCGPLCYKMEDAVH  128 (232)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHTSCHHHHHHHHHHHHHHHHHHHHGGGEETTTT-EEEETTEEECHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHhccCCC-ceeeCCcccchHHHHh
Confidence            445668889999999999999999999999999999999999999999999999988877766 6777877766655554


Q ss_pred             hcccchhhhhhcccC---ccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecC
Q psy11505        180 ECGFSEIYQQVKHSG---SLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLAN  256 (312)
Q Consensus       180 ~~~~~~~~~~i~~~~---~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  256 (312)
                      .+...++++.+..+.   ++|++|++||                                          ++++||+|||
T Consensus       129 ~~~~~~~~~~i~~f~~~l~~L~ld~~E~------------------------------------------alLkAivLf~  166 (232)
T d1xnxa_         129 AGFQYEFLESILHFHKNLKGLHLQEPEY------------------------------------------VLMAATALFS  166 (232)
T ss_dssp             TTCCHHHHHHHHHHHHHHHTTCCCHHHH------------------------------------------HHHHHHHHTC
T ss_pred             ccccHHHHHHHHHHHHHHHHhCCCHHHH------------------------------------------HHHHHHHHhc
Confidence            444456777766654   4999999999                                          9999999999


Q ss_pred             CCCc-ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505        257 SDVK-LDEFSSLKKFRNSILSSLGDCIYVL  285 (312)
Q Consensus       257 ~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~  285 (312)
                      ||++ |.++++|+++|++++.||.+|+..+
T Consensus       167 pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~  196 (232)
T d1xnxa_         167 PDRPGVTQREEIDQLQEEMALILNNHIMEQ  196 (232)
T ss_dssp             TTSTTCSCHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCcCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            9998 9999999999999999999999876

>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=99.91  E-value=2.7e-25  Score=191.70  Aligned_cols=141  Identities=18%  Similarity=0.206  Sum_probs=125.1

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhh
Q psy11505        101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE  180 (312)
Q Consensus       101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~  180 (312)
                      +...|..+.+.....+..+|+|||++|+|.+|+.+||+.|||++|+++++++.|+++.+...  +++.+|...+......
T Consensus        56 ~~~~~~~~~~~~~~~i~~vV~faK~iPgF~~L~~~DQi~LLk~~~~el~ll~~a~~~~~~~~--~~~~~~~~~~~~~~~~  133 (251)
T d1n83a_          56 REVMWQLCAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQNN--TVYFDGKYASPDVFKS  133 (251)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHSTTTTTSCHHHHHHHHHHHHHHHHHHHGGGGEETTTT--EEEETTEEECGGGGGG
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHcCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHhCCCCC--EEecCCeeecHHHHhh
Confidence            45568888999999999999999999999999999999999999999999999987776543  5666777777777777


Q ss_pred             cccchhhhhhcccCc---cCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCC
Q psy11505        181 CGFSEIYQQVKHSGS---LDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANS  257 (312)
Q Consensus       181 ~~~~~~~~~i~~~~~---~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  257 (312)
                      .+.+++.+.+..+..   +|++|++||                                          ++++||+||+|
T Consensus       134 ~~~~~~~~~~~~~~~~~~~L~ld~~E~------------------------------------------alL~AivL~~p  171 (251)
T d1n83a_         134 LGCEDFISFVFEFGKSLCSMHLTEDEI------------------------------------------ALFSAFVLMSA  171 (251)
T ss_dssp             GSCHHHHHHHHHHHHHHHTTCCCHHHH------------------------------------------HHHHHHHHSCT
T ss_pred             ccHHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHHcc
Confidence            777777777776554   999999999                                          99999999999


Q ss_pred             CCc-ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505        258 DVK-LDEFSSLKKFRNSILSSLGDCIYVL  285 (312)
Q Consensus       258 ~~~-l~~~~~~~~~~~~~~~~l~~~~~~~  285 (312)
                      |++ |+++++|+++|+++..||.+|+..+
T Consensus       172 d~~gL~~~~~Ve~lq~~~~~aL~~~~~~~  200 (251)
T d1n83a_         172 DRSWLQEKVKIEKLQQKIQLALQHVLQKN  200 (251)
T ss_dssp             TSTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CccccCCHHHHHHHHHHHHHHHHHHHHhc
Confidence            998 9999999999999999999999876

>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=99.91  E-value=4.1e-25  Score=192.06  Aligned_cols=165  Identities=16%  Similarity=0.218  Sum_probs=131.6

Q ss_pred             chhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccc-hhhHHh-
Q psy11505        100 PTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDL-VLDERQ-  177 (312)
Q Consensus       100 ~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~-~~~~~~-  177 (312)
                      .....+..+.+.....+..+|+|||++|+|.+|+.+||+.|||++|+++++++.|+++.+.+   ..+.+|. ...... 
T Consensus        71 ~~~~~~~~~~~~~~~~i~~vVefAK~iP~F~~L~~~DQi~LLK~~~~ElllL~~a~~~~~~~---~~~~~g~~~~~~~~~  147 (271)
T d2fvja1          71 VAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDG---VLISEGQGFMTREFL  147 (271)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEETTE---EEETTTTEEEEHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhCcChhhCCHHHHHHHHHHHHHHHHHHHHHHHcCCCC---CeeeCCCccchHHHH
Confidence            34567888999999999999999999999999999999999999999999999999876543   3443332 222221 


Q ss_pred             -hhhcccchhhh---hhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCcee
Q psy11505        178 -ARECGFSEIYQ---QVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLV  253 (312)
Q Consensus       178 -~~~~~~~~~~~---~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  253 (312)
                       .......++++   .+...+++|++|++||                                          ++++||+
T Consensus       148 ~~~~~~~~~~~~~i~~f~~~~~~L~ld~~E~------------------------------------------alLkAIv  185 (271)
T d2fvja1         148 KSLRKPFGDFMEPKFEFAVKFNALELDDSDL------------------------------------------AIFIAVI  185 (271)
T ss_dssp             HTSCTTGGGSSHHHHHHHHHHHTTCCCHHHH------------------------------------------HHHHHHH
T ss_pred             HHhhhhHHHHHHHHHHHHHHHHHhCCCHHHH------------------------------------------HHHHHHH
Confidence             12223334444   4444455999999999                                          9999999


Q ss_pred             ecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH------hh--------------------hh-ccccCCccchhHHHHH
Q psy11505        254 LANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL------RF--------------------WS-TVHKDGKVLMNKLFVE  305 (312)
Q Consensus       254 l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~------~~--------------------~~-~~~~~~~~~~~~~~~~  305 (312)
                      |||||++ |.+++.|+++|++++.||.+|+..+      ||                    +. +++..|.+++++|+.|
T Consensus       186 Lf~pd~~gL~~~~~Ve~lQ~~~~~aL~~y~~~~~p~~~~rf~kLL~~Lp~LR~l~~~~~e~l~~~k~~~~~~~l~pLl~E  265 (271)
T d2fvja1         186 ILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE  265 (271)
T ss_dssp             HTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHSTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCSSCCCHHHHH
T ss_pred             HHcccccCCccHHHHHHHHHHHHHHHHHHHHHhCCCchhHHHHHHHHhHHHHHHHHHHHHHHHHHhccCCCCCccHHHHH
Confidence            9999999 9999999999999999999999876      22                    22 3456889999999999


Q ss_pred             HHhh
Q psy11505        306 MLEA  309 (312)
Q Consensus       306 ~~~~  309 (312)
                      |+..
T Consensus       266 if~d  269 (271)
T d2fvja1         266 IYKD  269 (271)
T ss_dssp             HHTT
T ss_pred             HHHH
Confidence            9964

>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=99.91  E-value=4.8e-25  Score=191.02  Aligned_cols=165  Identities=15%  Similarity=0.193  Sum_probs=130.8

Q ss_pred             hHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHh-hhh
Q psy11505        102 LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQ-ARE  180 (312)
Q Consensus       102 ~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~-~~~  180 (312)
                      ...+.......+..+..+|+|||++|+|.+|+.+||++|||++|+++++++.|+++...+. .+.++++....+.. ...
T Consensus        69 ~~~~~~~~~~~~~~i~~iVewAK~iPgF~~L~~~DQi~LLK~~~~Ellil~~a~~~~~~~~-~~~~~~~~~~~~~~~~~~  147 (267)
T d2p54a1          69 VRIFHCCQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGM-LVAYGNGFITREFLKSLR  147 (267)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHGGGEETTEE-EETTTTEEEEHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhCcChhhCCHHHHHHHHHHHHHHHHHHHHHHhccCCCC-EEEeCCCccchHHHHHhc
Confidence            3345666666778899999999999999999999999999999999999999988776543 45556665444332 223


Q ss_pred             cccchhhhhhc---ccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCC
Q psy11505        181 CGFSEIYQQVK---HSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANS  257 (312)
Q Consensus       181 ~~~~~~~~~i~---~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  257 (312)
                      .+...+.+.+.   ..+++|++|++||                                          ++++||+||+|
T Consensus       148 ~~~~~~~~~~~~~~~~~~~L~ld~~E~------------------------------------------alLkAIvLf~p  185 (267)
T d2p54a1         148 KPFCDIMEPKFDFAMKFNALELDDSDI------------------------------------------SLFVAAIICCG  185 (267)
T ss_dssp             TTGGGTSHHHHHHHHHHHTTCCCHHHH------------------------------------------HHHHHHHHSCT
T ss_pred             chHHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHhcC
Confidence            33444444444   4455999999999                                          99999999999


Q ss_pred             CCc-ccchHHHHHHHHHHHHHhHhHHHHH------hh--------------------hh-ccccCCccchhHHHHHHHhh
Q psy11505        258 DVK-LDEFSSLKKFRNSILSSLGDCIYVL------RF--------------------WS-TVHKDGKVLMNKLFVEMLEA  309 (312)
Q Consensus       258 ~~~-l~~~~~~~~~~~~~~~~l~~~~~~~------~~--------------------~~-~~~~~~~~~~~~~~~~~~~~  309 (312)
                      |++ |.+..+|+++|++++.||.+|+..+      ||                    +. +++..+.+|+++|+.||+..
T Consensus       186 d~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~rf~kLL~~Lp~LR~l~~~~~e~l~~~k~~~~~~~l~pLl~Eif~d  265 (267)
T d2p54a1         186 DRPGLLNVGHIEKMQEGIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQLVTEHAQLVQIIKKTESDAALHPLLQEIYRD  265 (267)
T ss_dssp             TCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHTT
T ss_pred             CCCCcccHHHHHHHHHHHHHHHHHHHHhcCCChhhHHHHHHHHhHHHHHHHHHHHHHHHHHhccCCCCCccHHHHHHHHh
Confidence            998 9999999999999999999999877      22                    22 23568889999999999953

>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=99.90  E-value=6.1e-25  Score=193.57  Aligned_cols=140  Identities=16%  Similarity=0.117  Sum_probs=114.6

Q ss_pred             hHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhhc
Q psy11505        102 LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC  181 (312)
Q Consensus       102 ~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~~  181 (312)
                      ...+..+.++....+..+|+|||++|+|.+|+.+||++|||++|+++++++.|+++...+.  .++.++...........
T Consensus        96 ~~~l~~~~~~~~~~i~~iV~fAK~iP~F~~L~~~DQi~LLk~~~~el~~l~~a~~~~~~~~--~~~~~~~~~~~~~~~~~  173 (292)
T d1nrla_          96 FSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETG--TWECGRLSYCLEDTAGG  173 (292)
T ss_dssp             GTTHHHHHHHHHHHHHHHHHHHHHCHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTEETTTT--EEEETTEEEEECCCSSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCcCHhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCC--eeeCCCccccHHHhhhh
Confidence            3467888999999999999999999999999999999999999999999999999876654  33444444433332222


Q ss_pred             ccchhhhhhc---ccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCCC
Q psy11505        182 GFSEIYQQVK---HSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSD  258 (312)
Q Consensus       182 ~~~~~~~~i~---~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  258 (312)
                      +..++.+.+.   ..+++|++|++||                                          ++++||+|||||
T Consensus       174 ~~~~~~~~~~~~~~~l~~L~ld~~E~------------------------------------------~lLkAi~L~~pd  211 (292)
T d1nrla_         174 FQQLLLEPMLKFHYMLKKLQLHEEEY------------------------------------------VLMQAISLFSPD  211 (292)
T ss_dssp             HHHHTTSHHHHHHHHHHHTCCCHHHH------------------------------------------HHHHHHHHTCTT
T ss_pred             hHHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHhCCC
Confidence            2233444443   4455999999999                                          999999999999


Q ss_pred             Cc-ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505        259 VK-LDEFSSLKKFRNSILSSLGDCIYVL  285 (312)
Q Consensus       259 ~~-l~~~~~~~~~~~~~~~~l~~~~~~~  285 (312)
                      ++ |+++++|+++|++|..||.+|+..+
T Consensus       212 ~~gL~~~~~Ve~lq~~~~~aL~~y~~~~  239 (292)
T d1nrla_         212 RPGVLQHRVVDQLQEQFAITLKSYIECN  239 (292)
T ss_dssp             STTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCcccHHHHHHHHHHHHHHHHHHHHHh
Confidence            99 9999999999999999999999776

>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=99.89  E-value=3.5e-24  Score=185.46  Aligned_cols=165  Identities=17%  Similarity=0.171  Sum_probs=130.7

Q ss_pred             CchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhh
Q psy11505         99 DPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQA  178 (312)
Q Consensus        99 ~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~  178 (312)
                      ......+..+.......+..+|+|||++|+|.+|+.+||++|||++|+++++++.|++..+.   .+.+.+|..+.....
T Consensus        66 ~~~~~~f~~~~~~~~~~I~~iVefAK~iPgF~~L~~~DQi~LLK~~~~Ellil~~a~~~~~d---~~~~~~g~~~~~~~~  142 (265)
T d2b50b1          66 EISVHVFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNKD---GLLVANGSGFVTREF  142 (265)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHTSHHHHTSCHHHHHHHHHHHHHHHHHHHHGGGEETT---EEEETTTTEEEEHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHhcCcChhhCCHHHHHHHHHHHHHHHHHHHHHHHhCCC---CceEeCCcccccHHH
Confidence            33445566777788889999999999999999999999999999999999999999887643   566666544332222


Q ss_pred             hh---cccchhhhhh---cccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCce
Q psy11505        179 RE---CGFSEIYQQV---KHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTL  252 (312)
Q Consensus       179 ~~---~~~~~~~~~i---~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  252 (312)
                      ..   ....++.+.+   ...+.+|++|++||                                          ++++||
T Consensus       143 ~~~~~~~~~~~~~~~~~f~~~~~~L~ld~~E~------------------------------------------alLkAi  180 (265)
T d2b50b1         143 LRSLRKPFSDIIEPKFEFAVKFNALELDDSDL------------------------------------------ALFIAA  180 (265)
T ss_dssp             HHTSCHHHHHHHHHHHHHHHHHHTTCCCHHHH------------------------------------------HHHHHH
T ss_pred             HHHhhhhHHHHHHHHHHHHHHHHHhCCCHHHH------------------------------------------HHHHHH
Confidence            11   1223444444   44455999999999                                          999999


Q ss_pred             eecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH------hh--------------------hh-ccccCCccchhHHHH
Q psy11505        253 VLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL------RF--------------------WS-TVHKDGKVLMNKLFV  304 (312)
Q Consensus       253 ~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~------~~--------------------~~-~~~~~~~~~~~~~~~  304 (312)
                      +||+||++ ++++++|+++|+++++||.+|+..+      ||                    +. +++..|.+|+++|+.
T Consensus       181 iL~~pd~~~L~~~~~Ve~lQ~~~~~aL~~y~~~~~p~~~~rfakLL~~L~~LR~ls~~~~e~L~~~k~~~~~~~l~pLl~  260 (265)
T d2b50b1         181 IILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQQLFPKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQ  260 (265)
T ss_dssp             HHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTTSCCCHHHH
T ss_pred             hhcccCccccccHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCccHHHH
Confidence            99999998 9999999999999999999999876      22                    33 235689999999999


Q ss_pred             HHHh
Q psy11505        305 EMLE  308 (312)
Q Consensus       305 ~~~~  308 (312)
                      ||+.
T Consensus       261 Em~~  264 (265)
T d2b50b1         261 EIYK  264 (265)
T ss_dssp             HHHC
T ss_pred             HHhc
Confidence            9985

>d1lo1a_ g.39.1.2 (A:) Steroid hormone receptor Err2 DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Steroid hormone receptor Err2 DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=5.8e-17  Score=114.70  Aligned_cols=51  Identities=82%  Similarity=1.439  Sum_probs=46.8

Q ss_pred             CceeEcCCCCCcccccccccccccCchhHHHHhcccccccccccccccccc
Q psy11505          1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQK   51 (312)
Q Consensus         1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~~~~   51 (312)
                      +..|.|..+++|.|++..|+.||+|||+|||+|||++++||.+|++.++++
T Consensus        38 ~~~~~c~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~r~~~~r~k   88 (90)
T d1lo1a_          38 NIEYSCPATNECEITKRRRKSCQACRFMKALKVGMLKEGVRLDRVRGGRQK   88 (90)
T ss_dssp             TCCCCCSSCSCCCCCHHHHHHCHHHHHHHHHHHTCCGGGSCSSCCTTCCCC
T ss_pred             CCccchhcCCCCccCCCCccccchhhHHHHHHcCCCHHHhccccccccccC
Confidence            357899999999999999999999999999999999999999998877665

>d2hanb1 g.39.1.2 (B:5-87) Ecdysone receptor DNA-binding domain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Ecdysone receptor DNA-binding domain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.52  E-value=4.9e-16  Score=108.30  Aligned_cols=48  Identities=33%  Similarity=0.638  Sum_probs=43.7

Q ss_pred             CceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccccc
Q psy11505          1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG   48 (312)
Q Consensus         1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~   48 (312)
                      +..|.|..+++|.+++..|+.||+|||+|||++||++++||.+|+..+
T Consensus        34 ~~~~~c~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~~   81 (83)
T d2hanb1          34 SAVYCCKFGRACEMDMYMRRKCQECRLKKCLAVGMRPECVVPENQCAM   81 (83)
T ss_dssp             TCCCCCSSCSCCCCSTTGGGTCHHHHHHHHHHTTCCGGGSSCSSHHHH
T ss_pred             CCceeecCCCCcccCCcccccCccchHHHHHHcCCCHHHccccchhcc
Confidence            356899999999999999999999999999999999999999887543

>d1dszb_ g.39.1.2 (B:) Retinoid X receptor (RXR-alpha) DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Retinoid X receptor (RXR-alpha) DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=1.1e-15  Score=106.64  Aligned_cols=45  Identities=51%  Similarity=1.035  Sum_probs=42.0

Q ss_pred             ceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccc
Q psy11505          2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR   46 (312)
Q Consensus         2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~   46 (312)
                      ..|.|..+++|.+++..|+.||+|||+|||+|||++++||.+|++
T Consensus        40 ~~~~c~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~Rdr   84 (84)
T d1dszb_          40 LTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQR   84 (84)
T ss_dssp             CCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCCCCC
T ss_pred             CCeeccCCCCcccCCCCCccCCCCccHHHHHcCCChHHcccccCC
Confidence            568999999999999999999999999999999999999998863

>d1cita_ g.39.1.2 (A:) Orphan nuclear receptor NGFI-B DNA-binding domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Orphan nuclear receptor NGFI-B DNA-binding domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.51  E-value=2.3e-15  Score=106.37  Aligned_cols=49  Identities=55%  Similarity=1.053  Sum_probs=44.2

Q ss_pred             ceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccccccc
Q psy11505          2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQ   50 (312)
Q Consensus         2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~~~   50 (312)
                      ..|.|..+++|.++...|+.||+|||+|||+|||++++||.+++...+.
T Consensus        35 ~~~~c~~~~~c~~~~~~r~~Cr~CR~~KCl~~GM~~~~v~~~~~~~~r~   83 (89)
T d1cita_          35 AKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTDSLKGRRG   83 (89)
T ss_dssp             CCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHTTCCGGGSCCGGGTTCCS
T ss_pred             CceeecCCCCccccCCccccCchhhHHHHHHcCCCHHHhcccccccccC
Confidence            5688998999999999999999999999999999999999988765543

>d1dsza_ g.39.1.2 (A:) Retinoic acid receptor DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Retinoic acid receptor DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.49  E-value=2.1e-15  Score=103.05  Aligned_cols=43  Identities=53%  Similarity=0.965  Sum_probs=40.0

Q ss_pred             CceeEcCCCCCcccccccccccccCchhHHHHhcccccccccc
Q psy11505          1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLD   43 (312)
Q Consensus         1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~   43 (312)
                      +..|.|..+++|.+++..|..||+|||+|||+|||++++||.|
T Consensus        33 ~~~~~c~~~~~c~~~~~~r~~Cr~CR~~KCl~~GM~~~~vq~d   75 (75)
T d1dsza_          33 NMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRND   75 (75)
T ss_dssp             TCCCCCSSCSCCCCSTTTGGGCHHHHHHHHHHTTCCGGGSCCC
T ss_pred             CCceecccCCccccCCccccccchhHHHHHHHhCCCHHHccCC
Confidence            3578999999999999999999999999999999999999974

>d1kb2a_ g.39.1.2 (A:) Vitamin D3 receptor, VDR, DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Vitamin D3 receptor, VDR, DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.48  E-value=1.1e-15  Score=108.01  Aligned_cols=47  Identities=40%  Similarity=0.829  Sum_probs=42.9

Q ss_pred             ceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccccc
Q psy11505          2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG   48 (312)
Q Consensus         2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~   48 (312)
                      ..|.|..+++|.|++..|+.||+|||+|||+|||++++||.+|+...
T Consensus        35 ~~~~c~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~~   81 (89)
T d1kb2a_          35 ALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDEEVQR   81 (89)
T ss_dssp             CCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCHHHHHH
T ss_pred             CCeecCCCCccCCCCcCCccCchhhHHHHHHcCCCHhhccccchhch
Confidence            46889999999999999999999999999999999999999886543

>d1a6ya_ g.39.1.2 (A:) Orphan nuclear receptor reverb DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Orphan nuclear receptor reverb DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.46  E-value=3.8e-15  Score=102.55  Aligned_cols=43  Identities=44%  Similarity=1.011  Sum_probs=39.0

Q ss_pred             ceeE-cCCCCCcccccccccccccCchhHHHHhccccccccccc
Q psy11505          2 IEYT-CPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR   44 (312)
Q Consensus         2 ~~Y~-C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r   44 (312)
                      +.|. |..+++|.+++..|..||+|||+|||+|||++++||.+|
T Consensus        35 ~~~~~~~~~~~c~~~~~~r~~Cr~CR~~KCl~~GM~~~~vq~~R   78 (78)
T d1a6ya_          35 IQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGR   78 (78)
T ss_dssp             CCCCCCSSTTCCCCCTTTTTSCHHHHHHHHTTTTCCSTTCCCCC
T ss_pred             CceeeeccCCCcccCCCCCccchhhHHHHHHHhCCCHHHhcCCC
Confidence            5676 567789999999999999999999999999999999875

>d1r4ia_ g.39.1.2 (A:) Androgen receptor {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Androgen receptor
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.41  E-value=1.7e-14  Score=98.16  Aligned_cols=39  Identities=44%  Similarity=0.954  Sum_probs=36.3

Q ss_pred             CceeEcCCCCCcccccccccccccCchhHHHHhcccccc
Q psy11505          1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEG   39 (312)
Q Consensus         1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~ea   39 (312)
                      +..|.|..+++|.|++..|+.||+|||+|||+|||+++|
T Consensus        36 ~~~~~c~~~~~C~~~~~~r~~C~~CR~~KCl~vGM~~~A   74 (74)
T d1r4ia_          36 KQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLGA   74 (74)
T ss_dssp             CCCCCCSSSSCCCCCTTTTTTCHHHHHHHHHHHTCCSCC
T ss_pred             ccceeeecCCCcccCCCCcccchhhhHHHHHHcCCcCCC
Confidence            357899999999999999999999999999999999986

>d2nllb_ g.39.1.2 (B:) Thyroid hormone receptor (TR-beta) DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Thyroid hormone receptor (TR-beta) DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.38  E-value=1.2e-14  Score=105.71  Aligned_cols=47  Identities=38%  Similarity=0.751  Sum_probs=41.8

Q ss_pred             eeEcCCCCCcccccccccccccCchhHHHHhcccccccccccccccc
Q psy11505          3 EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGR   49 (312)
Q Consensus         3 ~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~~   49 (312)
                      .|.|.++++|.+++..|+.||+|||+|||+|||++++||.+|++.+.
T Consensus        39 ~~~c~~~~~c~~~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~~~   85 (103)
T d2nllb_          39 SYSCKYEGKCVIDKVTRNQCQECRFKKCIYVGMATDLVLDDSKRLAK   85 (103)
T ss_dssp             GCCCSSCTTCCCSTTTTTSCHHHHHHHHHHTTCCGGGSCCHHHHHHH
T ss_pred             eeecccCCCCcCCCCccCCCccccchhHHHhhccHHhhhccccchhh
Confidence            35677889999999999999999999999999999999998875543

>d1lata_ g.39.1.2 (A:) Glucocorticoid receptor DNA-binding domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Glucocorticoid receptor DNA-binding domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.33  E-value=1.1e-13  Score=93.41  Aligned_cols=38  Identities=47%  Similarity=0.960  Sum_probs=35.3

Q ss_pred             CceeEcCCCCCcccccccccccccCchhHHHHhccccc
Q psy11505          1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE   38 (312)
Q Consensus         1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~e   38 (312)
                      +..|.|..+++|.+++..|+.||+|||+|||+|||++|
T Consensus        34 ~~~~~c~~~~~C~~~~~~r~~Cr~CR~~KCl~~GM~~e   71 (71)
T d1lata_          34 QHNYLCKYEGKCIIDKIRRKNCPACRYRKCLQAGMNLE   71 (71)
T ss_dssp             CCCCCCSSCSCCCCSTTTTTTCHHHHHHHHHHTTCCCC
T ss_pred             CcceeeecCcccccccCccccCCccchhHHhHccCCCC
Confidence            35789999999999999999999999999999999986

>d1hcqa_ g.39.1.2 (A:) Estrogen receptor DNA-binding domain {Human and chicken (Homo sapiens) and (Gallus gallus) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Estrogen receptor DNA-binding domain
species: Human and chicken (Homo sapiens) and (Gallus gallus) [TaxId: 9606]

Probab=99.31  E-value=1.7e-13  Score=93.06  Aligned_cols=36  Identities=58%  Similarity=1.259  Sum_probs=34.0

Q ss_pred             ceeEcCCCCCcccccccccccccCchhHHHHhcccc
Q psy11505          2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLK   37 (312)
Q Consensus         2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~   37 (312)
                      ..|.|+.+++|.|+...|+.||+|||+|||+|||++
T Consensus        39 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~k   74 (74)
T d1hcqa_          39 NDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMK   74 (74)
T ss_dssp             CCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHHTCCC
T ss_pred             cccccccCCCCccCCCccccchHhhHHHHHHcCCcC
Confidence            568999999999999999999999999999999985

>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=98.88  E-value=2e-10  Score=79.57  Aligned_cols=41  Identities=51%  Similarity=1.040  Sum_probs=37.1

Q ss_pred             CCceeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505        205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ  245 (312)
Q Consensus       205 ~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (312)
                      .+..|.||++.++|+||||.+|++|++||+|+|.....+.+
T Consensus         4 ~~~~C~VC~~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~c   44 (84)
T d1dszb_           4 TKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTC   44 (84)
T ss_dssp             CCEECTTTCCEESSEETTEECCHHHHHHHHHHHHHTCCCCC
T ss_pred             CCCcCccCCCcCCccCCCHHHHHHhHHHHHHHHhcCCCeec
Confidence            35689999999999999999999999999999998887743

>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=98.83  E-value=4.7e-10  Score=81.01  Aligned_cols=38  Identities=53%  Similarity=1.076  Sum_probs=34.3

Q ss_pred             ceeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505        207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR  244 (312)
Q Consensus       207 ~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (312)
                      +.|.|||+.++|+|||+.+|+||++||+|++.....++
T Consensus         2 ~~C~VCg~~a~g~HfGv~sC~aCkaFFRR~v~~~~~~~   39 (103)
T d2nllb_           2 ELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPS   39 (103)
T ss_dssp             CBCTTTCSBCCSEETTEECCHHHHHHHHHHHHTTCGGG
T ss_pred             CcCccCCCcCCcccCchhhhHHHHHHhHHHhhccccce
Confidence            57999999999999999999999999999998765553

>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=98.82  E-value=4.6e-10  Score=77.59  Aligned_cols=38  Identities=53%  Similarity=1.153  Sum_probs=34.7

Q ss_pred             ceeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505        207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR  244 (312)
Q Consensus       207 ~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (312)
                      +.|.||++.++|+||||.+|++|++||+|++.....|.
T Consensus         1 e~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~   38 (83)
T d2hanb1           1 ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYC   38 (83)
T ss_dssp             CBCTTTCSBCCEEETTEEECHHHHHHHHHHHHTTCCCC
T ss_pred             CcCccCCCcCCccCcCHHhHhHhHHHHHHHHhcCCcee
Confidence            47999999999999999999999999999998777663

>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=98.81  E-value=4.9e-10  Score=75.68  Aligned_cols=39  Identities=49%  Similarity=1.037  Sum_probs=35.4

Q ss_pred             CceeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505        206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR  244 (312)
Q Consensus       206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (312)
                      ...|.||++.++|+||||.+|++|++||+|++.....+.
T Consensus         2 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~   40 (74)
T d1r4ia_           2 QKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYL   40 (74)
T ss_dssp             CCBCSSSCSBEEEEETTEEEEHHHHHHHHHHHTSCCCCC
T ss_pred             CCcCccCCCcCCccCCCHHhhHHHHHHHHHHHhccccee
Confidence            467999999999999999999999999999998777664

>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=98.81  E-value=6e-10  Score=78.04  Aligned_cols=39  Identities=44%  Similarity=1.037  Sum_probs=35.5

Q ss_pred             ceeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505        207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ  245 (312)
Q Consensus       207 ~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (312)
                      +.|.|||+.++|+||||.+|++|++||+|++.....+.+
T Consensus         1 r~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~c   39 (89)
T d1kb2a_           1 RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTC   39 (89)
T ss_dssp             CBCTTTCSBCCSEETTEECCHHHHHHHHHHHHTTCCCCC
T ss_pred             CCCeeCCCcCCccCCCHHHHHHHHHHHHHHHhcCCCeec
Confidence            479999999999999999999999999999988877743

>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=98.75  E-value=8.9e-10  Score=75.23  Aligned_cols=37  Identities=68%  Similarity=1.350  Sum_probs=34.1

Q ss_pred             eeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505        208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR  244 (312)
Q Consensus       208 ~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (312)
                      +|.||++.++|+||||.+|++|++||+|++.....++
T Consensus         2 iC~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~   38 (78)
T d1a6ya_           2 LCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYK   38 (78)
T ss_dssp             BCTTTSSBCCEEETTEEECHHHHHHHHHHHSSCCCCC
T ss_pred             CCeeCCCcCCcccCcchhhhhchhhhhhhhccCCcee
Confidence            6999999999999999999999999999998776664

>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=98.74  E-value=1.2e-09  Score=73.78  Aligned_cols=39  Identities=64%  Similarity=1.168  Sum_probs=35.3

Q ss_pred             CceeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505        206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR  244 (312)
Q Consensus       206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (312)
                      ...|.||++.++|+|||+.+|++|++||+|++.....+.
T Consensus         4 ~~~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~   42 (74)
T d1hcqa_           4 TRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYM   42 (74)
T ss_dssp             CCBCTTTCSBCCEEETTEEECHHHHHHHHHHHSSCCCCC
T ss_pred             CCCCccCCCcCCceEcCeeehHHHHHHHHHHHHcccccc
Confidence            356999999999999999999999999999998777764

>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=98.73  E-value=1.2e-09  Score=73.08  Aligned_cols=37  Identities=59%  Similarity=1.139  Sum_probs=34.2

Q ss_pred             eeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505        208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR  244 (312)
Q Consensus       208 ~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (312)
                      -|.||++.++|+||||.+|++|++||+|++.....+.
T Consensus         2 ~C~VC~~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~   38 (71)
T d1lata_           2 PCLVCSDEASGCHYGVLTCEGCKAFFKRAVEGQHNYL   38 (71)
T ss_dssp             BCTTTCSBCCEEETTEEECHHHHHHHHHHHHSCCCCC
T ss_pred             cCeeCCCcCCceEcCHhhHHHHHHHHHHHHhcCccee
Confidence            5899999999999999999999999999998777774

>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=98.69  E-value=2.2e-09  Score=72.63  Aligned_cols=37  Identities=54%  Similarity=1.162  Sum_probs=34.1

Q ss_pred             eeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505        209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ  245 (312)
Q Consensus       209 c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (312)
                      |.||++.++|+||||.+|++|++||+|++.....+.+
T Consensus         2 C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~c   38 (75)
T d1dsza_           2 CFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTC   38 (75)
T ss_dssp             CTTTCSCCCSEETTEECCHHHHHHHHHHHHTTCCCCC
T ss_pred             CccCCCcCCccCcCHHHhhhhHHHHHHHHhcCCceec
Confidence            8899999999999999999999999999988777744

>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=98.66  E-value=3.3e-09  Score=74.31  Aligned_cols=39  Identities=79%  Similarity=1.424  Sum_probs=35.5

Q ss_pred             CceeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505        206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR  244 (312)
Q Consensus       206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (312)
                      ...|.|||+.++++|||+.+|++|++||+|++.....+.
T Consensus         4 ~~~C~VCg~~~~~~hyG~~sC~aC~~FFRR~v~~~~~~~   42 (90)
T d1lo1a_           4 KRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYS   42 (90)
T ss_dssp             CCEETTTTEECSEESSSSEECHHHHHHHHHHHHTTCCCC
T ss_pred             CCcCCcCCCcCCceEcCeeechhhHHHHHHHHhcCCccc
Confidence            567999999999999999999999999999997777663

>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=98.66  E-value=3.3e-09  Score=74.27  Aligned_cols=37  Identities=59%  Similarity=1.089  Sum_probs=34.3

Q ss_pred             ceeeeeCCCCcccccccccchhHHHHHHHHhhhcccc
Q psy11505        207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY  243 (312)
Q Consensus       207 ~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  243 (312)
                      +.|.||++.++|+||||.+|++|++||+|++.....+
T Consensus         1 g~C~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~   37 (89)
T d1cita_           1 GRCAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKY   37 (89)
T ss_dssp             CCCSSSCCCCCEEETTEEECHHHHHHHHHHHHHTCCC
T ss_pred             CCCeECCCcCCccCCCcccchhhHHHHHHHHHcCCce
Confidence            4699999999999999999999999999999877776