Psyllid ID: psy16825

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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---
Protein Sequence
DGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEDLERNTEISCTQVIDRLEHVAVSKEEYYFLKALVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLR
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccHHHHHHcccccEEEccccccccccccccccccHHHHHHHHHHccccHHHcccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHccccHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccccccccEEccccccEEcEEccccEEcHHHHHHHHHHHHHccccccccccccccccccccccHHHHHHHHHHccccHHHcccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHcccccccEcccccccccccccccHHHHHHHHHcHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
dgikeeelprrlclvcgdvasgfhyGVASCEACKAFFKRTIqgnieytcpasndceiNKRRRKACQACRFQKCLRKGmlkegvrldrvrggrqkyrrnpdllsqqwppnksipsledlernteiSCTQVIDRLEHVAVSKEEYYFLKALVLANSDVKLDEFSSLKKFRNSILSSLgdciyvlr
Flexible Loop (DISEMBL)
dgikeeelprrLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIeytcpasndceiNKRRRKACQACrfqkclrkgmlkegvrldrvrggrqkyrrnpdllsqqwppnksipsledlerNTEISCTQVIDRLEHVAVSKEEYYFLKALVLANSDVKLDEfsslkkfrnsilsslgdciyvlr
Low Complexity Region (SEG)
DGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEDLERNTEISCTQVIDRLEHVAVSKEEYYFLKALVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLR
Disordered region (IsUnstruct)
*********RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV*********************************TEISCTQVIDRLEHVAVSKEEYYFLKALVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVL*
Disordered Region (DISOPRED)
************CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGML**************************************************************************************KFRNSILSSLGDCIYVLR
Disordered Region (DISEMBL)
DGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEDLERNTEISCTQVIDRLEHVAVSKEEYYFLKALVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLR
Disordered Region (DISPRO)
*******LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGML******************************************TEISCTQVIDRLEHVAVSKEEYYFLKALVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLR
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
DGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEDLERNTEISCTQVIDRLEHVAVSKEEYYFLKALVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLR
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	183	2.2.26 [Sep-21-2011]
Q6QMY5	422	Steroid hormone receptor	yes	N/A	0.540	0.234	0.83	1e-46
P11474	423	Steroid hormone receptor	yes	N/A	0.508	0.219	0.872	2e-46
Q5QJV7	422	Steroid hormone receptor	yes	N/A	0.508	0.220	0.872	2e-46
O08580	422	Steroid hormone receptor	yes	N/A	0.508	0.220	0.872	2e-46
P11475	433	Steroid hormone receptor	no	N/A	0.562	0.237	0.761	4e-45
Q5RAM2	435	Estrogen-related receptor	no	N/A	0.502	0.211	0.838	4e-45
P62510	458	Estrogen-related receptor	no	N/A	0.502	0.200	0.838	5e-45
P62509	458	Estrogen-related receptor	no	N/A	0.502	0.200	0.838	5e-45
P62508	458	Estrogen-related receptor	no	N/A	0.502	0.200	0.838	5e-45
O95718	508	Steroid hormone receptor	no	N/A	0.562	0.202	0.761	6e-45

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

 Score =  185 bits (470), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 83/100 (83%), Positives = 92/100 (92%)

Query: 8   LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
           LP+RLCLVCGDVASG+HYGVASCEACKAFFKRTIQG+IEY+CPASN+CEI KRRRKACQA
Sbjct: 74  LPKRLCLVCGDVASGYHYGVASCEACKAFFKRTIQGSIEYSCPASNECEITKRRRKACQA 133

Query: 68  CRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWP 107
           CRF KCLR GMLKEGVRLDRVRGGRQKY+R P++    +P
Sbjct: 134 CRFTKCLRVGMLKEGVRLDRVRGGRQKYKRRPEVDPLPFP 173

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

 Score =  185 bits (469), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 82/94 (87%), Positives = 90/94 (95%)

Query: 8   LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
           LP+RLCLVCGDVASG+HYGVASCEACKAFFKRTIQG+IEY+CPASN+CEI KRRRKACQA
Sbjct: 74  LPKRLCLVCGDVASGYHYGVASCEACKAFFKRTIQGSIEYSCPASNECEITKRRRKACQA 133

Query: 68  CRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL 101
           CRF KCLR GMLKEGVRLDRVRGGRQKY+R P++
Sbjct: 134 CRFTKCLRVGMLKEGVRLDRVRGGRQKYKRRPEV 167

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)

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

 Score =  185 bits (469), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 82/94 (87%), Positives = 90/94 (95%)

Query: 8   LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
           LP+RLCLVCGDVASG+HYGVASCEACKAFFKRTIQG+IEY+CPASN+CEI KRRRKACQA
Sbjct: 74  LPKRLCLVCGDVASGYHYGVASCEACKAFFKRTIQGSIEYSCPASNECEITKRRRKACQA 133

Query: 68  CRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL 101
           CRF KCLR GMLKEGVRLDRVRGGRQKY+R P++
Sbjct: 134 CRFTKCLRVGMLKEGVRLDRVRGGRQKYKRRPEV 167

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 =  185 bits (469), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 82/94 (87%), Positives = 90/94 (95%)

Query: 8   LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
           LP+RLCLVCGDVASG+HYGVASCEACKAFFKRTIQG+IEY+CPASN+CEI KRRRKACQA
Sbjct: 74  LPKRLCLVCGDVASGYHYGVASCEACKAFFKRTIQGSIEYSCPASNECEITKRRRKACQA 133

Query: 68  CRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL 101
           CRF KCLR GMLKEGVRLDRVRGGRQKY+R P++
Sbjct: 134 CRFTKCLRVGMLKEGVRLDRVRGGRQKYKRRPEV 167

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

 Score =  180 bits (457), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 83/109 (76%), Positives = 94/109 (86%), Gaps = 6/109 (5%)

Query: 8   LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
           +P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQGNIEY+CPA+N+CEI KRRRK+CQA
Sbjct: 98  IPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQA 157

Query: 68  CRFQKCLRKGMLKEGVRLDRVRGGRQKYRR------NPDLLSQQWPPNK 110
           CRF KCL+ GMLKEGVRLDRVRGGRQKY+R      +P L  Q  PP K
Sbjct: 158 CRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRLDSENSPYLSLQISPPAK 206

Nuclear receptor, may regulate ESR1 transcriptional activity.

Rattus norvegicus (taxid: 10116)

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

 Score =  180 bits (457), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 78/93 (83%), Positives = 88/93 (94%)

Query: 8   LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
           +P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQGNIEY+CPA+N+CEI KRRRK+CQA
Sbjct: 100 MPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQA 159

Query: 68  CRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPD 100
           CRF KCL+ GMLKEGVRLDRVRGGRQKY+R  D
Sbjct: 160 CRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRID 192

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

 Score =  180 bits (456), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 78/93 (83%), Positives = 88/93 (94%)

Query: 8   LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
           +P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQGNIEY+CPA+N+CEI KRRRK+CQA
Sbjct: 123 MPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQA 182

Query: 68  CRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPD 100
           CRF KCL+ GMLKEGVRLDRVRGGRQKY+R  D
Sbjct: 183 CRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRID 215

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 =  180 bits (456), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 78/93 (83%), Positives = 88/93 (94%)

Query: 8   LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
           +P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQGNIEY+CPA+N+CEI KRRRK+CQA
Sbjct: 123 MPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQA 182

Query: 68  CRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPD 100
           CRF KCL+ GMLKEGVRLDRVRGGRQKY+R  D
Sbjct: 183 CRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRID 215

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 =  180 bits (456), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 78/93 (83%), Positives = 88/93 (94%)

Query: 8   LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
           +P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQGNIEY+CPA+N+CEI KRRRK+CQA
Sbjct: 123 MPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQA 182

Query: 68  CRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPD 100
           CRF KCL+ GMLKEGVRLDRVRGGRQKY+R  D
Sbjct: 183 CRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRID 215

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

 Score =  179 bits (455), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 83/109 (76%), Positives = 94/109 (86%), Gaps = 6/109 (5%)

Query: 8   LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
           +P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQGNIEY+CPA+N+CEI KRRRK+CQA
Sbjct: 98  IPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQA 157

Query: 68  CRFQKCLRKGMLKEGVRLDRVRGGRQKYRR------NPDLLSQQWPPNK 110
           CRF KCL+ GMLKEGVRLDRVRGGRQKY+R      +P L  Q  PP K
Sbjct: 158 CRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRLDSESSPYLSLQISPPAK 206

Nuclear receptor, may regulate ESR1 transcriptional activity.

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	183
242021609	448	retinoid X receptor, putative [Pediculus	0.628	0.256	0.830	8e-52
213513284	415	estrogen-related receptor [Tribolium cas	0.546	0.240	0.92	2e-49
345496190	438	PREDICTED: steroid hormone receptor ERR2	0.612	0.255	0.822	2e-49
259906648	401	estrogen receptor-like protein [Teleogry	0.524	0.239	0.958	4e-49
109689232	505	estrogen receptor-related receptor homol	0.535	0.194	0.949	5e-49
345496188	450	PREDICTED: steroid hormone receptor ERR2	0.590	0.24	0.831	6e-49
170053275	446	estrogen-related receptor [Culex quinque	0.644	0.264	0.798	6e-49
158301679	507	AGAP001743-PA [Anopheles gambiae str. PE	0.535	0.193	0.949	7e-49
307201567	426	Steroid hormone receptor ERR2 [Harpegnat	0.612	0.262	0.822	8e-49
157136394	447	estrogen-related receptor (ERR) [Aedes a	0.535	0.219	0.939	8e-49

>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 =  208 bits (529), Expect = 8e-52,   Method: Compositional matrix adjust.
 Identities = 98/118 (83%), Positives = 104/118 (88%), Gaps = 3/118 (2%)

Query: 3   IKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRR 62
           I+E++LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPA+NDCEINKRRR
Sbjct: 106 IREDDLPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPAANDCEINKRRR 165

Query: 63  KACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL---LSQQWPPNKSIPSLED 117
           KACQACRFQKCLR GMLKEGVRLDRVRGGRQKYRRN D    +    P    +PSLED
Sbjct: 166 KACQACRFQKCLRMGMLKEGVRLDRVRGGRQKYRRNTDTPYQIHSMLPLKPYLPSLED 223

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|213513284|ref|NP_001135406.1| estrogen-related receptor [Tribolium castaneum] gi|270011014|gb|EFA07462.1| estrogen-related receptor [Tribolium castaneum]

 Score =  200 bits (509), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 92/100 (92%), Positives = 96/100 (96%)

Query: 1   DGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKR 60
           D +KEE+ PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPAS +CEINKR
Sbjct: 87  DEMKEEDSPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASGECEINKR 146

Query: 61  RRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPD 100
           RRKACQACRF+KCLR GMLKEGVRLDRVRGGRQKYRRNPD
Sbjct: 147 RRKACQACRFRKCLRSGMLKEGVRLDRVRGGRQKYRRNPD 186

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  200 bits (509), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 97/118 (82%), Positives = 107/118 (90%), Gaps = 6/118 (5%)

Query: 1   DGIKEEEL-PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINK 59
           DG+KEE++ PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPA+ +CEINK
Sbjct: 100 DGVKEEDMMPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPANGECEINK 159

Query: 60  RRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLED 117
           RRRKACQACRFQKCLR+GMLKEGVRLDRVRGGRQKYRR+ D     + P K+I +LED
Sbjct: 160 RRRKACQACRFQKCLRQGMLKEGVRLDRVRGGRQKYRRSTD----PYVPGKTI-TLED 212

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  199 bits (506), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 92/96 (95%), Positives = 93/96 (96%)

Query: 9   PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQAC 68
           PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPA+NDCEINKRRRKACQAC
Sbjct: 67  PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPAANDCEINKRRRKACQAC 126

Query: 69  RFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQ 104
           RFQKCLR GMLKEGVRLDRVRGGRQKYRRNPDL  Q
Sbjct: 127 RFQKCLRMGMLKEGVRLDRVRGGRQKYRRNPDLPYQ 162

Source: Teleogryllus emma

Species: Teleogryllus emma

Genus: Teleogryllus

Family: Gryllidae

Order: Orthoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|109689232|dbj|BAE96770.1| estrogen receptor-related receptor homolog [Anopheles stephensi]

 Score =  199 bits (505), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 94/99 (94%), Positives = 95/99 (95%), Gaps = 1/99 (1%)

Query: 1   DGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKR 60
           D IKEE LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKR
Sbjct: 108 DTIKEE-LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKR 166

Query: 61  RRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNP 99
           RRKACQACRF+KCL  GMLKEGVRLDRVRGGRQKYRRNP
Sbjct: 167 RRKACQACRFRKCLLMGMLKEGVRLDRVRGGRQKYRRNP 205

Source: Anopheles stephensi

Species: Anopheles stephensi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  198 bits (504), Expect = 6e-49,   Method: Compositional matrix adjust.
 Identities = 94/113 (83%), Positives = 103/113 (91%), Gaps = 5/113 (4%)

Query: 1   DGIKEEEL-PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINK 59
           DG+KEE++ PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPA+ +CEINK
Sbjct: 100 DGVKEEDMMPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPANGECEINK 159

Query: 60  RRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSI 112
           RRRKACQACRFQKCLR+GMLKEGVRLDRVRGGRQKYRR+ D     + P K+I
Sbjct: 160 RRRKACQACRFQKCLRQGMLKEGVRLDRVRGGRQKYRRSTD----PYVPGKTI 208

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170053275|ref|XP_001862599.1| estrogen-related receptor [Culex quinquefasciatus] gi|167873854|gb|EDS37237.1| estrogen-related receptor [Culex quinquefasciatus]

 Score =  198 bits (504), Expect = 6e-49,   Method: Compositional matrix adjust.
 Identities = 99/124 (79%), Positives = 104/124 (83%), Gaps = 6/124 (4%)

Query: 1   DGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKR 60
           D IKEE +PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKR
Sbjct: 71  DAIKEE-IPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKR 129

Query: 61  RRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNP-----DLLSQQWPPNKSIPSL 115
           RRKACQACRF+KCL  GMLKEGVRLDRVRGGRQKYRRNP      L   Q     +  SL
Sbjct: 130 RRKACQACRFRKCLLMGMLKEGVRLDRVRGGRQKYRRNPCTNPYQLQLTQSNSQYTAQSL 189

Query: 116 EDLE 119
           ED++
Sbjct: 190 EDIK 193

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|158301679|ref|XP_321343.4| AGAP001743-PA [Anopheles gambiae str. PEST] gi|157012589|gb|EAA00848.5| AGAP001743-PA [Anopheles gambiae str. PEST]

 Score =  198 bits (504), Expect = 7e-49,   Method: Compositional matrix adjust.
 Identities = 94/99 (94%), Positives = 95/99 (95%), Gaps = 1/99 (1%)

Query: 1   DGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKR 60
           D IKEE LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKR
Sbjct: 106 DTIKEE-LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKR 164

Query: 61  RRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNP 99
           RRKACQACRF+KCL  GMLKEGVRLDRVRGGRQKYRRNP
Sbjct: 165 RRKACQACRFRKCLLMGMLKEGVRLDRVRGGRQKYRRNP 203

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  198 bits (504), Expect = 8e-49,   Method: Compositional matrix adjust.
 Identities = 97/118 (82%), Positives = 106/118 (89%), Gaps = 6/118 (5%)

Query: 1   DGIKEEEL-PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINK 59
           DG+KEE++ PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPA+ +CEINK
Sbjct: 89  DGVKEEDMMPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPANGECEINK 148

Query: 60  RRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLED 117
           RRRKACQACRFQKCLR+GMLKEGVRLDRVRGGRQKYRR+ D     + P KS  +LED
Sbjct: 149 RRRKACQACRFQKCLRQGMLKEGVRLDRVRGGRQKYRRSTD----PYTPVKST-TLED 201

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157136394|ref|XP_001663736.1| estrogen-related receptor (ERR) [Aedes aegypti] gi|108869963|gb|EAT34188.1| AAEL013546-PA [Aedes aegypti]

 Score =  198 bits (503), Expect = 8e-49,   Method: Compositional matrix adjust.
 Identities = 93/99 (93%), Positives = 95/99 (95%), Gaps = 1/99 (1%)

Query: 1   DGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKR 60
           D IKEE +PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKR
Sbjct: 78  DAIKEE-IPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKR 136

Query: 61  RRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNP 99
           RRKACQACRF+KCL  GMLKEGVRLDRVRGGRQKYRRNP
Sbjct: 137 RRKACQACRFRKCLLMGMLKEGVRLDRVRGGRQKYRRNP 175

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	183
UNIPROTKB|F1MBX3	422	ESRRA "Uncharacterized protein	0.513	0.222	0.872	2.6e-51
UNIPROTKB|F1PFF7	613	ESRRA "Steroid hormone recepto	0.513	0.153	0.872	2.6e-51
UNIPROTKB|Q6QMY5	422	ESRRA "Steroid hormone recepto	0.513	0.222	0.872	2.6e-51
UNIPROTKB|F1RQP2	422	ESRRA "Uncharacterized protein	0.513	0.222	0.872	2.6e-51
MGI|MGI:1346831	422	Esrra "estrogen related recept	0.513	0.222	0.872	2.6e-51
RGD|1583866	422	Esrra "estrogen related recept	0.513	0.222	0.872	2.6e-51
UNIPROTKB|F1N0K9	478	LOC100852315 "Uncharacterized	0.508	0.194	0.838	2e-49
UNIPROTKB|E2QSQ7	441	ESRRB "Uncharacterized protein	0.508	0.210	0.838	2e-49
UNIPROTKB|F6V776	438	ESRRB "Uncharacterized protein	0.508	0.212	0.838	2e-49
UNIPROTKB|E7EWD9	508	ESRRB "Steroid hormone recepto	0.508	0.183	0.838	2e-49

UNIPROTKB|F1MBX3 ESRRA "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 462 (167.7 bits), Expect = 2.6e-51, Sum P(2) = 2.6e-51
 Identities = 82/94 (87%), Positives = 90/94 (95%)

Query:     8 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
             LP+RLCLVCGDVASG+HYGVASCEACKAFFKRTIQG+IEY+CPASN+CEI KRRRKACQA
Sbjct:    74 LPKRLCLVCGDVASGYHYGVASCEACKAFFKRTIQGSIEYSCPASNECEITKRRRKACQA 133

Query:    68 CRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL 101
             CRF KCLR GMLKEGVRLDRVRGGRQKY+R P++
Sbjct:   134 CRFTKCLRVGMLKEGVRLDRVRGGRQKYKRRPEV 167

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

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

GO:0005634 "nucleus" evidence=IEA

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

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

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005496 "steroid binding" evidence=IEA

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

UNIPROTKB|F1PFF7 ESRRA "Steroid hormone receptor ERR1" [Canis lupus familiaris (taxid:9615)]

 Score = 462 (167.7 bits), Expect = 2.6e-51, Sum P(2) = 2.6e-51
 Identities = 82/94 (87%), Positives = 90/94 (95%)

Query:     8 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
             LP+RLCLVCGDVASG+HYGVASCEACKAFFKRTIQG+IEY+CPASN+CEI KRRRKACQA
Sbjct:   265 LPKRLCLVCGDVASGYHYGVASCEACKAFFKRTIQGSIEYSCPASNECEITKRRRKACQA 324

Query:    68 CRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL 101
             CRF KCLR GMLKEGVRLDRVRGGRQKY+R P++
Sbjct:   325 CRFTKCLRVGMLKEGVRLDRVRGGRQKYKRRPEV 358

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

GO:0005634 "nucleus" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005496 "steroid binding" evidence=IEA

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

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

UNIPROTKB|Q6QMY5 ESRRA "Steroid hormone receptor ERR1" [Canis lupus familiaris (taxid:9615)]

 Score = 462 (167.7 bits), Expect = 2.6e-51, Sum P(2) = 2.6e-51
 Identities = 82/94 (87%), Positives = 90/94 (95%)

Query:     8 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
             LP+RLCLVCGDVASG+HYGVASCEACKAFFKRTIQG+IEY+CPASN+CEI KRRRKACQA
Sbjct:    74 LPKRLCLVCGDVASGYHYGVASCEACKAFFKRTIQGSIEYSCPASNECEITKRRRKACQA 133

Query:    68 CRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL 101
             CRF KCLR GMLKEGVRLDRVRGGRQKY+R P++
Sbjct:   134 CRFTKCLRVGMLKEGVRLDRVRGGRQKYKRRPEV 167

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005496 "steroid binding" evidence=IEA

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

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

UNIPROTKB|F1RQP2 ESRRA "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 462 (167.7 bits), Expect = 2.6e-51, Sum P(2) = 2.6e-51
 Identities = 82/94 (87%), Positives = 90/94 (95%)

Query:     8 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
             LP+RLCLVCGDVASG+HYGVASCEACKAFFKRTIQG+IEY+CPASN+CEI KRRRKACQA
Sbjct:    74 LPKRLCLVCGDVASGYHYGVASCEACKAFFKRTIQGSIEYSCPASNECEITKRRRKACQA 133

Query:    68 CRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL 101
             CRF KCLR GMLKEGVRLDRVRGGRQKY+R P++
Sbjct:   134 CRFTKCLRVGMLKEGVRLDRVRGGRQKYKRRPEV 167

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

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

GO:0005634 "nucleus" evidence=IEA

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

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

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005496 "steroid binding" evidence=IEA

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

MGI|MGI:1346831 Esrra "estrogen related receptor, alpha" [Mus musculus (taxid:10090)]

 Score = 462 (167.7 bits), Expect = 2.6e-51, Sum P(2) = 2.6e-51
 Identities = 82/94 (87%), Positives = 90/94 (95%)

Query:     8 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
             LP+RLCLVCGDVASG+HYGVASCEACKAFFKRTIQG+IEY+CPASN+CEI KRRRKACQA
Sbjct:    74 LPKRLCLVCGDVASGYHYGVASCEACKAFFKRTIQGSIEYSCPASNECEITKRRRKACQA 133

Query:    68 CRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL 101
             CRF KCLR GMLKEGVRLDRVRGGRQKY+R P++
Sbjct:   134 CRFTKCLRVGMLKEGVRLDRVRGGRQKYKRRPEV 167

GO:0003677 "DNA binding" evidence=IDA

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

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

GO:0005496 "steroid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0030278 "regulation of ossification" evidence=ISO

GO:0042127 "regulation of cell proliferation" evidence=ISO

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

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

GO:0045667 "regulation of osteoblast differentiation" evidence=ISO

GO:0045670 "regulation of osteoclast differentiation" evidence=ISO

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

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

GO:0046872 "metal ion binding" evidence=IEA

GO:0051216 "cartilage development" evidence=ISO

RGD|1583866 Esrra "estrogen related receptor, alpha" [Rattus norvegicus (taxid:10116)]

 Score = 462 (167.7 bits), Expect = 2.6e-51, Sum P(2) = 2.6e-51
 Identities = 82/94 (87%), Positives = 90/94 (95%)

Query:     8 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
             LP+RLCLVCGDVASG+HYGVASCEACKAFFKRTIQG+IEY+CPASN+CEI KRRRKACQA
Sbjct:    74 LPKRLCLVCGDVASGYHYGVASCEACKAFFKRTIQGSIEYSCPASNECEITKRRRKACQA 133

Query:    68 CRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL 101
             CRF KCLR GMLKEGVRLDRVRGGRQKY+R P++
Sbjct:   134 CRFTKCLRVGMLKEGVRLDRVRGGRQKYKRRPEV 167

GO:0003677 "DNA binding" evidence=ISO

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

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

GO:0005496 "steroid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;ISO

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0030278 "regulation of ossification" evidence=IMP

GO:0042127 "regulation of cell proliferation" evidence=IMP

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

GO:0045667 "regulation of osteoblast differentiation" evidence=IMP

GO:0045670 "regulation of osteoclast differentiation" evidence=IMP

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

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

GO:0051216 "cartilage development" evidence=IMP

UNIPROTKB|F1N0K9 LOC100852315 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 449 (163.1 bits), Expect = 2.0e-49, Sum P(2) = 2.0e-49
 Identities = 78/93 (83%), Positives = 88/93 (94%)

Query:     8 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
             +P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQGNIEY+CPA+N+CEI KRRRK+CQA
Sbjct:   143 IPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQA 202

Query:    68 CRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPD 100
             CRF KCL+ GMLKEGVRLDRVRGGRQKY+R  D
Sbjct:   203 CRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRLD 235

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

GO:0019827 "stem cell maintenance" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=IEA

GO:0001892 "embryonic placenta development" evidence=IEA

GO:0001834 "trophectodermal cell proliferation" evidence=IEA

GO:0001831 "trophectodermal cellular morphogenesis" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005496 "steroid binding" evidence=IEA

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

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

UNIPROTKB|E2QSQ7 ESRRB "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 449 (163.1 bits), Expect = 2.0e-49, Sum P(2) = 2.0e-49
 Identities = 78/93 (83%), Positives = 88/93 (94%)

Query:     8 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
             +P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQGNIEY+CPA+N+CEI KRRRK+CQA
Sbjct:    98 IPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQA 157

Query:    68 CRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPD 100
             CRF KCL+ GMLKEGVRLDRVRGGRQKY+R  D
Sbjct:   158 CRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRLD 190

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

GO:0005634 "nucleus" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005496 "steroid binding" evidence=IEA

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

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

UNIPROTKB|F6V776 ESRRB "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 449 (163.1 bits), Expect = 2.0e-49, Sum P(2) = 2.0e-49
 Identities = 78/93 (83%), Positives = 88/93 (94%)

Query:     8 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
             +P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQGNIEY+CPA+N+CEI KRRRK+CQA
Sbjct:   103 IPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQA 162

Query:    68 CRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPD 100
             CRF KCL+ GMLKEGVRLDRVRGGRQKY+R  D
Sbjct:   163 CRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRLD 195

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

GO:0005634 "nucleus" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005496 "steroid binding" evidence=IEA

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

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

UNIPROTKB|E7EWD9 ESRRB "Steroid hormone receptor ERR2" [Homo sapiens (taxid:9606)]

 Score = 449 (163.1 bits), Expect = 2.0e-49, Sum P(2) = 2.0e-49
 Identities = 78/93 (83%), Positives = 88/93 (94%)

Query:     8 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
             +P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQGNIEY+CPA+N+CEI KRRRK+CQA
Sbjct:   103 IPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQA 162

Query:    68 CRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPD 100
             CRF KCL+ GMLKEGVRLDRVRGGRQKY+R  D
Sbjct:   163 CRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRLD 195

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

---

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)
P11474	ERR1_HUMAN	No assigned EC number	0.8723	0.5081	0.2198	yes	N/A
Q6QMY5	ERR1_CANFA	No assigned EC number	0.83	0.5409	0.2345	yes	N/A
Q19345	NHR25_CAEEL	No assigned EC number	0.5476	0.4590	0.1468	yes	N/A
O08580	ERR1_MOUSE	No assigned EC number	0.8723	0.5081	0.2203	yes	N/A
Q5QJV7	ERR1_RAT	No assigned EC number	0.8723	0.5081	0.2203	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	183
cd07170	97	cd07170, NR_DBD_ERR, DNA-binding domain of estroge	2e-61
cd07155	75	cd07155, NR_DBD_ER_like, DNA-binding domain of est	7e-44
cd06916	72	cd06916, NR_DBD_like, DNA-binding domain of nuclea	5e-41
pfam00105	70	pfam00105, zf-C4, Zinc finger, C4 type (two domain	1e-38
cd07167	93	cd07167, NR_DBD_Lrh-1_like, The DNA-binding domain	1e-37
cd07171	82	cd07171, NR_DBD_ER, DNA-binding domain of estrogen	1e-35
cd06961	85	cd06961, NR_DBD_TR, DNA-binding domain of thyroid	8e-34
smart00399	70	smart00399, ZnF_C4, c4 zinc finger in nuclear horm	1e-32
cd07168	90	cd07168, NR_DBD_DHR4_like, DNA-binding domain of e	1e-32
cd06960	76	cd06960, NR_DBD_HNF4A, DNA-binding domain of hepto	1e-30
cd06969	75	cd06969, NR_DBD_NGFI-B, DNA-binding domain of the	7e-30
cd06964	85	cd06964, NR_DBD_RAR, DNA-binding domain of retinoi	1e-28
cd06967	87	cd06967, NR_DBD_TR2_like, DNA-binding domain of th	4e-28
cd07169	90	cd07169, NR_DBD_GCNF_like, DNA-binding domain of G	1e-27
cd07156	72	cd07156, NR_DBD_VDR_like, The DNA-binding domain o	1e-27
cd06956	77	cd06956, NR_DBD_RXR, DNA-binding domain of retinoi	1e-26
cd07179	74	cd07179, 2DBD_NR_DBD2, The second DNA-binding doma	3e-26
cd07158	73	cd07158, NR_DBD_Ppar_like, The DNA-binding domain	1e-25
cd07166	89	cd07166, NR_DBD_REV_ERB, DNA-binding domain of REV	1e-25
cd07172	78	cd07172, NR_DBD_GR_PR, DNA-binding domain of gluco	2e-25
cd07165	81	cd07165, NR_DBD_DmE78_like, DNA-binding domain of	2e-25
cd07164	78	cd07164, NR_DBD_PNR_like_1, DNA-binding domain of	3e-25
cd06965	84	cd06965, NR_DBD_Ppar, DNA-binding domain of peroxi	3e-25
cd06968	95	cd06968, NR_DBD_ROR, DNA-binding domain of Retinoi	1e-23
cd06958	73	cd06958, NR_DBD_COUP_TF, DNA-binding domain of chi	2e-23
cd07173	82	cd07173, NR_DBD_AR, DNA-binding domain of androgen	7e-23
cd07157	86	cd07157, 2DBD_NR_DBD1, The first DNA-binding domai	1e-22
cd06963	73	cd06963, NR_DBD_GR_like, The DNA binding domain of	2e-22
cd06966	94	cd06966, NR_DBD_CAR, DNA-binding domain of constit	6e-22
cd06959	73	cd06959, NR_DBD_EcR_like, The DNA-binding domain o	8e-22
cd06955	107	cd06955, NR_DBD_VDR, DNA-binding domain of vitamin	1e-21
cd07154	73	cd07154, NR_DBD_PNR_like, The DNA-binding domain o	1e-21
cd07162	87	cd07162, NR_DBD_PXR, DNA-binding domain of pregnan	1e-21
cd07160	101	cd07160, NR_DBD_LXR, DNA-binding domain of Liver X	1e-20
cd07161	91	cd07161, NR_DBD_EcR, DNA-binding domain of Ecdyson	2e-20
cd07163	92	cd07163, NR_DBD_TLX, DNA-binding domain of Tailles	2e-20
cd06970	92	cd06970, NR_DBD_PNR, DNA-binding domain of the pho	4e-20
cd06962	84	cd06962, NR_DBD_FXR, DNA-binding domain of Farneso	7e-20
cd06957	82	cd06957, NR_DBD_PNR_like_2, DNA-binding domain of	1e-19
cd06946	221	cd06946, NR_LBD_ERR, The ligand binding domain of	4e-15
cd07068	221	cd07068, NR_LBD_ER_like, The ligand binding domain	4e-12
cd06930	165	cd06930, NR_LBD_F2, Ligand-binding domain of nucle	8e-05

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

 Score =  185 bits (470), Expect = 2e-61
 Identities = 78/93 (83%), Positives = 87/93 (93%)

Query: 9   PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQAC 68
           P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQGNIEY+CPA+N+CEI KRRRK+CQAC
Sbjct: 3   PKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQAC 62

Query: 69  RFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL 101
           RF KCL+ GMLKEGVRLDRVRGGRQKY+R  D 
Sbjct: 63  RFMKCLKVGMLKEGVRLDRVRGGRQKYKRRIDA 95

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

>gnl|CDD|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 =  139 bits (353), Expect = 7e-44
 Identities = 59/75 (78%), Positives = 72/75 (96%)

Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQK 72
          CLVCGD+ASG+HYGVASCEACKAFFKRTIQGN+ Y+CP++++CE++K+RRK+CQACR QK
Sbjct: 1  CLVCGDIASGYHYGVASCEACKAFFKRTIQGNLGYSCPSTSECEVDKKRRKSCQACRLQK 60

Query: 73 CLRKGMLKEGVRLDR 87
          CL+ GMLKEGVRLDR
Sbjct: 61 CLKVGMLKEGVRLDR 75

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

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

 Score =  132 bits (335), Expect = 5e-41
 Identities = 45/72 (62%), Positives = 55/72 (76%)

Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQK 72
          C VCGD ASG+HYGV +CE CK FF+R+++ N+EYTCPA  +C I+KR R  CQACR +K
Sbjct: 1  CAVCGDKASGYHYGVLTCEGCKGFFRRSVRRNLEYTCPAGGNCVIDKRNRNRCQACRLKK 60

Query: 73 CLRKGMLKEGVR 84
          CL  GM KE VR
Sbjct: 61 CLAVGMRKEAVR 72

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

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

 Score =  126 bits (319), Expect = 1e-38
 Identities = 44/70 (62%), Positives = 51/70 (72%)

Query: 11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRF 70
           LC VCGD ASG+HYGV +CE CK FF+R+IQ NI YTCP + DC I+KR R  CQ CR 
Sbjct: 1  ELCKVCGDKASGYHYGVLTCEGCKGFFRRSIQKNIVYTCPFNKDCVIDKRNRNRCQYCRL 60

Query: 71 QKCLRKGMLK 80
          +KCL  GM K
Sbjct: 61 KKCLEVGMSK 70

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

>gnl|CDD|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 =  124 bits (313), Expect = 1e-37
 Identities = 48/84 (57%), Positives = 60/84 (71%)

Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQK 72
          C VCGD  SG+HYG+ +CE+CK FFKRT+Q    YTC  + +C+I+K +RK C  CRFQK
Sbjct: 1  CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKRYTCIENQNCQIDKTQRKRCPYCRFQK 60

Query: 73 CLRKGMLKEGVRLDRVRGGRQKYR 96
          CL  GM  E VR DR+RGGR K+ 
Sbjct: 61 CLSVGMKLEAVRADRMRGGRNKFG 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|143545 cd07171, NR_DBD_ER, DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers

 Score =  119 bits (299), Expect = 1e-35
 Identities = 48/81 (59%), Positives = 59/81 (72%)

Query: 9  PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQAC 68
              C VC D ASG+HYGV SCE CKAFFKR+IQG+ +Y CPA+N C I+K RRK+CQAC
Sbjct: 2  DTHFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQAC 61

Query: 69 RFQKCLRKGMLKEGVRLDRVR 89
          R +KC   GM+K G+R +R  
Sbjct: 62 RLRKCYEVGMMKGGIRRERRG 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|143519 cd06961, NR_DBD_TR, DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers

 Score =  114 bits (288), Expect = 8e-34
 Identities = 41/83 (49%), Positives = 55/83 (66%)

Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQ 71
           C+VCGD A+G+HY   +CE CK FF+RT+Q  + Y+C     CEI+K  R  CQ CRF+
Sbjct: 1  PCVVCGDKATGYHYRCITCEGCKGFFRRTVQKKLSYSCKGEGKCEIDKVTRNQCQECRFK 60

Query: 72 KCLRKGMLKEGVRLDRVRGGRQK 94
          KC+  GM K+ V  DR RG ++K
Sbjct: 61 KCIAVGMAKDLVLDDRKRGAKRK 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|197701 smart00399, ZnF_C4, c4 zinc finger in nuclear hormone receptors

 Score =  111 bits (280), Expect = 1e-32
 Identities = 42/70 (60%), Positives = 49/70 (70%)

Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQ 71
          LC VCGD ASGFH+GV SC ACKAFF+RT+    +Y C   N+C INKR R  C+ACR +
Sbjct: 1  LCCVCGDHASGFHFGVCSCRACKAFFRRTVNLRYKYRCDRKNNCSINKRYRCRCRACRLK 60

Query: 72 KCLRKGMLKE 81
          KCL  GM  E
Sbjct: 61 KCLGVGMDPE 70

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 =  111 bits (280), Expect = 1e-32
 Identities = 46/90 (51%), Positives = 59/90 (65%)

Query: 5  EEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKA 64
          +E+   +LC +C D A+G HYG+ +CE CK FFKRT+Q    YTC     CEI K +R  
Sbjct: 1  DEDESPKLCSICEDKATGLHYGIITCEGCKGFFKRTVQNKRVYTCVGDGRCEITKAQRNR 60

Query: 65 CQACRFQKCLRKGMLKEGVRLDRVRGGRQK 94
          CQ CRF+KC+RKGM+   VR DR+ GGR  
Sbjct: 61 CQYCRFRKCIRKGMMLAAVREDRMPGGRNS 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|143518 cd06960, NR_DBD_HNF4A, DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers

 Score =  106 bits (266), Expect = 1e-30
 Identities = 38/76 (50%), Positives = 51/76 (67%)

Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQK 72
          C VCGD A+G HYGV SC  CK FF+R+++ N  YTC    +C ++K +R AC+ CRF+K
Sbjct: 1  CAVCGDRATGKHYGVLSCNGCKGFFRRSVRKNRTYTCRFGGNCVVDKDKRNACRYCRFKK 60

Query: 73 CLRKGMLKEGVRLDRV 88
          CL  GM  E V+ +R 
Sbjct: 61 CLEVGMDPEAVQNERD 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|143527 cd06969, NR_DBD_NGFI-B, DNA-binding domain of the orphan nuclear receptor, nerve growth factor-induced-B

 Score =  104 bits (261), Expect = 7e-30
 Identities = 45/73 (61%), Positives = 55/73 (75%)

Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQ 71
          LC VCGD A+  HYGV +CE CK FFKRT+Q N +Y C A+ +C ++KRRR  CQ CRFQ
Sbjct: 2  LCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQ 61

Query: 72 KCLRKGMLKEGVR 84
          KCL+ GM+KE VR
Sbjct: 62 KCLQVGMVKEVVR 74

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

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

 Score =  101 bits (253), Expect = 1e-28
 Identities = 43/77 (55%), Positives = 52/77 (67%)

Query: 11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRF 70
          + C VC D +SG+HYGV++CE CK FF+R+IQ N+ YTC    +C INK  R  CQ CR 
Sbjct: 5  KPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRL 64

Query: 71 QKCLRKGMLKEGVRLDR 87
          QKC   GM KE VR DR
Sbjct: 65 QKCFEVGMSKESVRNDR 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|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 =  100 bits (250), Expect = 4e-28
 Identities = 45/80 (56%), Positives = 53/80 (66%)

Query: 8  LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
           P  LC+VCGD ASG HYG  SCE CK FFKR+I+ N+ Y+C  S DC INK  R  CQ 
Sbjct: 1  QPVELCVVCGDKASGRHYGAVSCEGCKGFFKRSIRKNLGYSCRGSKDCVINKHHRNRCQY 60

Query: 68 CRFQKCLRKGMLKEGVRLDR 87
          CR QKCL  GM  + V+ +R
Sbjct: 61 CRLQKCLAMGMKSDSVQCER 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|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 = 99.2 bits (247), Expect = 1e-27
 Identities = 40/84 (47%), Positives = 55/84 (65%)

Query: 11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRF 70
          R CL+CGD A+G HYG+ SCE CK FFKR+I     Y C    +C +++++R  CQ CR 
Sbjct: 7  RTCLICGDRATGLHYGIISCEGCKGFFKRSICNKRVYRCSRDKNCVMSRKQRNRCQYCRL 66

Query: 71 QKCLRKGMLKEGVRLDRVRGGRQK 94
           KCL+ GM ++ +R D + GGR K
Sbjct: 67 LKCLQMGMNRKAIREDGMPGGRNK 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|143531 cd07156, NR_DBD_VDR_like, The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers

 Score = 98.2 bits (245), Expect = 1e-27
 Identities = 36/69 (52%), Positives = 48/69 (69%)

Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQK 72
          C VCGD A+G+H+   +CE CK FF+R+++    +TCP + DCEI K  R+ CQACR +K
Sbjct: 1  CGVCGDRATGYHFNAMTCEGCKGFFRRSMKRKARFTCPFNGDCEITKDNRRHCQACRLKK 60

Query: 73 CLRKGMLKE 81
          CL  GM KE
Sbjct: 61 CLDIGMKKE 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|143514 cd06956, NR_DBD_RXR, DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers

 Score = 96.1 bits (239), Expect = 1e-26
 Identities = 43/76 (56%), Positives = 56/76 (73%)

Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQ 71
          +C +CGD ASG HYGV SCE CK FFKRT++ ++ YTC  + DC I+KR+R  CQ CR+Q
Sbjct: 2  ICAICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQ 61

Query: 72 KCLRKGMLKEGVRLDR 87
          KCL  GM +E V+ +R
Sbjct: 62 KCLAMGMKREAVQEER 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|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 = 95.3 bits (237), Expect = 3e-26
 Identities = 35/73 (47%), Positives = 46/73 (63%)

Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQK 72
          C VCG  +SGFH+G  +CE CK FF+RT   +  Y CP   +C I    R AC++CRF++
Sbjct: 1  CRVCGGKSSGFHFGALTCEGCKGFFRRTELSSNSYVCPGGQNCAITPATRNACKSCRFRR 60

Query: 73 CLRKGMLKEGVRL 85
          CL  GM K G R+
Sbjct: 61 CLAVGMSKTGSRI 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|143533 cd07158, NR_DBD_Ppar_like, The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family

 Score = 93.8 bits (233), Expect = 1e-25
 Identities = 42/73 (57%), Positives = 48/73 (65%), Gaps = 1/73 (1%)

Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYT-CPASNDCEINKRRRKACQACRFQ 71
          C VCGD ASGFHYGV SCE CK FF+RTIQ N+ Y  C     C I ++ R  CQ CRF+
Sbjct: 1  CKVCGDKASGFHYGVHSCEGCKGFFRRTIQHNLTYRRCLNGGKCVIQRKNRNRCQYCRFK 60

Query: 72 KCLRKGMLKEGVR 84
          KCL  GM +  VR
Sbjct: 61 KCLSVGMSRNAVR 73

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

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

 Score = 94.2 bits (234), Expect = 1e-25
 Identities = 42/78 (53%), Positives = 52/78 (66%), Gaps = 1/78 (1%)

Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEY-TCPASNDCEINKRRRKACQACRF 70
          LC VCGD ASGFHYGV +CE CK FF+R+IQ  I+Y  C  +  C I +  R  CQ CRF
Sbjct: 5  LCKVCGDKASGFHYGVHACEGCKGFFRRSIQQKIQYRKCTKNETCSIMRINRNRCQYCRF 64

Query: 71 QKCLRKGMLKEGVRLDRV 88
          +KCL  GM ++ VR  R+
Sbjct: 65 KKCLAVGMSRDAVRFGRI 82

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

 Score = 93.4 bits (232), Expect = 2e-25
 Identities = 40/77 (51%), Positives = 51/77 (66%)

Query: 9  PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQAC 68
          P+++CLVC D ASG HYGV +C +CK FFKR ++G   Y C   NDC I+K RRK C AC
Sbjct: 1  PQKICLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPAC 60

Query: 69 RFQKCLRKGMLKEGVRL 85
          R +KCL+ GM     + 
Sbjct: 61 RLRKCLQAGMNLGARKT 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|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 = 93.0 bits (231), Expect = 2e-25
 Identities = 44/77 (57%), Positives = 51/77 (66%)

Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQK 72
          C VCGD ASG+HYGV SCE CK FF+R+IQ  IEY C     CEI +  R  CQ CRF+K
Sbjct: 1  CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYRCLRDGKCEIIRLNRNRCQYCRFKK 60

Query: 73 CLRKGMLKEGVRLDRVR 89
          CL  GM K+ VR  R+ 
Sbjct: 61 CLAAGMSKDSVRYGRIP 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|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 = 92.9 bits (231), Expect = 3e-25
 Identities = 38/75 (50%), Positives = 52/75 (69%)

Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQK 72
          C VCGD ASG HYGV SC+ C+ FFKR+I+ N+ Y C  +  C ++  RR  CQACRF+K
Sbjct: 1  CRVCGDRASGKHYGVPSCDGCRGFFKRSIRRNLAYVCKENGSCVVDVARRNQCQACRFKK 60

Query: 73 CLRKGMLKEGVRLDR 87
          CL+  M ++ V+ +R
Sbjct: 61 CLQVNMNRDAVQHER 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|143523 cd06965, NR_DBD_Ppar, DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers

 Score = 92.5 bits (230), Expect = 3e-25
 Identities = 42/78 (53%), Positives = 51/78 (65%), Gaps = 3/78 (3%)

Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEY-TCPASNDCEINKRRRKACQACRF 70
           C VCGD ASGFHYGV +CE CK FF+RTI+  + Y  C  S  C+I+K+ R  CQ CRF
Sbjct: 1  ECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLVYKPCDLS--CKIHKKSRNKCQYCRF 58

Query: 71 QKCLRKGMLKEGVRLDRV 88
          QKCL  GM    +R  R+
Sbjct: 59 QKCLNVGMSHNAIRFGRM 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|143526 cd06968, NR_DBD_ROR, DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers

 Score = 89.1 bits (221), Expect = 1e-23
 Identities = 37/78 (47%), Positives = 51/78 (65%)

Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQK 72
          C +CGD +SG HYGV +CE CK FF+R+ Q N+ Y+CP   +C I++  R  CQ CR QK
Sbjct: 8  CKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVSYSCPRQKNCLIDRTNRNRCQHCRLQK 67

Query: 73 CLRKGMLKEGVRLDRVRG 90
          CL  GM ++ V+  R+  
Sbjct: 68 CLALGMSRDAVKFGRMSK 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|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 = 88.0 bits (218), Expect = 2e-23
 Identities = 36/72 (50%), Positives = 52/72 (72%)

Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQK 72
          C+VCGD +SG HYG  +CE CK+FFKR+++ N+ YTC  + +C I++  R  CQ CR +K
Sbjct: 1  CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRGNRNCPIDQHHRNQCQYCRLKK 60

Query: 73 CLRKGMLKEGVR 84
          CL+ GM +E V+
Sbjct: 61 CLKVGMRREAVQ 72

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

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

 Score = 86.9 bits (215), Expect = 7e-23
 Identities = 38/81 (46%), Positives = 52/81 (64%)

Query: 9  PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQAC 68
          P++ CL+CGD ASG HYG  +C +CK FFKR  +G  +Y C + NDC I+K RRK C +C
Sbjct: 2  PQKTCLICGDEASGCHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSC 61

Query: 69 RFQKCLRKGMLKEGVRLDRVR 89
          R +KC   GM     +L ++ 
Sbjct: 62 RLRKCFEAGMTLGARKLKKLG 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|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 = 86.0 bits (213), Expect = 1e-22
 Identities = 36/78 (46%), Positives = 44/78 (56%), Gaps = 2/78 (2%)

Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNI--EYTCPASNDCEINKRRRKACQACRF 70
          C VCG+ A+GFH+G   CEACK FF R+          CP    C I+K+ R  CQACR+
Sbjct: 3  CQVCGEPAAGFHHGAYVCEACKKFFMRSSNAISFTISECPNGGKCIIDKKNRTKCQACRY 62

Query: 71 QKCLRKGMLKEGVRLDRV 88
          +KCL  GM   G R  R 
Sbjct: 63 RKCLNVGMSLGGPRYGRR 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|143521 cd06963, NR_DBD_GR_like, The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers

 Score = 85.4 bits (211), Expect = 2e-22
 Identities = 39/73 (53%), Positives = 47/73 (64%)

Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQK 72
          CL+CGD ASG HYGV +C +CK FFKR  +G   Y C   NDC I+K RRK C ACR +K
Sbjct: 1  CLICGDEASGCHYGVLTCGSCKVFFKRAAEGQHNYLCAGRNDCIIDKIRRKNCPACRLRK 60

Query: 73 CLRKGMLKEGVRL 85
          C + GM     +L
Sbjct: 61 CYQAGMTLGARKL 73

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

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

 Score = 84.4 bits (209), Expect = 6e-22
 Identities = 34/71 (47%), Positives = 45/71 (63%)

Query: 11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRF 70
          ++C VCGD A G+++   +CE+CKAFF+R    N E+ CP +  CEIN   R+ CQ CR 
Sbjct: 1  KICGVCGDKALGYNFNAITCESCKAFFRRNALKNKEFKCPFNESCEINVVTRRFCQKCRL 60

Query: 71 QKCLRKGMLKE 81
           KC   GM KE
Sbjct: 61 DKCFAIGMKKE 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|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 = 83.6 bits (207), Expect = 8e-22
 Identities = 35/70 (50%), Positives = 44/70 (62%)

Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQ 71
           C+VCGD ASGFHYGV SCE CK FF+R++     Y C   N CE++   R+ CQ CR +
Sbjct: 1  NCVVCGDKASGFHYGVLSCEGCKGFFRRSVTKGAVYACKFGNKCEMDMYMRRKCQECRLR 60

Query: 72 KCLRKGMLKE 81
          KC   GM  +
Sbjct: 61 KCKAAGMRPD 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|143513 cd06955, NR_DBD_VDR, DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers

 Score = 84.6 bits (209), Expect = 1e-21
 Identities = 36/76 (47%), Positives = 52/76 (68%)

Query: 11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRF 70
          R+C VCGD A+GFH+   +CE CK FF+R+++    +TCP + DC I K  R+ CQACR 
Sbjct: 7  RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRL 66

Query: 71 QKCLRKGMLKEGVRLD 86
          ++C+  GM+KE +  D
Sbjct: 67 KRCVDIGMMKEFILTD 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|143529 cd07154, NR_DBD_PNR_like, The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family

 Score = 83.4 bits (206), Expect = 1e-21
 Identities = 39/73 (53%), Positives = 50/73 (68%), Gaps = 1/73 (1%)

Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASN-DCEINKRRRKACQACRFQ 71
          C VCGD +SG HYGV +C+ C  FFKR+I+ N+ YTC A N  C ++K RR  CQACR +
Sbjct: 1  CKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNLLYTCKAGNGSCVVDKARRNQCQACRLK 60

Query: 72 KCLRKGMLKEGVR 84
          KCL   M K+ V+
Sbjct: 61 KCLEVSMNKDAVQ 73

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

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

 Score = 83.4 bits (206), Expect = 1e-21
 Identities = 34/70 (48%), Positives = 44/70 (62%)

Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQ 71
          +C VCGD A+G+H+   +CE CK FF+R ++ N    CP    C I K  R+ CQACR +
Sbjct: 1  ICRVCGDRATGYHFNAMTCEGCKGFFRRAMKRNARLCCPFQKGCVITKSNRRQCQACRLR 60

Query: 72 KCLRKGMLKE 81
          KCL  GM KE
Sbjct: 61 KCLSIGMKKE 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|143534 cd07160, NR_DBD_LXR, DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers

 Score = 81.5 bits (201), Expect = 1e-20
 Identities = 33/72 (45%), Positives = 45/72 (62%)

Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQ 71
          +C VCGD ASGFHY V SCE CK FF+R++    +Y C     C+++   R+ CQ CR +
Sbjct: 20 VCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAQYVCKNGGKCQMDMYMRRKCQECRLR 79

Query: 72 KCLRKGMLKEGV 83
          KC   GM ++ V
Sbjct: 80 KCREAGMREQCV 91

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

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

 Score = 80.7 bits (199), Expect = 2e-20
 Identities = 35/75 (46%), Positives = 46/75 (61%)

Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQ 71
          LCLVCGD ASG+HY   +CE CK FF+R++  +  Y C     CE++   R+ CQ CR +
Sbjct: 3  LCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYHCKYGRACEMDMYMRRKCQECRLK 62

Query: 72 KCLRKGMLKEGVRLD 86
          KCL  GM  E V  +
Sbjct: 63 KCLSVGMRPECVVPE 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|143537 cd07163, NR_DBD_TLX, DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers

 Score = 80.6 bits (199), Expect = 2e-20
 Identities = 34/77 (44%), Positives = 49/77 (63%), Gaps = 2/77 (2%)

Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASN--DCEINKRRRKACQACRF 70
          C VCGD +SG HYG+ +C+ C  FFKR+I+ N +Y C +     C ++K  R  C+ACR 
Sbjct: 9  CKVCGDRSSGKHYGIYACDGCSGFFKRSIRRNRQYVCKSKGQGGCPVDKTHRNQCRACRL 68

Query: 71 QKCLRKGMLKEGVRLDR 87
          +KC   GM K+ V+ +R
Sbjct: 69 KKCFEVGMNKDAVQHER 85

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

>gnl|CDD|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 = 80.0 bits (197), Expect = 4e-20
 Identities = 37/80 (46%), Positives = 52/80 (65%), Gaps = 1/80 (1%)

Query: 9  PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPA-SNDCEINKRRRKACQA 67
          P  LC VCGD +SG HYG+ +C  C  FFKR+++  + Y C A +  C ++K  R  CQA
Sbjct: 5  PGLLCRVCGDTSSGKHYGIYACNGCSGFFKRSVRRKLIYRCQAGTGMCPVDKAHRNQCQA 64

Query: 68 CRFQKCLRKGMLKEGVRLDR 87
          CR +KCL+ GM K+ V+ +R
Sbjct: 65 CRLKKCLQAGMNKDAVQNER 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|143520 cd06962, NR_DBD_FXR, DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers

 Score = 78.9 bits (194), Expect = 7e-20
 Identities = 35/70 (50%), Positives = 45/70 (64%)

Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQ 71
          LC+VCGD ASG+HY   +CE CK FF+R+I  N  Y C    +CE++   R+ CQ CR +
Sbjct: 3  LCVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCEMDMYMRRKCQECRLR 62

Query: 72 KCLRKGMLKE 81
          KC   GML E
Sbjct: 63 KCKEMGMLAE 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|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 = 78.7 bits (194), Expect = 1e-19
 Identities = 36/76 (47%), Positives = 47/76 (61%), Gaps = 1/76 (1%)

Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASN-DCEINKRRRKACQACRFQ 71
          C VCGD + G HYGV  C+ C  FFKR+++  I YTC A N +C ++K RR  C  CR Q
Sbjct: 1  CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKGIIYTCIAGNGNCVVDKARRNWCPFCRLQ 60

Query: 72 KCLRKGMLKEGVRLDR 87
          KC   GM +  V+ +R
Sbjct: 61 KCFAVGMNRAAVQEER 76

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

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

 Score = 70.1 bits (172), Expect = 4e-15
 Identities = 21/59 (35%), Positives = 36/59 (61%), Gaps = 1/59 (1%)

Query: 126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVKL-DEFSSLKKFRNSILSSLGDCIYVLR 183
           C Q++ RL+ + + KEEY  LKAL LANSD    ++  ++++ R+++L +L D      
Sbjct: 113 CLQLVRRLQRLRLEKEEYVLLKALALANSDSVHIEDVEAVRQLRDALLEALSDYEAGRH 171

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 = 61.9 bits (151), Expect = 4e-12
 Identities = 20/59 (33%), Positives = 37/59 (62%), Gaps = 1/59 (1%)

Query: 126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVLR 183
             Q++ R   + + +EEY  LKA++LANSDV+ L++  ++++ R++IL +L D      
Sbjct: 113 LLQLVRRFRELGLQREEYVCLKAIILANSDVRHLEDREAVQQLRDAILDALVDVEAKRH 171

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

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

 Score = 40.7 bits (96), Expect = 8e-05
 Identities = 12/51 (23%), Positives = 27/51 (52%), Gaps = 1/51 (1%)

Query: 128 QVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGD 177
           +++ +L  + +  +EY  LKA+VL N D+  L     +++ +     +L +
Sbjct: 89  ELLSKLRSLQLDPKEYACLKAIVLFNPDLPGLKNQQQVEELQEKAQQALQE 139

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	183
KOG4215|consensus	432		100.0
KOG4217|consensus	605		100.0
KOG4216|consensus	479		100.0
KOG4218|consensus	475		100.0
cd07170	97	NR_DBD_ERR DNA-binding domain of estrogen related	100.0
cd06961	85	NR_DBD_TR DNA-binding domain of thyroid hormone re	99.98
cd06964	85	NR_DBD_RAR DNA-binding domain of retinoic acid rec	99.98
cd07160	101	NR_DBD_LXR DNA-binding domain of Liver X receptors	99.98
cd07168	90	NR_DBD_DHR4_like DNA-binding domain of ecdysone-in	99.97
cd06967	87	NR_DBD_TR2_like DNA-binding domain of the TR2 and	99.97
cd06956	77	NR_DBD_RXR DNA-binding domain of retinoid X recept	99.97
cd06970	92	NR_DBD_PNR DNA-binding domain of the photoreceptor	99.97
cd06957	82	NR_DBD_PNR_like_2 DNA-binding domain of the photor	99.97
cd07171	82	NR_DBD_ER DNA-binding domain of estrogen receptors	99.97
cd07163	92	NR_DBD_TLX DNA-binding domain of Tailless (TLX) is	99.97
cd07169	90	NR_DBD_GCNF_like DNA-binding domain of Germ cell n	99.97
cd07155	75	NR_DBD_ER_like DNA-binding domain of estrogen rece	99.97
cd07166	89	NR_DBD_REV_ERB DNA-binding domain of REV-ERB recep	99.97
cd07165	81	NR_DBD_DmE78_like DNA-binding domain of Drosophila	99.97
cd07164	78	NR_DBD_PNR_like_1 DNA-binding domain of the photor	99.97
cd07167	93	NR_DBD_Lrh-1_like The DNA-binding domain of Lrh-1	99.97
cd07161	91	NR_DBD_EcR DNA-binding domain of Ecdysone receptor	99.97
cd06962	84	NR_DBD_FXR DNA-binding domain of Farnesoid X recep	99.97
cd06960	76	NR_DBD_HNF4A DNA-binding domain of heptocyte nucle	99.97
cd06969	75	NR_DBD_NGFI-B DNA-binding domain of the orphan nuc	99.97
cd06968	95	NR_DBD_ROR DNA-binding domain of Retinoid-related	99.97
cd07179	74	2DBD_NR_DBD2 The second DNA-binding domain (DBD) o	99.97
cd06966	94	NR_DBD_CAR DNA-binding domain of constitutive andr	99.97
KOG4846|consensus	538		99.97
cd07172	78	NR_DBD_GR_PR DNA-binding domain of glucocorticoid	99.97
cd07156	72	NR_DBD_VDR_like The DNA-binding domain of vitamin	99.97
cd06958	73	NR_DBD_COUP_TF DNA-binding domain of chicken ovalb	99.97
cd07173	82	NR_DBD_AR DNA-binding domain of androgen receptor	99.97
cd06959	73	NR_DBD_EcR_like The DNA-binding domain of Ecdysone	99.97
cd06965	84	NR_DBD_Ppar DNA-binding domain of peroxisome proli	99.97
cd06963	73	NR_DBD_GR_like The DNA binding domain of GR_like n	99.97
cd07154	73	NR_DBD_PNR_like The DNA-binding domain of the phot	99.97
cd07157	86	2DBD_NR_DBD1 The first DNA-binding domain (DBD) of	99.97
cd06955	107	NR_DBD_VDR DNA-binding domain of vitamin D recepto	99.97
cd06916	72	NR_DBD_like DNA-binding domain of nuclear receptor	99.97
cd07162	87	NR_DBD_PXR DNA-binding domain of pregnane X recept	99.97
cd07158	73	NR_DBD_Ppar_like The DNA-binding domain of peroxis	99.97
smart00399	70	ZnF_C4 c4 zinc finger in nuclear hormone receptors	99.96
PF00105	70	zf-C4: Zinc finger, C4 type (two domains); InterPr	99.95
cd07076	247	NR_LBD_GR Ligand binding domain of the glucocortic	99.44
cd06934	226	NR_LBD_PXR_like The ligand binding domain of xenob	99.4
cd06937	231	NR_LBD_RAR The ligand binding domain (LBD) of reti	99.4
cd06940	189	NR_LBD_REV_ERB The ligand binding domain of REV-ER	99.39
cd06935	243	NR_LBD_TR The ligand binding domain of thyroid hor	99.39
cd07073	246	NR_LBD_AR Ligand binding domain of the nuclear rec	99.37
cd06939	241	NR_LBD_ROR_like The ligand binding domain of Retin	99.36
cd06933	238	NR_LBD_VDR The ligand binding domain of vitamin D	99.36
cd07349	222	NR_LBD_SHP The ligand binding domain of DAX1 prote	99.35
cd07069	241	NR_LBD_Lrh-1 The ligand binding domain of the live	99.35
cd06947	246	NR_LBD_GR_Like Ligand binding domain of nuclear ho	99.35
cd06932	259	NR_LBD_PPAR The ligand binding domain of peroxisom	99.35
cd07070	237	NR_LBD_SF-1 The ligand binding domain of nuclear r	99.35
cd06950	206	NR_LBD_Tlx_PNR_like The ligand binding domain of T	99.34
cd06951	222	NR_LBD_Dax1_like The ligand binding domain of DAX1	99.33
cd07348	238	NR_LBD_NGFI-B The ligand binding domain of Nurr1,	99.33
cd07075	248	NR_LBD_MR Ligand binding domain of the mineralocor	99.33
cd06954	236	NR_LBD_LXR The ligand binding domain of Liver X re	99.32
cd06953	213	NR_LBD_DHR4_like The ligand binding domain of orph	99.31
cd06941	195	NR_LBD_DmE78_like The ligand binding domain of Dro	99.31
cd06936	221	NR_LBD_Fxr The ligand binding domain of Farnesoid	99.3
cd06945	239	NR_LBD_Nurr1_like The ligand binding domain of Nur	99.29
cd07074	248	NR_LBD_PR Ligand binding domain of the progesteron	99.28
cd07071	238	NR_LBD_Nurr1 The ligand binding domain of Nurr1, a	99.28
cd06943	207	NR_LBD_RXR_like The ligand binding domain of the r	99.27
cd06944	237	NR_LBD_Ftz-F1_like The ligand binding domain of FT	99.26
cd07072	239	NR_LBD_DHR38_like Ligand binding domain of DHR38_l	99.26
cd06949	235	NR_LBD_ER Ligand binding domain of Estrogen recept	99.26
cd06948	236	NR_LBD_COUP-TF Ligand binding domain of chicken ov	99.25
cd06946	221	NR_LBD_ERR The ligand binding domain of estrogen r	99.23
cd06929	174	NR_LBD_F1 Ligand-binding domain of nuclear recepto	99.22
cd06930	165	NR_LBD_F2 Ligand-binding domain of nuclear recepto	99.18
cd07068	221	NR_LBD_ER_like The ligand binding domain of estrog	99.16
cd06942	191	NR_LBD_Sex_1_like The ligand binding domain of Cae	99.15
cd07350	232	NR_LBD_Dax1 The ligand binding domain of DAX1 prot	99.14
cd06938	231	NR_LBD_EcR The ligand binding domain (LBD) of the	99.12
cd06952	222	NR_LBD_TR2_like The ligand binding domain of the o	99.11
cd06931	222	NR_LBD_HNF4_like The ligand binding domain of hept	98.98
cd06157	168	NR_LBD The ligand binding domain of nuclear recept	98.69
smart00430	163	HOLI Ligand binding domain of hormone receptors.	98.67
PF00104	203	Hormone_recep: Ligand-binding domain of nuclear ho	98.07
PF01412	116	ArfGap: Putative GTPase activating protein for Arf	89.51

>KOG4215|consensus

Probab=100.00  E-value=3.7e-51  Score=323.82  Aligned_cols=173  Identities=34%  Similarity=0.661  Sum_probs=152.7

Q ss_pred             CCCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeeccc
Q psy16825          9 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV   88 (183)
Q Consensus         9 ~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~   88 (183)
                      ....|.||||++.|.|||+.+|+||||||||+|.++..|+|+.+.+|.|||+.|+.||+|||+||+++||+++|||.+|+
T Consensus        18 ~~~~CaICGDkaTGKHYGA~SCdGCKGFFRRSVrk~~~YtCRF~k~C~VDKdkRNaCRyCRfqKC~~aGMK~eAiQnERD   97 (432)
T KOG4215|consen   18 VAEFCAICGDKATGKHYGAISCDGCKGFFRRSVRKNHQYTCRFNKQCVVDKDKRNACRYCRFQKCVRAGMKREAIQNERD   97 (432)
T ss_pred             ccchhheeCCcccccccceeecCcchHHHHHHHHhcceeeeeccccccccchhhhhhhHhhHHHHHHhcccHHhhhcccc
Confidence            34679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccccccCCCCC--CC---------------------------CC---CC------------------------CCCCC
Q psy16825         89 RGGRQKYRRNPDL--LS---------------------------QQ---WP------------------------PNKSI  112 (183)
Q Consensus        89 ~~~~~~~~~~~~~--~~---------------------------~~---~~------------------------~~k~i  112 (183)
                      +.+.++.......  .+                           .+   -+                        |.|.+
T Consensus        98 rIg~Rr~~~~~~n~~~~~id~L~~aE~~~~q~~~srs~~~~~~~~d~r~~~~n~~~at~~Dv~eSm~qqLlllVEWAK~i  177 (432)
T KOG4215|consen   98 RIGSRRPSYEAGNENSPSIDALVQAEALVRQLRSSRSGGVPGIDGDIRQGPPNKKIATENDVCESMKQQLLLLVEWAKYI  177 (432)
T ss_pred             cccccCCCCCCCCCCchhHHHHHhHHHHHhhhhccccccCcCcchhhhcCccccccccHHHHHHHHHHHHHHHHHHHHhc
Confidence            9877654433211  00                           00   00                        11889


Q ss_pred             CCccccccccc--------------------------------------------------chhhhhhhhchhcccChhH
Q psy16825        113 PSLEDLERNTE--------------------------------------------------ISCTQVIDRLEHVAVSKEE  142 (183)
Q Consensus       113 P~f~~L~~~dq--------------------------------------------------~~~~~lv~~~~~l~~~~~E  142 (183)
                      |.|.+++.+||                                                  +++.+++..|++|++|..|
T Consensus       178 ~~F~el~l~DqvaLLk~~a~~hllLg~a~RSm~l~~v~ll~N~~v~~~~~~~~~eis~v~~RIiDElv~Pmr~L~md~~E  257 (432)
T KOG4215|consen  178 PPFCELPLDDQVALLKAHAGQHLLLGAAFRSMHLKDVCLLNNTYVLHRHAPDLPEISRVAPRIIDELVNPMRRLQMDEIE  257 (432)
T ss_pred             cchhcCCchhHHHHHHccchhhhhhhhhhccccccceEEecCceeeccCCCChHHHHHHHHHHHHHHhhHHHHhccchHH
Confidence            99999999999                                                  5678999999999999999


Q ss_pred             HHHHHHHHhcCCCCC-CCchh--HHHHHHHHHHHHHHHHHHh
Q psy16825        143 YYFLKALVLANSDVK-LDEFS--SLKKFRNSILSSLGDCIYV  181 (183)
Q Consensus       143 ~~~lkai~L~~~d~~-L~~~~--~v~~~~~~~~~~L~~~~~~  181 (183)
                      |+|||||+||+||+. |++..  .|++.+++++.+|..||.-
T Consensus       258 y~cLKAi~FfdP~akGis~~s~~~I~~aR~~vl~sLe~yi~d  299 (432)
T KOG4215|consen  258 YVCLKAIAFFDPDAKGLSDPSQIRIREARNRVLKSLEAYISD  299 (432)
T ss_pred             HHHHHHHHhcCccccccCCchHhHHHHHHHHHHHHHHHHHhh
Confidence            999999999999986 99988  8999999999999999964

>KOG4217|consensus

Probab=100.00  E-value=4.2e-40  Score=267.88  Aligned_cols=172  Identities=38%  Similarity=0.699  Sum_probs=149.7

Q ss_pred             CCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecccc
Q psy16825         10 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR   89 (183)
Q Consensus        10 ~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~   89 (183)
                      .+.|.||||.+.-.||||-+|+|||+||+|+|+++..|+|.++.+|.|||..||+||+|||||||+|||-++-|+.+--+
T Consensus       269 e~~CAVCgDnAaCqHYGvRTCEGCKGFFKRTVQKnaKYvClanKnCPVDKRrRnRCQyCRfQKCL~VGMVKEVVRtdSLk  348 (605)
T KOG4217|consen  269 EGLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLAVGMVKEVVRTDSLK  348 (605)
T ss_pred             cceeeecCChHHhhhcCccccccchHHHHHHHhcCCeeEeecCCCCCcchhhhhhchhhhHhHHHHhhhhhhheeccccc
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999999988777


Q ss_pred             cccccccCCCCCCCCC--CCCC----------------------------------------------------------
Q psy16825         90 GGRQKYRRNPDLLSQQ--WPPN----------------------------------------------------------  109 (183)
Q Consensus        90 ~~~~~~~~~~~~~~~~--~~~~----------------------------------------------------------  109 (183)
                      +++.+....+......  .|+.                                                          
T Consensus       349 GRRGRLpSKpKs~q~sppSpPi~LltalvrAh~Dstp~~~~ldys~~q~~~~~~~~tdA~~vqqfy~lLtgsl~virk~a  428 (605)
T KOG4217|consen  349 GRRGRLPSKPKSRQPSPPSPPISLLTALVRAHVDSTPSTMTLDYSRFQELVPHFSGTDALHVQQFYDLLTGSLEVIRKWA  428 (605)
T ss_pred             cccCCCCCCCCCCCCCCCCCchHHHHHHHHHhhcCCCCcchhhHHHhccccccccccHHHHHHHHHHHhhhhHHHHHHHH
Confidence            7776655444331110  1110                                                          


Q ss_pred             CCCCCccccccccc------------------------------------------------chhhhhhhhchhcccChh
Q psy16825        110 KSIPSLEDLERNTE------------------------------------------------ISCTQVIDRLEHVAVSKE  141 (183)
Q Consensus       110 k~iP~f~~L~~~dq------------------------------------------------~~~~~lv~~~~~l~~~~~  141 (183)
                      ..||+|.+|+..||                                                +.+.+|...+..+++|..
T Consensus       429 ekiPgf~el~paDq~lLlesaflelfvlRlAyRs~~~e~kliFcsG~vlhr~qC~rgfgewidsi~~FS~~l~~l~idi~  508 (605)
T KOG4217|consen  429 EKIPGFAELPPADQDLLLESAFLELFVLRLAYRSNPSEDKLIFCSGLVLHRLQCLRGFGEWIDSIREFSRSLHSLNIDIS  508 (605)
T ss_pred             HhCcCcccCChhhHHHHHHHHHHHHHHHHHHHhcCCCCCeEEEecchhhhHHHHHHHHHHHHHHHHHHHHHhhhchhhHH
Confidence            56999999999999                                                334567888889999999


Q ss_pred             HHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHHHHHHHh
Q psy16825        142 EYYFLKALVLANSDVKLDEFSSLKKFRNSILSSLGDCIYV  181 (183)
Q Consensus       142 E~~~lkai~L~~~d~~L~~~~~v~~~~~~~~~~L~~~~~~  181 (183)
                      -|+||.|+.+..--++|.++..||++|++|+.+|.||+..
T Consensus       509 AfacL~aLa~iTErhGL~epkrVeelqnkIi~~LKDHvt~  548 (605)
T KOG4217|consen  509 AFACLSALALITERHGLKEPKRVEELQNKIINCLKDHVTG  548 (605)
T ss_pred             HHHHHHHHHhhhhhhcCCCcchHHHHHHHHHHHHHHHhhh
Confidence            9999999999998888999999999999999999999853

>KOG4216|consensus

Probab=100.00  E-value=8.9e-39  Score=255.06  Aligned_cols=82  Identities=45%  Similarity=1.053  Sum_probs=78.5

Q ss_pred             cccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecccccc
Q psy16825         12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG   91 (183)
Q Consensus        12 ~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~~~   91 (183)
                      +|.||||.++|.||||++|+|||+||||+-..+..|.|+...+|.||...||+||+||+||||++||.++||.++|+..+
T Consensus        48 PCKiCGDKSSGiHYGVITCEGCKGFFRRSQ~s~a~YsCpRqknC~iDRtnRNRCQ~CRLqKClaLGMSRDAVKFGRMSKK  127 (479)
T KOG4216|consen   48 PCKICGDKSSGIHYGVITCEGCKGFFRRSQQSNANYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSKK  127 (479)
T ss_pred             eeeeccCCCCcceeeeEeeccchHhhhhhhhccccccCCcccCCcccccccchhhHHHHHHHHHhccchhhHHhccccHh
Confidence            59999999999999999999999999999999999999999999999999999999999999999999999999997665


Q ss_pred             cc
Q psy16825         92 RQ   93 (183)
Q Consensus        92 ~~   93 (183)
                      .+
T Consensus       128 QR  129 (479)
T KOG4216|consen  128 QR  129 (479)
T ss_pred             hH
Confidence            54

>KOG4218|consensus

Probab=100.00  E-value=3.5e-37  Score=242.83  Aligned_cols=85  Identities=59%  Similarity=1.193  Sum_probs=81.5

Q ss_pred             CCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecccc
Q psy16825         10 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR   89 (183)
Q Consensus        10 ~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~   89 (183)
                      .+.|.||||+.+|+|||-.+|+.||+||+|+|++++.|.|....+|.|||..|.+|.+|||||||.+||+.+||+.+|++
T Consensus        15 ~ElCPVCGDkVSGYHYGLLTCESCKGFFKRTVQNnK~YtC~e~qnC~iDkTqRKRCP~CRFQKCLtvGMklEAVRADRMR   94 (475)
T KOG4218|consen   15 GELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKQYTCSEEQNCHIDKTQRKRCPSCRFQKCLTVGMKLEAVRADRMR   94 (475)
T ss_pred             ccccccccCccccceeeeeehhhhhhHHHHHhhcCcceecccccccccchHhhccCCchhHHHHhhhhhhHHHHHHhhhc
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccccc
Q psy16825         90 GGRQK   94 (183)
Q Consensus        90 ~~~~~   94 (183)
                      +++.+
T Consensus        95 GGRNK   99 (475)
T KOG4218|consen   95 GGRNK   99 (475)
T ss_pred             ccccc
Confidence            87753

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

Probab=100.00  E-value=4.6e-34  Score=192.37  Aligned_cols=89  Identities=87%  Similarity=1.599  Sum_probs=82.2

Q ss_pred             CCCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeeccc
Q psy16825          9 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV   88 (183)
Q Consensus         9 ~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~   88 (183)
                      +...|.|||++++|+||||++|+||++||||+|..+..|.|..+++|.+++..+..|++|||+|||++||++++||.+|+
T Consensus         3 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~vq~~r~   82 (97)
T cd07170           3 PKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRV   82 (97)
T ss_pred             CCCCCeecCCcCcceEECceeehhhhHHHHHHhccCCceeecCCCccccCcccCccCCccccchhhhcCCCHHHcccccC
Confidence            45679999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccccccccC
Q psy16825         89 RGGRQKYRR   97 (183)
Q Consensus        89 ~~~~~~~~~   97 (183)
                      ..++.+...
T Consensus        83 ~~~~~~~~~   91 (97)
T cd07170          83 RGGRQKYKR   91 (97)
T ss_pred             CCCCCCccC
Confidence            777655443

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

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

Probab=99.98  E-value=6.9e-34  Score=187.77  Aligned_cols=83  Identities=49%  Similarity=1.070  Sum_probs=79.2

Q ss_pred             cccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecccccc
Q psy16825         12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG   91 (183)
Q Consensus        12 ~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~~~   91 (183)
                      +|.|||++++|+||||.+|+||++||||+|..+..|.|..+++|.+++..++.|++|||+||+++||++++||.+|++..
T Consensus         1 ~C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~~   80 (85)
T cd06961           1 PCVVCGDKATGYHYRCITCEGCKGFFRRTVQKKLSYSCKGEGKCEIDKVTRNQCQECRFKKCIAVGMAKDLVLDDRKRGA   80 (85)
T ss_pred             CCceeCCcCcceEEChhhhhhhhHhhHhhhccCCccccCCCCccccCccccccCccchhhhhhhccCCHHHcccccCccc
Confidence            49999999999999999999999999999999999999999999999999999999999999999999999999999887


Q ss_pred             ccc
Q psy16825         92 RQK   94 (183)
Q Consensus        92 ~~~   94 (183)
                      +++
T Consensus        81 ~~~   83 (85)
T cd06961          81 KRK   83 (85)
T ss_pred             ccc
Confidence            654

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

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

Probab=99.98  E-value=1.1e-33  Score=186.63  Aligned_cols=82  Identities=52%  Similarity=1.037  Sum_probs=77.6

Q ss_pred             CCCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeeccc
Q psy16825          9 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV   88 (183)
Q Consensus         9 ~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~   88 (183)
                      ....|.|||++++|+||||.+|+||++||||+|..+..|.|..+++|.+++..+..|++|||+|||++||++++||.+|+
T Consensus         3 ~~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~R~   82 (85)
T cd06964           3 IYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRN   82 (85)
T ss_pred             cCCCCcccCCcCcccEECcceeeeeeeEEeeeecCCCCeECCCCCccccCCcccccCccchhhhhhhhCCCHHHhhcccc
Confidence            34679999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cc
Q psy16825         89 RG   90 (183)
Q Consensus        89 ~~   90 (183)
                      +.
T Consensus        83 ~~   84 (85)
T cd06964          83 KK   84 (85)
T ss_pred             CC
Confidence            63

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

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

Probab=99.98  E-value=2.8e-33  Score=189.69  Aligned_cols=82  Identities=40%  Similarity=0.881  Sum_probs=77.7

Q ss_pred             CCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecccc
Q psy16825         10 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR   89 (183)
Q Consensus        10 ~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~   89 (183)
                      ...|.|||++++|+||||.+|+||++||||+|..+..|.|..+++|.+++..+..|++|||+|||++||++++||.+|++
T Consensus        18 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~~~   97 (101)
T cd07160          18 NEVCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAQYVCKNGGKCQMDMYMRRKCQECRLRKCREAGMREQCVLSEEQI   97 (101)
T ss_pred             CCCCeecCCcCcceEECcceehhhhhhhhhcccccCccccCCCCccccCCcccccCccchhHHHHHhCCCHHHhcChhhh
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999999876


Q ss_pred             cc
Q psy16825         90 GG   91 (183)
Q Consensus        90 ~~   91 (183)
                      ..
T Consensus        98 ~~   99 (101)
T cd07160          98 RL   99 (101)
T ss_pred             hh
Confidence            53

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

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

Probab=99.97  E-value=2.6e-33  Score=186.80  Aligned_cols=85  Identities=53%  Similarity=1.102  Sum_probs=80.1

Q ss_pred             CCCCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecc
Q psy16825          8 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR   87 (183)
Q Consensus         8 ~~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r   87 (183)
                      +....|.|||++++|+||||.+|+||++||||++..+..|.|..+++|.+++..+..|++|||+||+++||++++|+.+|
T Consensus         4 ~~~~~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R   83 (90)
T cd07168           4 ESPKLCSICEDKATGLHYGIITCEGCKGFFKRTVQNKRVYTCVGDGRCEITKAQRNRCQYCRFRKCIRKGMMLAAVREDR   83 (90)
T ss_pred             ccCCCCcccCCcCcceEECceehhhhhHhhhhhhcCCCCccCCCCCCccccccccccccccchhhhhhcCCCHHHhhccc
Confidence            34567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccc
Q psy16825         88 VRGGR   92 (183)
Q Consensus        88 ~~~~~   92 (183)
                      +|+.+
T Consensus        84 ~~~~~   88 (90)
T cd07168          84 MPGGR   88 (90)
T ss_pred             CCCCC
Confidence            98664

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=99.97  E-value=2.2e-33  Score=185.99  Aligned_cols=83  Identities=54%  Similarity=1.056  Sum_probs=78.7

Q ss_pred             CCCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeeccc
Q psy16825          9 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV   88 (183)
Q Consensus         9 ~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~   88 (183)
                      |...|.|||++++|+||||.+|+||++||||++..+..|.|..+++|.+++..+..|++|||+||+++||++++||.+|+
T Consensus         2 ~~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~R~   81 (87)
T cd06967           2 PVELCVVCGDKASGRHYGAVSCEGCKGFFKRSIRKNLGYSCRGSKDCVINKHHRNRCQYCRLQKCLAMGMKSDSVQCERK   81 (87)
T ss_pred             CCCCCeecCCcCCcCEeCcceEeeeeeEeeeeeeCCCCcccCCCCccccCccccccCccchhhhhhHcCCCHHHhccccC
Confidence            45679999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccc
Q psy16825         89 RGG   91 (183)
Q Consensus        89 ~~~   91 (183)
                      +..
T Consensus        82 ~~~   84 (87)
T cd06967          82 PID   84 (87)
T ss_pred             CCC
Confidence            754

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

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

Probab=99.97  E-value=2.4e-33  Score=182.07  Aligned_cols=76  Identities=57%  Similarity=1.167  Sum_probs=73.6

Q ss_pred             cccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecc
Q psy16825         12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR   87 (183)
Q Consensus        12 ~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r   87 (183)
                      .|.|||++++|+||||.+|+||++||||+|..+..|.|+.+++|.+++..++.|++|||+||+++||++++||.+|
T Consensus         2 ~C~VC~~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r   77 (77)
T cd06956           2 ICAICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER   77 (77)
T ss_pred             CCcccCCcCcceEECceeehhHHHHHHHHhhCCCccccCCCCccccCCCccccCccchhHHHhHhCCCHHHhccCC
Confidence            5999999999999999999999999999999999999999999999999999999999999999999999999876

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

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

Probab=99.97  E-value=4.5e-33  Score=185.96  Aligned_cols=84  Identities=44%  Similarity=0.965  Sum_probs=78.2

Q ss_pred             CCCCcccccCCCCcccccccccccchhhhhhccccCCceeecCCC-CCccccccccccccchhhhHHhhhcccccceeec
Q psy16825          8 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPAS-NDCEINKRRRKACQACRFQKCLRKGMLKEGVRLD   86 (183)
Q Consensus         8 ~~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~-~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~   86 (183)
                      .|...|.|||++++|+||||.+|+||++||||+|..+..|.|..+ ++|.+++..+..|++|||+||+++||++++||.+
T Consensus         4 ~p~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~   83 (92)
T cd06970           4 NPGLLCRVCGDTSSGKHYGIYACNGCSGFFKRSVRRKLIYRCQAGTGMCPVDKAHRNQCQACRLKKCLQAGMNKDAVQNE   83 (92)
T ss_pred             CCCCCCeecCCcCcccEECccEEeeeeeEeeeeeecCCCceeecCCCcCccCCCccccCccchhhHhhHhCCCHHHcccc
Confidence            345579999999999999999999999999999999999999885 8999999999999999999999999999999999


Q ss_pred             ccccc
Q psy16825         87 RVRGG   91 (183)
Q Consensus        87 r~~~~   91 (183)
                      |++..
T Consensus        84 R~~~~   88 (92)
T cd06970          84 RQPRN   88 (92)
T ss_pred             cCccc
Confidence            98654

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

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

Probab=99.97  E-value=3.1e-33  Score=183.56  Aligned_cols=80  Identities=43%  Similarity=0.904  Sum_probs=75.7

Q ss_pred             ccccCCCCcccccccccccchhhhhhccccCCceeecC-CCCCccccccccccccchhhhHHhhhcccccceeecccccc
Q psy16825         13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCP-ASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG   91 (183)
Q Consensus        13 C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~-~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~~~   91 (183)
                      |.|||++++|+||||++|+||++||||+|..+..|.|. .+++|.+++..++.|++|||+||+++||++++|+.+|+|..
T Consensus         1 C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~p~~   80 (82)
T cd06957           1 CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKGIIYTCIAGNGNCVVDKARRNWCPFCRLQKCFAVGMNRAAVQEERGPRK   80 (82)
T ss_pred             CCccCccCcceEECcceEeeeeeEEEEeecCCCceEccCccCCCccCCCccCcccCcchhhcccccCCHHHhccccCcCC
Confidence            89999999999999999999999999999999999998 46899999999999999999999999999999999998765


Q ss_pred             c
Q psy16825         92 R   92 (183)
Q Consensus        92 ~   92 (183)
                      +
T Consensus        81 ~   81 (82)
T cd06957          81 L   81 (82)
T ss_pred             C
Confidence            4

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=99.97  E-value=4.1e-33  Score=182.60  Aligned_cols=79  Identities=61%  Similarity=1.244  Sum_probs=75.2

Q ss_pred             CCCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecc
Q psy16825          9 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR   87 (183)
Q Consensus         9 ~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r   87 (183)
                      +...|.|||++++|+||||.+|+||++||||+|..+..|.|..+++|.+++..+..|++|||+|||++||++++|+.+|
T Consensus         2 ~~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~~   80 (82)
T cd07171           2 DTHFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRRER   80 (82)
T ss_pred             CCCCCeecCCcCcceEECceeehhhHHhHHHHeeCCCceeCCCCCccccCCcccccCccchhHHHhHhcCCHHHHHHhh
Confidence            4567999999999999999999999999999999999999999999999999999999999999999999999998876

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

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

Probab=99.97  E-value=4.9e-33  Score=186.22  Aligned_cols=83  Identities=41%  Similarity=0.920  Sum_probs=77.5

Q ss_pred             CCCcccccCCCCcccccccccccchhhhhhccccCCceeecCC--CCCccccccccccccchhhhHHhhhcccccceeec
Q psy16825          9 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPA--SNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLD   86 (183)
Q Consensus         9 ~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~--~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~   86 (183)
                      ....|.|||++++|+||||.+|+||++||||++..+..|.|..  +++|.+++..+..|++|||+||+++||++++||.+
T Consensus         5 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~   84 (92)
T cd07163           5 LDIPCKVCGDRSSGKHYGIYACDGCSGFFKRSIRRNRQYVCKSKGQGGCPVDKTHRNQCRACRLKKCFEVGMNKDAVQHE   84 (92)
T ss_pred             cCCCCcccCCcCcccEECceeeeeeeeEEeeeecCCCCcCCCCCCCCCCccCCCccccCccchhhhhhhhcCCHHHhhcc
Confidence            3567999999999999999999999999999999999999987  47999999999999999999999999999999999


Q ss_pred             ccccc
Q psy16825         87 RVRGG   91 (183)
Q Consensus        87 r~~~~   91 (183)
                      |+|..
T Consensus        85 r~p~~   89 (92)
T cd07163          85 RGPRN   89 (92)
T ss_pred             cCcCC
Confidence            98754

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

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

Probab=99.97  E-value=7.3e-33  Score=184.49  Aligned_cols=84  Identities=46%  Similarity=1.068  Sum_probs=79.6

Q ss_pred             CCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecccc
Q psy16825         10 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR   89 (183)
Q Consensus        10 ~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~   89 (183)
                      ...|.|||++++|+||||++|+||++||||++..+..|.|..+++|.+++..+..|++|||+||+++||++++|+.+|++
T Consensus         6 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~   85 (90)
T cd07169           6 QRTCLICGDRATGLHYGIISCEGCKGFFKRSICNKRVYRCSRDKNCVMSRKQRNRCQYCRLLKCLQMGMNRKAIREDGMP   85 (90)
T ss_pred             CCCCeecCCcCcceEECcceehhhHHHHHHHhcCCCceecCCCCcccccccccccccccchhhhccccCCHHHhccccCC
Confidence            45699999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cccc
Q psy16825         90 GGRQ   93 (183)
Q Consensus        90 ~~~~   93 (183)
                      +.+.
T Consensus        86 ~~~~   89 (90)
T cd07169          86 GGRN   89 (90)
T ss_pred             CCCC
Confidence            7653

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).

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

Probab=99.97  E-value=5.8e-33  Score=179.52  Aligned_cols=75  Identities=79%  Similarity=1.549  Sum_probs=72.7

Q ss_pred             ccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecc
Q psy16825         13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR   87 (183)
Q Consensus        13 C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r   87 (183)
                      |.|||++++|+||||.+|+||++||||++..+..|.|+.+++|.+++..+..|++|||+||+++||++++||.+|
T Consensus         1 C~VC~~~~~g~hygv~sC~aCk~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r   75 (75)
T cd07155           1 CLVCGDIASGYHYGVASCEACKAFFKRTIQGNLGYSCPSTSECEVDKKRRKSCQACRLQKCLKVGMLKEGVRLDR   75 (75)
T ss_pred             CcccCccCcceEEChhhhhhhHHHHHHHhhCCCceeCCcCCCcccCCcccccCccchhhhhhHhCCCHHHcccCC
Confidence            899999999999999999999999999999999999999999999999999999999999999999999999876

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

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

Probab=99.97  E-value=5.2e-33  Score=184.98  Aligned_cols=83  Identities=51%  Similarity=1.064  Sum_probs=78.2

Q ss_pred             CCcccccCCCCcccccccccccchhhhhhccccCCcee-ecCCCCCccccccccccccchhhhHHhhhcccccceeeccc
Q psy16825         10 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEY-TCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV   88 (183)
Q Consensus        10 ~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~-~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~   88 (183)
                      ...|.|||++++|+||||.+|+||++||||+|..+..| .|..+++|.+++..+..|++|||+||+++||++++||.+|+
T Consensus         3 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~   82 (89)
T cd07166           3 VVLCKVCGDKASGFHYGVHACEGCKGFFRRSIQQKIQYRKCTKNETCSIMRINRNRCQYCRFKKCLAVGMSRDAVRFGRI   82 (89)
T ss_pred             CCCCcccCccCcceEEChhhhhhHhhEecceeEcCCcchhhccCCcccccccccccccchhhhhcccccCCHHHhcCCCC
Confidence            35699999999999999999999999999999999999 59999999999999999999999999999999999999998


Q ss_pred             cccc
Q psy16825         89 RGGR   92 (183)
Q Consensus        89 ~~~~   92 (183)
                      |.+.
T Consensus        83 ~~~~   86 (89)
T cd07166          83 PKRE   86 (89)
T ss_pred             CCcc
Confidence            8655

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

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

Probab=99.97  E-value=9e-33  Score=181.06  Aligned_cols=79  Identities=56%  Similarity=1.129  Sum_probs=76.3

Q ss_pred             ccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecccccc
Q psy16825         13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG   91 (183)
Q Consensus        13 C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~~~   91 (183)
                      |.|||++++|+||||.+|+||++||||++..+..|.|..+++|.+++..+..|++|||+|||++||++++||.+|+|++
T Consensus         1 C~VCg~~~~g~hyG~~sC~aC~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~V~~~r~~~~   79 (81)
T cd07165           1 CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYRCLRDGKCEIIRLNRNRCQYCRFKKCLAAGMSKDSVRYGRIPNR   79 (81)
T ss_pred             CCccCccCcceEECchhhhhHHHHHHhHhccCCceeCCCCCCccccccccccccchhhhhcccccCCHHHcccCCCCcc
Confidence            8999999999999999999999999999999999999999999999999999999999999999999999999998854

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,

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

Probab=99.97  E-value=9.7e-33  Score=179.76  Aligned_cols=78  Identities=49%  Similarity=1.070  Sum_probs=75.3

Q ss_pred             ccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeeccccc
Q psy16825         13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG   90 (183)
Q Consensus        13 C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~~   90 (183)
                      |.|||++++|+||||.+|+||++||||++..+..|.|..+++|.+++..+..|++|||+|||++||++++||.+|+|.
T Consensus         1 C~VCg~~~~g~hyG~~~C~~C~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~   78 (78)
T cd07164           1 CRVCGDRASGKHYGVPSCDGCRGFFKRSIRRNLAYVCKENGSCVVDVARRNQCQACRFKKCLQVNMNRDAVQHERAPR   78 (78)
T ss_pred             CcccCccCcceEECcchhhhhhhhhhhhccCCCCccCCCCCcccccCcccccCccchhhhhhHhcCCHHHhccCCCCC
Confidence            899999999999999999999999999999999999999999999999999999999999999999999999999863

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

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

Probab=99.97  E-value=9.6e-33  Score=184.56  Aligned_cols=82  Identities=59%  Similarity=1.187  Sum_probs=77.9

Q ss_pred             ccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeeccccccc
Q psy16825         13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGR   92 (183)
Q Consensus        13 C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~~~~   92 (183)
                      |.|||++++|+||||.+|+||++||||+|..+..|.|+.+++|.+++..++.|++|||+||+++||++++||.+|.++.+
T Consensus         1 C~VCg~~a~g~hyGv~sC~aCk~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~Vq~~r~~~~~   80 (93)
T cd07167           1 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMRGGR   80 (93)
T ss_pred             CcccCccCcceEECchhhhhHHHHHHHHeeCCCccccCCCCccccCccccCcCCCcccchhhhccCCHHHhhhcccCCCc
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999987665


Q ss_pred             cc
Q psy16825         93 QK   94 (183)
Q Consensus        93 ~~   94 (183)
                      .+
T Consensus        81 ~~   82 (93)
T cd07167          81 NK   82 (93)
T ss_pred             cc
Confidence            43

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

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

Probab=99.97  E-value=1e-32  Score=184.07  Aligned_cols=82  Identities=43%  Similarity=0.912  Sum_probs=77.0

Q ss_pred             CcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeeccccc
Q psy16825         11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG   90 (183)
Q Consensus        11 ~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~~   90 (183)
                      ..|.|||++++|+||||.+|+||++||||+|..+..|.|..+++|.+++..+..|++|||+||+++||++++||.+++..
T Consensus         2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~~~   81 (91)
T cd07161           2 ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYHCKYGRACEMDMYMRRKCQECRLKKCLSVGMRPECVVPESQCA   81 (91)
T ss_pred             CCCeeCCCcCcceEECceeehhhHHHHHHHhccCCceecCCCCccccCccccccCccchhhHHhHcCCCHHHcCchhhhh
Confidence            45999999999999999999999999999999999999999999999999999999999999999999999999997654


Q ss_pred             cc
Q psy16825         91 GR   92 (183)
Q Consensus        91 ~~   92 (183)
                      .+
T Consensus        82 ~~   83 (91)
T cd07161          82 IK   83 (91)
T ss_pred             HH
Confidence            44

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

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

Probab=99.97  E-value=1.1e-32  Score=181.40  Aligned_cols=80  Identities=44%  Similarity=0.956  Sum_probs=75.4

Q ss_pred             CcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeeccccc
Q psy16825         11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG   90 (183)
Q Consensus        11 ~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~~   90 (183)
                      ..|.|||++++|+||||++|+||++||||++..+..|.|..+++|.+++..+..|++|||+||+++||++++|+.++...
T Consensus         2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~~~   81 (84)
T cd06962           2 ELCVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCEMDMYMRRKCQECRLRKCKEMGMLAECLLTEIQCK   81 (84)
T ss_pred             CCCeecCCcCcceEECcceeecceeeeeeeeccCCceecCCCCcCccCccccccCccchhhHHHHhCCChHHccCHHHHh
Confidence            35999999999999999999999999999999999999999999999999999999999999999999999999887543

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

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

Probab=99.97  E-value=2.4e-32  Score=177.24  Aligned_cols=76  Identities=50%  Similarity=1.060  Sum_probs=73.5

Q ss_pred             ccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeeccc
Q psy16825         13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV   88 (183)
Q Consensus        13 C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~   88 (183)
                      |.|||++++|+||||.+|+||++||||++..+..|.|..+++|.+++..+..|++|||+|||++||++++|+.+|+
T Consensus         1 C~vCg~~~~~~hygv~~C~aC~~FFrR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~   76 (76)
T cd06960           1 CAVCGDRATGKHYGVLSCNGCKGFFRRSVRKNRTYTCRFGGNCVVDKDKRNACRYCRFKKCLEVGMDPEAVQNERD   76 (76)
T ss_pred             CCccCccCcccEECcceeeeehheeCccccCCCceeCCCCCcccccCcccccCccchhhhhhhcCCCHHHcccCCC
Confidence            8999999999999999999999999999999999999999999999999999999999999999999999999875

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

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

Probab=99.97  E-value=2.5e-32  Score=176.40  Aligned_cols=74  Identities=61%  Similarity=1.182  Sum_probs=71.2

Q ss_pred             CcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhccccccee
Q psy16825         11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR   84 (183)
Q Consensus        11 ~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~   84 (183)
                      ++|.|||++++|+||||.+|+||++||||++..+..|.|..+++|.+++..+..|++|||+||+++||++++||
T Consensus         1 ~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~   74 (75)
T cd06969           1 GLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLQVGMVKEVVR   74 (75)
T ss_pred             CCCeecCCcCcceEECcceeeeeeeeeeeeeecCCcccCCcCCccccCCcccccCcccHhHHHHHhCCCHHHcc
Confidence            36999999999999999999999999999999999999999999999999999999999999999999999986

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

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

Probab=99.97  E-value=3.7e-32  Score=182.74  Aligned_cols=84  Identities=44%  Similarity=1.023  Sum_probs=79.2

Q ss_pred             CCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecccc
Q psy16825         10 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR   89 (183)
Q Consensus        10 ~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~   89 (183)
                      ...|.|||++++|+||||++|+||++||||++..+..|.|..+++|.+++..+..|++|||+||+++||++++|+.+|.+
T Consensus         5 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~V~~~r~~   84 (95)
T cd06968           5 VIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVSYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMS   84 (95)
T ss_pred             ccCCcccCCcCcceEECceeehhhHHhhHHheeCCCceecCCCcccccccCCceeccccchhhcccccCChhhcccCcCC
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cccc
Q psy16825         90 GGRQ   93 (183)
Q Consensus        90 ~~~~   93 (183)
                      .+.+
T Consensus        85 ~~~~   88 (95)
T cd06968          85 KKQR   88 (95)
T ss_pred             hhhh
Confidence            6654

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

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

Probab=99.97  E-value=4.1e-32  Score=175.00  Aligned_cols=74  Identities=47%  Similarity=1.108  Sum_probs=71.2

Q ss_pred             ccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeec
Q psy16825         13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLD   86 (183)
Q Consensus        13 C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~   86 (183)
                      |.|||++++|+||||.+|+||++||||++..+..|.|..+++|.+++..+..|++|||+||+++||++++|+++
T Consensus         1 C~VCg~~~~g~hygv~sC~aC~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~   74 (74)
T cd07179           1 CRVCGGKSSGFHFGALTCEGCKGFFRRTELSSNSYVCPGGQNCAITPATRNACKSCRFRRCLAVGMSKTGSRIG   74 (74)
T ss_pred             CcccCccCcceEECceeehhHHHHHHHHhhCCCcccCCCCCccccCCcccccCccchhHHHHHhCCCHhHeeCc
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999863

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.

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

Probab=99.97  E-value=1.4e-32  Score=184.49  Aligned_cols=82  Identities=41%  Similarity=0.909  Sum_probs=77.9

Q ss_pred             cccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecccccc
Q psy16825         12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG   91 (183)
Q Consensus        12 ~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~~~   91 (183)
                      .|.|||++++|+||||++|+||++||||++..+..|.|..+++|.++...+..|++|||+|||++||++++|+.+|+...
T Consensus         2 ~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~r~~~~   81 (94)
T cd06966           2 ICGVCGDKALGYNFNAITCESCKAFFRRNALKNKEFKCPFNESCEINVVTRRFCQKCRLDKCFAIGMKKEWIMSEEDKSE   81 (94)
T ss_pred             CCeeCCCcCcceEECcceeeeehheehhcccCCCccccCCCCccccCccccccCccchhhhCcccCCCHHHccchhhhhH
Confidence            59999999999999999999999999999999999999999999999999999999999999999999999999987765


Q ss_pred             cc
Q psy16825         92 RQ   93 (183)
Q Consensus        92 ~~   93 (183)
                      ++
T Consensus        82 ~r   83 (94)
T cd06966          82 KR   83 (94)
T ss_pred             HH
Confidence            54

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

>KOG4846|consensus

Probab=99.97  E-value=8e-32  Score=216.78  Aligned_cols=82  Identities=51%  Similarity=1.093  Sum_probs=77.8

Q ss_pred             CcccccCCCCcccccccccccchhhhhhccccCCcee-ecCCCCCccccccccccccchhhhHHhhhcccccceeecccc
Q psy16825         11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEY-TCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR   89 (183)
Q Consensus        11 ~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~-~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~   89 (183)
                      -.|.||||+++|+||||.+|+|||+||||+|+.+..| .|-+..+|.|.++.||+||+|||+|||.|||.+++|++++++
T Consensus       133 ~lCkVCgDkASGfHYGV~aCEGCKGFFRRSIQqkI~YrrClk~e~C~I~R~nRNRCQ~CRfKKCL~vGMSrDaVRFG~m~  212 (538)
T KOG4846|consen  133 SLCKVCGDKASGFHYGVTACEGCKGFFRRSIQQKIDYRRCLKQEVCEIKRENRNRCQYCRFKKCLDVGMSRDAVRFGQMK  212 (538)
T ss_pred             EeehhhccccccceeceeecccchHHHHHHHHHhhhHHHHhhhhceehhhhccchhhhhhHHHHHhcccchhhhhhcccc
Confidence            3699999999999999999999999999999999999 699999999999999999999999999999999999999876


Q ss_pred             ccc
Q psy16825         90 GGR   92 (183)
Q Consensus        90 ~~~   92 (183)
                      .+.
T Consensus       213 ~rn  215 (538)
T KOG4846|consen  213 FRN  215 (538)
T ss_pred             ccc
Confidence            544

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

Probab=99.97  E-value=7.1e-32  Score=175.25  Aligned_cols=76  Identities=53%  Similarity=1.127  Sum_probs=71.7

Q ss_pred             CCCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhccccccee
Q psy16825          9 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR   84 (183)
Q Consensus         9 ~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~   84 (183)
                      |...|.|||++++|+||||++|+||++||||++..+..|.|..+++|.+++..++.|++|||+||+++||+..++.
T Consensus         1 ~~~~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~   76 (78)
T cd07172           1 PQKICLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCLQAGMNLGARK   76 (78)
T ss_pred             CCCCCeecCCcCcceEECceeehhhHHhHHHHeeCCCceeCCCCCccccCCcccccCccchhHHHHHhCCCccccc
Confidence            3567999999999999999999999999999999999999999999999999999999999999999999988764

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

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

Probab=99.97  E-value=4.9e-32  Score=173.85  Aligned_cols=72  Identities=50%  Similarity=1.118  Sum_probs=69.4

Q ss_pred             ccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhccccccee
Q psy16825         13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR   84 (183)
Q Consensus        13 C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~   84 (183)
                      |.|||++++|+||||.+|+||++||||++..+..|.|..+++|.+++..++.|++|||+||+++||++++|.
T Consensus         1 C~VC~~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   72 (72)
T cd07156           1 CGVCGDRATGYHFNAMTCEGCKGFFRRSMKRKARFTCPFNGDCEITKDNRRHCQACRLKKCLDIGMKKEMIL   72 (72)
T ss_pred             CCccCccCcccEECcceehhhhhhhchhccCcCccccCCCCccccCCcccccCccchhHHHHHhCCCHHHcC
Confidence            899999999999999999999999999999999999999999999999999999999999999999999873

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

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

Probab=99.97  E-value=5.9e-32  Score=173.90  Aligned_cols=72  Identities=50%  Similarity=1.152  Sum_probs=70.0

Q ss_pred             ccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhccccccee
Q psy16825         13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR   84 (183)
Q Consensus        13 C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~   84 (183)
                      |.|||++++|+||||.+|+||++||||++..+..|.|..+++|.+++..++.|++|||+|||++||++++||
T Consensus         1 C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   72 (73)
T cd06958           1 CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRGNRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQ   72 (73)
T ss_pred             CCccCccCcceEEChhhhhhhhhhhhhhhcCCCceeCCCCCcCccCCcccccCccchhhHhhHhCCCHHHcc
Confidence            899999999999999999999999999999999999999999999999999999999999999999999987

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

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

Probab=99.97  E-value=6.5e-32  Score=176.79  Aligned_cols=78  Identities=49%  Similarity=1.096  Sum_probs=72.3

Q ss_pred             CCCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeec
Q psy16825          9 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLD   86 (183)
Q Consensus         9 ~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~   86 (183)
                      +...|.|||++++|+||||++|+||++||||+|..+..|.|..+++|.+++..++.|++|||+||+++||++.....+
T Consensus         2 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~~~~~   79 (82)
T cd07173           2 PQKTCLICGDEASGCHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCFEAGMTLGARKLK   79 (82)
T ss_pred             CCCCCeecCCcCcceEECcchhhhHHHHHHHHhcCCCceecCCCCccccCCCccCcCcchhhhhhhhcCCCcChHHhh
Confidence            456799999999999999999999999999999999999999999999999999999999999999999988765443

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

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

Probab=99.97  E-value=7.7e-32  Score=173.37  Aligned_cols=73  Identities=48%  Similarity=1.043  Sum_probs=70.0

Q ss_pred             cccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhccccccee
Q psy16825         12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR   84 (183)
Q Consensus        12 ~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~   84 (183)
                      +|.|||++++|+||||.+|+||++||||++..+..|.|+.+++|.+++..+..|++|||+||+++||+++.|+
T Consensus         1 ~C~vCg~~~~~~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~   73 (73)
T cd06959           1 NCVVCGDKASGFHYGVLSCEGCKGFFRRSVTKGAVYACKFGNKCEMDMYMRRKCQECRLRKCKAAGMRPDCLL   73 (73)
T ss_pred             CCceeCCcCcceEECceeehhhHHHHHHhhcCCCCccCCCCCcCCcCCcccccCccchhHHHHHhCCChhhcC
Confidence            5999999999999999999999999999999999999999999999999999999999999999999998873

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

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

Probab=99.97  E-value=7.3e-32  Score=177.72  Aligned_cols=80  Identities=53%  Similarity=1.074  Sum_probs=74.2

Q ss_pred             cccccCCCCcccccccccccchhhhhhccccCCceee-cCCCCCccccccccccccchhhhHHhhhcccccceeeccccc
Q psy16825         12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYT-CPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG   90 (183)
Q Consensus        12 ~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~-C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~~   90 (183)
                      .|.|||++++|+||||.+|+||++||||++..+..|. |...  |.+++..++.|++|||+||+++||++++|+.+|++.
T Consensus         1 ~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~~C~~~--C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~~~   78 (84)
T cd06965           1 ECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLVYKPCDLS--CKIHKKSRNKCQYCRFQKCLNVGMSHNAIRFGRMPR   78 (84)
T ss_pred             CCcccCccCcceEEChhhhhhhhhheeeeeecCCCccccccC--CCcCccccccccchhhhhhhhccCCHHHcccCCCCc
Confidence            4999999999999999999999999999999999995 9753  999999999999999999999999999999999976


Q ss_pred             ccc
Q psy16825         91 GRQ   93 (183)
Q Consensus        91 ~~~   93 (183)
                      ..+
T Consensus        79 ~~~   81 (84)
T cd06965          79 VEK   81 (84)
T ss_pred             hhh
Confidence            553

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

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

Probab=99.97  E-value=1.3e-31  Score=172.12  Aligned_cols=72  Identities=53%  Similarity=1.120  Sum_probs=69.3

Q ss_pred             ccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhccccccee
Q psy16825         13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR   84 (183)
Q Consensus        13 C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~   84 (183)
                      |.|||++++|+||||++|+||++||||++..+..|.|+.+++|.+++..++.|++|||+||+++||+++++.
T Consensus         1 C~VCg~~a~~~hygv~sC~aCk~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~a~~   72 (73)
T cd06963           1 CLICGDEASGCHYGVLTCGSCKVFFKRAAEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCYQAGMTLGARK   72 (73)
T ss_pred             CcccCccCcceEECceeehhhhHhHHHhhcCCCceeCCCCCccccCCcccccCccchhhHHHHcCCChhhcc
Confidence            899999999999999999999999999999999999999999999999999999999999999999998863

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

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

Probab=99.97  E-value=7.5e-32  Score=173.51  Aligned_cols=72  Identities=51%  Similarity=1.106  Sum_probs=69.2

Q ss_pred             ccccCCCCcccccccccccchhhhhhccccCCceeecC-CCCCccccccccccccchhhhHHhhhccccccee
Q psy16825         13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCP-ASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR   84 (183)
Q Consensus        13 C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~-~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~   84 (183)
                      |.|||++++|+||||.+|+||++||||++..+..|.|. .+++|.+++..+..|++|||+||+++||++++||
T Consensus         1 C~vCg~~~~~~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~vq   73 (73)
T cd07154           1 CKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNLLYTCKAGNGSCVVDKARRNQCQACRLKKCLEVSMNKDAVQ   73 (73)
T ss_pred             CcccCccCcceEECcceeeeeeeEeeeeecCCCCcccCCCCCCCccCCcccccCccchhhHhhHhCCChHHCC
Confidence            89999999999999999999999999999999999998 6789999999999999999999999999999886

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

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

Probab=99.97  E-value=1.2e-31  Score=177.32  Aligned_cols=78  Identities=46%  Similarity=0.925  Sum_probs=73.2

Q ss_pred             cccccCCCCcccccccccccchhhhhhccccCCc--eeecCCCCCccccccccccccchhhhHHhhhcccccceeecccc
Q psy16825         12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNI--EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR   89 (183)
Q Consensus        12 ~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~--~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~   89 (183)
                      .|.|||++++|+||||.+|+||++||||++..+.  .|.|..+++|.+++..++.|++|||+|||++||++++++.+|+.
T Consensus         2 ~C~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~~~~~~   81 (86)
T cd07157           2 TCQVCGEPAAGFHHGAYVCEACKKFFMRSSNAISFTISECPNGGKCIIDKKNRTKCQACRYRKCLNVGMSLGGPRYGRRS   81 (86)
T ss_pred             CCcccCCcCcccEECcceeeEeeeEEecceecCCCccccCCCCCccccCccccccCccchhhHHhHcCCCcccccccccc
Confidence            5999999999999999999999999999998764  89999999999999999999999999999999999999988763

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.

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

Probab=99.97  E-value=8.5e-32  Score=184.13  Aligned_cols=77  Identities=47%  Similarity=1.072  Sum_probs=73.3

Q ss_pred             CCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeec
Q psy16825         10 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLD   86 (183)
Q Consensus        10 ~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~   86 (183)
                      ...|.|||++++|+||||++|+||++||||+|..+..|.|..+++|.+++..++.|++|||+|||++||++++|+.+
T Consensus         6 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~   82 (107)
T cd06955           6 PRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTD   82 (107)
T ss_pred             CCCCeecCCcCcccEECcceeeeecceecceeccCCccccCCCCccccccCCccccccchhHHHHHcCCCchhccCH
Confidence            35699999999999999999999999999999999999999999999999999999999999999999999888877

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

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

Probab=99.97  E-value=8.9e-32  Score=172.74  Aligned_cols=72  Identities=63%  Similarity=1.309  Sum_probs=69.7

Q ss_pred             ccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhccccccee
Q psy16825         13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR   84 (183)
Q Consensus        13 C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~   84 (183)
                      |.|||++++|+||||.+|+||++||||++..+..|.|..+++|.+++..+..|++|||+||+++||++++||
T Consensus         1 C~vC~~~~~~~hygv~sC~aC~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   72 (72)
T cd06916           1 CAVCGDKASGYHYGVLTCEGCKGFFRRSVRRNLEYTCPAGGNCVIDKRNRNRCQACRLKKCLAVGMRKEAVR   72 (72)
T ss_pred             CCccCccCcccEECcceeeeeeeeEeEeecCCCCccCCCCCccccCCcccccCccchhhHhhHhCCChHHcC
Confidence            899999999999999999999999999999999999999999999999999999999999999999999885

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

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

Probab=99.97  E-value=8.4e-32  Score=178.69  Aligned_cols=78  Identities=45%  Similarity=0.990  Sum_probs=74.1

Q ss_pred             cccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecccc
Q psy16825         12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR   89 (183)
Q Consensus        12 ~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~   89 (183)
                      +|.|||++++|+||||.+|+||++||||++..+..|.|..+++|.+++..++.|++|||+||+++||++++|+.++..
T Consensus         1 ~C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~~~   78 (87)
T cd07162           1 ICRVCGDRATGYHFNAMTCEGCKGFFRRAMKRNARLCCPFQKGCVITKSNRRQCQACRLRKCLSIGMKKELIMSDEAV   78 (87)
T ss_pred             CCcccCCcCcceEECcceehhhHHHHHhhhccCceeEcCCCCceecCCcccccCccchhhHHhHhCCCHHHccCHHHH
Confidence            499999999999999999999999999999999999999999999999999999999999999999999999988543

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

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

Probab=99.97  E-value=1.7e-31  Score=171.96  Aligned_cols=72  Identities=58%  Similarity=1.207  Sum_probs=69.5

Q ss_pred             ccccCCCCcccccccccccchhhhhhccccCCcee-ecCCCCCccccccccccccchhhhHHhhhccccccee
Q psy16825         13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEY-TCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR   84 (183)
Q Consensus        13 C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~-~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~   84 (183)
                      |.|||++++|+||||.+|+||++||||++..+..| .|+.+++|.+++..+..|++|||+|||++||++++|+
T Consensus         1 C~VCg~~~~g~hyGv~~C~aC~~FFRR~v~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   73 (73)
T cd07158           1 CKVCGDKASGFHYGVHSCEGCKGFFRRTIQHNLTYRRCLNGGKCVIQRKNRNRCQYCRFKKCLSVGMSRNAVR   73 (73)
T ss_pred             CcccCccCcceEECcchhhHHHHHHhhhhcCCCCcccCCCCCCcCCCccccccCccchhhhhhHccCChHHcC
Confidence            89999999999999999999999999999999999 8999999999999999999999999999999999875

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=99.96  E-value=6.2e-30  Score=163.54  Aligned_cols=70  Identities=60%  Similarity=1.177  Sum_probs=67.0

Q ss_pred             cccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhccccc
Q psy16825         12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE   81 (183)
Q Consensus        12 ~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~   81 (183)
                      .|.|||++++|+||||.+|+||++||||+|..+..|.|..+++|.+++..+..|++|||+||+++||+++
T Consensus         1 ~C~vC~~~~~~~hygv~~C~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~   70 (70)
T smart00399        1 LCCVCGDHASGFHFGVCSCRACKAFFRRTVNLRYKYRCDRKNNCSINKRYRCRCRACRLKKCLGVGMDPE   70 (70)
T ss_pred             CCeEeCCcCcccEeCCcEechhhhhhhhheeCCCCeecCCCcccccCCCccccCccCcChhHhhccCcCC
Confidence            4999999999999999999999999999999999999999999999999999999999999999999864

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

Probab=99.95  E-value=3.4e-29  Score=160.35  Aligned_cols=70  Identities=53%  Similarity=1.186  Sum_probs=62.5

Q ss_pred             CcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccc
Q psy16825         11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLK   80 (183)
Q Consensus        11 ~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~   80 (183)
                      ..|.|||++++|+||||.+|++|++||||++..+..+.|..+++|.+++..+..|++|||+||+++||++
T Consensus         1 ~~C~VCg~~~~~~~ygv~sC~~C~~FFrR~~~~~~~~~C~~~~~C~i~~~~~~~C~~CRf~KCl~~GM~k   70 (70)
T PF00105_consen    1 KKCKVCGDPASGYHYGVLSCNACKMFFRRSVKKKKPYKCKKNGNCKIDKDNRRKCRSCRFQKCLEVGMKK   70 (70)
T ss_dssp             -BSTTTSSBESEEETTEEEEHHHHHHHHHHHHTTCG-STSSSST---STTTTTTSHHHHHHHHHHTTBSG
T ss_pred             CCCeECCCccCcccccccccccceeeeeecccccccccccccccccccccCCCEeCcchHHHHHHHCCcC
Confidence            3699999999999999999999999999999999889999999999999999999999999999999974

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 ....

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

Probab=99.44  E-value=1.6e-13  Score=107.60  Aligned_cols=57  Identities=26%  Similarity=0.355  Sum_probs=53.6

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCC-CCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANS-DVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~-d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +++++.+|++|++|.+||+|||||+|||| |.+ |.+...|+.+|++++.+|.+||..+
T Consensus       116 l~e~~~~~r~L~ld~~EfacLKAIvLfnp~d~~GL~~~~~Ve~lqe~~~~aL~~yi~~~  174 (247)
T cd07076         116 MLYVSSELHRLQVSYEEYLCMKTLLLLSTVPKDGLKSQELFDEIRMTYIKELGKAIVKR  174 (247)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence            56899999999999999999999999999 875 9999999999999999999999865

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

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

Probab=99.40  E-value=5.9e-13  Score=103.54  Aligned_cols=58  Identities=17%  Similarity=0.297  Sum_probs=53.4

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhcC
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVLR  183 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~~  183 (183)
                      +.+++.+|+.|++|..||+||+||+||+||++ |.+...|+.+|++++.+|.+|+..+|
T Consensus       121 ~~~~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~  179 (226)
T cd06934         121 LLRFHYTLRKLQLQEEEYVLMQAMSLFSPDRPGVTQHDVIDQLQEKMALTLKSYIDSKR  179 (226)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCcCCcChHHHHHHHHHHHHHHHHHHHHcC
Confidence            35678899999999999999999999999986 99999999999999999999997653

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

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

Probab=99.40  E-value=5.5e-13  Score=104.03  Aligned_cols=57  Identities=19%  Similarity=0.232  Sum_probs=53.4

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|+.|++|..||+||+||+||+||.+ |.+...|+++|++++.+|.+|+...
T Consensus       124 ~~~~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~  181 (231)
T cd06937         124 VFTFANQLLPLEMDDTEIGLLSAICLICGDRQDLEEPDRVEKLQEPLLEALKIYARKR  181 (231)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCccCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            45799999999999999999999999999986 9999999999999999999999754

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

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

Probab=99.39  E-value=7.5e-13  Score=100.29  Aligned_cols=57  Identities=19%  Similarity=0.329  Sum_probs=53.4

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|+.+++|.+||++|+||+|+|||.+ |.+...|+++|++++.+|.+|+...
T Consensus        98 ~~~~~~~l~~L~ld~~E~a~LkAivLf~pd~~~L~~~~~Ve~lq~~~~~aL~~~~~~~  155 (189)
T cd06940          98 MFDFSEKLNSLQLSDEEMGLFTAVVLVSADRSGLENVNLVEALQETLIRALRTLIAKN  155 (189)
T ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCcCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            46789999999999999999999999999986 9999999999999999999998753

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

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

Probab=99.39  E-value=7.2e-13  Score=104.10  Aligned_cols=76  Identities=20%  Similarity=0.254  Sum_probs=69.1

Q ss_pred             CCCCCCCccccccccc-------------------------------------------------chhhhhhhhchhccc
Q psy16825        108 PNKSIPSLEDLERNTE-------------------------------------------------ISCTQVIDRLEHVAV  138 (183)
Q Consensus       108 ~~k~iP~f~~L~~~dq-------------------------------------------------~~~~~lv~~~~~l~~  138 (183)
                      +.|.+|+|.+|+.+||                                                 ..+.+++.+|+.|++
T Consensus        71 fAK~iPgF~~L~~~DQi~LLk~~~~ElliL~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~f~~~l~~L~l  150 (243)
T cd06935          71 FAKKLPMFTELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLSGEMAVTREQLKNGGLGVVSDAIFDLGVSLSSFNL  150 (243)
T ss_pred             HHhcCCccccCChHHHHHHHHHhHHHHHHHHHHHHhCcCCCeEEeeCCeEeeHHHHHhcChHHHHHHHHHHHHHHHhcCC
Confidence            3599999999999999                                                 234579999999999


Q ss_pred             ChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhcC
Q psy16825        139 SKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVLR  183 (183)
Q Consensus       139 ~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~~  183 (183)
                      |.+||++|+||+||+||++ |.+...|+++|++++.+|.+|+..+|
T Consensus       151 d~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~  196 (243)
T cd06935         151 DDTEVALLQAVLLMSSDRPGLACVERIEKLQDSFLLAFEHYINYRK  196 (243)
T ss_pred             CHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhC
Confidence            9999999999999999986 99999999999999999999997643

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

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

Probab=99.37  E-value=1e-12  Score=103.22  Aligned_cols=57  Identities=18%  Similarity=0.289  Sum_probs=52.6

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCC-CCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANS-DVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~-d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.++++|++|.+||+|||||+|||| |++ |.+.+.|+.+|++++.+|.+||...
T Consensus       116 l~~~~~~l~~L~ld~~EyacLKAIiLfnp~d~~gL~~~~~Ve~lQe~~~~aL~~yi~~~  174 (246)
T cd07073         116 MRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFFDELRMNYIKELDRIIACK  174 (246)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCcccccCHHHHHHHHHHHHHHHHHHHHhc
Confidence            34788999999999999999999999999 875 9999999999999999999999764

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

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

Probab=99.36  E-value=1.1e-12  Score=102.86  Aligned_cols=75  Identities=23%  Similarity=0.298  Sum_probs=68.7

Q ss_pred             CCCCCCCccccccccc------------------------------------------------chhhhhhhhchhcccC
Q psy16825        108 PNKSIPSLEDLERNTE------------------------------------------------ISCTQVIDRLEHVAVS  139 (183)
Q Consensus       108 ~~k~iP~f~~L~~~dq------------------------------------------------~~~~~lv~~~~~l~~~  139 (183)
                      +.|.+|+|.+|+.+||                                                ..+.+++.+++.|++|
T Consensus        67 fAK~IPgF~~L~~~DQi~LLk~~~~Ellll~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~l~~L~ld  146 (241)
T cd06939          67 FAKRIPGFMELCQNDQIVLLKAGSLEVVLVRMSRAFNPSNNTVLFDGKYAPIDLFKSLGCDDLISAVFDFAKSLCELKLT  146 (241)
T ss_pred             HHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhCCCCCEEEECCccccHHHHHHcCcHHHHHHHHHHHHHHHhcCCC
Confidence            3488999999999999                                                2256889999999999


Q ss_pred             hhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        140 KEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       140 ~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      ..||+||+||+|++||++ |.+...|+++|++++.+|.+|+...
T Consensus       147 ~~E~all~AivL~~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~  190 (241)
T cd06939         147 EDEIALFSALVLISADRPGLQEKRKVEKLQQKIELALRHVLQKN  190 (241)
T ss_pred             HHHHHHHHHHHHhcCCCcCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999987 9999999999999999999999764

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

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

Probab=99.36  E-value=1.3e-12  Score=102.28  Aligned_cols=57  Identities=14%  Similarity=0.240  Sum_probs=52.6

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|+.|++|.+||+||+||+||+||++ |.+...|+.+|++++.+|.+|+..+
T Consensus       125 l~~~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~  182 (238)
T cd06933         125 LVKFQVGLKKLNLHEEEHVLLMAICILSPDRPGVQDHALIEAIQDRLSDTLQTYIRCR  182 (238)
T ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHHHHCCCCCCCcchHHHHHHHHHHHHHHHHHHHhc
Confidence            34677889999999999999999999999986 9999999999999999999999764

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

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

Probab=99.35  E-value=1.6e-12  Score=100.81  Aligned_cols=57  Identities=23%  Similarity=0.328  Sum_probs=53.0

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +++++.+|++|++|.+||++||||+|||||.+ |.+...|+.+|++++.+|.+|+...
T Consensus       117 l~e~~~~l~~L~ld~~Eya~LkaivLf~pd~~gl~~~~~V~~lqe~~~~aL~~~~~~~  174 (222)
T cd07349         117 LQCCLNKFWSLDLSPKEYAYLKGTILFNPDVPGLTASSHVGHLQQEAQWALCEVLEPL  174 (222)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHcCCCcccCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            45778899999999999999999999999987 9999999999999999999999754

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.

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

Probab=99.35  E-value=1.4e-12  Score=102.26  Aligned_cols=56  Identities=25%  Similarity=0.405  Sum_probs=52.6

Q ss_pred             hhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        127 TQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       127 ~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      ++++.+|+.|++|..||+|||||+|||||++ |.+...|+.+|++++.+|.+|+...
T Consensus       132 ~e~~~~lr~L~ld~~E~a~LKaivLfnpd~~gL~~~~~Ve~lQe~~~~aL~~yi~~~  188 (241)
T cd07069         132 QELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCN  188 (241)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence            4688999999999999999999999999987 9999999999999999999999753

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).

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

Probab=99.35  E-value=1.5e-12  Score=102.31  Aligned_cols=56  Identities=20%  Similarity=0.331  Sum_probs=52.0

Q ss_pred             hhhhhhchhcccChhHHHHHHHHHhcCC-CCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        127 TQVIDRLEHVAVSKEEYYFLKALVLANS-DVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       127 ~~lv~~~~~l~~~~~E~~~lkai~L~~~-d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      .+++.+|++|++|.+||+|||||+|||+ |.+ |.+...|+++|++++.+|.+||..+
T Consensus       117 ~e~~~~l~~L~ld~~E~acLKAIvLfn~~d~~gL~~~~~Ve~lqe~i~~AL~~yi~~~  174 (246)
T cd06947         117 RQISQEFVRLQVTYEEFLCMKVLLLLSTIPKDGLKSQAAFDEMRMNYIKELRKAIVKR  174 (246)
T ss_pred             HHHHHHHHhcCCCHHHHHHHHHHHHcCCCccccccCHHHHHHHHHHHHHHHHHHHHHh
Confidence            4678999999999999999999999999 765 9999999999999999999999754

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

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

Probab=99.35  E-value=1.8e-12  Score=102.75  Aligned_cols=57  Identities=11%  Similarity=0.213  Sum_probs=53.3

Q ss_pred             hhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhcC
Q psy16825        127 TQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVLR  183 (183)
Q Consensus       127 ~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~~  183 (183)
                      .+++.+|+.|++|.+||+||+||+|++||++ |.+...|+++|++++.+|.+|+...+
T Consensus       151 ~e~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~~i~~~~  208 (259)
T cd06932         151 FEFAEKFNALELTDSELALFCAVIILSPDRPGLINRKPVERIQEHVLQALELQLKKNH  208 (259)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHhCCCcccCcCHHHHHHHHHHHHHHHHHHHhhhC
Confidence            4789999999999999999999999999987 99999999999999999999997653

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

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

Probab=99.35  E-value=1.5e-12  Score=101.89  Aligned_cols=56  Identities=25%  Similarity=0.353  Sum_probs=52.5

Q ss_pred             hhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        127 TQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       127 ~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      .+++.+|++|++|.+||+||+||+|||||++ |++.+.|+.+|++++.+|.+||...
T Consensus       130 ~e~~~kl~~L~ld~~Ey~~LkaIiLfnpd~~gL~~~~~Ve~lQe~~~~aL~~y~~~~  186 (237)
T cd07070         130 QELVLQLHALQLDRQEFVCLKFLILFSLDVKFLNNHSLVKDAQEKANAALLDYTLCH  186 (237)
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHhcCCCccCCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence            4689999999999999999999999999986 9999999999999999999999753

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

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

Probab=99.34  E-value=2e-12  Score=99.19  Aligned_cols=57  Identities=19%  Similarity=0.335  Sum_probs=53.1

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||++||||+|+|||++ |++...|+++|++++.+|.+|+...
T Consensus       112 i~~~~~~~~~L~ld~~EyalLKai~L~npd~~~L~~~~~Ve~lq~~~~~aL~~y~~~~  169 (206)
T cd06950         112 LQETLSRFRQLRVDATEFACLKAIVLFKPETRGLKDPAQVEALQDQAQLMLNKHIRTR  169 (206)
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            45788999999999999999999999999986 9999999999999999999999753

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

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

Probab=99.33  E-value=2.1e-12  Score=100.14  Aligned_cols=56  Identities=16%  Similarity=0.176  Sum_probs=52.7

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +++++.+|++|++|..||++||||+|||||.+ | +...|+++|++++.+|.+||...
T Consensus       120 l~e~~~~l~~L~ld~~Eya~LkAivLfnpD~~gl-~~~~Ve~lQe~~~~aL~~yi~~~  176 (222)
T cd06951         120 IQQFLMKCWSLDLDCKEYAYLKGAVLFTPVPPLL-CPHYIEALQKEAQQALNEHTMMT  176 (222)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCcc-CHHHHHHHHHHHHHHHHHHHHhh
Confidence            56899999999999999999999999999987 9 99999999999999999999754

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.

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

Probab=99.33  E-value=2.8e-12  Score=100.33  Aligned_cols=73  Identities=21%  Similarity=0.327  Sum_probs=66.6

Q ss_pred             CCCCCCCccccccccc------------------------------------------------chhhhhhhhchhcccC
Q psy16825        108 PNKSIPSLEDLERNTE------------------------------------------------ISCTQVIDRLEHVAVS  139 (183)
Q Consensus       108 ~~k~iP~f~~L~~~dq------------------------------------------------~~~~~lv~~~~~l~~~  139 (183)
                      +.|.+|+|.+|+.+||                                                ..+.+++.+|+.|++|
T Consensus        60 wAK~iPgF~~L~~~DQi~LLk~~w~El~vL~~a~r~~~~~~~l~f~~~~~~~r~~~~~~~~~~~~~i~ef~~~l~~L~ld  139 (238)
T cd07348          60 WAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNPEEGKLIFCNGVVLHRTQCVRGFGDWIDSILEFSQSLHRMNLD  139 (238)
T ss_pred             HHccCCCccCCChHHHHHHHHHHHHHHHHHHHHHHcCCCCCeEEeeCCeeecHHHHHhhHHHHHHHHHHHHHHHHHcCCC
Confidence            3499999999999999                                                2246789999999999


Q ss_pred             hhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHh
Q psy16825        140 KEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYV  181 (183)
Q Consensus       140 ~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~  181 (183)
                      .+||+||+||+|+ +|++ |.+...|+.+|++++.+|.+|+..
T Consensus       140 ~~E~a~LkAIvLf-~Dr~gL~~~~~Ve~lQe~~~~aL~~yi~~  181 (238)
T cd07348         140 VSAFSCLAALVII-TDRHGLKEPKRVEELQNRLISCLKEHVSG  181 (238)
T ss_pred             HHHHHHHHHHHHc-CCCcCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999 7876 999999999999999999999975

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

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

Probab=99.33  E-value=2.4e-12  Score=101.09  Aligned_cols=56  Identities=18%  Similarity=0.288  Sum_probs=51.6

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCC-C-CCCchhHHHHHHHHHHHHHHHHHHh
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSD-V-KLDEFSSLKKFRNSILSSLGDCIYV  181 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d-~-~L~~~~~v~~~~~~~~~~L~~~~~~  181 (183)
                      +.+++.+|++|++|.+||+|||||+||||| . +|++...|+.+|++++.+|.+||..
T Consensus       116 ~~e~~~~l~~L~Ld~~E~acLKAIvLfn~d~~~gL~~~~~Ve~lqe~~~~aL~~yi~~  173 (248)
T cd07075         116 MHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKDGLKSQAAFEEMRTNYIKELRKMVTK  173 (248)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            457889999999999999999999999996 4 4999999999999999999999974

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

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

Probab=99.32  E-value=3.1e-12  Score=100.16  Aligned_cols=57  Identities=12%  Similarity=0.294  Sum_probs=53.3

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||++|+||+|||||++ |.+...|+.+|++++.+|.+|+...
T Consensus       130 i~~~~~~l~~L~ld~~E~~lL~aivLf~pd~~gL~~~~~V~~lQ~~~~~aL~~y~~~~  187 (236)
T cd06954         130 IFEFSKSMRELQLDDAEYALLIAINIFSADRPNVQDHHRVERLQETYVEALHSYIKIK  187 (236)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHhhccCCcccCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence            35789999999999999999999999999986 9999999999999999999999754

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

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

Probab=99.31  E-value=3.7e-12  Score=98.22  Aligned_cols=56  Identities=27%  Similarity=0.393  Sum_probs=52.0

Q ss_pred             hhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        127 TQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       127 ~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      .+++.+|+++++|.+||++|+||+|||||.+ |++.+.|+++|++++.+|.+||...
T Consensus       118 ~~l~~~l~~L~ld~eEy~lLkAIvLfnpd~~gLs~~~~Ve~lQ~~~~~aL~~y~~~~  174 (213)
T cd06953         118 TYLLAKFRQLKVSNEEYVCLKVINFLNQDIDGLTNASQLESLQKRYWYVLQDFTELN  174 (213)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            3678899999999999999999999999986 9999999999999999999999754

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).

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

Probab=99.31  E-value=4e-12  Score=96.76  Aligned_cols=58  Identities=19%  Similarity=0.212  Sum_probs=53.6

Q ss_pred             hhhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        125 SCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       125 ~~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      .+.+++.+|++|++|.+||++|+||+||+||.+ |.+.+.|+++|++++.+|.+||...
T Consensus        87 ~~~~~~~~l~~L~ld~~E~allkAi~Lf~pd~~gl~~~~~Ve~lq~~~~~aL~~~i~~~  145 (195)
T cd06941          87 ALFEFSDSFNSLGLSDTEVALFCAVVLLSPDRIGLSEPKKVAILQDRVLEALKVQVSRN  145 (195)
T ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            356789999999999999999999999999985 9999999999999999999998754

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

>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=99.30  E-value=4.7e-12  Score=98.16  Aligned_cols=57  Identities=18%  Similarity=0.314  Sum_probs=52.2

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||+||+||+|||||++ |++...|+.+|++++.+|.+||...
T Consensus       119 i~~~~~kl~~L~l~~~E~~lLkaIvL~npd~~gL~~~~~Ve~~Q~~~~~aL~~y~~~~  176 (221)
T cd06936         119 MFNFYKSMGELKMTQEEYALLTAITILFPDRPYLKDKEAVEKLQEPLLDLLQKFCKLY  176 (221)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCcCCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            34678888999999999999999999999986 9999999999999999999999654

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

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

Probab=99.29  E-value=5.2e-12  Score=99.02  Aligned_cols=74  Identities=23%  Similarity=0.324  Sum_probs=67.3

Q ss_pred             CCCCCCccccccccc------------------------------------------------chhhhhhhhchhcccCh
Q psy16825        109 NKSIPSLEDLERNTE------------------------------------------------ISCTQVIDRLEHVAVSK  140 (183)
Q Consensus       109 ~k~iP~f~~L~~~dq------------------------------------------------~~~~~lv~~~~~l~~~~  140 (183)
                      .|.+|+|.+|+.+||                                                ..+.+++.+|+.|+++.
T Consensus        61 AK~IPgF~~L~~~DQi~LLk~~w~El~~L~~a~r~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~i~~f~~~l~~L~ld~  140 (239)
T cd06945          61 AEKIPGFKDLHREDQDLLLESAFLELFVLRLAYRSNPVDGKLVFCNGLVLHRLQCVRGFGEWLDSILAFSSSLQSLLLDD  140 (239)
T ss_pred             HHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCceEeeCCceecHHHHHHhHHHHHHHHHHHHHHHHHHhCCh
Confidence            488999999999999                                                22456778999999999


Q ss_pred             hHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        141 EEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       141 ~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      .||++|+||+|++||++ |.+.+.|+++|++++.+|.+|+...
T Consensus       141 ~E~~~LkaivL~~pD~~gL~~~~~Ve~lQe~~~~aL~~y~~~~  183 (239)
T cd06945         141 ISAFCCLALLLLITERHGLKEPKKVEELQNKIISCLRDHVTSN  183 (239)
T ss_pred             HHHHHHHHHHHhCCCccccCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999986 9999999999999999999999764

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

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

Probab=99.28  E-value=4.8e-12  Score=99.31  Aligned_cols=56  Identities=27%  Similarity=0.387  Sum_probs=51.0

Q ss_pred             hhhhhhchhcccChhHHHHHHHHHhcCC-CCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        127 TQVIDRLEHVAVSKEEYYFLKALVLANS-DVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       127 ~~lv~~~~~l~~~~~E~~~lkai~L~~~-d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      ++++.+|+++++|.+||+|||||+|||| |++ |++...|+++|++|+.+|.+||..+
T Consensus       117 ~e~~~~~~~L~ld~~Ey~cLKAIvLfnp~d~~gL~~q~~Ve~lR~~y~~aL~~yi~~~  174 (248)
T cd07074         117 WQIPQEFVKLQVSQEEFLCMKALLLLNTIPLEGLRSQTQFDEMRSSYIRELIKAIGLR  174 (248)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHCCCCcCCCCCCHHHHHHHHHHHHHHHHHHHHHc
Confidence            3578899999999999999999999999 665 9999999999999999999997543

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

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

Probab=99.28  E-value=7.7e-12  Score=97.89  Aligned_cols=73  Identities=19%  Similarity=0.359  Sum_probs=66.1

Q ss_pred             CCCCCCccccccccc------------------------------------------------chhhhhhhhchhcccCh
Q psy16825        109 NKSIPSLEDLERNTE------------------------------------------------ISCTQVIDRLEHVAVSK  140 (183)
Q Consensus       109 ~k~iP~f~~L~~~dq------------------------------------------------~~~~~lv~~~~~l~~~~  140 (183)
                      .|.+|+|.+|+.+||                                                ..+.+++.+|+.|++|.
T Consensus        61 AK~iPgF~~L~~~DQi~LLk~~~~Ell~L~~a~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~i~ef~~~l~~L~ld~  140 (238)
T cd07071          61 AEKIPGFTDLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIFCNGVVLHRLQCVRGFGEWIDSIVEFSSNLQNMNIDI  140 (238)
T ss_pred             hccCCCccCCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCCceEeeCCceechhhhhhcHHHHHHHHHHHHHHHHhcCCCH
Confidence            499999999999999                                                22468999999999999


Q ss_pred             hHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        141 EEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       141 ~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +||+||+||+|++ |.+ |.+...|+++|++++.+|.+|+..+
T Consensus       141 ~E~alLkAIvLf~-D~~gL~~~~~Ve~lQe~~~~aL~~yi~~~  182 (238)
T cd07071         141 SAFSCIAALAMVT-ERHGLKEPKRVEELQNKIVNCLKDHVTFN  182 (238)
T ss_pred             HHHHHHHHHHHcC-CCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999995 765 9999999999999999999999753

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).

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

Probab=99.27  E-value=9.1e-12  Score=95.59  Aligned_cols=57  Identities=23%  Similarity=0.388  Sum_probs=52.8

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||++|+||+|||||.. |++...|+++|++++.+|.+|+...
T Consensus       117 ~~~~~~~l~~L~ld~~E~~lLkaI~L~~pd~~~L~~~~~v~~~q~~~~~aL~~y~~~~  174 (207)
T cd06943         117 LTELVVKMRDLKMDRTELGCLRAIILFNPDVKGLKSRQEVESLREKVYASLEEYCRQK  174 (207)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            45789999999999999999999999999985 9999999999999999999999653

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

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

Probab=99.26  E-value=8.1e-12  Score=97.84  Aligned_cols=57  Identities=23%  Similarity=0.412  Sum_probs=53.1

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||+|||||+|||||++ |++...|+++|++++.+|.+|+...
T Consensus       129 i~~~~~~l~~L~ld~~E~~lLkaIiL~npd~~gL~~~~~Ve~~q~~~~~aL~~y~~~~  186 (237)
T cd06944         129 AQELVNKLRELQFDRQEFVCLKFLILFNPDVKGLENRQLVESVQEQVNAALLDYTLCN  186 (237)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHcCCCcCCCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            45889999999999999999999999999986 9999999999999999999998654

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

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

Probab=99.26  E-value=9.6e-12  Score=97.37  Aligned_cols=73  Identities=22%  Similarity=0.310  Sum_probs=65.8

Q ss_pred             CCCCCCCccccccccc------------------------------------------------chhhhhhhhchhcccC
Q psy16825        108 PNKSIPSLEDLERNTE------------------------------------------------ISCTQVIDRLEHVAVS  139 (183)
Q Consensus       108 ~~k~iP~f~~L~~~dq------------------------------------------------~~~~~lv~~~~~l~~~  139 (183)
                      +.|.+|+|.+|+.+||                                                ..+.+++.+|+.|++|
T Consensus        61 wAK~IPgF~~L~~~DQi~LLk~~w~Ell~L~~a~r~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~i~ef~~~l~~L~ld  140 (239)
T cd07072          61 FAEKIPGFPDLCKEDQELLFQSASLELFVLRLAYRTAPEDTKLTFCNGVVLHKQQCQRSFGDWLHAILEFSKSLHAMDID  140 (239)
T ss_pred             HhccCCCccCCCHHHHHHHHHHhHHHHHHHHHHHHccCCCCeEEeeCCeeecHHHHHhhHHHHHHHHHHHHHHHHHcCCC
Confidence            3599999999999999                                                2245889999999999


Q ss_pred             hhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHh
Q psy16825        140 KEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYV  181 (183)
Q Consensus       140 ~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~  181 (183)
                      .+||+||+||+||+ |.+ |.+...|+++|++++.+|.+|+..
T Consensus       141 ~~E~a~LkAivLf~-dr~gL~~~~~Ve~lQe~~~~aL~~yi~~  182 (239)
T cd07072         141 ISAFACLCALTLIT-ERHGLKEPHKVEQLQMKIISSLRDHVTY  182 (239)
T ss_pred             HHHHHHHHHHHHhC-CCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999996 664 999999999999999999999974

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).

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

Probab=99.26  E-value=8.3e-12  Score=97.63  Aligned_cols=57  Identities=25%  Similarity=0.368  Sum_probs=51.8

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCC-C-----CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDV-K-----LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~-~-----L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|+.+++|.+||+|||||+|||||+ +     |++...|+++|++++.+|.+||...
T Consensus       119 ~~~~~~~l~~L~ld~~EyalLKAIvLfnpd~~g~~~~~l~~~~~Ve~lq~~~~~aL~~y~~~~  181 (235)
T cd06949         119 LLATASRFRELQLQREEYVCLKAIILLNSSVYTFLLESLESRRQVQRLLDKITDALVHACSKR  181 (235)
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHcCCCcCCcccccccCHHHHHHHHHHHHHHHHHHHHhc
Confidence            3568889999999999999999999999997 4     6788999999999999999999754

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

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

Probab=99.25  E-value=1e-11  Score=97.17  Aligned_cols=56  Identities=21%  Similarity=0.371  Sum_probs=52.3

Q ss_pred             hhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        127 TQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       127 ~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      .+++.+|++|++|.+||++||||+|+|||.+ |++...|+++|++++.+|.+|+...
T Consensus       119 ~~l~~~l~~L~ld~~E~~lLkaiiL~npd~~~L~~~~~v~~~q~~~~~aL~~y~~~~  175 (236)
T cd06948         119 QEQVEKLKALHVDSAEFSCLKAIVLFTSDACGLSDPAHIESLQEKSQCALEEYVRTQ  175 (236)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHcCcccccccCHHHHHHHHHHHHHHHHHHHHHh
Confidence            4788999999999999999999999999985 9999999999999999999999754

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

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

Probab=99.23  E-value=1.9e-11  Score=94.79  Aligned_cols=57  Identities=37%  Similarity=0.648  Sum_probs=52.7

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||++|+||+|+|||.. +.+...|+++|++|+.+|.+||...
T Consensus       113 ~~~~~~~l~~L~l~~~E~~lLkai~L~npd~~~l~~~~~v~~~q~~~~~aL~~y~~~~  170 (221)
T cd06946         113 CLQLVRRLQRLRLEKEEYVLLKALALANSDSVHIEDVEAVRQLRDALLEALSDYEAGR  170 (221)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            45799999999999999999999999999975 9999999999999999999999643

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-

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

Probab=99.22  E-value=2.6e-11  Score=90.43  Aligned_cols=57  Identities=21%  Similarity=0.427  Sum_probs=52.8

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+++++++|.+||++|+||+||+||.. |++...|++.|++++.+|.+|+...
T Consensus        88 ~~~~~~~l~~L~l~~~E~~llkai~l~~pd~~~l~~~~~v~~~q~~~~~aL~~y~~~~  145 (174)
T cd06929          88 LFEFAEKMNKLQLDDNEYALLTAIVLFSPDRPGLQDVDTVEKLQERLLEALQRYLKVN  145 (174)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcccCcCHHHHHHHHHHHHHHHHHHHHhc
Confidence            45789999999999999999999999999985 9999999999999999999998654

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=99.18  E-value=5.2e-11  Score=87.87  Aligned_cols=58  Identities=22%  Similarity=0.385  Sum_probs=53.3

Q ss_pred             hhhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        125 SCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       125 ~~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      .+.+++.+|+++++|.+||++|+||+|++||.. |++...|++.|++++.+|.+|+...
T Consensus        86 ~~~~~~~~l~~L~l~~~E~~lLkai~l~~p~~~~l~~~~~v~~~q~~~~~aL~~~~~~~  144 (165)
T cd06930          86 RLQELLSKLRSLQLDPKEYACLKAIVLFNPDLPGLKNQQQVEELQEKAQQALQEYIRKR  144 (165)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHHHHHHHHHHHhh
Confidence            346799999999999999999999999999985 9999999999999999999999753

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).

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

Probab=99.16  E-value=6e-11  Score=92.00  Aligned_cols=57  Identities=35%  Similarity=0.581  Sum_probs=52.9

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|+++++|.+||++|+||+|+|||+. |.+...|++.|++++.+|.+||...
T Consensus       113 ~~~~~~~l~~L~ld~~E~~lLkaIil~npd~~~L~~~~~V~~~q~~~~~aL~~y~~~~  170 (221)
T cd07068         113 LLQLVRRFRELGLQREEYVCLKAIILANSDVRHLEDREAVQQLRDAILDALVDVEAKR  170 (221)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHcCCCccCccCHHHHHHHHHHHHHHHHHHHHHh
Confidence            45789999999999999999999999999986 8999999999999999999998754

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

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

Probab=99.15  E-value=8.2e-11  Score=89.27  Aligned_cols=55  Identities=16%  Similarity=0.189  Sum_probs=51.7

Q ss_pred             hhhhhhchhcccChhHHHHHHHHHhcCCC--CC-CCchhHHHHHHHHHHHHHHHHHHh
Q psy16825        127 TQVIDRLEHVAVSKEEYYFLKALVLANSD--VK-LDEFSSLKKFRNSILSSLGDCIYV  181 (183)
Q Consensus       127 ~~lv~~~~~l~~~~~E~~~lkai~L~~~d--~~-L~~~~~v~~~~~~~~~~L~~~~~~  181 (183)
                      .+++.+|++|++|.+||++|+||+|++||  .. |++...|+.+|+.++.+|.+|+..
T Consensus        88 ~~~~~~l~~L~l~~~E~~lL~Aivl~~pd~~~~~l~~~~~v~~~q~~l~~~L~~~~~~  145 (191)
T cd06942          88 LQFANKILTLNLTNAELALLCAAELLQPDSLGIQLEETAKSNLQLSVLFQFLKSVLFK  145 (191)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCCccchHHHHHHHHHHHHHHHHHHHh
Confidence            47999999999999999999999999999  76 999999999999999999999864

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).

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

Probab=99.14  E-value=8.8e-11  Score=91.60  Aligned_cols=58  Identities=19%  Similarity=0.330  Sum_probs=54.7

Q ss_pred             hhhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        125 SCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       125 ~~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      .+++++.+|+.|++|..||++||||+|||||++ |.+...|+++|++++.+|.+|+...
T Consensus       128 ~l~e~~~~l~~L~ld~~E~a~LkAivLf~pD~~~L~~~~~Ve~lQe~~~~aL~~yi~~~  186 (232)
T cd07350         128 AIKAFLAKCWSLDISTKEYAYLKGTVLFNPDLPGLQCVQYIQGLQWEAQQALNEHVRMI  186 (232)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcccCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            467999999999999999999999999999987 9999999999999999999999754

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.

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

Probab=99.12  E-value=1.4e-10  Score=90.54  Aligned_cols=58  Identities=19%  Similarity=0.216  Sum_probs=51.9

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHHHHHHHhcC
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLR  183 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~L~~~~~v~~~~~~~~~~L~~~~~~~~  183 (183)
                      +.+++.+|++|++|.+||++|+||+||++..+|++...|+++|++++.+|.+||..++
T Consensus       125 l~~~~~~l~~L~ld~~E~~lL~AI~Lf~d~~~L~~~~~Ve~~Q~~~~~aL~~y~~~~~  182 (231)
T cd06938         125 LFRFCRAMCSMKVDNAEYALLTAIVIFSDRPGLLQPKKVEKIQEIYLEALRAYVDNRR  182 (231)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHccCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence            3457999999999999999999999998555699999999999999999999997653

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

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

Probab=99.11  E-value=1.4e-10  Score=90.03  Aligned_cols=56  Identities=23%  Similarity=0.394  Sum_probs=52.0

Q ss_pred             hhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        127 TQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       127 ~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      .+++.+|+++++|..||++|+||+|++||+. +++...|+++|++++.+|.+|+...
T Consensus       116 ~~~~~~l~~L~ld~~E~~~LkaiiLf~~d~~~l~~~~~v~~lq~~i~~aL~~y~~~~  172 (222)
T cd06952         116 QEFVNSMQKLDVDDHEYAYLKAIVLFSPDHPGQELRQQIEKLQEKALMELRDYVGKT  172 (222)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHhCCCCcCCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence            4678999999999999999999999999986 9999999999999999999999643

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

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

Probab=98.98  E-value=1.1e-09  Score=84.95  Aligned_cols=56  Identities=29%  Similarity=0.430  Sum_probs=52.1

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHh
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYV  181 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~  181 (183)
                      +.+++.+|+++++|.+||++|+||+|++||.. |++.+.++.+|++++.+|.+|+..
T Consensus       118 ~~~~~~~l~~L~l~~~E~~lLkaiil~~p~~~~ls~~~~i~~~r~~~~~aL~~y~~~  174 (222)
T cd06931         118 LDELVLPLRDLNIDDNEYACLKAIVFFDPDAKGLSDPQKIKRLRFQVQVSLEDYIND  174 (222)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHcCCCccCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            45789999999999999999999999999986 999999999999999999999853

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

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

Probab=98.69  E-value=4.4e-08  Score=71.65  Aligned_cols=59  Identities=25%  Similarity=0.395  Sum_probs=52.9

Q ss_pred             chhhhhhhhchhcccChhHHHHHHHHHhcCCCCC--CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        124 ISCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK--LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       124 ~~~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~--L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      ..+.+++.+|.++++|.+|+++|+|++|++|+..  +.....+++.|+++..+|.+|+...
T Consensus        86 ~~~~~~~~~~~~L~l~~~E~~~l~ai~l~~~~~~~s~~~~~~~~~~~~~~~~~L~~y~~~~  146 (168)
T cd06157          86 RLLFEFVNPLRALKLDDEEYALLKAIVLFSPDRKESLEDRKIVEELQERLLEALQDYLRKN  146 (168)
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHh
Confidence            3456899999999999999999999999999975  6777889999999999999998653

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

>smart00430 HOLI Ligand binding domain of hormone receptors

Probab=98.67  E-value=2.7e-08  Score=72.43  Aligned_cols=59  Identities=25%  Similarity=0.344  Sum_probs=52.9

Q ss_pred             chhhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCch--hHHHHHHHHHHHHHHHHHHhc
Q psy16825        124 ISCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEF--SSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       124 ~~~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~--~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      ..+.+++.+|++|+++.+|+++|+++++++|+.. +.+.  ..++++|+.+..+|.+|+...
T Consensus        80 ~~~~~~~~~l~~L~l~~~E~~~l~ai~l~~~~~~~l~~~~~~~~~~~~~~~~~~L~~y~~~~  141 (163)
T smart00430       80 RILQELVKPLRELKLDDEEYALLKAILLFNPAGPGLSEEGKEILEKLQEKLANALHDYYLKN  141 (163)
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHcChhhhhhChHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            4456899999999999999999999999999875 8877  789999999999999998653

>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=98.07  E-value=9.2e-06  Score=61.14  Aligned_cols=55  Identities=27%  Similarity=0.478  Sum_probs=48.1

Q ss_pred             hhhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CC-chhH-HHHHHHHHHHHHHHHH
Q psy16825        125 SCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LD-EFSS-LKKFRNSILSSLGDCI  179 (183)
Q Consensus       125 ~~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~-~~~~-v~~~~~~~~~~L~~~~  179 (183)
                      .+..++.+|.++++|.+||+++++++|++|+.. +. +... ++.+|+++..+|.+|+
T Consensus       106 ~~~~~~~~~~~l~l~~~E~~~l~~l~l~~~~~~~~~~~~~~~~~~~r~~~~~~L~~y~  163 (203)
T PF00104_consen  106 YMNEVLRPFRRLKLDEEEFALLKALILFNPDYPGLSEETREIVEELRDRIIQALHSYY  163 (203)
T ss_dssp             HHHHHHHHHHHTT-BHHHHHHHHHHHHSSTTSTTHS-SHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhhHHHHHHHHHhhhcccccccccchhHHHHHHHHHHHHHHHHHH
Confidence            455789999999999999999999999999876 66 5555 8899999999999998

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 ....

>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []

Probab=89.51  E-value=0.2  Score=34.79  Aligned_cols=33  Identities=21%  Similarity=0.642  Sum_probs=23.9

Q ss_pred             CCCCcccccCCCCc---ccccccccccchhhhhhcc
Q psy16825          8 LPRRLCLVCGDVAS---GFHYGVASCEACKAFFKRT   40 (183)
Q Consensus         8 ~~~~~C~vC~~~~~---~~hyg~~~C~~C~~FFrR~   40 (183)
                      +....|.-||.+..   ...||++.|..|++.+|-.
T Consensus        11 ~~N~~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~l   46 (116)
T PF01412_consen   11 PGNKVCADCGAPNPTWASLNYGIFLCLECAGIHRSL   46 (116)
T ss_dssp             TTCTB-TTT-SBS--EEETTTTEEE-HHHHHHHHHH
T ss_pred             cCcCcCCCCCCCCCCEEEeecChhhhHHHHHHHHHh
Confidence            44678999998775   3789999999999997764

The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	183
1lo1_A	98	Estrogen Related Receptor 2 Dna Binding Domain In C		9e-43
1hcq_A	84	The Crystal Structure Of The Estrogen Receptor Dna-		4e-26
2ff0_A	102	Solution Structure Of Steroidogenic Factor 1 Dna Bi		4e-25
2a66_A	113	Human Liver Receptor Homologue Dna-Binding Domain (		9e-25
1hcp_A	76	Dna Recognition By The Oestrogen Receptor: From Sol		1e-23
4aa6_E	71	The Oestrogen Receptor Recognizes An Imperfectly Pa		4e-23
4aa6_A	71	The Oestrogen Receptor Recognizes An Imperfectly Pa		4e-23
3dzu_A	467	Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp		2e-22
1cit_A	89	Dna-Binding Mechanism Of The Monomeric Orphan Nucle		7e-22
1ynw_B	99	Crystal Structure Of Vitamin D Receptor And 9-Cis R		1e-21
1dsz_B	85	Structure Of The RxrRAR DNA-Binding Domain Heterodi		3e-21
1rxr_A	83	High Resolution Solution Structure Of The Retinoid		3e-20
1by4_A	82	Structure And Mechanism Of The Homodimeric Assembly		3e-20
1hlz_A	94	Crystal Structure Of The Orphan Nuclear Receptor Re		7e-20
1r0n_A	81	Crystal Structure Of Heterodimeric Ecdsyone Recepto		9e-20
1dsz_A	86	Structure Of The RxrRAR DNA-Binding Domain Heterodi		1e-19
2han_A	93	Structural Basis Of Heterodimeric Ecdysteroid Recep		3e-19
4hn5_A	117	Gr Dna Binding Domain - Tslp Ngre Complex Length =		3e-19
1r0o_A	86	Crystal Structure Of The Heterodimeric Ecdysone Rec		4e-19
1hra_A	80	The Solution Structure Of The Human Retinoic Acid R		6e-19
1r4o_A	92	Crystallographic Analysis Of The Interaction Of The		2e-18
4hn6_A	114	Gr Dna Binding Domain R460d/d462r - Tslp Ngre Compl		2e-18
1r4r_B	92	Crystallographic Analysis Of The Interaction Of The		2e-18
1glu_A	81	Crystallographic Analysis Of The Interaction Of The		2e-18
2c7a_A	78	Structure Of The Progesterone Receptor-Dna Complex		2e-18
1ynw_A	110	Crystal Structure Of Vitamin D Receptor And 9-Cis R		2e-18
2nll_A	66	Retinoid X Receptor-Thyroid Hormone Receptor Dna-Bi		6e-18
1kb2_A	110	Crystal Structure Of Vdr Dna-Binding Domain Bound T		6e-18
1lat_A	82	Glucocorticoid Receptor MutantDNA COMPLEX Length =		7e-18
1gdc_A	72	Refined Solution Structure Of The Glucocorticoid Re		8e-18
3g9p_B	90	Gr Dna Binding Domain:sgk 16bp Complex-7 Length = 9		8e-18
2gda_A	72	Refined Solution Structure Of The Glucocorticoid Re		9e-18
1r4i_A	105	Crystal Structure Of Androgen Receptor Dna-Binding		2e-17
3dzu_D	419	Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp		2e-17
2ebl_A	89	Solution Structure Of The Zinc Finger, C4-type Doma		2e-17
1rgd_A	71	Structure Refinement Of The Glucocorticoid Receptor		3e-17
2env_A	88	Solution Sturcture Of The C4-Type Zinc Finger Domai		8e-17
3cbb_A	78	Crystal Structure Of Hepatocyte Nuclear Factor 4alp		2e-16
3g6t_A	91	Gr Gamma Dna-Binding Domain:fkbp5 16bp Complex-34 L		2e-16
2nll_B	103	Retinoid X Receptor-Thyroid Hormone Receptor Dna-Bi		6e-16
3m9e_A	105	Thyroid Hormone Beta Dna Binding Domain Homodimer W		3e-15
1r0n_B	109	Crystal Structure Of Heterodimeric Ecdsyone Recepto		8e-15
2han_B	119	Structural Basis Of Heterodimeric Ecdysteroid Recep		9e-15

>pdb|1LO1|A Chain A, Estrogen Related Receptor 2 Dna Binding Domain In Complex With Dna Length = 98

Iteration: 1
 Score =  169 bits (427), Expect = 9e-43,   Method: Compositional matrix adjust.
 Identities = 77/93 (82%), Positives = 87/93 (93%)
Query: 8   LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
           +P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQGNIEY+CPA+N+CEI KRRRK+CQA
Sbjct: 2   IPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQA 61
Query: 68  CRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPD 100
           CRF K L+ GMLKEGVRLDRVRGGRQKY+R  D
Sbjct: 62  CRFMKALKVGMLKEGVRLDRVRGGRQKYKRRLD 94

>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 =  114 bits (284), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 53/81 (65%), Positives = 63/81 (77%), Gaps = 1/81 (1%)
Query: 11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRF 70
          R C VC D ASG+HYGV SCE CKAFFKR+IQG+ +Y CPA+N C I+K RRK+CQACR 
Sbjct: 5  RYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRL 64
Query: 71 QKCLRKGMLKEGVRLDRVRGG 91
          +KC   GM+K G+R DR RGG
Sbjct: 65 RKCYEVGMMKGGIRKDR-RGG 84

>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 =  110 bits (276), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 55/98 (56%), Positives = 67/98 (68%), Gaps = 4/98 (4%)
Query: 12  LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQ 71
           LC VCGD  SG+HYG+ +CE+CK FFKRT+Q N  YTC  S  C+I+K +RK C  CRFQ
Sbjct: 3   LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKHYTCTESQSCKIDKTQRKRCPFCRFQ 62
Query: 72  KCLRKGMLKEGVRLDRVRGGRQK----YRRNPDLLSQQ 105
           KCL  GM  E VR DR+RGGR K    Y+R+  L  Q+
Sbjct: 63  KCLTVGMRLEAVRADRMRGGRNKFGPMYKRDRALKQQK 100

>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 =  109 bits (272), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 54/98 (55%), Positives = 68/98 (69%), Gaps = 4/98 (4%)
Query: 12  LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQ 71
           LC VCGD  SG+HYG+ +CE+CK FFKRT+Q N  YTC  + +C+I+K +RK C  CRFQ
Sbjct: 11  LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQNCQIDKTQRKRCPYCRFQ 70
Query: 72  KCLRKGMLKEGVRLDRVRGGRQK----YRRNPDLLSQQ 105
           KCL  GM  E VR DR+RGGR K    Y+R+  L  Q+
Sbjct: 71  KCLSVGMKLEAVRADRMRGGRNKFGPMYKRDRALKQQK 108

>pdb|1HCP|A Chain A, Dna Recognition By The Oestrogen Receptor: From Solution To The Crystal Length = 76

Iteration: 1
 Score =  105 bits (263), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 47/72 (65%), Positives = 56/72 (77%)
Query: 11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRF 70
          R C VC D ASG+HYGV SCE CKAFFKR+IQG+ +Y CPA+N C I+K RRK+CQACR 
Sbjct: 5  RYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRL 64
Query: 71 QKCLRKGMLKEG 82
          +KC   GM+K G
Sbjct: 65 RKCYEVGMMKGG 76

>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 =  103 bits (258), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 46/70 (65%), Positives = 55/70 (78%)
Query: 11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRF 70
          R C VC D ASG+HYGV SCE CKAFFKR+IQG+ +Y CPA+N C I+K RRK+CQACR 
Sbjct: 2  RYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRL 61
Query: 71 QKCLRKGMLK 80
          +KC   GM+K
Sbjct: 62 RKCYEVGMMK 71

>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 =  103 bits (258), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 46/70 (65%), Positives = 55/70 (78%)
Query: 11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRF 70
          R C VC D ASG+HYGV SCE CKAFFKR+IQG+ +Y CPA+N C I+K RRK+CQACR 
Sbjct: 2  RYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRL 61
Query: 71 QKCLRKGMLK 80
          +KC   GM+K
Sbjct: 62 RKCYEVGMMK 71

>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 =  101 bits (252), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 44/81 (54%), Positives = 59/81 (72%)
Query: 10  RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACR 69
           + +C +CGD +SG HYGV SCE CK FFKRT++ ++ YTC  + DC I+KR+R  CQ CR
Sbjct: 137 KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCR 196
Query: 70  FQKCLRKGMLKEGVRLDRVRG 90
           +QKCL  GM +E V+ +R RG
Sbjct: 197 YQKCLAMGMKREAVQEERQRG 217

>pdb|1CIT|A Chain A, Dna-Binding Mechanism Of The Monomeric Orphan Nuclear Receptor Ngfi-B Length = 89

Iteration: 1
 Score = 99.8 bits (247), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 49/87 (56%), Positives = 60/87 (68%)
Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQK 72
          C VCGD AS  HYGV +CE CK FFKRT+Q + +Y C A+ DC ++KRRR  CQ CRFQK
Sbjct: 3  CAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQK 62
Query: 73 CLRKGMLKEGVRLDRVRGGRQKYRRNP 99
          CL  GM+KE VR D ++G R +    P
Sbjct: 63 CLAVGMVKEVVRTDSLKGRRGRLPSKP 89

>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 = 99.4 bits (246), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 44/83 (53%), Positives = 59/83 (71%)
Query: 8  LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
            + +C +CGD +SG HYGV SCE CK FFKRT++ ++ YTC  + DC I+KR+R  CQ 
Sbjct: 1  FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQY 60
Query: 68 CRFQKCLRKGMLKEGVRLDRVRG 90
          CR+QKCL  GM +E V+ +R RG
Sbjct: 61 CRYQKCLAMGMKREAVQEERQRG 83

>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 = 97.8 bits (242), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 44/83 (53%), Positives = 59/83 (71%)
Query: 8  LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
            + +C +CGD +SG HYGV SCE CK FFKRT++ ++ YTC  + DC I+KR+R  CQ 
Sbjct: 3  FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQY 62
Query: 68 CRFQKCLRKGMLKEGVRLDRVRG 90
          CR+QKCL  GM +E V+ +R RG
Sbjct: 63 CRYQKCLAMGMKREAVQEERQRG 85

>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 = 94.4 bits (233), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 43/82 (52%), Positives = 58/82 (70%)
Query: 9  PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQAC 68
           + +C +CGD +SG HYGV SCE CK FFKRT++ ++ YTC  + DC I+KR+R  CQ C
Sbjct: 2  TKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYC 61
Query: 69 RFQKCLRKGMLKEGVRLDRVRG 90
          R+QK L  GM +E V+ +R RG
Sbjct: 62 RYQKALAMGMKREAVQEERQRG 83

>pdb|1BY4|A Chain A, Structure And Mechanism Of The Homodimeric Assembly Of The Rxr On Dna Length = 82

Iteration: 1
 Score = 94.4 bits (233), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 42/80 (52%), Positives = 57/80 (71%)
Query: 8  LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
            + +C +CGD +SG HYGV SCE CK FFKRT++ ++ YTC  + DC I+KR+R  CQ 
Sbjct: 3  FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQY 62
Query: 68 CRFQKCLRKGMLKEGVRLDR 87
          CR+QKCL  GM +E V+ +R
Sbjct: 63 CRYQKCLAMGMKREAVQEER 82

>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 = 93.2 bits (230), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 44/78 (56%), Positives = 55/78 (70%), Gaps = 1/78 (1%)
Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYT-CPASNDCEINKRRRKACQACRF 70
          LC VCGDVASGFHYGV +CE CK FF+R+IQ NI+Y  C  + +C I +  R  CQ CRF
Sbjct: 9  LCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRF 68
Query: 71 QKCLRKGMLKEGVRLDRV 88
          +KCL  GM ++ VR  R+
Sbjct: 69 KKCLSVGMSRDAVRFGRI 86

>pdb|1R0N|A Chain A, Crystal Structure Of Heterodimeric Ecdsyone Receptor Dna Binding Complex Length = 81

Iteration: 1
 Score = 92.8 bits (229), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 41/77 (53%), Positives = 55/77 (71%)
Query: 8  LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
            + +C +CGD +SG HYGV SCE CK FFKRT++ ++ YTC  + DC I+KR+R  CQ 
Sbjct: 1  FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQY 60
Query: 68 CRFQKCLRKGMLKEGVR 84
          CR+QKCL  GM +E V+
Sbjct: 61 CRYQKCLAMGMKREAVQ 77

>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 = 92.8 bits (229), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 43/75 (57%), Positives = 51/75 (68%)
Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQK 72
          C VC D +SG+HYGV++CE CK FF+R+IQ N+ YTC    +C INK  R  CQ CR QK
Sbjct: 7  CFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQK 66
Query: 73 CLRKGMLKEGVRLDR 87
          C   GM KE VR DR
Sbjct: 67 CFEVGMSKESVRNDR 81

>pdb|2HAN|A Chain A, Structural Basis Of Heterodimeric Ecdysteroid Receptor Interaction With Natural Response Element Hsp27 Gene Promoter Length = 93

Iteration: 1
 Score = 90.9 bits (224), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 42/79 (53%), Positives = 56/79 (70%)
Query: 9  PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQAC 68
           + LC +CGD ASG HYGV SCE CK FFKRT++ ++ Y C  + +C I+KR+R  CQ C
Sbjct: 9  SKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYACRENRNCIIDKRQRNRCQYC 68
Query: 69 RFQKCLRKGMLKEGVRLDR 87
          R+QKCL  GM +E V+ +R
Sbjct: 69 RYQKCLTCGMKREAVQEER 87

>pdb|4HN5|A Chain A, Gr Dna Binding Domain - Tslp Ngre Complex Length = 117

Iteration: 1
 Score = 90.9 bits (224), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 41/70 (58%), Positives = 50/70 (71%)
Query: 9  PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQAC 68
          P +LCLVC D ASG HYGV +C +CK FFKR ++G   Y C   NDC I+K RRK C AC
Sbjct: 28 PPKLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPAC 87
Query: 69 RFQKCLRKGM 78
          R++KCL+ GM
Sbjct: 88 RYRKCLQAGM 97

>pdb|1R0O|A Chain A, Crystal Structure Of The Heterodimeric Ecdysone Receptor Dna-Binding Complex Length = 86

Iteration: 1
 Score = 90.9 bits (224), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 42/79 (53%), Positives = 56/79 (70%)
Query: 9  PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQAC 68
           + LC +CGD ASG HYGV SCE CK FFKRT++ ++ Y C  + +C I+KR+R  CQ C
Sbjct: 7  SKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYACRENRNCIIDKRQRNRCQYC 66
Query: 69 RFQKCLRKGMLKEGVRLDR 87
          R+QKCL  GM +E V+ +R
Sbjct: 67 RYQKCLTCGMKREAVQEER 85

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

Iteration: 1
 Score = 90.1 bits (222), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 43/79 (54%), Positives = 53/79 (67%), Gaps = 2/79 (2%)
Query: 8  LPR--RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKAC 65
          +PR  + C VC D +SG+HYGV++CE CK FF+R+IQ N+ YTC    +C INK  R  C
Sbjct: 1  MPRVYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMIYTCHRDKNCVINKVTRNRC 60
Query: 66 QACRFQKCLRKGMLKEGVR 84
          Q CR QKC   GM KE VR
Sbjct: 61 QYCRLQKCFEVGMSKESVR 79

>pdb|1R4O|A Chain A, Crystallographic Analysis Of The Interaction Of The Glucocorticoid Receptor With Dna Length = 92

Iteration: 1
 Score = 88.6 bits (218), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 41/70 (58%), Positives = 49/70 (70%)
Query: 9  PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQAC 68
          P R CLVC D ASG HYGV +C +CK FFKR ++G   Y C   NDC I+K RRK C AC
Sbjct: 3  PARPCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPAC 62
Query: 69 RFQKCLRKGM 78
          R++KCL+ GM
Sbjct: 63 RYRKCLQAGM 72

>pdb|4HN6|A Chain A, Gr Dna Binding Domain R460d/d462r - Tslp Ngre Complex Length = 114

Iteration: 1
 Score = 88.6 bits (218), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 40/74 (54%), Positives = 50/74 (67%)
Query: 5  EEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKA 64
          +   P +LCLVC D ASG HYGV +C +CK FFKR ++G   Y C   N C I+K RRK 
Sbjct: 21 QSNAPPKLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGDNRCIIDKIRRKN 80
Query: 65 CQACRFQKCLRKGM 78
          C ACR++KCL+ GM
Sbjct: 81 CPACRYRKCLQAGM 94

>pdb|1R4R|B Chain B, Crystallographic Analysis Of The Interaction Of The Glucocorticoid Receptor With Dna Length = 92

Iteration: 1
 Score = 88.6 bits (218), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 41/70 (58%), Positives = 49/70 (70%)
Query: 9  PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQAC 68
          P R CLVC D ASG HYGV +C +CK FFKR ++G   Y C   NDC I+K RRK C AC
Sbjct: 3  PARPCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPAC 62
Query: 69 RFQKCLRKGM 78
          R++KCL+ GM
Sbjct: 63 RYRKCLQAGM 72

>pdb|1GLU|A Chain A, Crystallographic Analysis Of The Interaction Of The Glucocorticoid Receptor With Dna Length = 81

Iteration: 1
 Score = 88.2 bits (217), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 41/70 (58%), Positives = 49/70 (70%)
Query: 9  PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQAC 68
          P R CLVC D ASG HYGV +C +CK FFKR ++G   Y C   NDC I+K RRK C AC
Sbjct: 3  PARPCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPAC 62
Query: 69 RFQKCLRKGM 78
          R++KCL+ GM
Sbjct: 63 RYRKCLQAGM 72

>pdb|2C7A|A Chain A, Structure Of The Progesterone Receptor-Dna Complex Length = 78

Iteration: 1
 Score = 88.2 bits (217), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 39/74 (52%), Positives = 52/74 (70%)
Query: 9  PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQAC 68
          P+++CL+CGD ASG HYGV +C +CK FFKR ++G   Y C   NDC ++K RRK C AC
Sbjct: 1  PQKICLICGDEASGCHYGVLTCGSCKVFFKRAMEGQHNYLCAGRNDCIVDKIRRKNCPAC 60
Query: 69 RFQKCLRKGMLKEG 82
          R +KC + GM+  G
Sbjct: 61 RLRKCCQAGMVLGG 74

>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 = 88.2 bits (217), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 37/76 (48%), Positives = 53/76 (69%)
Query: 11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRF 70
          R+C VCGD A+GFH+   +CE CK FF+R+++    +TC A+ DC I K  R+ACQACR 
Sbjct: 7  RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCAANGDCRITKDNRRACQACRL 66
Query: 71 QKCLRKGMLKEGVRLD 86
          ++C+  GM+KE +  D
Sbjct: 67 KRCVDIGMMKEFILTD 82

>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 = 86.7 bits (213), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 39/66 (59%), Positives = 49/66 (74%)
Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQK 72
          C +CGD +SG HYGV SCE CK FFKRT++ ++ YTC  + DC I+KR+R  CQ CR+QK
Sbjct: 1  CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQK 60
Query: 73 CLRKGM 78
          CL  GM
Sbjct: 61 CLAMGM 66

>pdb|1KB2|A Chain A, Crystal Structure Of Vdr Dna-Binding Domain Bound To Mouse Osteopontin (Spp) Response Element Length = 110

Iteration: 1
 Score = 86.7 bits (213), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 36/76 (47%), Positives = 52/76 (68%)
Query: 11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRF 70
          R+C VCGD A+GFH+   +CE CK FF+R+++    +TCP + DC I K  R+ CQACR 
Sbjct: 7  RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRL 66
Query: 71 QKCLRKGMLKEGVRLD 86
          ++C+  GM+KE +  D
Sbjct: 67 KRCVDIGMMKEFILTD 82

>pdb|1LAT|A Chain A, Glucocorticoid Receptor MutantDNA COMPLEX Length = 82

Iteration: 1
 Score = 86.7 bits (213), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 41/70 (58%), Positives = 48/70 (68%)
Query: 9  PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQAC 68
          P R CLVC D ASG HYGV +CE CKAFFKR ++G   Y C     C I+K RRK C AC
Sbjct: 3  PARPCLVCSDEASGCHYGVLTCEGCKAFFKRAVEGQHNYLCKYEGKCIIDKIRRKNCPAC 62
Query: 69 RFQKCLRKGM 78
          R++KCL+ GM
Sbjct: 63 RYRKCLQAGM 72

>pdb|1GDC|A Chain A, Refined Solution Structure Of The Glucocorticoid Receptor Dna-Binding Domain Length = 72

Iteration: 1
 Score = 86.3 bits (212), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 40/67 (59%), Positives = 48/67 (71%)
Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQ 71
          LCLVC D ASG HYGV +C +CK FFKR ++G   Y C   NDC I+K RRK C ACR++
Sbjct: 1  LCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYR 60
Query: 72 KCLRKGM 78
          KCL+ GM
Sbjct: 61 KCLQAGM 67

>pdb|3G9P|B Chain B, Gr Dna Binding Domain:sgk 16bp Complex-7 Length = 90

Iteration: 1
 Score = 86.3 bits (212), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 39/68 (57%), Positives = 48/68 (70%)
Query: 11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRF 70
           +CLVC D ASG HYGV +C +CK FFKR ++G   Y C   NDC I+K RRK C ACR+
Sbjct: 3  HMCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRY 62
Query: 71 QKCLRKGM 78
          +KCL+ GM
Sbjct: 63 RKCLQAGM 70

>pdb|2GDA|A Chain A, Refined Solution Structure Of The Glucocorticoid Receptor Dna-Binding Domain Length = 72

Iteration: 1
 Score = 86.3 bits (212), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 40/67 (59%), Positives = 48/67 (71%)
Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQ 71
          LCLVC D ASG HYGV +C +CK FFKR ++G   Y C   NDC I+K RRK C ACR++
Sbjct: 1  LCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYR 60
Query: 72 KCLRKGM 78
          KCL+ GM
Sbjct: 61 KCLQAGM 67

>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 = 85.5 bits (210), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 37/70 (52%), Positives = 48/70 (68%)
Query: 9  PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQAC 68
          P++ CL+CGD ASG HYG  +C +CK FFKR  +G  +Y C + NDC I+K RRK C +C
Sbjct: 6  PQKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSC 65
Query: 69 RFQKCLRKGM 78
          R +KC   GM
Sbjct: 66 RLRKCYEAGM 75

>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 = 85.5 bits (210), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 41/77 (53%), Positives = 50/77 (64%), Gaps = 3/77 (3%)
Query: 13  CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYT-CPASNDCEINKRRRKACQACRFQ 71
           C VCGD ASGFHYGV +CE CK FF+RTI+  + Y  C    +C I+K+ R  CQ CRFQ
Sbjct: 53  CRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLIYDRCDL--NCRIHKKSRNKCQYCRFQ 110
Query: 72  KCLRKGMLKEGVRLDRV 88
           KCL  GM    +R  R+
Sbjct: 111 KCLAVGMSHNAIRFGRM 127

>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 = 84.7 bits (208), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 37/72 (51%), Positives = 53/72 (73%)
Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQK 72
          C+VCGD +SG HYG  +CE CK+FFKR+++ N+ YTC A+ +C I++  R  CQ CR +K
Sbjct: 10 CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRANRNCPIDQHHRNQCQYCRLKK 69
Query: 73 CLRKGMLKEGVR 84
          CL+ GM +E V+
Sbjct: 70 CLKVGMRREAVQ 81

>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 = 84.3 bits (207), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 39/66 (59%), Positives = 47/66 (71%)
Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQK 72
          CLVC D ASG HYGV +C +CK FFKR ++G   Y C   NDC I+K RRK C ACR++K
Sbjct: 1  CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRK 60
Query: 73 CLRKGM 78
          CL+ GM
Sbjct: 61 CLQAGM 66

>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 = 83.2 bits (204), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 40/74 (54%), Positives = 47/74 (63%), Gaps = 1/74 (1%)
Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQK 72
          C VCGD ASGFHYGV +CE CK FF+RTI+  +EY       C+I K+ R  CQ CRFQK
Sbjct: 10 CRVCGDKASGFHYGVHACEGCKGFFRRTIRMKLEYE-KCERSCKIQKKNRNKCQYCRFQK 68
Query: 73 CLRKGMLKEGVRLD 86
          CL  GM    +R  
Sbjct: 69 CLALGMSHNAIRFG 82

>pdb|3CBB|A Chain A, Crystal Structure Of Hepatocyte Nuclear Factor 4alpha In Complex With Dna: Diabetes Gene Product Length = 78

Iteration: 1
 Score = 82.0 bits (201), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 36/76 (47%), Positives = 52/76 (68%)
Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQ 71
          LC +CGD A+G HYG +SC+ CK FF+R+++ N  Y+C  S  C ++K +R  C+ CR +
Sbjct: 2  LCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLK 61
Query: 72 KCLRKGMLKEGVRLDR 87
          KC R GM KE V+ +R
Sbjct: 62 KCFRAGMKKEAVQNER 77

>pdb|3G6T|A Chain A, Gr Gamma Dna-Binding Domain:fkbp5 16bp Complex-34 Length = 91

Iteration: 1
 Score = 81.6 bits (200), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 39/68 (57%), Positives = 48/68 (70%), Gaps = 1/68 (1%)
Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQG-NIEYTCPASNDCEINKRRRKACQACRF 70
          +CLVC D ASG HYGV +C +CK FFKR ++G    Y C   NDC I+K RRK C ACR+
Sbjct: 4  MCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGRQHNYLCAGRNDCIIDKIRRKNCPACRY 63
Query: 71 QKCLRKGM 78
          +KCL+ GM
Sbjct: 64 RKCLQAGM 71

>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 = 80.1 bits (196), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 40/85 (47%), Positives = 53/85 (62%), Gaps = 2/85 (2%)
Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIE--YTCPASNDCEINKRRRKACQACR 69
          LC+VCGD A+G+HY   +CE CK FF+RTIQ N+   Y+C     C I+K  R  CQ CR
Sbjct: 3  LCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQECR 62
Query: 70 FQKCLRKGMLKEGVRLDRVRGGRQK 94
          F+KC+  GM  + V  D  R  ++K
Sbjct: 63 FKKCIYVGMATDLVLDDSKRLAKRK 87

>pdb|3M9E|A Chain A, Thyroid Hormone Beta Dna Binding Domain Homodimer With Inverted Palindrome Tre Length = 105

Iteration: 1
 Score = 78.2 bits (191), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 39/85 (45%), Positives = 53/85 (62%), Gaps = 2/85 (2%)
Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIE--YTCPASNDCEINKRRRKACQACR 69
          LC+VCGD A+G+HY   +CE CK FF+RTIQ ++   Y+C     C I+K  R  CQ CR
Sbjct: 5  LCVVCGDKATGYHYRCITCEGCKGFFRRTIQKSLHPSYSCKYEGKCIIDKVTRNQCQECR 64
Query: 70 FQKCLRKGMLKEGVRLDRVRGGRQK 94
          F+KC+  GM  + V  D  R  ++K
Sbjct: 65 FKKCIYVGMATDLVLDDSKRLAKRK 89

>pdb|1R0N|B Chain B, Crystal Structure Of Heterodimeric Ecdsyone Receptor Dna Binding Complex Length = 109

Iteration: 1
 Score = 76.3 bits (186), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 35/72 (48%), Positives = 45/72 (62%)
Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQ 71
          LCLVCGD ASG+HY   +CE CK FF+R++  +  Y C     CE++   R+ CQ CR +
Sbjct: 8  LCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECRLK 67
Query: 72 KCLRKGMLKEGV 83
          KCL  GM  E V
Sbjct: 68 KCLAVGMRPECV 79

>pdb|2HAN|B Chain B, Structural Basis Of Heterodimeric Ecdysteroid Receptor Interaction With Natural Response Element Hsp27 Gene Promoter Length = 119

Iteration: 1
 Score = 76.3 bits (186), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 35/72 (48%), Positives = 45/72 (62%)
Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQ 71
          LCLVCGD ASG+HY   +CE CK FF+R++  +  Y C     CE++   R+ CQ CR +
Sbjct: 10 LCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECRLK 69
Query: 72 KCLRKGMLKEGV 83
          KCL  GM  E V
Sbjct: 70 KCLAVGMRPECV 81

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	183
1lo1_A	98	Steroid hormone receptor ERR2; estrogen related re	3e-52
2a66_A	113	Orphan nuclear receptor NR5A2; protein-DNA complex	1e-48
1cit_A	89	NGFI-B, protein (orphan nuclear receptor NGFI-B);	1e-47
1r4i_A	105	Androgen receptor; AR, steroid receptor, protein-D	2e-47
3g9m_A	90	Glucocorticoid receptor; glucocorticoid, DNA-bindi	8e-46
1hcq_A	84	Protein (estrogen receptor); protein-DNA complex,	8e-46
1ynw_B	99	Retinoic acid receptor RXR-alpha, retinoid X recep	3e-45
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	1e-44
1kb2_A	110	Vitamin D3 receptor; VDR, nuclear receptor, protei	2e-44
1dsz_B	85	RXR-alpha, retinoic acid receptor RXR-alpha; RAR,	2e-44
2han_A	93	Protein ultraspiracle; transcription regulation, t	7e-44
1dsz_A	86	RAR-alpha, retinoic acid receptor alpha; RAR, nucl	3e-43
1a6y_A	94	Orphan nuclear receptor NR1D1; orphan receptor, DN	2e-41
2han_B	119	Ecdysone receptor; transcription regulation, trans	4e-41
2ebl_A	89	COUP transcription factor 1; DNA-binding, metal-bi	6e-39
2nll_B	103	Protein (thyroid hormone receptor); complex (trans	6e-38
3cbb_A	78	HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DN	6e-38
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	4e-37
3k6p_A	248	Steroid hormone receptor ERR1; estrogen related re	7e-08
3ltx_A	243	Estrogen receptor; constitutive, nuclear receptor,	2e-07
2e2r_A	244	Estrogen-related receptor gamma; ERR gamma, BPA, n	3e-07
1z5x_E	310	Ecdysone receptor ligand binding domain; ponastero	5e-07
3tx7_B	352	Nuclear receptor subfamily 5 group A member 2; LRH	6e-07
3plz_A	257	FTZ-F1 related protein; alpha helical sandwhich, f	1e-06
1ovl_A	271	Orphan nuclear receptor NURR1 (MSe 414, 496, 511);	1e-06
1ovl_A	271	Orphan nuclear receptor NURR1 (MSe 414, 496, 511);	3e-04
1pzl_A	237	Hepatocyte nuclear factor 4-alpha; transcription;	2e-06
1g2n_A	264	Ultraspiracle protein; antiparallel alpha-helical	3e-06
1ymt_A	246	Steroidogenic factor 1; SF-1, ligand-binding domai	4e-06
2nxx_A	235	Ultraspiracle (USP, NR2B4); hormone receptor, APO	9e-06
3vhv_A	260	Mineralocorticoid receptor; nuclear receptor, tran	9e-06
2iz2_A	243	FTZ-F1 alpha, nuclear hormone receptor FTZ-F1; nuc	1e-05
3mnp_A	261	Glucocorticoid receptor; protein-ligand complex, s	1e-05
1lbd_A	282	RXR_LBD, retinoid X receptor; transcription factor	2e-05
1lbd_A	282	RXR_LBD, retinoid X receptor; transcription factor	3e-04
3vhu_A	294	Mineralocorticoid receptor; nuclear receptor, tran	2e-05
1sqn_A	261	PR, progesterone receptor; nuclear receptor, stero	3e-05
3oll_A	240	Estrogen receptor beta; steroid binding, phosphory	8e-05
1xpc_A	248	Estrogen receptor; nuclear receptor, transcription	8e-05
1t7r_A	269	Androgen receptor; nuclear receptor, transcription	8e-05
2p1t_A	240	Retinoic acid receptor RXR-alpha; protein-ligand c	1e-04
2ocf_A	298	Estrogen receptor; estrogen receptor, LBD, monobod	4e-04
1hg4_A	279	Ultraspiracle; nuclear hormone receptor, transcrip	7e-04
3cjw_A	244	COUP transcription factor 2; COUP-TFII, nuclear re	7e-04
2hc4_A	302	Vitamin D receptor; alpha helical sandwich, gene r	8e-04

>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 =  161 bits (409), Expect = 3e-52
 Identities = 77/93 (82%), Positives = 87/93 (93%)

Query: 8   LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
           +P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQGNIEY+CPA+N+CEI KRRRK+CQA
Sbjct: 2   IPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQA 61

Query: 68  CRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPD 100
           CRF K L+ GMLKEGVRLDRVRGGRQKY+R  D
Sbjct: 62  CRFMKALKVGMLKEGVRLDRVRGGRQKYKRRLD 94

>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 =  152 bits (386), Expect = 1e-48
 Identities = 53/111 (47%), Positives = 68/111 (61%)

Query: 2   GIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRR 61
           G   +E    LC VCGD  SG+HYG+ +CE+CK FFKRT+Q N  YTC  + +C+I+K +
Sbjct: 1   GEFGDEDLEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQNCQIDKTQ 60

Query: 62  RKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSI 112
           RK C  CRFQKCL  GM  E VR DR+RGGR K+              K++
Sbjct: 61  RKRCPYCRFQKCLSVGMKLEAVRADRMRGGRNKFGPMYKRDRALKQQKKAL 111

>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 =  149 bits (378), Expect = 1e-47
 Identities = 49/87 (56%), Positives = 60/87 (68%)

Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQK 72
          C VCGD AS  HYGV +CE CK FFKRT+Q + +Y C A+ DC ++KRRR  CQ CRFQK
Sbjct: 3  CAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQK 62

Query: 73 CLRKGMLKEGVRLDRVRGGRQKYRRNP 99
          CL  GM+KE VR D ++G R +    P
Sbjct: 63 CLAVGMVKEVVRTDSLKGRRGRLPSKP 89

>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 =  149 bits (377), Expect = 2e-47
 Identities = 38/92 (41%), Positives = 54/92 (58%)

Query: 9   PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQAC 68
           P++ CL+CGD ASG HYG  +C +CK FFKR  +G  +Y C + NDC I+K RRK C +C
Sbjct: 6   PQKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSC 65

Query: 69  RFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPD 100
           R +KC   GM     +L ++   + +      
Sbjct: 66  RLRKCYEAGMTLGARKLKKLGNLKLQEEGENS 97

>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 =  144 bits (366), Expect = 8e-46
 Identities = 42/86 (48%), Positives = 54/86 (62%)

Query: 11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRF 70
           +CLVC D ASG HYGV +C +CK FFKR ++G   Y C   NDC I+K RRK C ACR+
Sbjct: 3  HMCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRY 62

Query: 71 QKCLRKGMLKEGVRLDRVRGGRQKYR 96
          +KCL+ GM  E  +  +   G Q+  
Sbjct: 63 RKCLQAGMNLEARKTKKKIKGIQQAT 88

>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 =  144 bits (365), Expect = 8e-46
 Identities = 51/82 (62%), Positives = 61/82 (74%)

Query: 9  PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQAC 68
            R C VC D ASG+HYGV SCE CKAFFKR+IQG+ +Y CPA+N C I+K RRK+CQAC
Sbjct: 3  ETRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQAC 62

Query: 69 RFQKCLRKGMLKEGVRLDRVRG 90
          R +KC   GM+K G+R DR  G
Sbjct: 63 RLRKCYEVGMMKGGIRKDRRGG 84

>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 =  143 bits (363), Expect = 3e-45
 Identities = 45/98 (45%), Positives = 61/98 (62%)

Query: 8   LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
             + +C +CGD +SG HYGV SCE CK FFKRT++ ++ YTC  + DC I+KR+R  CQ 
Sbjct: 1   FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQY 60

Query: 68  CRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQ 105
           CR+QKCL  GM +E V+ +R RG  +         S  
Sbjct: 61  CRYQKCLAMGMKREAVQEERQRGKDRNENEVESTSSAN 98

>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 =  152 bits (385), Expect = 1e-44
 Identities = 46/115 (40%), Positives = 67/115 (58%), Gaps = 2/115 (1%)

Query: 9   PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQAC 68
            + +C +CGD +SG HYGV SCE CK FFKRT++ ++ YTC  + DC I+KR+R  CQ C
Sbjct: 136 TKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYC 195

Query: 69  RFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEDLERNTE 123
           R+QKCL  GM +E V+ +R RG  +         +     +  +  + + E   E
Sbjct: 196 RYQKCLAMGMKREAVQEERQRGKDRNENEVES--TSSANEDMPVERILEAELAVE 248

>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 =  141 bits (358), Expect = 2e-44
 Identities = 40/109 (36%), Positives = 62/109 (56%), Gaps = 3/109 (2%)

Query: 6   EELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKAC 65
           +    R+C VCGD A+GFH+   +CE CK FF+R+++    +TCP + DC I K  R+ C
Sbjct: 2   DRNVPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHC 61

Query: 66  QACRFQKCLRKGMLKEGVRLDRVRGGRQKY---RRNPDLLSQQWPPNKS 111
           QACR ++C+  GM+KE +  D     +++    R+  + L     P  S
Sbjct: 62  QACRLKRCVDIGMMKEFILTDEEVQRKREMILKRKEEEALKDSLRPKLS 110

>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 =  140 bits (356), Expect = 2e-44
 Identities = 44/83 (53%), Positives = 59/83 (71%)

Query: 8  LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
            + +C +CGD +SG HYGV SCE CK FFKRT++ ++ YTC  + DC I+KR+R  CQ 
Sbjct: 3  FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQY 62

Query: 68 CRFQKCLRKGMLKEGVRLDRVRG 90
          CR+QKCL  GM +E V+ +R RG
Sbjct: 63 CRYQKCLAMGMKREAVQEERQRG 85

>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 =  139 bits (353), Expect = 7e-44
 Identities = 43/84 (51%), Positives = 57/84 (67%)

Query: 9  PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQAC 68
           + LC +CGD ASG HYGV SCE CK FFKRT++ ++ Y C  + +C I+KR+R  CQ C
Sbjct: 9  SKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYACRENRNCIIDKRQRNRCQYC 68

Query: 69 RFQKCLRKGMLKEGVRLDRVRGGR 92
          R+QKCL  GM +E V+ +R    R
Sbjct: 69 RYQKCLTCGMKREAVQEERQGIHR 92

>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 =  138 bits (349), Expect = 3e-43
 Identities = 43/84 (51%), Positives = 54/84 (64%)

Query: 9  PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQAC 68
            + C VC D +SG+HYGV++CE CK FF+R+IQ N+ YTC    +C INK  R  CQ C
Sbjct: 3  IYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYC 62

Query: 69 RFQKCLRKGMLKEGVRLDRVRGGR 92
          R QKC   GM KE VR DR +  +
Sbjct: 63 RLQKCFEVGMSKESVRNDRNKKKK 86

>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 =  133 bits (337), Expect = 2e-41
 Identities = 47/89 (52%), Positives = 59/89 (66%), Gaps = 2/89 (2%)

Query: 9  PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYT-CPASNDCEINKRRRKACQA 67
             LC VCGDVASGFHYGV +CE CK FF+R+IQ NI+Y  C  + +C I +  R  CQ 
Sbjct: 6  MVLLCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQ 65

Query: 68 CRFQKCLRKGMLKEGVRLDRVRGGRQKYR 96
          CRF+KCL  GM ++ VR  R+   R+K R
Sbjct: 66 CRFKKCLSVGMSRDAVRFGRIP-KREKQR 93

>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 =  133 bits (337), Expect = 4e-41
 Identities = 37/109 (33%), Positives = 56/109 (51%), Gaps = 3/109 (2%)

Query: 11  RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRF 70
            LCLVCGD ASG+HY   +CE CK FF+R++  +  Y C     CE++   R+ CQ CR 
Sbjct: 9   ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECRL 68

Query: 71  QKCLRKGMLKEGVRLDRVRGGRQKYR---RNPDLLSQQWPPNKSIPSLE 116
           +KCL  GM  E V  +     +++ +   +  D ++         P + 
Sbjct: 69  KKCLAVGMRPECVVPENQCAMKRREKKAQKEKDKMTTSPSSQHGSPGIH 117

>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 =  127 bits (321), Expect = 6e-39
 Identities = 37/80 (46%), Positives = 53/80 (66%)

Query: 9  PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQAC 68
              C+VCGD +SG HYG  +CE CK+FFKR+++ N+ YTC A+ +C I++  R  CQ C
Sbjct: 6  SGIECVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRANRNCPIDQHHRNQCQYC 65

Query: 69 RFQKCLRKGMLKEGVRLDRV 88
          R +KCL+ GM +E V+    
Sbjct: 66 RLKKCLKVGMRREAVQRGSG 85

>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 =  125 bits (315), Expect = 6e-38
 Identities = 40/85 (47%), Positives = 53/85 (62%), Gaps = 2/85 (2%)

Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIE--YTCPASNDCEINKRRRKACQACR 69
          LC+VCGD A+G+HY   +CE CK FF+RTIQ N+   Y+C     C I+K  R  CQ CR
Sbjct: 3  LCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQECR 62

Query: 70 FQKCLRKGMLKEGVRLDRVRGGRQK 94
          F+KC+  GM  + V  D  R  ++K
Sbjct: 63 FKKCIYVGMATDLVLDDSKRLAKRK 87

>3cbb_A HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DNA binding domain, nuclear; zinc finger; 2.00A {Homo sapiens} Length = 78

 Score =  124 bits (313), Expect = 6e-38
 Identities = 36/76 (47%), Positives = 52/76 (68%)

Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQ 71
          LC +CGD A+G HYG +SC+ CK FF+R+++ N  Y+C  S  C ++K +R  C+ CR +
Sbjct: 2  LCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLK 61

Query: 72 KCLRKGMLKEGVRLDR 87
          KC R GM KE V+ +R
Sbjct: 62 KCFRAGMKKEAVQNER 77

>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 =  131 bits (331), Expect = 4e-37
 Identities = 41/89 (46%), Positives = 51/89 (57%), Gaps = 1/89 (1%)

Query: 9   PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQAC 68
               C VCGD ASGFHYGV +CE CK FF+RTI+  + Y     N C I+K+ R  CQ C
Sbjct: 49  MAIECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLIYDRCDLN-CRIHKKSRNKCQYC 107

Query: 69  RFQKCLRKGMLKEGVRLDRVRGGRQKYRR 97
           RFQKCL  GM    +R  R+    ++   
Sbjct: 108 RFQKCLAVGMSHNAIRFGRMPQAEKEKLL 136

>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 = 49.7 bits (119), Expect = 7e-08
 Identities = 17/56 (30%), Positives = 35/56 (62%), Gaps = 1/56 (1%)

Query: 125 SCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCI 179
           +  Q++ RL+ + + +EEY  LKAL LANSD   +++  ++++ R ++  +L +  
Sbjct: 133 ALLQLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQLREALHEALLEYE 188

>3ltx_A Estrogen receptor; constitutive, nuclear receptor, DNA-binding, metal-binding, nucleus, transcription, transcription regulation, zinc-finger; 2.60A {Crassostrea gigas} Length = 243

 Score = 48.5 bits (116), Expect = 2e-07
 Identities = 13/53 (24%), Positives = 30/53 (56%), Gaps = 1/53 (1%)

Query: 128 QVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCI 179
            V +++    + K+E   L+A+VL N++V+ L  ++ +   + S+L ++ D  
Sbjct: 125 AVSEQMMQNHLHKDELLLLQAMVLVNAEVRRLASYNQIFNMQQSLLDAIVDTA 177

>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 = 47.8 bits (114), Expect = 3e-07
 Identities = 15/53 (28%), Positives = 33/53 (62%), Gaps = 1/53 (1%)

Query: 128 QVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCI 179
           Q++ + + + + KEE+  LKA+ LANSD   +++  +++K ++ +  +L D  
Sbjct: 136 QLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQDYE 188

>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 = 47.5 bits (113), Expect = 5e-07
 Identities = 13/99 (13%), Positives = 29/99 (29%), Gaps = 16/99 (16%)

Query: 53  NDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRR------NPDLLSQQW 106
             C + KR+ K  Q  + +         +G++ +          +         +  +Q 
Sbjct: 21  FQCAV-KRKEKKAQKDKDKPNSTTSCSPDGIKQEIDPQRLDTDSQLLSVNGVKPITPEQE 79

Query: 107 PPNKSI---------PSLEDLERNTEISCTQVIDRLEHV 136
                +         PS ED++R    +  +     E  
Sbjct: 80  ELIHRLVYFQNEYEHPSPEDIKRIVNAAPEEENVAEERF 118

>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 = 47.3 bits (112), Expect = 6e-07
 Identities = 14/55 (25%), Positives = 29/55 (52%), Gaps = 1/55 (1%)

Query: 126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCI 179
             +++ +L  +   + E+  LK LVL + DVK L+ F  ++  +  + ++L D  
Sbjct: 242 AQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYT 296

>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 = 46.3 bits (110), Expect = 1e-06
 Identities = 14/55 (25%), Positives = 29/55 (52%), Gaps = 1/55 (1%)

Query: 126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCI 179
             +++ +L  +   + E+  LK LVL + DVK L+ F  ++  +  + ++L D  
Sbjct: 147 AQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYT 201

>1ovl_A Orphan nuclear receptor NURR1 (MSe 414, 496, 511); NUUR1, LBD, transcription; 2.20A {Homo sapiens} SCOP: a.123.1.1 Length = 271

 Score = 46.2 bits (110), Expect = 1e-06
 Identities = 12/41 (29%), Positives = 20/41 (48%)

Query: 78  MLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEDL 118
           M+KE VR D ++G R +    P    +  PP+  +  +  L
Sbjct: 1   MVKEVVRTDSLKGRRGRLPSKPKSPQEPSPPSPPVSLISAL 41

>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 = 39.3 bits (92), Expect = 3e-04
 Identities = 9/52 (17%), Positives = 24/52 (46%)

Query: 128 QVIDRLEHVAVSKEEYYFLKALVLANSDVKLDEFSSLKKFRNSILSSLGDCI 179
           +    L+++ +    +  + AL +      L E   +++ +N I++ L D +
Sbjct: 161 EFSSNLQNMNIDISAFSCIAALAMVTERHGLKEPKRVEELQNKIVNCLKDHV 212

>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 = 45.5 bits (108), Expect = 2e-06
 Identities = 19/80 (23%), Positives = 39/80 (48%), Gaps = 1/80 (1%)

Query: 101 LLSQQWPPNKSIPSLEDLERNTEISCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LD 159
           LL   +   +  P L ++ R +     +++   + + +   EY +LKA++  + D K L 
Sbjct: 103 LLGNDYIVPRHCPELAEMSRVSIRILDELVLPFQELQIDDNEYAYLKAIIFFDPDAKGLS 162

Query: 160 EFSSLKKFRNSILSSLGDCI 179
           +   +K+ R+ +  SL D I
Sbjct: 163 DPGKIKRLRSQVQVSLEDYI 182

>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 = 45.2 bits (107), Expect = 3e-06
 Identities = 15/80 (18%), Positives = 34/80 (42%), Gaps = 1/80 (1%)

Query: 101 LLSQQWPPNKSIPSLEDLERNTEISCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LD 159
            L      +++      + +  +   +++  ++  + V + EY  LKA++L N DVK L 
Sbjct: 122 CLMPGMTLHRNSALQAGVGQIFDRVLSELSLKMRTLRVDQAEYVALKAIILLNPDVKGLK 181

Query: 160 EFSSLKKFRNSILSSLGDCI 179
               ++  R  +   L +  
Sbjct: 182 NRQEVEVLREKMFLCLDEYC 201

>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 = 44.8 bits (106), Expect = 4e-06
 Identities = 16/83 (19%), Positives = 33/83 (39%), Gaps = 6/83 (7%)

Query: 98  NPDLLSQQWPPNKSIPSLEDLERNTEISCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK 157
             ++                + R  E+       +L  + + ++E+  LK L+L + DVK
Sbjct: 113 GQEVELSTVAVQAGSLLHSLVLRAQELVL-----QLHALQLDRQEFVCLKFLILFSLDVK 167

Query: 158 -LDEFSSLKKFRNSILSSLGDCI 179
            L+  S +K  +    ++L D  
Sbjct: 168 FLNNHSLVKDAQEKANAALLDYT 190

>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 = 43.5 bits (103), Expect = 9e-06
 Identities = 11/53 (20%), Positives = 28/53 (52%), Gaps = 1/53 (1%)

Query: 128 QVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCI 179
           +++++++ + + K E   L+A++L N DV+ +     ++  R  I   L +  
Sbjct: 126 ELVNKMKEMKMDKTELGCLRAIILYNPDVRGIKSVQEVEMLREKIYGVLEEYT 178

>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 = 43.8 bits (103), Expect = 9e-06
 Identities = 11/56 (19%), Positives = 27/56 (48%), Gaps = 2/56 (3%)

Query: 126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK--LDEFSSLKKFRNSILSSLGDCI 179
             Q+  +   + ++ EEY  +K L+L ++  K  L   ++ ++ R + +  L   +
Sbjct: 128 MHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKDGLKSQAAFEEMRTNYIKELRKMV 183

>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 = 43.4 bits (102), Expect = 1e-05
 Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 2/54 (3%)

Query: 128 QVIDRLEHVAVSKEEYYFLKALVLANSDVK--LDEFSSLKKFRNSILSSLGDCI 179
            +   L+ + VS EEY  +K L+L +S  K  L       + R + +  LG  I
Sbjct: 132 FISTELQRLQVSYEEYLCMKTLLLLSSVPKEGLKSQELFDEIRMTYIKELGKAI 185

>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 = 42.9 bits (101), Expect = 2e-05
 Identities = 7/62 (11%), Positives = 18/62 (29%), Gaps = 5/62 (8%)

Query: 62  RKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEDLERN 121
                +    +       +E V+ +R RG  +         +     +  +  + + E  
Sbjct: 7   HHHHSSGLVPRG---SHKREAVQEERQRGKDRNENEVE--STSSANEDMPVERILEAELA 61

Query: 122 TE 123
            E
Sbjct: 62  VE 63

>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 = 39.0 bits (91), Expect = 3e-04
 Identities = 13/53 (24%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 128 QVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCI 179
           +++ ++  + + K E   L+A+VL N D K L   + ++  R  + +SL    
Sbjct: 172 ELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYC 224

>3vhu_A Mineralocorticoid receptor; nuclear receptor, transcription factor, activating mutation, hypertension, antagonist, spironolactone; HET: SNL; 2.11A {Homo sapiens} Length = 294

 Score = 43.0 bits (101), Expect = 2e-05
 Identities = 11/56 (19%), Positives = 27/56 (48%), Gaps = 2/56 (3%)

Query: 126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK--LDEFSSLKKFRNSILSSLGDCI 179
             Q+  +   + ++ EEY  +K L+L ++  K  L   ++ ++ R + +  L   +
Sbjct: 162 MHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKDGLKSQAAFEEMRTNYIKELRKMV 217

>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 = 42.2 bits (99), Expect = 3e-05
 Identities = 14/54 (25%), Positives = 26/54 (48%), Gaps = 2/54 (3%)

Query: 128 QVIDRLEHVAVSKEEYYFLKALVLANSDVK--LDEFSSLKKFRNSILSSLGDCI 179
           Q+      + VS+EE+  +K L+L N+     L   +  ++ R+S +  L   I
Sbjct: 131 QIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELIKAI 184

>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 = 40.9 bits (96), Expect = 8e-05
 Identities = 13/60 (21%), Positives = 23/60 (38%), Gaps = 8/60 (13%)

Query: 128 QVIDRLEHVAVSKEEYYFLKALVLANSDVK--------LDEFSSLKKFRNSILSSLGDCI 179
               R   + +  +EY  +KA++L NS +          D    L    N++  +L   I
Sbjct: 122 ATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNAVTDALVWVI 181

>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 = 40.9 bits (96), Expect = 8e-05
 Identities = 13/61 (21%), Positives = 25/61 (40%), Gaps = 9/61 (14%)

Query: 128 QVIDRLEHVAVSKEEYYFLKALVLANSDVK---------LDEFSSLKKFRNSILSSLGDC 178
               R   + +  EE+  LK+++L NS V          L+E   + +  + I  +L   
Sbjct: 124 ATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHL 183

Query: 179 I 179
           +
Sbjct: 184 M 184

>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 = 40.7 bits (95), Expect = 8e-05
 Identities = 10/58 (17%), Positives = 22/58 (37%), Gaps = 2/58 (3%)

Query: 128 QVIDRLEHVAVSKEEYYFLKALVLANSDVK--LDEFSSLKKFRNSILSSLGDCIYVLR 183
            +      + ++ +E+  +KAL+L +      L       + R + +  L   I   R
Sbjct: 139 HLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFFDELRMNYIKELDRIIACKR 196

>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 = 40.1 bits (94), Expect = 1e-04
 Identities = 13/53 (24%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 128 QVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCI 179
           +++ ++  + + K E   L+A+VL N D K L   + ++  R  + +SL    
Sbjct: 130 ELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYC 182

>2ocf_A Estrogen receptor; estrogen receptor, LBD, monobody, estradiol, hormone-growth complex; HET: CME EST; 2.95A {Homo sapiens} Length = 298

 Score = 39.1 bits (91), Expect = 4e-04
 Identities = 13/61 (21%), Positives = 25/61 (40%), Gaps = 9/61 (14%)

Query: 128 QVIDRLEHVAVSKEEYYFLKALVLANSDVK---------LDEFSSLKKFRNSILSSLGDC 178
               R   + +  EE+  LK+++L NS V          L+E   + +  + I  +L   
Sbjct: 133 ATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHL 192

Query: 179 I 179
           +
Sbjct: 193 M 193

>1hg4_A Ultraspiracle; nuclear hormone receptor, transcription factor, ligand binding; HET: LPP; 2.4A {Drosophila melanogaster} SCOP: a.123.1.1 Length = 279

 Score = 38.0 bits (88), Expect = 7e-04
 Identities = 11/80 (13%), Positives = 38/80 (47%), Gaps = 1/80 (1%)

Query: 101 LLSQQWPPNKSIPSLEDLERNTEISCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LD 159
            L+Q +  +++      +    +   +++  +++ + + + E   LKA++L N D++ + 
Sbjct: 136 FLNQSFSYHRNSAIKAGVSAIFDRILSELSVKMKRLNLDRRELSCLKAIILYNPDIRGIK 195

Query: 160 EFSSLKKFRNSILSSLGDCI 179
             + ++  R  + + L +  
Sbjct: 196 SRAEIEMCREKVYACLDEHC 215

>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 = 37.8 bits (88), Expect = 7e-04
 Identities = 13/53 (24%), Positives = 28/53 (52%), Gaps = 1/53 (1%)

Query: 128 QVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCI 179
           + +++L+ + V   EY  LKA+VL  SD   L + + ++  +     +L + +
Sbjct: 127 EQVEKLKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVESLQEKSQCALEEYV 179

>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 = 37.9 bits (88), Expect = 8e-04
 Identities = 4/28 (14%), Positives = 8/28 (28%)

Query: 65 CQACRFQKCLRKGMLKEGVRLDRVRGGR 92
              RF+  +R+G +             
Sbjct: 29 SDFVRFRPPVREGPVTRSASRAASLHSL 56

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	183
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	100.0
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	100.0
2ebl_A	89	COUP transcription factor 1; DNA-binding, metal-bi	100.0
1dsz_B	85	RXR-alpha, retinoic acid receptor RXR-alpha; RAR,	100.0
3cbb_A	78	HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DN	100.0
1ynw_B	99	Retinoic acid receptor RXR-alpha, retinoid X recep	100.0
1lo1_A	98	Steroid hormone receptor ERR2; estrogen related re	100.0
2han_A	93	Protein ultraspiracle; transcription regulation, t	100.0
1dsz_A	86	RAR-alpha, retinoic acid receptor alpha; RAR, nucl	100.0
1cit_A	89	NGFI-B, protein (orphan nuclear receptor NGFI-B);	100.0
2a66_A	113	Orphan nuclear receptor NR5A2; protein-DNA complex	100.0
1hcq_A	84	Protein (estrogen receptor); protein-DNA complex,	100.0
1a6y_A	94	Orphan nuclear receptor NR1D1; orphan receptor, DN	100.0
2han_B	119	Ecdysone receptor; transcription regulation, trans	100.0
4hn5_A	117	Glucocorticoid receptor; glucocorticoid receptor,	100.0
1kb2_A	110	Vitamin D3 receptor; VDR, nuclear receptor, protei	100.0
3g9m_A	90	Glucocorticoid receptor; glucocorticoid, DNA-bindi	100.0
1r4i_A	105	Androgen receptor; AR, steroid receptor, protein-D	100.0
2nll_B	103	Protein (thyroid hormone receptor); complex (trans	100.0
2lze_A	87	A primordial catalytic fold generated by in vitro	99.85
1lbd_A	282	RXR_LBD, retinoid X receptor; transcription factor	99.74
1xdk_B	303	RAR-beta, retinoic acid receptor, beta; nuclear re	99.48
3vi8_A	273	Peroxisome proliferator-activated receptor alpha;	99.43
1ovl_A	271	Orphan nuclear receptor NURR1 (MSe 414, 496, 511);	99.39
3cqv_A	199	Nuclear receptor subfamily 1 group D member 2; rev	99.33
1fcy_A	236	RAR-gamma-1, retinoic acid receptor gamma-1; isoty	99.31
3v3e_B	257	Nuclear receptor subfamily 4 group A member 1; orp	99.3
3l0l_A	248	Nuclear receptor ROR-gamma; nuclear receptor, rorg	99.3
2e2r_A	244	Estrogen-related receptor gamma; ERR gamma, BPA, n	99.28
3ltx_A	243	Estrogen receptor; constitutive, nuclear receptor,	99.28
3u9q_A	269	Peroxisome proliferator-activated receptor gamma;	99.27
3n00_A	245	REV-ERBA-alpha; reverba ncorid1, anti-parallel B-s	99.27
3kmr_A	266	Retinoic acid receptor alpha; nuclear receptor tra	99.27
3k6p_A	248	Steroid hormone receptor ERR1; estrogen related re	99.26
2iz2_A	243	FTZ-F1 alpha, nuclear hormone receptor FTZ-F1; nuc	99.26
1n83_A	270	Nuclear receptor ROR-alpha; three-layered alpha he	99.26
2hc4_A	302	Vitamin D receptor; alpha helical sandwich, gene r	99.25
1xvp_B	246	Orphan nuclear receptor NR1I3; CAR, RXR, citco, SR	99.25
3cjw_A	244	COUP transcription factor 2; COUP-TFII, nuclear re	99.25
1osh_A	232	BIle acid receptor; nuclear receptor, ligand bindi	99.25
3b0t_A	254	Vitamin D3 receptor; nuclear receptor, transcripti	99.24
3p0u_A	249	Nuclear receptor subfamily 2 group C member 2; lig	99.24
1nq7_A	244	Nuclear receptor ROR-beta; ligand-binding domain,	99.24
2nxx_A	235	Ultraspiracle (USP, NR2B4); hormone receptor, APO	99.23
3ilz_A	267	Thyroid hormone receptor, alpha isoform 1 variant;	99.23
3ipq_A	283	Oxysterols receptor LXR-alpha; LXR homodimer, LXR	99.21
2o4j_A	292	Vitamin D3 receptor; nuclear receptor-ligand compl	99.21
3mnp_A	261	Glucocorticoid receptor; protein-ligand complex, s	99.21
3vhv_A	260	Mineralocorticoid receptor; nuclear receptor, tran	99.2
1ymt_A	246	Steroidogenic factor 1; SF-1, ligand-binding domai	99.2
3plz_A	257	FTZ-F1 related protein; alpha helical sandwhich, f	99.2
1pdu_A	244	DHR38, nuclear hormone receptor HR38; nuclear rece	99.19
1t7r_A	269	Androgen receptor; nuclear receptor, transcription	99.19
2r40_D	266	Ecdysone receptor, 20-hydroxy-ecdysone receptor; n	99.18
3tx7_B	352	Nuclear receptor subfamily 5 group A member 2; LRH	99.17
1nrl_A	316	Orphan nuclear receptor PXR; PXR, xenobiotic, SRC-	99.17
1sqn_A	261	PR, progesterone receptor; nuclear receptor, stero	99.16
2p1t_A	240	Retinoic acid receptor RXR-alpha; protein-ligand c	99.16
3vhu_A	294	Mineralocorticoid receptor; nuclear receptor, tran	99.15
2nxx_E	248	Ecdysone receptor (ECR, NRH1); hormone receptor, A	99.15
1z5x_E	310	Ecdysone receptor ligand binding domain; ponastero	99.12
2ocf_A	298	Estrogen receptor; estrogen receptor, LBD, monobod	99.11
1xpc_A	248	Estrogen receptor; nuclear receptor, transcription	99.1
3up3_A	243	Acedaf-12; ligand binding domain, nematode, steroi	99.07
1yye_A	268	ER-beta, estrogen receptor beta; ER-beta, nuclear	99.06
3oll_A	240	Estrogen receptor beta; steroid binding, phosphory	99.03
1pzl_A	237	Hepatocyte nuclear factor 4-alpha; transcription;	99.01
3f5c_B	268	Nuclear receptor subfamily 0 group B member 1; tra	99.0
1l2j_A	271	Estrogen receptor beta; nuclear receptor, transcri	99.0
1g2n_A	264	Ultraspiracle protein; antiparallel alpha-helical	98.98
1hg4_A	279	Ultraspiracle; nuclear hormone receptor, transcrip	98.94
3gyt_A	244	Nuclear hormone receptor of the steroid/thyroid ho	98.9
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	84.73

>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=2.5e-44  Score=304.06  Aligned_cols=173  Identities=36%  Similarity=0.687  Sum_probs=145.9

Q ss_pred             CCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecccc
Q psy16825         10 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR   89 (183)
Q Consensus        10 ~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~   89 (183)
                      ...|.|||++++|+||||.+|+|||+||||+|.++..|.|+.+++|.+++..|+.||+|||+||+++||++++||.+|++
T Consensus       137 ~~~C~VCg~~a~g~hygv~sC~~Ck~FFrR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~  216 (467)
T 3dzy_A          137 KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQR  216 (467)
T ss_dssp             CEECTTTSSEECSEETTEECCHHHHHHHHHHHHTTCCCCCSSSSCCCCCSSSSSSCHHHHHHHHHHTTCCGGGCCCCSCC
T ss_pred             CCcceeCCCCCCCCcCCCcchhhhhHhccccccCCCceeCCCCCCCCCCcccccccccchhhhhhhccccchhhhccccc
Confidence            34699999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cccccccCCCC--CCC-------------------C---C-----------CC-----------------CCCCCCCccc
Q psy16825         90 GGRQKYRRNPD--LLS-------------------Q---Q-----------WP-----------------PNKSIPSLED  117 (183)
Q Consensus        90 ~~~~~~~~~~~--~~~-------------------~---~-----------~~-----------------~~k~iP~f~~  117 (183)
                      ...+.......  ...                   .   .           .+                 +.+.+|+|.+
T Consensus       217 ~k~r~~~~~~~~~~~~~~~~~~~ll~a~~~~e~~~~~~~~~~~~~~~~~~~~~~~~l~e~a~~~L~~vVeWAK~iP~F~~  296 (467)
T 3dzy_A          217 GKDRNENEVESTSSANEDMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSE  296 (467)
T ss_dssp             CCCCSCSSCTTSTTCSCSSCHHHHHHHHHC----------------------CCTTHHHHHHHHHHHHHHHHHHSTTSTT
T ss_pred             cccccccccccccccCCCCchhhhhhhhhhhcccchhhhhhcccCCCCcccchHHHHHHHHHHHHHHHHHHHHhCcchhc
Confidence            64432110000  000                   0   0           00                 0166899999


Q ss_pred             cccccc--------------------------------------------------chhhhhhhhchhcccChhHHHHHH
Q psy16825        118 LERNTE--------------------------------------------------ISCTQVIDRLEHVAVSKEEYYFLK  147 (183)
Q Consensus       118 L~~~dq--------------------------------------------------~~~~~lv~~~~~l~~~~~E~~~lk  147 (183)
                      |+.+||                                                  ..+.+++.+|++|++|.+||++|+
T Consensus       297 L~~~DQi~LLK~~w~elliL~~a~rs~~~~~~~ll~~g~~i~~~~~~~~~~~~~~~~il~~lv~~l~~L~ld~~E~~lLk  376 (467)
T 3dzy_A          297 LPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLR  376 (467)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHHHHHHTSSSTTBCCCSSSCCCBTHHHHTTTCHHHHHHHHHHTHHHHHHHTCCHHHHHHHH
T ss_pred             CCHHHHHHHHHhHHHHHHHHHHHHHhccCCCceEecCCceechhhhhhhcchHHHHHHHHHHHHHHHHhcCCHHHHHHHH
Confidence            999999                                                  123478999999999999999999


Q ss_pred             HHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        148 ALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       148 ai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      ||+||+||+. |++...|+++|++++.+|.+|+...
T Consensus       377 AIvLfnpd~~gL~~~~~Ve~lQe~~~~aL~~Y~~~~  412 (467)
T 3dzy_A          377 AIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHK  412 (467)
T ss_dssp             HHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhCcCCCCCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence            9999999986 9999999999999999999999654

>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=3.1e-43  Score=294.12  Aligned_cols=172  Identities=30%  Similarity=0.577  Sum_probs=143.2

Q ss_pred             CCcccccCCCCcccccccccccchhhhhhccccCCceee-cCCCCCccccccccccccchhhhHHhhhcccccceeeccc
Q psy16825         10 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYT-CPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV   88 (183)
Q Consensus        10 ~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~-C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~   88 (183)
                      ...|.|||++++|+||||.+|+|||+||||+|..+..|. |  .++|.+++..|+.|++|||+||+++||++++||.+|+
T Consensus        50 ~~~C~vC~~~~~g~hygv~~C~~C~~FFrR~~~~~~~~~~c--~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~vq~~R~  127 (419)
T 3dzy_D           50 AIECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLIYDRC--DLNCRIHKKSRNKCQYCRFQKCLAVGMSHNAIRFGRM  127 (419)
T ss_dssp             CCCCSSSCSCCCSBCSSSBCCHHHHHHHHHHHTTTCCCCCC--CSCCCCCTTGGGTCHHHHHHHHHHTTCCGGGCCCSCC
T ss_pred             CCcCeECCCcCCCCccCcccchhhhHHHccchhcccccccc--cCCCCcccccCccchhhhHHHHhhcccchhheecccc
Confidence            456999999999999999999999999999999998885 6  4689999999999999999999999999999999998


Q ss_pred             ccccccccCCCC--------C-------------------------------------C-C------------------C
Q psy16825         89 RGGRQKYRRNPD--------L-------------------------------------L-S------------------Q  104 (183)
Q Consensus        89 ~~~~~~~~~~~~--------~-------------------------------------~-~------------------~  104 (183)
                      +...+.......        .                                     . +                  .
T Consensus       128 ~~~~k~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~a~~~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~l~~ae~~~~~~  207 (419)
T 3dzy_D          128 PQAEKEKLLAEISSDIDQLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFK  207 (419)
T ss_dssp             TTTTGGGSTTTTTSTTTTSCSTTHHHHHHHHHHHHHHHTTCSSCHHHHHHHHHCCSSSCCCEEECSHHHHHCCC------
T ss_pred             cccccccccccccccccCCCCchhhHHHHHHHHHHhhhccCCccchhccccccCCCCCCCCcccccchhhhhcccccccc
Confidence            754432110000        0                                     0 0                  0


Q ss_pred             C------------------------------CCCCCCCCCccccccccc-------------------------------
Q psy16825        105 Q------------------------------WPPNKSIPSLEDLERNTE-------------------------------  123 (183)
Q Consensus       105 ~------------------------------~~~~k~iP~f~~L~~~dq-------------------------------  123 (183)
                      .                              +.+.|.+|+|.+|+.+||                               
T Consensus       208 ~~~~~~~~~~e~~~~~~~~~~~~~~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w~Ell~L~~a~~~~~~~~~~~~~~  287 (419)
T 3dzy_D          208 HITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQ  287 (419)
T ss_dssp             ----------CHHHHHHHHHHHHHHHHHHHHHHHHTTSTTTTTSCHHHHHHHHHHHHHHHHHHHHGGGBCSSEEEEGGGT
T ss_pred             cCCCcccccchhhhHHHHHHHHHHHHHHHHHHHHhccCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCceeecCc
Confidence            0                              011288999999999999                               


Q ss_pred             -------------------chhhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhcC
Q psy16825        124 -------------------ISCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVLR  183 (183)
Q Consensus       124 -------------------~~~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~~  183 (183)
                                         ..+.+++.+|+.|++|.+||+||+||+||+||++ |.+...|+++|++++.+|.+|+..++
T Consensus       288 ~~~~~~~~~~~~~~~~~l~~~i~~f~~~l~~L~ld~~E~alLkAivLf~pD~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~  367 (419)
T 3dzy_D          288 GFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNH  367 (419)
T ss_dssp             EEEEHHHHHSSSGGGSGGGHHHHHHHHHHHHTCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             ccccHHHHHhhhhhHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence                               0123677899999999999999999999999987 99999999999999999999997653

>2ebl_A COUP transcription factor 1; DNA-binding, metal-binding, nuclear protein, receptor, transcription regulation, zinc, EAR3, erbal3 tfcoup1; NMR {Homo sapiens}

Probab=100.00  E-value=2.5e-37  Score=204.09  Aligned_cols=85  Identities=44%  Similarity=0.927  Sum_probs=79.9

Q ss_pred             CCCCCCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceee
Q psy16825          6 EELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRL   85 (183)
Q Consensus         6 ~~~~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~   85 (183)
                      ++++...|.|||++++|+||||++|+||++||||+|..+..|.|+.+++|.+++..|+.|++|||+|||++||++++||.
T Consensus         3 ~~~~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~   82 (89)
T 2ebl_A            3 SGSSGIECVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRANRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQR   82 (89)
T ss_dssp             CCCSSCBCTTTCSBCCSEETTEECCHHHHHHHHHHHTTTCCCCCSSCSCCCCCSSSSSCCSHHHHHHHHHHTCCHHHHSC
T ss_pred             CCCCCCCCcEeCCCCcceEeCchhhHHhhhhhheeeeeccceecccCccCCcCccCccccccchHHHhhhccCCHHHccc
Confidence            34456679999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccc
Q psy16825         86 DRVRG   90 (183)
Q Consensus        86 ~r~~~   90 (183)
                      +|++.
T Consensus        83 ~R~~~   87 (89)
T 2ebl_A           83 GSGPS   87 (89)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            99864

>1dsz_B RXR-alpha, retinoic acid receptor RXR-alpha; RAR, nuclear receptor, protein-DNA, transcription/DNA complex; HET: DNA; 1.70A {Homo sapiens} SCOP: g.39.1.2 PDB: 1by4_A* 1rxr_A 1r0n_A 1r0o_A 2nll_A*

Probab=100.00  E-value=4.9e-37  Score=201.22  Aligned_cols=82  Identities=52%  Similarity=1.111  Sum_probs=78.0

Q ss_pred             CCCCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecc
Q psy16825          8 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR   87 (183)
Q Consensus         8 ~~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r   87 (183)
                      .+...|.|||++++|+||||++|+||++||||+|..+..|.|+.+++|.+++..++.|++|||+|||++||++++||.+|
T Consensus         3 ~~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R   82 (85)
T 1dsz_B            3 FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER   82 (85)
T ss_dssp             SCCEECTTTCCEESSEETTEECCHHHHHHHHHHHHHTCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCCC
T ss_pred             CCCCCCCEeCCCCCceeeCccchHHHHHHHHHhhccccceeecccccccccccccccCcchhHHHHhHcCCCHHHhhccc
Confidence            34567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cc
Q psy16825         88 VR   89 (183)
Q Consensus        88 ~~   89 (183)
                      ++
T Consensus        83 ~~   84 (85)
T 1dsz_B           83 QR   84 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>3cbb_A HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DNA binding domain, nuclear; zinc finger; 2.00A {Homo sapiens}

Probab=100.00  E-value=1.2e-36  Score=196.43  Aligned_cols=77  Identities=47%  Similarity=1.063  Sum_probs=73.4

Q ss_pred             cccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeeccc
Q psy16825         12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV   88 (183)
Q Consensus        12 ~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~   88 (183)
                      .|.|||++++|+||||++|+||++||||+|..+..|.|+.+++|.+++..++.|++|||+|||++||++++||.+|+
T Consensus         2 ~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~Rd   78 (78)
T 3cbb_A            2 LCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNERD   78 (78)
T ss_dssp             BCTTTSSBCCSEETTEECCHHHHHHHHHHHHTTCCCCCSSCSCCCCSTTTTTTCHHHHHHHHHHHTCCGGGCCCC--
T ss_pred             CCeEeCCCCCceEeCCcchhhhceeeeEEEecccCcccccccccCcCccccccChhhhhHHHhHcCCCHHHccccCC
Confidence            59999999999999999999999999999999999999999999999999999999999999999999999999875

>1ynw_B Retinoic acid receptor RXR-alpha, retinoid X receptor; VDR, nuclear receptor, protein-DNA complex, transcripti complex; 3.00A {Homo sapiens} SCOP: g.39.1.2

Probab=100.00  E-value=1.5e-36  Score=204.22  Aligned_cols=85  Identities=52%  Similarity=1.093  Sum_probs=71.9

Q ss_pred             CCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecccc
Q psy16825         10 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR   89 (183)
Q Consensus        10 ~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~   89 (183)
                      ...|.|||++++|+||||++|+||++||||+|..+..|.|+.+++|.+++..++.|++|||+|||++||++++||.+|++
T Consensus         3 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~   82 (99)
T 1ynw_B            3 KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQR   82 (99)
T ss_dssp             --CBTTTBSCCCBCCTTSCBCSHHHHHHHHHHHTTCCCCCSSSSCCCCCSTTSSSCHHHHHHHHHHTTCCSTTCC-----
T ss_pred             CCCCceeCCCCcceeeCccchHHHHHHHHhhhccccccccCCCCcccccccCCccCccccHHHHhHcCCCHHHhhhcccc
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccccc
Q psy16825         90 GGRQK   94 (183)
Q Consensus        90 ~~~~~   94 (183)
                      ...+.
T Consensus        83 ~~~~~   87 (99)
T 1ynw_B           83 GKDRN   87 (99)
T ss_dssp             -----
T ss_pred             ccccC
Confidence            76643

>1lo1_A Steroid hormone receptor ERR2; estrogen related receptor 2, DNA binding domain, HERR2, hormone nuclear receptor; NMR {Homo sapiens} SCOP: g.39.1.2

Probab=100.00  E-value=8.3e-37  Score=205.08  Aligned_cols=89  Identities=84%  Similarity=1.550  Sum_probs=82.9

Q ss_pred             CCCCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecc
Q psy16825          8 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR   87 (183)
Q Consensus         8 ~~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r   87 (183)
                      .+...|.|||++++|+||||++|+||++||||+|..+..|.|+.+++|.+++..++.|++|||+|||++||++++||.+|
T Consensus         2 ~~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R   81 (98)
T 1lo1_A            2 IPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKALKVGMLKEGVRLDR   81 (98)
T ss_dssp             CCCCEETTTTEECSEESSSSEECHHHHHHHHHHHHTTCCCCCSSCSCCCCCHHHHHHCHHHHHHHHHHHTCCGGGSCSSC
T ss_pred             CCCCCCcEeCCCCcCeeeCccchhhhhhhheeeecccCccccCccccccccccccccccchhHHHHhHcCCCHHHeeccc
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccccccc
Q psy16825         88 VRGGRQKYR   96 (183)
Q Consensus        88 ~~~~~~~~~   96 (183)
                      ++..+.+..
T Consensus        82 ~~~~r~k~~   90 (98)
T 1lo1_A           82 VRGGRQKYK   90 (98)
T ss_dssp             CTTCCCCCC
T ss_pred             ccCcccccC
Confidence            887775543

>2han_A Protein ultraspiracle; transcription regulation, transcription factor, DNA-binding, nuclear protein, nuclear receptor, zinc finger; 1.95A {Drosophila melanogaster} SCOP: g.39.1.2

Probab=100.00  E-value=1.2e-36  Score=202.63  Aligned_cols=84  Identities=51%  Similarity=1.035  Sum_probs=76.0

Q ss_pred             CCCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeeccc
Q psy16825          9 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV   88 (183)
Q Consensus         9 ~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~   88 (183)
                      ....|.|||++++|+||||++|+||++||||+|..+..|.|+.+++|.+++..++.|++|||+|||++||++++||.+|+
T Consensus         9 ~~~~C~VCgd~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~   88 (93)
T 2han_A            9 SKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYACRENRNCIIDKRQRNRCQYCRYQKCLTCGMKREAVQEERQ   88 (93)
T ss_dssp             -CCBCTTTCSBCCEEETTEEECHHHHHHHHHHHHHTCCCCCSSCSCCCCSTTTGGGCHHHHHHHHHHHTCCGGGSCCCC-
T ss_pred             CCCCCcEeCCCCcCeecCcchhHHHHHHHHhhhccccCcCcCCCCcCCcCCCCCccCccccHHHHhHhCCCHHHhhhccC
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cccc
Q psy16825         89 RGGR   92 (183)
Q Consensus        89 ~~~~   92 (183)
                      +..+
T Consensus        89 ~~~~   92 (93)
T 2han_A           89 GIHR   92 (93)
T ss_dssp             ----
T ss_pred             cccC
Confidence            6543

>1dsz_A RAR-alpha, retinoic acid receptor alpha; RAR, nuclear receptor, protein-DNA, transcription/DNA complex; HET: DNA; 1.70A {Homo sapiens} SCOP: g.39.1.2 PDB: 1hra_A

Probab=100.00  E-value=2.2e-36  Score=198.69  Aligned_cols=82  Identities=52%  Similarity=1.043  Sum_probs=73.7

Q ss_pred             CCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecccc
Q psy16825         10 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR   89 (183)
Q Consensus        10 ~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~   89 (183)
                      ...|.|||++++|+||||++|+||++||||+|..+..|.|+.+++|.+++..++.|++|||+|||++||++++||.+|++
T Consensus         4 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~   83 (86)
T 1dsz_A            4 YKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNK   83 (86)
T ss_dssp             --CCTTTCSCCCSEETTEECCHHHHHHHHHHHHTTCCCCCSSCSCCCCSTTTGGGCHHHHHHHHHHTTCCGGGSCCC---
T ss_pred             CCCCcEECCCccceeeCchhHHHHHHHHHHHhhcccceeeccCCccccCccccccchhhhHHHHHHhCCCHHHhhhcccc
Confidence            35699999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             cc
Q psy16825         90 GG   91 (183)
Q Consensus        90 ~~   91 (183)
                      .+
T Consensus        84 ~k   85 (86)
T 1dsz_A           84 KK   85 (86)
T ss_dssp             --
T ss_pred             cc
Confidence            53

>1cit_A NGFI-B, protein (orphan nuclear receptor NGFI-B); early immediate response gene product, transcription factor, monomeric protein-DNA complex; HET: DNA; 2.70A {Rattus norvegicus} SCOP: g.39.1.2

Probab=100.00  E-value=2.9e-36  Score=199.19  Aligned_cols=84  Identities=57%  Similarity=1.087  Sum_probs=78.8

Q ss_pred             CcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeeccccc
Q psy16825         11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG   90 (183)
Q Consensus        11 ~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~~   90 (183)
                      +.|.|||++++|+||||++|+||++||||+|..+..|.|+.+++|.+++..++.|++|||+|||++||++++||.++...
T Consensus         1 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~~~~~   80 (89)
T 1cit_A            1 GRCAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTDSLKG   80 (89)
T ss_dssp             CCCSSSCCCCCEEETTEEECHHHHHHHHHHHHHTCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHTTCCGGGSCCGGGTT
T ss_pred             CCCeEeCCCCcceEeCccchhhhhhhceeeEEecceeeeccCCccccCCCCcccChhhhhHHHhHcCCCHHHeecccccC
Confidence            36999999999999999999999999999999999999999999999999999999999999999999999999988766


Q ss_pred             cccc
Q psy16825         91 GRQK   94 (183)
Q Consensus        91 ~~~~   94 (183)
                      .+.+
T Consensus        81 ~r~r   84 (89)
T 1cit_A           81 RRGR   84 (89)
T ss_dssp             CCSC
T ss_pred             cccc
Confidence            5544

>2a66_A Orphan nuclear receptor NR5A2; protein-DNA complex, zinc finger, DNA- binding domain, transcription factor, FTZ-F1, C-terminal extension; 2.20A {Homo sapiens} PDB: 2ff0_A

Probab=100.00  E-value=4e-36  Score=206.39  Aligned_cols=90  Identities=57%  Similarity=1.108  Sum_probs=80.2

Q ss_pred             CCCCCCCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhccccccee
Q psy16825          5 EEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR   84 (183)
Q Consensus         5 ~~~~~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~   84 (183)
                      +++.+...|.|||++++|+||||++|+||++||||+|..+..|.|+.+++|.+++..++.|++|||+|||++||++++||
T Consensus         4 ~~~~~~~~C~VCgd~a~G~HyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~R~~Cr~CR~~KCl~vGM~~~~vq   83 (113)
T 2a66_A            4 GDEDLEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVR   83 (113)
T ss_dssp             ------CBCTTTCCBEEEEETTEEEEHHHHHHHHHHHHTTCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSC
T ss_pred             CCCCCCCCCcEeCCCCcceeeCcccHHHHHHHHhhhhhccccccccccccCCcCCCccccccchhHHHHhHhCCCHHHhc
Confidence            34555678999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eccccccccc
Q psy16825         85 LDRVRGGRQK   94 (183)
Q Consensus        85 ~~r~~~~~~~   94 (183)
                      .+|++..+.+
T Consensus        84 ~~R~~~~r~~   93 (113)
T 2a66_A           84 ADRMRGGRNK   93 (113)
T ss_dssp             TTCCCSSCCT
T ss_pred             cccccCCCCC
Confidence            9998776643

>1hcq_A Protein (estrogen receptor); protein-DNA complex, complexed with drug, transcription/DNA complex; HET: DNA; 2.40A {Homo sapiens} SCOP: g.39.1.2 PDB: 1hcp_A 4aa6_A

Probab=100.00  E-value=7.8e-36  Score=195.08  Aligned_cols=79  Identities=63%  Similarity=1.256  Sum_probs=69.0

Q ss_pred             CCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeeccc
Q psy16825         10 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV   88 (183)
Q Consensus        10 ~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~   88 (183)
                      ...|.|||++++|+||||++|+||++||||+|..+..|.|+.+++|.+++..++.|++|||+|||++||++++||.+|.
T Consensus         4 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~   82 (84)
T 1hcq_A            4 TRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRKDRR   82 (84)
T ss_dssp             CCBCTTTCSBCCEEETTEEECHHHHHHHHHHHSSCCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHHTCCC--------
T ss_pred             CCcCcEECCCCCCeeeCccchHHhhhhhhhccccccccccccCccCCcCCcCcccChhhhhHHHhHcCCCHHHhcccCC
Confidence            4579999999999999999999999999999999999999999999999999999999999999999999999999885

>1a6y_A Orphan nuclear receptor NR1D1; orphan receptor, DNA-binding, reverb, REV- ERB, transcription regulation, transcription/DNA complex; HET: DNA 5IU; 2.30A {Homo sapiens} SCOP: g.39.1.2 PDB: 1ga5_A* 1hlz_A

Probab=100.00  E-value=6.9e-36  Score=199.33  Aligned_cols=84  Identities=52%  Similarity=1.094  Sum_probs=74.8

Q ss_pred             CCcccccCCCCcccccccccccchhhhhhccccCCcee-ecCCCCCccccccccccccchhhhHHhhhcccccceeeccc
Q psy16825         10 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEY-TCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV   88 (183)
Q Consensus        10 ~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~-~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~   88 (183)
                      ...|.|||++++|+||||++|+||++||||+|..+..| .|..+++|.+++..++.|++|||+|||++||++++||.+|+
T Consensus         7 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~   86 (94)
T 1a6y_A            7 VLLCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGRI   86 (94)
T ss_dssp             -CBCTTTSSBCCEEETTEEECHHHHHHHHHHHSSCCCCCCCSSTTCCCCCTTTTTSCHHHHHHHHTTTTCCSTTCCCCC-
T ss_pred             CCcCcEeCCCCcceEeCccchhhhhhehheeeecccceEEccCCCCCccCccccccccchhHHHhhHccCCHHHhccCcC
Confidence            46799999999999999999999999999999999999 59999999999999999999999999999999999999998


Q ss_pred             ccccc
Q psy16825         89 RGGRQ   93 (183)
Q Consensus        89 ~~~~~   93 (183)
                      +...+
T Consensus        87 ~~~~k   91 (94)
T 1a6y_A           87 PKREK   91 (94)
T ss_dssp             -----
T ss_pred             cCchh
Confidence            76543

>2han_B Ecdysone receptor; transcription regulation, transcription factor, DNA-binding, nuclear protein, nuclear receptor, zinc finger; 1.95A {Drosophila melanogaster} SCOP: g.39.1.2 PDB: 1r0o_B 1r0n_B

Probab=100.00  E-value=2.4e-35  Score=204.86  Aligned_cols=83  Identities=42%  Similarity=0.915  Sum_probs=78.4

Q ss_pred             CCCCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecc
Q psy16825          8 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR   87 (183)
Q Consensus         8 ~~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r   87 (183)
                      .....|.|||++++|+||||++|+||++||||+|..+..|.|+.+++|.+++..++.|++|||+|||++||++++|+.++
T Consensus         6 ~~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r   85 (119)
T 2han_B            6 VQEELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECRLKKCLAVGMRPECVVPEN   85 (119)
T ss_dssp             CCSCBCTTTCSBCCEEETTEEECHHHHHHHHHHHHTTCCCCCSSCSCCCCSTTGGGTCHHHHHHHHHHTTCCGGGSSCSS
T ss_pred             CCCCcCeEeCCcCCcceECchhHHhhHHhhhhheEeccccccccccccccCccccccchhhHHHHHHHhCCCHHHccchh
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             ccc
Q psy16825         88 VRG   90 (183)
Q Consensus        88 ~~~   90 (183)
                      +..
T Consensus        86 ~~~   88 (119)
T 2han_B           86 QCA   88 (119)
T ss_dssp             HHH
T ss_pred             hhh
Confidence            654

>4hn5_A Glucocorticoid receptor; glucocorticoid receptor, steroid receptors, NGRE, repre transcription; HET: DNA; 1.90A {Homo sapiens} PDB: 4hn6_A*

Probab=100.00  E-value=4.7e-35  Score=202.03  Aligned_cols=87  Identities=49%  Similarity=1.012  Sum_probs=70.8

Q ss_pred             CCCCCCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceee
Q psy16825          6 EELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRL   85 (183)
Q Consensus         6 ~~~~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~   85 (183)
                      ++.+...|.|||++++|+||||.+|+||++||||+|..+..|.|+.+++|.+++..++.|++|||+||+++||++++||.
T Consensus        25 ~~~~~~~C~VCgd~a~G~HyGv~sC~aCk~FFRRsv~~~~~y~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~avq~  104 (117)
T 4hn5_A           25 SNAPPKLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEARKT  104 (117)
T ss_dssp             -----CBCTTTCSBCCEEETTEEECHHHHHHHHHHHSSCCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHHTCCTTC---
T ss_pred             CCCCCCcCCcCCCcCcccccCCcccchhhhhhhcceecCCceecCCCCccccCcccccCCcccchHHHhHcCCCHHHhcc
Confidence            34456789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccccc
Q psy16825         86 DRVRGGR   92 (183)
Q Consensus        86 ~r~~~~~   92 (183)
                      +|.....
T Consensus       105 kR~~k~~  111 (117)
T 4hn5_A          105 KKKIKGI  111 (117)
T ss_dssp             -------
T ss_pred             ccccccc
Confidence            8865433

>1kb2_A Vitamin D3 receptor; VDR, nuclear receptor, protein-DNA complex, transcription/DNA complex; 2.70A {Homo sapiens} SCOP: g.39.1.2 PDB: 1kb4_A 1kb6_A 1ynw_A

Probab=100.00  E-value=4e-35  Score=200.88  Aligned_cols=82  Identities=44%  Similarity=0.981  Sum_probs=76.4

Q ss_pred             CCCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeeccc
Q psy16825          9 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV   88 (183)
Q Consensus         9 ~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~   88 (183)
                      ....|.|||++++|+||||++|+||++||||+|..+..|.|+.+++|.+++..++.|++|||+|||++||++++|+.+|.
T Consensus         5 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~   84 (110)
T 1kb2_A            5 VPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDEE   84 (110)
T ss_dssp             --CBCTTTCSBCCSEETTEECCHHHHHHHHHHHHTTCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCHHH
T ss_pred             cCCCCcEeCCCCCceEeCchhHhhhhhhheeeeecccceeeCCCCCccCCcccceecccccHhhhhhcCCcHHhcccHHH
Confidence            34679999999999999999999999999999999999999999999999999999999999999999999999988876


Q ss_pred             cc
Q psy16825         89 RG   90 (183)
Q Consensus        89 ~~   90 (183)
                      ..
T Consensus        85 ~q   86 (110)
T 1kb2_A           85 VQ   86 (110)
T ss_dssp             HH
T ss_pred             Hh
Confidence            54

>3g9m_A Glucocorticoid receptor; glucocorticoid, DNA-binding, allostery, lever ARM, transcription, hormone; HET: DNA; 1.61A {Rattus norvegicus} SCOP: g.39.1.2 PDB: 3g6p_A* 3g6q_B* 3g6r_B* 3g6u_A* 3g8u_A* 3g8x_A* 3g97_B* 3g99_A* 3g9i_A* 3g9j_A* 3fyl_A* 3g9o_B* 3g9p_B* 3g6t_A* 1r4o_A 1r4r_A 1glu_A* 1gdc_A 2gda_A 1rgd_A ...

Probab=100.00  E-value=8.2e-35  Score=193.21  Aligned_cols=82  Identities=50%  Similarity=1.033  Sum_probs=75.1

Q ss_pred             CcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeeccccc
Q psy16825         11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG   90 (183)
Q Consensus        11 ~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~~   90 (183)
                      ..|.|||++++|+||||.+|+||++||||+|..+..|.|..+++|.+++..++.|++|||+|||++||++++||.+|...
T Consensus         3 ~~C~VCg~~a~g~hyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~avq~~r~~~   82 (90)
T 3g9m_A            3 HMCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEARKTKKKIK   82 (90)
T ss_dssp             CBCTTTCSBCCEEETTEEECHHHHHHHHHHHHSCCCCCCSSSSCCCCCTTGGGTCHHHHHHHHHHHTCCTTHHHHHC---
T ss_pred             CcCccCCCcCcccccCCccchhHhHHhhhhhhcCCceeCCCCCccccCcccccCCcchhhHHHHHcCCCHHHhccccccc
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999998655


Q ss_pred             cc
Q psy16825         91 GR   92 (183)
Q Consensus        91 ~~   92 (183)
                      ..
T Consensus        83 ~~   84 (90)
T 3g9m_A           83 GI   84 (90)
T ss_dssp             --
T ss_pred             cc
Confidence            44

>1r4i_A Androgen receptor; AR, steroid receptor, protein-DNA complex, transcription/DNA complex; 3.10A {Rattus norvegicus} SCOP: g.39.1.2

Probab=100.00  E-value=1.8e-34  Score=195.91  Aligned_cols=83  Identities=46%  Similarity=1.022  Sum_probs=71.7

Q ss_pred             CCCCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecc
Q psy16825          8 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR   87 (183)
Q Consensus         8 ~~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r   87 (183)
                      ++...|.|||++++|+||||++|+||++||||+|..+..|.|+.+++|.+++..|+.|++|||+|||++||++++++..+
T Consensus         5 ~~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~~k~~k   84 (105)
T 1r4i_A            5 PPQKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLGARKLKK   84 (105)
T ss_dssp             -CCCBCSSSCSBEEEEETTEEEEHHHHHHHHHHHTSCCCCCCSSSSCCCCCTTTTTTCHHHHHHHHHHHTCCSCC-----
T ss_pred             CCCCCCcEeCCCCCceEeCCcchhhhhhhhceeEEecCceeeccCCccccCccccccchhchHHHHHhhhcccchhhhcc
Confidence            44678999999999999999999999999999999999999999999999999999999999999999999999998877


Q ss_pred             ccc
Q psy16825         88 VRG   90 (183)
Q Consensus        88 ~~~   90 (183)
                      .+.
T Consensus        85 ~~~   87 (105)
T 1r4i_A           85 LGN   87 (105)
T ss_dssp             ---
T ss_pred             ccc
Confidence            643

>2nll_B Protein (thyroid hormone receptor); complex (transcription regulation/DNA), DNA-binding, nuclear protein, zinc- finger, multigene family; HET: DNA 5IU; 1.90A {Homo sapiens} SCOP: g.39.1.2 PDB: 3m9e_A*

Probab=100.00  E-value=8.1e-35  Score=197.26  Aligned_cols=83  Identities=47%  Similarity=0.985  Sum_probs=77.2

Q ss_pred             CcccccCCCCcccccccccccchhhhhhccccCCc--eeecCCCCCccccccccccccchhhhHHhhhcccccceeeccc
Q psy16825         11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNI--EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV   88 (183)
Q Consensus        11 ~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~--~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~   88 (183)
                      ..|.|||++++|+||||+||+||++||||+|..+.  .|.|+.+++|.+++..++.|++|||+||+++||++++||.++.
T Consensus         2 ~~C~VCgd~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~~~   81 (103)
T 2nll_B            2 ELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQECRFKKCIYVGMATDLVLDDSK   81 (103)
T ss_dssp             CBCTTTCSBCCSEETTEECCHHHHHHHHHHHHTTCGGGCCCSSCTTCCCSTTTTTSCHHHHHHHHHHTTCCGGGSCCHHH
T ss_pred             CCCeEeCCcCcCeecCcccHHHhhhhheecccccccchhhhhccCCcCcCccCccccchhhhHhhhHhCCCHHHhhhhhh
Confidence            46999999999999999999999999999999875  8999999999999999999999999999999999999999987


Q ss_pred             ccccc
Q psy16825         89 RGGRQ   93 (183)
Q Consensus        89 ~~~~~   93 (183)
                      +..+.
T Consensus        82 ~~~k~   86 (103)
T 2nll_B           82 RLAKR   86 (103)
T ss_dssp             HHHHH
T ss_pred             hHHhh
Confidence            65443

>2lze_A A primordial catalytic fold generated by in vitro evolution; ligase, de novo protein; NMR {Synthetic construct}

Probab=99.85  E-value=2.5e-22  Score=131.18  Aligned_cols=69  Identities=23%  Similarity=0.263  Sum_probs=61.0

Q ss_pred             ccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceee
Q psy16825         15 VCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRL   85 (183)
Q Consensus        15 vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~   85 (183)
                      ....++.+.||+++ |.+|++||||++ .+..|.|+.+++|.|++..|+.|++|||+|||+|||+...+..
T Consensus         9 ~p~~p~~g~h~c~v-Cgd~asfFRRt~-~~~~y~C~~~~~C~i~~~~R~~C~~CR~qKCl~VgM~~~~~~~   77 (87)
T 2lze_A            9 DPLEPRGGKHICAI-CGNNAEDYKHTD-MDLTYTDRDYKNCESYHKCSDLCQYCRYQKDLAIHHQHHHGGS   77 (87)
T ss_dssp             CTTCCSCCSSSCSS-SSSSSSSCTTTT-TSCTTTSCCCCCCCCSSCCSSSCSGGGTSCCHHHHCSSCCCCC
T ss_pred             CCcCCCCCCEEccC-CCCccceECccc-CCCeeEcCCCCccccCCCccCcCCcccChhhccCcCEeccCcc
Confidence            34467889999987 999999999995 6788999999999999999999999999999999998775543

>1lbd_A RXR_LBD, retinoid X receptor; transcription factor, nuclear receptor, structural proteomic europe, spine, structural genomics; 2.70A {Homo sapiens} SCOP: a.123.1.1 PDB: 1z5x_U* 2q60_A

Probab=99.74  E-value=2.3e-18  Score=136.78  Aligned_cols=56  Identities=25%  Similarity=0.383  Sum_probs=52.3

Q ss_pred             hhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        127 TQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       127 ~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      .+++.+|++|++|.+||+||+||+||+||++ |++...|+.+|++++.+|.+|+...
T Consensus       171 ~~~~~~l~~L~ld~~E~~lLkaivL~~pd~~gLs~~~~v~~lq~~~~~~L~~y~~~~  227 (282)
T 1lbd_A          171 TELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHK  227 (282)
T ss_dssp             HHHHHHTTTTCCCHHHHHHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhcCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            4689999999999999999999999999986 9999999999999999999999754

>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=99.48  E-value=4.5e-14  Score=113.21  Aligned_cols=57  Identities=21%  Similarity=0.257  Sum_probs=52.8

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +..++.+|++|++|.+||+||+||+||+||++ |.+...|+.+|++++.+|.+||...
T Consensus       157 i~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~  214 (303)
T 1xdk_B          157 VFTFANQLLPLEMDDTETGLLSAICLICGDRQDLEEPTKVDKLQEPLLEALKIYIRKR  214 (303)
T ss_dssp             HHHHHHHHGGGCCCHHHHHHHHHHHHSCSCSSSCSSHHHHHHHTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHHHHHHHHHHHh
Confidence            34688999999999999999999999999986 9999999999999999999999754

>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=99.43  E-value=1.6e-13  Score=108.40  Aligned_cols=75  Identities=15%  Similarity=0.238  Sum_probs=69.2

Q ss_pred             CCCCCCccccccccc--------------------------------------------------chhhhhhhhchhccc
Q psy16825        109 NKSIPSLEDLERNTE--------------------------------------------------ISCTQVIDRLEHVAV  138 (183)
Q Consensus       109 ~k~iP~f~~L~~~dq--------------------------------------------------~~~~~lv~~~~~l~~  138 (183)
                      .|.+|+|.+|+.+||                                                  ..+.+++.+|+.|++
T Consensus        96 AK~iPgF~~L~~~DQi~LLk~~w~ElllL~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~L~l  175 (273)
T 3vi8_A           96 AKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGMLVAYGNGFITREFLKSLRKPFCDIMEPKFDFAMKFNALEL  175 (273)
T ss_dssp             GGGSTTTTTSCHHHHHHHHHHHHHHHHHHHHGGGEETTEEEETTTTEEEEHHHHHHSCTTTHHHHHHHHHHHHHHHTTCC
T ss_pred             HccCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeeeeCCCccchHHHHHhhhhHHHHHHHHHHHHHHHHHhCC
Confidence            489999999999999                                                  235689999999999


Q ss_pred             ChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhcC
Q psy16825        139 SKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVLR  183 (183)
Q Consensus       139 ~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~~  183 (183)
                      |.+||+||+||+||+||++ |.+...|+.+|++++.+|.+||..++
T Consensus       176 d~~E~alLkAivLf~pd~~gL~~~~~Ve~lqe~~~~aL~~yi~~~~  221 (273)
T 3vi8_A          176 DDSDISLFVAAIICCGDRPGLLNVGHIEKMQEGIVHVLRLHLQSNH  221 (273)
T ss_dssp             CHHHHHHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CHHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHhC
Confidence            9999999999999999987 99999999999999999999998654

>1ovl_A Orphan nuclear receptor NURR1 (MSe 414, 496, 511); NUUR1, LBD, transcription; 2.20A {Homo sapiens} SCOP: a.123.1.1

Probab=99.39  E-value=3.5e-13  Score=106.28  Aligned_cols=57  Identities=16%  Similarity=0.284  Sum_probs=51.9

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||+||+||+|||+..+|++...|+++|++++.+|.+||...
T Consensus       159 l~~~~~~l~~L~ld~~E~~lLkAivL~~~~~gL~~~~~v~~lq~~~~~aL~~y~~~~  215 (271)
T 1ovl_A          159 IVEFSSNLQNMNIDISAFSCIAALAMVTERHGLKEPKRVEELQNKIVNCLKDHVTFN  215 (271)
T ss_dssp             HHHHHHHHHTTCCCHHHHHHHHHHHHSSCCTTCSCHHHHHHHHHHHHHHHHHHHHGG
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCcHHHHHHHHHHHHHHHHHHHHhc
Confidence            357899999999999999999999999975559999999999999999999999753

>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=99.33  E-value=1.3e-12  Score=98.53  Aligned_cols=57  Identities=19%  Similarity=0.372  Sum_probs=53.3

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||++|+||+|||||++ |++...|+++|++++.+|.+|+...
T Consensus       106 i~~~~~~~~~L~ld~~E~~lLkaivL~~pd~~gL~~~~~v~~~q~~~~~aL~~y~~~~  163 (199)
T 3cqv_A          106 MFEFSEKLNALQLSDEEMSLFTAVVLVSADRSGIENVNSVEALQETLIRALRTLIMKN  163 (199)
T ss_dssp             HHHHHHHHHTTCCCHHHHHHHHHHHHHTSCCTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCCCCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence            45789999999999999999999999999986 9999999999999999999999754

>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=99.31  E-value=2.8e-12  Score=99.10  Aligned_cols=57  Identities=19%  Similarity=0.188  Sum_probs=52.9

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||+||+||+||+||++ |++...|+++|++++.+|.+||...
T Consensus       130 i~~~~~~l~~L~ld~~E~~lLkaivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~  187 (236)
T 1fcy_A          130 VFAFAGQLLPLEMDDTETGLLSAICLICGDRMDLEEPEKVDKLQEPLLEALRLYARRR  187 (236)
T ss_dssp             HHHHHHHHGGGCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            34688999999999999999999999999986 9999999999999999999999754

>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=99.30  E-value=2.1e-12  Score=101.22  Aligned_cols=73  Identities=23%  Similarity=0.300  Sum_probs=66.1

Q ss_pred             CCCCCCccccccccc------------------------------------------------chhhhhhhhchhcccCh
Q psy16825        109 NKSIPSLEDLERNTE------------------------------------------------ISCTQVIDRLEHVAVSK  140 (183)
Q Consensus       109 ~k~iP~f~~L~~~dq------------------------------------------------~~~~~lv~~~~~l~~~~  140 (183)
                      .|.+|+|.+|+.+||                                                ..+.+++.+|++|++|.
T Consensus        72 AK~iP~F~~L~~~DQi~LLk~~w~ElllL~~a~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~L~ld~  151 (257)
T 3v3e_B           72 AEKIPGFAELSPADQDLLLESAFLELFILRLAYRSKPGEGKLIFCSGLVLHRLQCARGFGDWIDSILAFSRSLHSLLVDV  151 (257)
T ss_dssp             HHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHSBGGGTEEECTTSBEEEHHHHHHHHTTHHHHHHHHHHHHHHTTCCH
T ss_pred             HHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhccCCCCeeEeCCCccccHHHHHhhhHHHHHHHHHHHHHHHhcCCCH
Confidence            388999999999999                                                23567899999999999


Q ss_pred             hHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHHHHHHHh
Q psy16825        141 EEYYFLKALVLANSDVKLDEFSSLKKFRNSILSSLGDCIYV  181 (183)
Q Consensus       141 ~E~~~lkai~L~~~d~~L~~~~~v~~~~~~~~~~L~~~~~~  181 (183)
                      +||+||+||+||++..+|.+...|+++|++++.+|.+|+..
T Consensus       152 ~E~a~LkAivLfsd~~gL~~~~~Ve~lqe~~~~aL~~yi~~  192 (257)
T 3v3e_B          152 PAFACLSALVLITDRHGLQEPRRVEELQNRIASCLKEHVAA  192 (257)
T ss_dssp             HHHHHHHHHHHSSCCTTCSSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999994456999999999999999999999964

>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=99.30  E-value=2.3e-12  Score=100.40  Aligned_cols=57  Identities=18%  Similarity=0.211  Sum_probs=53.3

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||+||+||+|||||++ |.+...|+++|++++.+|.+|+...
T Consensus       141 l~~~~~~l~~L~ld~~E~~lLkAivLfnpd~~gL~~~~~ve~lqe~~~~aL~~y~~~~  198 (248)
T 3l0l_A          141 IFDFSHSLSALHFSEDEIALYTALVLINAHRPGLQEKRKVEQLQYNLELAFHHHLCKT  198 (248)
T ss_dssp             HHHHHHHHHTTCCCHHHHHHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCCccHHHHHHHHHHHHHHHHHHHHhh
Confidence            45789999999999999999999999999986 9999999999999999999999764

>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=99.28  E-value=4.4e-12  Score=98.55  Aligned_cols=57  Identities=26%  Similarity=0.425  Sum_probs=53.0

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||++|+||+|||||++ |++...|+++|++++.+|.+|+...
T Consensus       134 l~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~  191 (244)
T 2e2r_A          134 ILQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQ  191 (244)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHHHHHHTCCCTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhccCCCCCcCHHHHHHHHHHHHHHHHHHHHhc
Confidence            35789999999999999999999999999986 9999999999999999999999754

>3ltx_A Estrogen receptor; constitutive, nuclear receptor, DNA-binding, metal-binding, nucleus, transcription, transcription regulation, zinc-finger; 2.60A {Crassostrea gigas}

Probab=99.28  E-value=4.6e-12  Score=98.36  Aligned_cols=57  Identities=23%  Similarity=0.437  Sum_probs=53.0

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||+||+||+|||||++ |++...|+++|++++.+|.+|+...
T Consensus       123 i~~~~~~l~~L~ld~~E~~lLkaivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~  180 (243)
T 3ltx_A          123 VAAVSEQMMQNHLHKDELLLLQAMVLVNAEVRRLASYNQIFNMQQSLLDAIVDTAQKY  180 (243)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHHTSCCSCCTTHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            34788999999999999999999999999986 9999999999999999999999754

>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=99.27  E-value=4.9e-12  Score=99.71  Aligned_cols=56  Identities=9%  Similarity=0.211  Sum_probs=52.6

Q ss_pred             hhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        127 TQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       127 ~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      .+++.+|++|++|.+||+||+||+|||||++ |.+...|+++|++++.+|.+||..+
T Consensus       161 ~~~~~~l~~L~ld~~E~alLkAIvLfnpd~~gL~~~~~Ve~lqe~~~~aL~~y~~~~  217 (269)
T 3u9q_A          161 FEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLN  217 (269)
T ss_dssp             HHHHHHHHTTCCCHHHHHHHHHHHHTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhcCCHHHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHHHHHHHHHHHh
Confidence            4688999999999999999999999999986 9999999999999999999999764

>3n00_A REV-ERBA-alpha; reverba ncorid1, anti-parallel B-sheet, transcription regula; 2.60A {Homo sapiens}

Probab=99.27  E-value=3.6e-12  Score=99.20  Aligned_cols=57  Identities=19%  Similarity=0.371  Sum_probs=53.5

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||+||+||+|||||++ |++...|+++|++++.+|.+||...
T Consensus       151 i~~~~~~l~~L~ld~~E~~lLkAIvL~npd~~gL~~~~~ve~lq~~~~~aL~~y~~~~  208 (245)
T 3n00_A          151 MFDFSEKLNSLALTEEELGLFTAVVLVSADRSGMENSASVEQLQETLLRALRALVLKN  208 (245)
T ss_dssp             HHHHHHHHHHTCCCHHHHHHHHHHHHHTSCCTTCSSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHHHHHHHHHHHh
Confidence            45799999999999999999999999999986 9999999999999999999999764

>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=99.27  E-value=6e-12  Score=99.06  Aligned_cols=56  Identities=16%  Similarity=0.214  Sum_probs=52.6

Q ss_pred             hhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        127 TQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       127 ~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      ..++.+|++|++|.+||+||+||+||+||++ |++...|+++|++++.+|.+||..+
T Consensus       155 ~~~~~~l~~L~ld~~E~~lLkAIvL~~pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~  211 (266)
T 3kmr_A          155 FAFANQLLPLEMDDAETGLLSAICLICGDRQDLEQPDRVDMLQEPLLEALKVYVRKR  211 (266)
T ss_dssp             HHHHHHHGGGCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            4678999999999999999999999999986 9999999999999999999999764

>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=99.26  E-value=5.5e-12  Score=98.26  Aligned_cols=57  Identities=30%  Similarity=0.457  Sum_probs=53.3

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|+++++|.+||++|+||+|||||++ |++...|+++|++++.+|.+|+..+
T Consensus       134 l~~~~~~l~~L~ld~~E~~lLkAivL~npd~~gL~~~~~ve~lq~~~~~aL~~y~~~~  191 (248)
T 3k6p_A          134 LLQLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQLREALHEALLEYEAGR  191 (248)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHHHHHHHTCCCTTCSCHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            45789999999999999999999999999986 9999999999999999999999764

>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=99.26  E-value=5.1e-12  Score=99.66  Aligned_cols=57  Identities=19%  Similarity=0.247  Sum_probs=53.1

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||+||+||+|||||++ |.+...|+++|++++.+|.+||...
T Consensus       150 i~~~~~~l~~L~ld~~E~~lLkAivLfnpd~~gL~~~~~ve~lq~~~~~aL~~y~~~~  207 (270)
T 1n83_A          150 VFEFGKSLCSMHLTEDEIALFSAFVLMSADRSWLQEKVKIEKLQQKIQLALQHVLQKN  207 (270)
T ss_dssp             HHHHHHHHHTTCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            45789999999999999999999999999986 9999999999999999999999754

>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=99.25  E-value=9e-12  Score=99.74  Aligned_cols=56  Identities=16%  Similarity=0.273  Sum_probs=52.2

Q ss_pred             hhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        127 TQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       127 ~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      .+++.+|++|++|.+||+||+||+|||||++ |.+...|+++|++++.+|.+||...
T Consensus       191 ~~~~~~l~~L~ld~~E~alLkAIvLfnpd~~gL~~~~~Ve~lqe~~~~aL~~y~~~~  247 (302)
T 2hc4_A          191 VKFQVGLKKLKLHEEEHVLLMAICLLSPDRPGVQDHVRIEALQDRLCDVLQAYIRIQ  247 (302)
T ss_dssp             HHHHHHHHTTCCCHHHHHHHHHHHHTCSCSTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence            4678899999999999999999999999986 9999999999999999999999754

>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=99.25  E-value=4.3e-12  Score=98.64  Aligned_cols=56  Identities=16%  Similarity=0.261  Sum_probs=52.2

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHh
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYV  181 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~  181 (183)
                      +.+++.+|++|++|.+||+||+||+|||||++ |++...|+++|++++.+|.+||..
T Consensus       140 i~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~  196 (246)
T 1xvp_B          140 LFHFHGTLRKLQLQEPEYVLLAAMALFSPDRPGVTQRDEIDQLQEEMALTLQSYIKG  196 (246)
T ss_dssp             HHHHHHHHHHTCCCHHHHHHHHHHHHSCSSSTTCSCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            34678899999999999999999999999986 999999999999999999999974

>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=99.25  E-value=6.2e-12  Score=97.62  Aligned_cols=56  Identities=23%  Similarity=0.398  Sum_probs=52.1

Q ss_pred             hhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        127 TQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       127 ~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      .+++.+|++|++|.+||+||+||+|+|||++ |++...|+++|++++.+|.+|+...
T Consensus       126 ~~~~~~~~~L~ld~~E~~lLkaivL~~pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~  182 (244)
T 3cjw_A          126 QEQVEKLKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVESLQEKSQCALEEYVRSQ  182 (244)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            4678899999999999999999999999986 9999999999999999999999754

>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=99.25  E-value=8.6e-12  Score=96.07  Aligned_cols=57  Identities=18%  Similarity=0.359  Sum_probs=52.5

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +..++.+|++|++|.+||+||+||+|||||++ |++...|+++|++++.+|.+|+...
T Consensus       125 i~~~~~~l~~L~ld~~E~~lLkaivL~~pd~~gL~~~~~v~~~q~~~~~aL~~y~~~~  182 (232)
T 1osh_A          125 MFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLCKIH  182 (232)
T ss_dssp             HHHHHHHHHTTCCCHHHHHHHHHHHHTCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCCChHHHHHHHHHHHHHHHHHHHHH
Confidence            34578999999999999999999999999986 9999999999999999999999754

>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=99.24  E-value=6.9e-12  Score=97.91  Aligned_cols=57  Identities=14%  Similarity=0.233  Sum_probs=53.0

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||+||+||+|||||++ |++...|+++|++++.+|.+||...
T Consensus       144 l~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~  201 (254)
T 3b0t_A          144 LIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRLSNTLQTYIRCR  201 (254)
T ss_dssp             HHHHHHHHHTTCCCHHHHHHHHHHHHSCSCSTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCccCCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence            34688999999999999999999999999986 9999999999999999999999764

>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=99.24  E-value=8.8e-12  Score=97.13  Aligned_cols=57  Identities=25%  Similarity=0.393  Sum_probs=53.0

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||+||+||+|+|||++ |.+...|+++|++++.+|.+|+..+
T Consensus       128 l~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~  185 (249)
T 3p0u_A          128 LQEFCNSMAKLDIDGYEYAYLKAIVLFSPDHPGLTSTSQIEKFQEAAQMELQDYVQAT  185 (249)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHTCSCSTTCCCSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhCCCHHHHHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHh
Confidence            34688999999999999999999999999986 9999999999999999999999764

>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=99.24  E-value=4.7e-12  Score=98.38  Aligned_cols=57  Identities=21%  Similarity=0.228  Sum_probs=53.1

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||+||+||+|||||++ |++...|+.+|++++.+|.+||...
T Consensus       135 i~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~  192 (244)
T 1nq7_A          135 AFDFAKNLCSLQLTEEEIALFSSAVLISPDRAWLLEPRKVQKLQEKIYFALQHVIQKN  192 (244)
T ss_dssp             HHHHHHHHHTTCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            34789999999999999999999999999986 9999999999999999999999764

>2nxx_A Ultraspiracle (USP, NR2B4); hormone receptor, APO and holo ligand binding pocket, hormone/growth factor complex; HET: P1A; 2.75A {Tribolium castaneum}

Probab=99.23  E-value=7.4e-12  Score=96.65  Aligned_cols=57  Identities=19%  Similarity=0.418  Sum_probs=53.2

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||+||+||+|+|||++ |++...|+++|++++.+|.+|+...
T Consensus       124 ~~~~~~~l~~L~ld~~E~~lLkaivL~~pd~~gL~~~~~v~~~q~~~~~aL~~y~~~~  181 (235)
T 2nxx_A          124 LSELVNKMKEMKMDKTELGCLRAIILYNPDVRGIKSVQEVEMLREKIYGVLEEYTRTT  181 (235)
T ss_dssp             HHHTHHHHHHHTCCHHHHHHHHHHHHCCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            45789999999999999999999999999986 9999999999999999999999754

>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=99.23  E-value=5.7e-12  Score=99.20  Aligned_cols=57  Identities=16%  Similarity=0.202  Sum_probs=53.2

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||+||+||+|||||++ |.+...|+++|++++.+|.+||...
T Consensus       156 i~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~  213 (267)
T 3ilz_A          156 IFELGKSLSAFNLDDTEVALLQAVLLMSTDRSGLLXVDKIEKSQEAYLLAFEHYVNHR  213 (267)
T ss_dssp             HHHHHHHHGGGCCCHHHHHHHHHHHHSCCCSSSCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCchHHHHHHHHHHHHHHHHHHHHHh
Confidence            45788999999999999999999999999986 9999999999999999999999754

>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=99.21  E-value=1.1e-11  Score=98.45  Aligned_cols=57  Identities=9%  Similarity=0.255  Sum_probs=53.1

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||+||+||+|||||++ |.+...|+++|++++.+|.+||...
T Consensus       175 l~~~~~~l~~L~ld~~E~~lLkAIvL~npd~~gL~~~~~ve~lq~~~~~aL~~y~~~~  232 (283)
T 3ipq_A          175 IFEFSRAMNELQLNDAEFALLIAISIFSADRPNVQDQLQVERLQHTYVEALHAYVSIH  232 (283)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHHHHHTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCCCcHHHHHHHHHHHHHHHHHHHHHh
Confidence            45788999999999999999999999999986 9999999999999999999999754

>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=99.21  E-value=1.1e-11  Score=98.77  Aligned_cols=56  Identities=14%  Similarity=0.234  Sum_probs=52.5

Q ss_pred             hhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        127 TQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       127 ~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      .+++.+|++|++|.+||+||+||+|||||++ |++...|+++|++++.+|.+||..+
T Consensus       148 ~~~~~~l~~L~ld~~E~~lLkAIvLfnpd~~gL~~~~~Ve~lq~~~~~aL~~y~~~~  204 (292)
T 2o4j_A          148 IKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCR  204 (292)
T ss_dssp             HHHHHHHHHTCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHHHHHHHHHHHh
Confidence            4688999999999999999999999999986 9999999999999999999999764

>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=99.21  E-value=1.2e-11  Score=97.12  Aligned_cols=57  Identities=26%  Similarity=0.355  Sum_probs=52.8

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCC-CCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANS-DVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~-d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||+||+||+|||| |++ |++...|+++|++++.+|.+||...
T Consensus       130 l~~~~~~l~~L~ld~~E~~lLkAIvL~np~d~~gL~~~~~ve~lq~~~~~aL~~y~~~~  188 (261)
T 3mnp_A          130 MLFISTELQRLQVSYEEYLCMKTLLLLSSVPKEGLKSQELFDEIRMTYIKELGKAIAKR  188 (261)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHHHHHTSEEETTCCTTHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHcCCCCcCCCccHHHHHHHHHHHHHHHHHHHHhh
Confidence            34689999999999999999999999999 876 9999999999999999999999765

>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=99.20  E-value=1.1e-11  Score=97.17  Aligned_cols=57  Identities=18%  Similarity=0.301  Sum_probs=52.3

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCC-CCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANS-DVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~-d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||+||+||+|||| |++ |++...|+++|++++.+|.+||...
T Consensus       128 l~~~~~~l~~L~ld~~E~~lLkAIvLfnp~d~~gL~~~~~ve~lqe~~~~aL~~y~~~~  186 (260)
T 3vhv_A          128 MHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKDGLKSQAAFEEMRTNYIKELRKMVTKC  186 (260)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHHHHHTSEEETTCCTTHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHcCCcCCCCCcCHHHHHHHHHHHHHHHHHHHHhc
Confidence            45789999999999999999999999999 875 9999999999999999999999754

>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=99.20  E-value=1.3e-11  Score=95.94  Aligned_cols=57  Identities=25%  Similarity=0.344  Sum_probs=52.5

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||+||+||+|||||++ |++...|+++|++++.+|.+|+...
T Consensus       136 ~~~~~~~~~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~  193 (246)
T 1ymt_A          136 AQELVLQLHALQLDRQEFVCLKFLILFSLDVKFLNNHSLVKDAQEKANAALLDYTLSH  193 (246)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHTCSCGGGSSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHhcCCcccccccHHHHHHHHHHHHHHHHHHHHhc
Confidence            34678899999999999999999999999986 9999999999999999999999754

>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=99.20  E-value=1.5e-11  Score=96.35  Aligned_cols=56  Identities=25%  Similarity=0.405  Sum_probs=52.4

Q ss_pred             hhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        127 TQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       127 ~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      .+++.+|++|++|.+||+||+||+|||||++ |++...|+++|++++.+|.+|+...
T Consensus       148 ~~~~~~l~~L~ld~~E~~lLkAivL~npd~~gL~~~~~ve~lq~~~~~aL~~y~~~~  204 (257)
T 3plz_A          148 QELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCN  204 (257)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHSCTTCCSCTTHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHh
Confidence            4688999999999999999999999999986 9999999999999999999999764

>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=99.19  E-value=2.1e-11  Score=94.83  Aligned_cols=55  Identities=20%  Similarity=0.277  Sum_probs=50.7

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCC-CCCchhHHHHHHHHHHHHHHHHHHh
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDV-KLDEFSSLKKFRNSILSSLGDCIYV  181 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~-~L~~~~~v~~~~~~~~~~L~~~~~~  181 (183)
                      +.+++.+|++|++|.+||+||+||+||+ |. +|++...|+++|++++.+|.+||..
T Consensus       132 l~~~~~~l~~L~ld~~E~~lLkAIvLfn-d~~gL~~~~~ve~lq~~~~~aL~~y~~~  187 (244)
T 1pdu_A          132 IMEFSRSLHNLEIDISAFACLCALTLIT-ERHGLREPKKVEQLQMKIIGSLRDHVTY  187 (244)
T ss_dssp             HHHHHHHHHHHCCCHHHHHHHHHHHHSS-CCTTCSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhC-CCCCCccHHHHHHHHHHHHHHHHHHHHH
Confidence            4578999999999999999999999998 65 4999999999999999999999964

>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=99.19  E-value=1.8e-11  Score=96.40  Aligned_cols=57  Identities=18%  Similarity=0.289  Sum_probs=52.3

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCC-CCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANS-DVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~-d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||+||+||+|||| |++ |++...|+++|++++.+|.+|+..+
T Consensus       137 i~~~~~~l~~L~ld~~E~~lLkAIvLfnp~~~~gL~~~~~ve~lq~~~~~aL~~y~~~~  195 (269)
T 1t7r_A          137 MRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFFDELRMNYIKELDRIIACK  195 (269)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHTSEEETTCCTTHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHcCCCccCCCccHHHHHHHHHHHHHHHHHHHHHh
Confidence            35788999999999999999999999999 775 9999999999999999999999643

>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=99.18  E-value=1.9e-11  Score=96.17  Aligned_cols=56  Identities=16%  Similarity=0.192  Sum_probs=52.0

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||+||+||+||| |++ |++...|+++|++++.+|.+||..+
T Consensus       154 l~~~~~~l~~L~ld~~E~~lLkAivL~n-d~~gL~~~~~v~~lq~~~~~aL~~y~~~~  210 (266)
T 2r40_D          154 LLHFCRCMYSMMMDNVHYALLTAIVIFS-DRPGLEQPLLVEEIQRYYLNTLRVYILNQ  210 (266)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHHHHHHTS-CCTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcccCCHHHHHHHhhheeec-CCCCCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence            4578999999999999999999999999 876 9999999999999999999999764

>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=99.17  E-value=2.8e-11  Score=98.70  Aligned_cols=56  Identities=25%  Similarity=0.405  Sum_probs=47.8

Q ss_pred             hhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        127 TQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       127 ~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      .+++.+|++|++|.+||+||+||+|||||+. |++...|+++|++++.+|.+|+...
T Consensus       243 ~~l~~~l~~L~ld~~EyalLkAIvLfnpd~~gLs~~~~Ve~lQe~~~~aL~~y~~~~  299 (352)
T 3tx7_B          243 QELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCN  299 (352)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHSCSCC------CHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHHHHh
Confidence            4688899999999999999999999999986 9999999999999999999999754

>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=99.17  E-value=1.2e-11  Score=99.48  Aligned_cols=57  Identities=16%  Similarity=0.234  Sum_probs=52.8

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||+||+||+|||||++ |.+...|+.+|++|+.+|.+||...
T Consensus       205 i~~~~~~l~~L~ld~~E~alLkAIvLfnpd~~gL~~~~~Ve~lqe~~~~aL~~y~~~~  262 (316)
T 1nrl_A          205 MLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECN  262 (316)
T ss_dssp             HHHHHHHHHHTCCCHHHHHHHHHHHHTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHHHHHHHHHHHh
Confidence            34678899999999999999999999999986 9999999999999999999999764

>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=99.16  E-value=2.5e-11  Score=95.18  Aligned_cols=56  Identities=25%  Similarity=0.385  Sum_probs=51.9

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCC-CCC-CCchhHHHHHHHHHHHHHHHHHHh
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANS-DVK-LDEFSSLKKFRNSILSSLGDCIYV  181 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~-d~~-L~~~~~v~~~~~~~~~~L~~~~~~  181 (183)
                      +.+++.+|++|++|.+||+||+||+|||| |++ |++...|+++|++++.+|.+||..
T Consensus       129 i~~~~~~l~~L~ld~~E~~lLkAIvLfnp~~~~gL~~~~~ve~lq~~~~~aL~~y~~~  186 (261)
T 1sqn_A          129 MWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELIKAIGL  186 (261)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHHHHHTSEECTTCCTTHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHcCCCcccccccHHHHHHHHHHHHHHHHHHHHh
Confidence            34678999999999999999999999999 775 999999999999999999999964

>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=99.16  E-value=4.1e-11  Score=92.69  Aligned_cols=56  Identities=25%  Similarity=0.383  Sum_probs=52.2

Q ss_pred             hhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        127 TQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       127 ~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      .+++.+|++|++|.+||++|+||+|++||.. |.+...|+++|++++.+|.+|+...
T Consensus       129 ~~~~~~l~~L~ld~~E~~~Lkai~l~~pd~~gl~~~~~ve~~q~~~~~~L~~y~~~~  185 (240)
T 2p1t_A          129 TELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHK  185 (240)
T ss_dssp             HHTHHHHHHTTCCHHHHHHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhCCCHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            4689999999999999999999999999986 9999999999999999999999754

>3vhu_A Mineralocorticoid receptor; nuclear receptor, transcription factor, activating mutation, hypertension, antagonist, spironolactone; HET: SNL; 2.11A {Homo sapiens}

Probab=99.15  E-value=2.4e-11  Score=96.86  Aligned_cols=57  Identities=18%  Similarity=0.301  Sum_probs=51.5

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCC-CCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANS-DVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~-d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||+||+||+|||| |++ |++...|+++|++++.+|.+||...
T Consensus       162 l~~~~~~l~~L~ld~~EyalLkAIvLfnp~d~~gL~~~~~Ve~lQe~~~~aL~~y~~~~  220 (294)
T 3vhu_A          162 MHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKDGLKSQAAFEEMRTNYIKELRKMVTKC  220 (294)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHHHHHTSEEETTCCTTHHHHHHHHHHHHHHHHHHHC--
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCcHHHHHHHHHHHHHHHHHHHHhc
Confidence            45688999999999999999999999999 875 9999999999999999999999653

>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=99.15  E-value=4.4e-11  Score=93.08  Aligned_cols=56  Identities=20%  Similarity=0.203  Sum_probs=51.2

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||+||+||+||+ |++ |++...|+++|++++.+|.+|+...
T Consensus       138 i~~~~~~l~~L~ld~~E~~lLkAivL~~-d~~gL~~~~~v~~lq~~~~~aL~~y~~~~  194 (248)
T 2nxx_E          138 LLHFCRTMYSMRVDNAEYALLTAIVIFS-ERPALIEGWKVEKIQEIYLEALRAYVDNR  194 (248)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHTC-CCSSCTTHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHcC-CCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            3468899999999999999999999997 765 9999999999999999999999764

>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=99.12  E-value=6.1e-11  Score=95.21  Aligned_cols=56  Identities=18%  Similarity=0.224  Sum_probs=51.2

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||+||+||+||+ |++ |.+...|+++|++++.+|.+||...
T Consensus       202 i~~~~~~l~~L~ld~~E~alLkAIvLf~-d~~gL~~~~~Ve~lqe~~~~aL~~y~~~~  258 (310)
T 1z5x_E          202 LLRFCRHMCAMKVDNAEYALLTAIVIFS-ERPSLSEGWKVEKIQEIYIEALKAYVENR  258 (310)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHHHHHTC-CCTTCTTHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHcC-CCCCCccHHHHHHHHHHHHHHHHHHHHHH
Confidence            3468899999999999999999999997 765 9999999999999999999999754

>2ocf_A Estrogen receptor; estrogen receptor, LBD, monobody, estradiol, hormone-growth complex; HET: CME EST; 2.95A {Homo sapiens}

Probab=99.11  E-value=3.9e-11  Score=95.89  Aligned_cols=55  Identities=25%  Similarity=0.368  Sum_probs=47.6

Q ss_pred             hhhhhhchhcccChhHHHHHHHHHhcCCCC--------C-CCchhHHHHHHHHHHHHHHHHHHh
Q psy16825        127 TQVIDRLEHVAVSKEEYYFLKALVLANSDV--------K-LDEFSSLKKFRNSILSSLGDCIYV  181 (183)
Q Consensus       127 ~~lv~~~~~l~~~~~E~~~lkai~L~~~d~--------~-L~~~~~v~~~~~~~~~~L~~~~~~  181 (183)
                      .+++.+|++|++|.+||+||+||+|||||+        + |.+...|+++|++++.+|.+||..
T Consensus       132 ~~~~~~l~~L~ld~~Ey~lLkAIvLfnpd~~~LS~~~~~gL~~~~~ve~lqe~~~~aL~~y~~~  195 (298)
T 2ocf_A          132 LATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAK  195 (298)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHHHCSCCC-----------CHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhHhhhCcCHHHHHHHHHHHHcCCCccccccccccccccHHHHHHHHHHHHHHHHHHHHh
Confidence            457899999999999999999999999997        4 778889999999999999999965

>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=99.10  E-value=2.6e-11  Score=94.31  Aligned_cols=56  Identities=25%  Similarity=0.355  Sum_probs=49.8

Q ss_pred             hhhhhhchhcccChhHHHHHHHHHhcCCCC--------C-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        127 TQVIDRLEHVAVSKEEYYFLKALVLANSDV--------K-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       127 ~~lv~~~~~l~~~~~E~~~lkai~L~~~d~--------~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      .+++.+|++|++|.+||+||+||+|||||+        + |.+...|+++|++++.+|.+|+...
T Consensus       123 ~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~~ls~~~~~gl~~~~~v~~lq~~~~~aL~~y~~~~  187 (248)
T 1xpc_A          123 LATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKA  187 (248)
T ss_dssp             HHHHHHHHHHTCCHHHHHHHHHHHHHHTTTTCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHHcCCcccccccccccccccHHHHHHHHHHHHHHHHHHHHcc
Confidence            457899999999999999999999999997        3 5667789999999999999999753

>3up3_A Acedaf-12; ligand binding domain, nematode, steroid binding protein- transcription complex; HET: XCA; 1.25A {Ancylostoma ceylanicum} PDB: 3up0_A*

Probab=99.07  E-value=4.2e-11  Score=93.01  Aligned_cols=56  Identities=7%  Similarity=0.080  Sum_probs=50.6

Q ss_pred             hhhhhhhchh-cccChhHHHHHHHHHhcCCCCCCCch---hHHHHHHHHHHHHHHHHHHh
Q psy16825        126 CTQVIDRLEH-VAVSKEEYYFLKALVLANSDVKLDEF---SSLKKFRNSILSSLGDCIYV  181 (183)
Q Consensus       126 ~~~lv~~~~~-l~~~~~E~~~lkai~L~~~d~~L~~~---~~v~~~~~~~~~~L~~~~~~  181 (183)
                      +.+++.+|++ |++|.+||+||+||+||+|+.+|.++   ..|+++|++++.+|.+||..
T Consensus       133 l~~~~~~~~~~L~ld~~E~alLkAivLfsp~~gL~~~~~~~~Ve~lQe~~~~aL~~y~~~  192 (243)
T 3up3_A          133 FLQFFKIFHEDIRSNDLVISMIMLIVLFSPRDSITDPEDRRIIARHHEQFSALLNRYLES  192 (243)
T ss_dssp             HHHHHHTSCHHHHTCHHHHHHHHHHHHSCCCTTCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHhhcCCCCCCCCcchHHHHHHHHHHHHHHHHHHHHH
Confidence            4578889997 99999999999999999999559876   79999999999999999964

>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=99.06  E-value=1.5e-10  Score=91.17  Aligned_cols=55  Identities=24%  Similarity=0.303  Sum_probs=46.9

Q ss_pred             hhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCc-------hhHHHHHHHHHHHHHHHHHHh
Q psy16825        127 TQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDE-------FSSLKKFRNSILSSLGDCIYV  181 (183)
Q Consensus       127 ~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~-------~~~v~~~~~~~~~~L~~~~~~  181 (183)
                      .+++.+|++|++|.+||+||+||+|||||++ |.+       ...|+++|++++.+|.+|+..
T Consensus       119 ~~~~~~l~~L~ld~~E~~lLkAIvLfnpd~~gLs~~~~~~~~~~~v~~~q~~~~~aL~~y~~~  181 (268)
T 1yye_A          119 LATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAK  181 (268)
T ss_dssp             HHHHHHHHHHTCCHHHHHHHHHHHHHTCCC----------CCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHHcCCCCCCcccchhhHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4578999999999999999999999999975 754       568999999999999999965

>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=99.03  E-value=3e-10  Score=87.82  Aligned_cols=56  Identities=23%  Similarity=0.289  Sum_probs=48.7

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCc-------hhHHHHHHHHHHHHHHHHHHh
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDE-------FSSLKKFRNSILSSLGDCIYV  181 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~-------~~~v~~~~~~~~~~L~~~~~~  181 (183)
                      +.+++.+|++|++|.+||+||+||+|||||++ |++       ...|+.+|+++..+|.+|+..
T Consensus       120 l~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~gLs~~~~~~~~~~~v~~~q~~~~~aL~~y~~~  183 (240)
T 3oll_A          120 LLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAK  183 (240)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHHCSCCCCCCCCC--CHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHcCCCCCCcccccchhhHHHHHHHHHHHHHHHHHHHHhc
Confidence            34688999999999999999999999999975 654       357889999999999999964

>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=99.01  E-value=2.5e-10  Score=87.92  Aligned_cols=57  Identities=25%  Similarity=0.463  Sum_probs=52.7

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|.+|++|.+||++|+|++|++||.+ |++...|+++|++++.+|.+|+..+
T Consensus       128 ~~~l~~~l~~L~ld~~E~~~L~ai~l~~~~~~~l~~~~~ve~~q~~~~~~L~~y~~~~  185 (237)
T 1pzl_A          128 LDELVLPFQELQIDDNEYAYLKAIIFFDPDAKGLSDPGKIKRLRSQVQVSLEDYINDR  185 (237)
T ss_dssp             HHHTHHHHHHHTCCHHHHHHHHHHHHCCTTCTTCSCHHHHHHHHHHHHHHHHHHHHSS
T ss_pred             HHHHHHHHHhhCCCHHHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHHHHHhc
Confidence            45789999999999999999999999999986 9999999999999999999998653

>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=99.00  E-value=5.3e-10  Score=87.98  Aligned_cols=59  Identities=19%  Similarity=0.250  Sum_probs=55.1

Q ss_pred             chhhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        124 ISCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       124 ~~~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      ..+.+++.+|++|++|.+||++|+||+|+|||++ |.+...|+++|++++.+|.+||...
T Consensus       157 ~~l~~~~~~l~~L~ld~~E~~lLkAivL~npd~~gL~~~~~ve~lq~~~~~aL~~y~~~~  216 (268)
T 3f5c_B          157 QAIKSFFFKCWSLNIDTKEYAYLKGTVLFNPDLPGLQCVKYIEGLQWRTQQILTEHIRMM  216 (268)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHHHHH
Confidence            3567899999999999999999999999999986 9999999999999999999999764

>1l2j_A Estrogen receptor beta; nuclear receptor, transcription factor, antagonist transcription receptor; HET: ETC; 2.95A {Homo sapiens} SCOP: a.123.1.1

Probab=99.00  E-value=3.2e-10  Score=89.37  Aligned_cols=55  Identities=24%  Similarity=0.306  Sum_probs=45.7

Q ss_pred             hhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCch-------hHHHHHHHHHHHHHHHHHHh
Q psy16825        127 TQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEF-------SSLKKFRNSILSSLGDCIYV  181 (183)
Q Consensus       127 ~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~-------~~v~~~~~~~~~~L~~~~~~  181 (183)
                      .+++.+|++|++|.+||+||+||+|||||+. |++.       ..|+++|++++.+|.+||..
T Consensus       147 ~~~~~~l~~L~ld~~E~~lLkAIvLfnpd~~gLs~~~~~~~~~~~v~~~q~~~~~aL~~y~~~  209 (271)
T 1l2j_A          147 LATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAK  209 (271)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHHHC----CCCCGGGHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHHcCCCcCCCccchhhHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4578999999999999999999999999975 7653       46778899999999999964

>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=98.98  E-value=7.1e-10  Score=86.95  Aligned_cols=58  Identities=24%  Similarity=0.370  Sum_probs=54.1

Q ss_pred             hhhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        125 SCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       125 ~~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      .+.+++.+|++|++|.+||+||+||+|||||++ |++...|+++|++++.+|.+|+...
T Consensus       146 ~~~~~~~~~~~L~ld~~E~~lLkAivL~npd~~gL~~~~~ve~lq~~~~~aL~~y~~~~  204 (264)
T 1g2n_A          146 VLSELSLKMRTLRVDQAEYVALKAIILLNPDVKGLKNRQEVEVLREKMFLCLDEYCRRS  204 (264)
T ss_dssp             HHHHTHHHHHHTTCCHHHHHHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHHHHHHHHHHHh
Confidence            456899999999999999999999999999986 9999999999999999999999754

>1hg4_A Ultraspiracle; nuclear hormone receptor, transcription factor, ligand binding; HET: LPP; 2.4A {Drosophila melanogaster} SCOP: a.123.1.1

Probab=98.94  E-value=1.2e-09  Score=86.34  Aligned_cols=57  Identities=16%  Similarity=0.357  Sum_probs=53.4

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||+||+||+|||||++ |++...|+++|++++.+|.+|+...
T Consensus       161 ~~~~~~~~~~L~ld~~E~~lLkAivL~npd~~gL~~~~~v~~lq~~~~~aL~~y~~~~  218 (279)
T 1hg4_A          161 LSELSVKMKRLNLDRRELSCLKAIILYNPDIRGIKSRAEIEMCREKVYACLDEHCRLE  218 (279)
T ss_dssp             HHHTHHHHHHHTCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            46789999999999999999999999999986 9999999999999999999999754

>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=98.90  E-value=8.7e-10  Score=85.62  Aligned_cols=47  Identities=19%  Similarity=0.229  Sum_probs=41.9

Q ss_pred             cccChhHHHHHHHHHhcCCCCC-CC---chhHHHHHHHHHHHHHHHHHHhc
Q psy16825        136 VAVSKEEYYFLKALVLANSDVK-LD---EFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       136 l~~~~~E~~~lkai~L~~~d~~-L~---~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +..+..||+||+||+||+||++ |.   +...|+++|++++.+|.+|+...
T Consensus       143 l~~~~~E~alLkAivLfspDr~gL~~~~d~~~Ve~lQe~~~~aL~~y~~~~  193 (244)
T 3gyt_A          143 VRKNDLAIDIIVLMVLFDSKREGLVSQQDKETVEKLHRNYESLLHRYLYSI  193 (244)
T ss_dssp             HHTCHHHHHHHHHHHHSCTTSTTCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhHHHHHHHHHHHHHhccCCCCCccccHHHHHHHHHHHHHHHHHHHHHh
Confidence            4456679999999999999987 98   78899999999999999999754

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=84.73  E-value=0.72  Score=26.64  Aligned_cols=55  Identities=18%  Similarity=0.434  Sum_probs=33.3

Q ss_pred             CCCCCCCCCCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhh
Q psy16825          2 GIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRF   70 (183)
Q Consensus         2 ~~~~~~~~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~   70 (183)
                      |+.++......|.||++..     .++.|.+|...|.-.        |....-=.+. ...+.|..|+-
T Consensus         1 ~s~g~~~~~~~C~vC~~~g-----~ll~Cd~C~~~~H~~--------Cl~ppl~~~p-~g~W~C~~C~~   55 (56)
T 2yql_A            1 GSSGSSGHEDFCSVCRKSG-----QLLMCDTCSRVYHLD--------CLDPPLKTIP-KGMWICPRCQD   55 (56)
T ss_dssp             CCCCCCSSCCSCSSSCCSS-----CCEECSSSSCEECSS--------SSSSCCCSCC-CSSCCCHHHHC
T ss_pred             CCCCcCCCCCCCccCCCCC-----eEEEcCCCCcceECc--------cCCCCcCCCC-CCceEChhhhC
Confidence            3445555567799999852     577899998777554        5331111111 24567887753

---

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	183
d1lo1a_	90	g.39.1.2 (A:) Steroid hormone receptor Err2 DNA-bi	1e-33
d1dszb_	84	g.39.1.2 (B:) Retinoid X receptor (RXR-alpha) DNA-	4e-31
d1cita_	89	g.39.1.2 (A:) Orphan nuclear receptor NGFI-B DNA-b	1e-30
d1kb2a_	89	g.39.1.2 (A:) Vitamin D3 receptor, VDR, DNA-bindin	2e-28
d1a6ya_	78	g.39.1.2 (A:) Orphan nuclear receptor reverb DNA-b	3e-27
d2hanb1	83	g.39.1.2 (B:5-87) Ecdysone receptor DNA-binding do	4e-27
d1r4ia_	74	g.39.1.2 (A:) Androgen receptor {Rat (Rattus norve	2e-26
d1dsza_	75	g.39.1.2 (A:) Retinoic acid receptor DNA-binding d	4e-26
d1hcqa_	74	g.39.1.2 (A:) Estrogen receptor DNA-binding domain	9e-25
d1lata_	71	g.39.1.2 (A:) Glucocorticoid receptor DNA-binding	2e-24
d2nllb_	103	g.39.1.2 (B:) Thyroid hormone receptor (TR-beta) D	2e-21
d1pdua_	230	a.123.1.1 (A:) Nuclear hormone receptor HR38 {Frui	3e-04
d2qw4a1	233	a.123.1.1 (A:32-264) Orphan nuclear receptor NR4A1	5e-04
d1sqna_	251	a.123.1.1 (A:) Progesterone receptor {Human (Homo	0.001
d3d24a1	227	a.123.1.1 (A:194-420) Steroid hormone receptor ERR	0.002
d1nhza_	247	a.123.1.1 (A:) Glucocorticoid receptor {Human (Hom	0.002
d1xvpb_	246	a.123.1.1 (B:) Orphan nuclear receptor NR1I3 (CAR)	0.003
d1ovla_	236	a.123.1.1 (A:) Orphan nuclear receptor NURR1 {Huma	0.003
d1hg4a_	265	a.123.1.1 (A:) Ultraspiracle protein, usp {Drosoph	0.004

>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 =  112 bits (282), Expect = 1e-33
 Identities = 75/89 (84%), Positives = 85/89 (95%)

Query: 8  LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
          +P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQGNIEY+CPA+N+CEI KRRRK+CQA
Sbjct: 2  IPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQA 61

Query: 68 CRFQKCLRKGMLKEGVRLDRVRGGRQKYR 96
          CRF K L+ GMLKEGVRLDRVRGGRQKY+
Sbjct: 62 CRFMKALKVGMLKEGVRLDRVRGGRQKYK 90

>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 =  106 bits (265), Expect = 4e-31
 Identities = 43/82 (52%), Positives = 58/82 (70%)

Query: 8  LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQA 67
            + +C +CGD +SG HYGV SCE CK FFKRT++ ++ YTC  + DC I+KR+R  CQ 
Sbjct: 3  FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQY 62

Query: 68 CRFQKCLRKGMLKEGVRLDRVR 89
          CR+QKCL  GM +E V+ +R R
Sbjct: 63 CRYQKCLAMGMKREAVQEERQR 84

>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 =  105 bits (262), Expect = 1e-30
 Identities = 49/87 (56%), Positives = 60/87 (68%)

Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQK 72
          C VCGD AS  HYGV +CE CK FFKRT+Q + +Y C A+ DC ++KRRR  CQ CRFQK
Sbjct: 3  CAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQK 62

Query: 73 CLRKGMLKEGVRLDRVRGGRQKYRRNP 99
          CL  GM+KE VR D ++G R +    P
Sbjct: 63 CLAVGMVKEVVRTDSLKGRRGRLPSKP 89

>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 = 99.7 bits (248), Expect = 2e-28
 Identities = 36/84 (42%), Positives = 55/84 (65%)

Query: 11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRF 70
          R+C VCGD A+GFH+   +CE CK FF+R+++    +TCP + DC I K  R+ CQACR 
Sbjct: 1  RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRL 60

Query: 71 QKCLRKGMLKEGVRLDRVRGGRQK 94
          ++C+  GM+KE +  D     +++
Sbjct: 61 KRCVDIGMMKEFILTDEEVQRKRE 84

>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 = 96.2 bits (239), Expect = 3e-27
 Identities = 44/77 (57%), Positives = 54/77 (70%), Gaps = 1/77 (1%)

Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYT-CPASNDCEINKRRRKACQACRF 70
          LC VCGDVASGFHYGV +CE CK FF+R+IQ NI+Y  C  + +C I +  R  CQ CRF
Sbjct: 2  LCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRF 61

Query: 71 QKCLRKGMLKEGVRLDR 87
          +KCL  GM ++ VR  R
Sbjct: 62 KKCLSVGMSRDAVRFGR 78

>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 = 95.8 bits (238), Expect = 4e-27
 Identities = 35/81 (43%), Positives = 47/81 (58%)

Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQ 71
          LCLVCGD ASG+HY   +CE CK FF+R++  +  Y C     CE++   R+ CQ CR +
Sbjct: 2  LCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECRLK 61

Query: 72 KCLRKGMLKEGVRLDRVRGGR 92
          KCL  GM  E V  +     +
Sbjct: 62 KCLAVGMRPECVVPENQCAMK 82

>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 = 94.4 bits (234), Expect = 2e-26
 Identities = 37/73 (50%), Positives = 48/73 (65%)

Query: 9  PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQAC 68
          P++ CL+CGD ASG HYG  +C +CK FFKR  +G  +Y C + NDC I+K RRK C +C
Sbjct: 1  PQKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSC 60

Query: 69 RFQKCLRKGMLKE 81
          R +KC   GM   
Sbjct: 61 RLRKCYEAGMTLG 73

>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 = 93.2 bits (231), Expect = 4e-26
 Identities = 42/74 (56%), Positives = 50/74 (67%)

Query: 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQK 72
          C VC D +SG+HYGV++CE CK FF+R+IQ N+ YTC    +C INK  R  CQ CR QK
Sbjct: 2  CFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQK 61

Query: 73 CLRKGMLKEGVRLD 86
          C   GM KE VR D
Sbjct: 62 CFEVGMSKESVRND 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 = 89.8 bits (222), Expect = 9e-25
 Identities = 46/72 (63%), Positives = 55/72 (76%)

Query: 9  PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQAC 68
            R C VC D ASG+HYGV SCE CKAFFKR+IQG+ +Y CPA+N C I+K RRK+CQAC
Sbjct: 3  ETRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQAC 62

Query: 69 RFQKCLRKGMLK 80
          R +KC   GM+K
Sbjct: 63 RLRKCYEVGMMK 74

>d1lata_ g.39.1.2 (A:) Glucocorticoid receptor DNA-binding domain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 71

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Glucocorticoid receptor DNA-binding domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 88.6 bits (219), Expect = 2e-24
 Identities = 41/71 (57%), Positives = 48/71 (67%)

Query: 11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRF 70
          R CLVC D ASG HYGV +CE CKAFFKR ++G   Y C     C I+K RRK C ACR+
Sbjct: 1  RPCLVCSDEASGCHYGVLTCEGCKAFFKRAVEGQHNYLCKYEGKCIIDKIRRKNCPACRY 60

Query: 71 QKCLRKGMLKE 81
          +KCL+ GM  E
Sbjct: 61 RKCLQAGMNLE 71

>d2nllb_ g.39.1.2 (B:) Thyroid hormone receptor (TR-beta) DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Thyroid hormone receptor (TR-beta) DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 82.1 bits (202), Expect = 2e-21
 Identities = 39/88 (44%), Positives = 52/88 (59%), Gaps = 2/88 (2%)

Query: 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYT--CPASNDCEINKRRRKACQACR 69
          LC+VCGD A+G+HY   +CE CK FF+RTIQ N+  +  C     C I+K  R  CQ CR
Sbjct: 3  LCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQECR 62

Query: 70 FQKCLRKGMLKEGVRLDRVRGGRQKYRR 97
          F+KC+  GM  + V  D  R  ++K   
Sbjct: 63 FKKCIYVGMATDLVLDDSKRLAKRKLIE 90

>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 = 37.7 bits (87), Expect = 3e-04
 Identities = 16/87 (18%), Positives = 30/87 (34%), Gaps = 2/87 (2%)

Query: 95  YRRNPDLLSQQWPPNKSIPSLEDLERNTEI--SCTQVIDRLEHVAVSKEEYYFLKALVLA 152
           YR   D     +     +   + L    E      +    L ++ +    +  L AL L 
Sbjct: 88  YRARIDDTKLIFCNGTVLHRTQCLRSFGEWLNDIMEFSRSLHNLEIDISAFACLCALTLI 147

Query: 153 NSDVKLDEFSSLKKFRNSILSSLGDCI 179
                L E   +++ +  I+ SL D +
Sbjct: 148 TERHGLREPKKVEQLQMKIIGSLRDHV 174

>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 = 37.3 bits (86), Expect = 5e-04
 Identities = 18/91 (19%), Positives = 31/91 (34%), Gaps = 2/91 (2%)

Query: 95  YRRNPDLLSQQWPPNKSIPSLEDLERNTEI--SCTQVIDRLEHVAVSKEEYYFLKALVLA 152
           YR  P      +     +  L+      +   S       L  + V    +  L ALVL 
Sbjct: 91  YRSKPGEGKLIFCSGLVLHRLQCARGFGDWIDSILAFSRSLHSLLVDVPAFACLSALVLI 150

Query: 153 NSDVKLDEFSSLKKFRNSILSSLGDCIYVLR 183
                L E   +++ +N I S L + +  + 
Sbjct: 151 TDRHGLQEPRRVEELQNRIASCLKEHVAAVA 181

>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 = 36.2 bits (83), Expect = 0.001
 Identities = 14/61 (22%), Positives = 29/61 (47%), Gaps = 2/61 (3%)

Query: 125 SCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK--LDEFSSLKKFRNSILSSLGDCIYVL 182
           +  Q+      + VS+EE+  +K L+L N+     L   +  ++ R+S +  L   I + 
Sbjct: 119 TMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELIKAIGLR 178

Query: 183 R 183
           +
Sbjct: 179 Q 179

>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 = 35.4 bits (81), Expect = 0.002
 Identities = 17/53 (32%), Positives = 34/53 (64%), Gaps = 1/53 (1%)

Query: 128 QVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCI 179
           Q++ RL+ + + +EEY  LKAL LANSD   +++  ++++ R ++  +L +  
Sbjct: 118 QLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQLREALHEALLEYE 170

>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 = 35.5 bits (81), Expect = 0.002
 Identities = 17/57 (29%), Positives = 24/57 (42%), Gaps = 2/57 (3%)

Query: 125 SCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK--LDEFSSLKKFRNSILSSLGDCI 179
               V   L  + VS EEY  +K L+L +S  K  L       + R + +  LG  I
Sbjct: 116 HMLYVSSELHRLQVSYEEYLCMKTLLLLSSVPKDGLKSQELFDEIRMTYIKELGKAI 172

>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 = 35.0 bits (80), Expect = 0.003
 Identities = 9/56 (16%), Positives = 21/56 (37%), Gaps = 1/56 (1%)

Query: 125 SCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCI 179
                   L  + + + EY  L A+ L + D   + +   + + +  +  +L   I
Sbjct: 139 LLFHFHGTLRKLQLQEPEYVLLAAMALFSPDRPGVTQRDEIDQLQEEMALTLQSYI 194

>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 = 34.6 bits (79), Expect = 0.003
 Identities = 16/87 (18%), Positives = 35/87 (40%), Gaps = 2/87 (2%)

Query: 95  YRRNPDLLSQQWPPNKSIPSLEDLERNTEI--SCTQVIDRLEHVAVSKEEYYFLKALVLA 152
           YR NP      +     +  L+ +    E   S  +    L+++ +    +  + AL + 
Sbjct: 91  YRSNPVEGKLIFCNGVVLHRLQCVRGFGEWIDSIVEFSSNLQNMNIDISAFSCIAALAMV 150

Query: 153 NSDVKLDEFSSLKKFRNSILSSLGDCI 179
                L E   +++ +N I++ L D +
Sbjct: 151 TERHGLKEPKRVEELQNKIVNCLKDHV 177

>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 = 34.3 bits (78), Expect = 0.004
 Identities = 11/80 (13%), Positives = 38/80 (47%), Gaps = 1/80 (1%)

Query: 101 LLSQQWPPNKSIPSLEDLERNTEISCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LD 159
            L+Q +  +++      +    +   +++  +++ + + + E   LKA++L N D++ + 
Sbjct: 128 FLNQSFSYHRNSAIKAGVSAIFDRILSELSVKMKRLNLDRRELSCLKAIILYNPDIRGIK 187

Query: 160 EFSSLKKFRNSILSSLGDCI 179
             + ++  R  + + L +  
Sbjct: 188 SRAEIEMCREKVYACLDEHC 207

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	183
d1lo1a_	90	Steroid hormone receptor Err2 DNA-binding domain {	100.0
d1dszb_	84	Retinoid X receptor (RXR-alpha) DNA-binding domain	100.0
d2hanb1	83	Ecdysone receptor DNA-binding domain {Fruit fly (D	100.0
d1dsza_	75	Retinoic acid receptor DNA-binding domain {Human (	100.0
d1kb2a_	89	Vitamin D3 receptor, VDR, DNA-binding domain {Huma	100.0
d1a6ya_	78	Orphan nuclear receptor reverb DNA-binding domain	100.0
d1r4ia_	74	Androgen receptor {Rat (Rattus norvegicus) [TaxId:	100.0
d1cita_	89	Orphan nuclear receptor NGFI-B DNA-binding domain	100.0
d2nllb_	103	Thyroid hormone receptor (TR-beta) DNA-binding dom	99.97
d1lata_	71	Glucocorticoid receptor DNA-binding domain {Rat (R	99.97
d1hcqa_	74	Estrogen receptor DNA-binding domain {Human and ch	99.97
d1osha_	231	Bile acid receptor FXR {Human (Homo sapiens) [TaxI	99.37
d1xnxa_	232	Orphan nuclear receptor NR1I3 (CAR) {Mouse (Mus mu	99.36
d1ie9a_	255	Vitamin D nuclear receptor {Human (Homo sapiens) [	99.36
d1xvpb_	246	Orphan nuclear receptor NR1I3 (CAR) {Human (Homo s	99.36
d1pq9a_	239	Oxysterols receptor LXR-beta {Human (Homo sapiens)	99.34
d2p54a1	267	Peroxisome proliferator activated receptor alpha,	99.33
d1n46a_	251	Thyroid hormone receptor beta (TR-beta) {Human (Ho	99.33
d1g2na_	256	Ultraspiracle protein, usp {Heliothis virescens [T	99.33
d2fvja1	271	Peroxisome proliferator activated receptor gamma,	99.32
d2e2ra1	223	Orphan nuclear receptor ERR3 {Human (Homo sapiens)	99.32
d1fcya_	236	Retinoic acid receptor gamma (RAR-gamma) {Human (H	99.31
d1hg4a_	265	Ultraspiracle protein, usp {Drosophila melanogaste	99.29
d1pk5a_	242	Orphan nuclear receptor NR5a2 (LRH-1) {Mouse (Mus	99.28
d1nrla_	292	Pregnane x receptor, PXR {Human (Homo sapiens) [Ta	99.28
d1n83a_	251	Orphan nuclear receptor ROR-alpha {Human (Homo sap	99.27
d1pzla_	233	Hepatocyte nuclear factor 4-alpha {Human (Homo sap	99.27
d3d24a1	227	Steroid hormone receptor ERR1 {Human (Homo sapiens	99.27
d1ovla_	236	Orphan nuclear receptor NURR1 {Human (Homo sapiens	99.26
d1nhza_	247	Glucocorticoid receptor {Human (Homo sapiens) [Tax	99.25
d1pdua_	230	Nuclear hormone receptor HR38 {Fruit fly (Drosophi	99.25
d2qw4a1	233	Orphan nuclear receptor NR4A1 {Human (Homo sapiens	99.24
d1sqna_	251	Progesterone receptor {Human (Homo sapiens) [TaxId	99.23
d2b50b1	265	Peroxisome proliferator-activated receptor delta,	99.22
d1t7ra_	250	Androgen receptor {Chimpanzee (Pan troglodytes) [T	99.22
d1nq7a_	244	Orphan nuclear receptor ROR-beta {Rat (Rattus norv	99.22
d2r40d1	243	Ecdysone receptor {Noctuid moth (Heliothis viresce	99.21
d2p1ta1	230	Retinoid-X receptor alpha (RXR-alpha) {Human (Homo	99.19
d1xpca_	245	Estrogen receptor alpha {Human (Homo sapiens) [Tax	99.05
d2j7ya1	236	Estrogen receptor beta {Rat (Rattus norvegicus) [T	98.91
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	90.43
d1dcqa2	122	Pyk2-associated protein beta ARF-GAP domain {Mouse	86.39

>d1lo1a_ g.39.1.2 (A:) Steroid hormone receptor Err2 DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Steroid hormone receptor Err2 DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.8e-36  Score=198.43  Aligned_cols=87  Identities=85%  Similarity=1.546  Sum_probs=81.9

Q ss_pred             CCCCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecc
Q psy16825          8 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR   87 (183)
Q Consensus         8 ~~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r   87 (183)
                      .|..+|.|||++++|+||||++|+||++||||+|..+..|.|..+++|.+++..++.|++|||+|||++||++++||.+|
T Consensus         2 ~P~~~C~VCg~~~~~~hyG~~sC~aC~~FFRR~v~~~~~~~c~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~r   81 (90)
T d1lo1a_           2 IPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKALKVGMLKEGVRLDR   81 (90)
T ss_dssp             CCCCEETTTTEECSEESSSSEECHHHHHHHHHHHHTTCCCCCSSCSCCCCCHHHHHHCHHHHHHHHHHHTCCGGGSCSSC
T ss_pred             CCCCcCCcCCCcCCceEcCeeechhhHHHHHHHHhcCCccchhcCCCCccCCCCccccchhhHHHHHHcCCCHHHhcccc
Confidence            35678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccccc
Q psy16825         88 VRGGRQK   94 (183)
Q Consensus        88 ~~~~~~~   94 (183)
                      ++.++++
T Consensus        82 ~~~~r~k   88 (90)
T d1lo1a_          82 VRGGRQK   88 (90)
T ss_dssp             CTTCCCC
T ss_pred             ccccccC
Confidence            8876654

>d1dszb_ g.39.1.2 (B:) Retinoid X receptor (RXR-alpha) DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Retinoid X receptor (RXR-alpha) DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=3.5e-36  Score=194.68  Aligned_cols=82  Identities=52%  Similarity=1.111  Sum_probs=77.7

Q ss_pred             CCCCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecc
Q psy16825          8 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR   87 (183)
Q Consensus         8 ~~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r   87 (183)
                      .+..+|.|||++++|+||||.+|+||++||||+|..+..|.|..+++|.+++..++.|++|||+|||++||++++||.+|
T Consensus         3 ~~~~~C~VC~~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~c~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~R   82 (84)
T d1dszb_           3 FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER   82 (84)
T ss_dssp             SCCEECTTTCCEESSEETTEECCHHHHHHHHHHHHHTCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCCC
T ss_pred             CCCCcCccCCCcCCccCCCHHHHHHhHHHHHHHHhcCCCeeccCCCCcccCCCCCccCCCCccHHHHHcCCChHHccccc
Confidence            44567999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             cc
Q psy16825         88 VR   89 (183)
Q Consensus        88 ~~   89 (183)
                      ++
T Consensus        83 dr   84 (84)
T d1dszb_          83 QR   84 (84)
T ss_dssp             CC
T ss_pred             CC
Confidence            63

>d2hanb1 g.39.1.2 (B:5-87) Ecdysone receptor DNA-binding domain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Ecdysone receptor DNA-binding domain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=100.00  E-value=4.4e-36  Score=193.93  Aligned_cols=81  Identities=43%  Similarity=0.915  Sum_probs=77.1

Q ss_pred             CcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeeccccc
Q psy16825         11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG   90 (183)
Q Consensus        11 ~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~~   90 (183)
                      ++|.|||++++|+||||.+|+||++||||+|..+..|.|..+++|.+++..++.|++|||+|||++||++++||.+|+..
T Consensus         1 e~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~c~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~   80 (83)
T d2hanb1           1 ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECRLKKCLAVGMRPECVVPENQCA   80 (83)
T ss_dssp             CBCTTTCSBCCEEETTEEECHHHHHHHHHHHHTTCCCCCSSCSCCCCSTTGGGTCHHHHHHHHHHTTCCGGGSSCSSHHH
T ss_pred             CcCccCCCcCCccCcCHHhHhHhHHHHHHHHhcCCceeecCCCCcccCCcccccCccchHHHHHHcCCCHHHccccchhc
Confidence            47999999999999999999999999999999999999999999999999999999999999999999999999988754


Q ss_pred             c
Q psy16825         91 G   91 (183)
Q Consensus        91 ~   91 (183)
                      .
T Consensus        81 ~   81 (83)
T d2hanb1          81 M   81 (83)
T ss_dssp             H
T ss_pred             c
Confidence            3

>d1dsza_ g.39.1.2 (A:) Retinoic acid receptor DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Retinoic acid receptor DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=6.5e-35  Score=185.07  Aligned_cols=75  Identities=56%  Similarity=1.123  Sum_probs=72.6

Q ss_pred             cccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeec
Q psy16825         12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLD   86 (183)
Q Consensus        12 ~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~   86 (183)
                      +|.|||++++|+||||.+|+||++||||+|..+..|.|..+++|.+++..+..|++|||+|||++||++++||.|
T Consensus         1 PC~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~c~~~~~c~~~~~~r~~Cr~CR~~KCl~~GM~~~~vq~d   75 (75)
T d1dsza_           1 PCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRND   75 (75)
T ss_dssp             CCTTTCSCCCSEETTEECCHHHHHHHHHHHHTTCCCCCSSCSCCCCSTTTGGGCHHHHHHHHHHTTCCGGGSCCC
T ss_pred             CCccCCCcCCccCcCHHHhhhhHHHHHHHHhcCCceecccCCccccCCccccccchhHHHHHHHhCCCHHHccCC
Confidence            599999999999999999999999999999999999999999999999999999999999999999999999875

>d1kb2a_ g.39.1.2 (A:) Vitamin D3 receptor, VDR, DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Vitamin D3 receptor, VDR, DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=2.4e-35  Score=192.88  Aligned_cols=82  Identities=44%  Similarity=0.999  Sum_probs=77.5

Q ss_pred             CcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeeccccc
Q psy16825         11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG   90 (183)
Q Consensus        11 ~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~~   90 (183)
                      .+|.|||++++|+||||++|+||++||||+|..+..|.|..+++|.+++..++.|++|||+|||++||++++||.+|++.
T Consensus         1 r~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~c~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~   80 (89)
T d1kb2a_           1 RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDEEVQ   80 (89)
T ss_dssp             CBCTTTCSBCCSEETTEECCHHHHHHHHHHHHTTCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCHHHHH
T ss_pred             CCCeeCCCcCCccCCCHHHHHHHHHHHHHHHhcCCCeecCCCCccCCCCcCCccCchhhHHHHHHcCCCHhhccccchhc
Confidence            47999999999999999999999999999999999999998999999999999999999999999999999999998765


Q ss_pred             cc
Q psy16825         91 GR   92 (183)
Q Consensus        91 ~~   92 (183)
                      ..
T Consensus        81 ~k   82 (89)
T d1kb2a_          81 RK   82 (89)
T ss_dssp             HH
T ss_pred             hh
Confidence            44

>d1a6ya_ g.39.1.2 (A:) Orphan nuclear receptor reverb DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Orphan nuclear receptor reverb DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=6.2e-35  Score=186.52  Aligned_cols=76  Identities=57%  Similarity=1.160  Sum_probs=72.1

Q ss_pred             cccccCCCCcccccccccccchhhhhhccccCCceeec-CCCCCccccccccccccchhhhHHhhhcccccceeecc
Q psy16825         12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTC-PASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR   87 (183)
Q Consensus        12 ~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C-~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r   87 (183)
                      +|.|||++++|+||||.+|+||++||||++..+..|.| ..+++|.+++..+..|++|||+|||++||++++||.+|
T Consensus         2 iC~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~~~~~~~~c~~~~~~r~~Cr~CR~~KCl~~GM~~~~vq~~R   78 (78)
T d1a6ya_           2 LCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGR   78 (78)
T ss_dssp             BCTTTSSBCCEEETTEEECHHHHHHHHHHHSSCCCCCCCSSTTCCCCCTTTTTSCHHHHHHHHTTTTCCSTTCCCCC
T ss_pred             CCeeCCCcCCcccCcchhhhhchhhhhhhhccCCceeeeccCCCcccCCCCCccchhhHHHHHHHhCCCHHHhcCCC
Confidence            69999999999999999999999999999999999975 66788999999999999999999999999999999876

>d1r4ia_ g.39.1.2 (A:) Androgen receptor {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Androgen receptor
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=100.00  E-value=7.2e-35  Score=184.25  Aligned_cols=74  Identities=50%  Similarity=1.116  Sum_probs=70.8

Q ss_pred             CCCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccc
Q psy16825          9 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEG   82 (183)
Q Consensus         9 ~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~   82 (183)
                      |.+.|.|||++++|+||||.+|+||++||||++..+..|.|..+++|.+++..++.|++|||+|||++||+.+|
T Consensus         1 P~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~c~~~~~C~~~~~~r~~C~~CR~~KCl~vGM~~~A   74 (74)
T d1r4ia_           1 PQKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLGA   74 (74)
T ss_dssp             CCCBCSSSCSBEEEEETTEEEEHHHHHHHHHHHTSCCCCCCSSSSCCCCCTTTTTTCHHHHHHHHHHHTCCSCC
T ss_pred             CCCcCccCCCcCCccCCCHHhhHHHHHHHHHHHhcccceeeecCCCcccCCCCcccchhhhHHHHHHcCCcCCC
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999875

>d1cita_ g.39.1.2 (A:) Orphan nuclear receptor NGFI-B DNA-binding domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Orphan nuclear receptor NGFI-B DNA-binding domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=100.00  E-value=1.5e-34  Score=189.26  Aligned_cols=84  Identities=57%  Similarity=1.087  Sum_probs=78.5

Q ss_pred             CcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeeccccc
Q psy16825         11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG   90 (183)
Q Consensus        11 ~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~~   90 (183)
                      +.|+|||++++|+||||.+|+||++||||++..+..|.|..+++|.+++..++.|++|||+|||++||++++||.++...
T Consensus         1 g~C~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~c~~~~~c~~~~~~r~~Cr~CR~~KCl~~GM~~~~v~~~~~~~   80 (89)
T d1cita_           1 GRCAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTDSLKG   80 (89)
T ss_dssp             CCCSSSCCCCCEEETTEEECHHHHHHHHHHHHHTCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHTTCCGGGSCCGGGTT
T ss_pred             CCCeECCCcCCccCCCcccchhhHHHHHHHHHcCCceeecCCCCccccCCccccCchhhHHHHHHcCCCHHHhccccccc
Confidence            46999999999999999999999999999999999999999999999999999999999999999999999999988766


Q ss_pred             cccc
Q psy16825         91 GRQK   94 (183)
Q Consensus        91 ~~~~   94 (183)
                      .+.+
T Consensus        81 ~r~~   84 (89)
T d1cita_          81 RRGR   84 (89)
T ss_dssp             CCSC
T ss_pred             ccCC
Confidence            5544

>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=99.97  E-value=1.9e-34  Score=193.95  Aligned_cols=82  Identities=46%  Similarity=0.948  Sum_probs=74.9

Q ss_pred             CcccccCCCCcccccccccccchhhhhhccccCCcee--ecCCCCCccccccccccccchhhhHHhhhcccccceeeccc
Q psy16825         11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEY--TCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV   88 (183)
Q Consensus        11 ~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~--~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~   88 (183)
                      +.|.|||++++|+||||+||+||++||||+|..+..+  .|..+++|.+++..++.|++|||+|||+|||++++|+.+|+
T Consensus         2 ~~C~VCg~~a~g~HfGv~sC~aCkaFFRR~v~~~~~~~~~c~~~~~c~~~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~   81 (103)
T d2nllb_           2 ELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQECRFKKCIYVGMATDLVLDDSK   81 (103)
T ss_dssp             CBCTTTCSBCCSEETTEECCHHHHHHHHHHHHTTCGGGCCCSSCTTCCCSTTTTTSCHHHHHHHHHHTTCCGGGSCCHHH
T ss_pred             CcCccCCCcCCcccCchhhhHHHHHHhHHHhhccccceeecccCCCCcCCCCccCCCccccchhHHHhhccHHhhhcccc
Confidence            4699999999999999999999999999999987665  45778999999999999999999999999999999999987


Q ss_pred             cccc
Q psy16825         89 RGGR   92 (183)
Q Consensus        89 ~~~~   92 (183)
                      +...
T Consensus        82 ~~~~   85 (103)
T d2nllb_          82 RLAK   85 (103)
T ss_dssp             HHHH
T ss_pred             chhh
Confidence            6544

>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=99.97  E-value=1.2e-33  Score=177.31  Aligned_cols=71  Identities=58%  Similarity=1.156  Sum_probs=68.3

Q ss_pred             CcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhccccc
Q psy16825         11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE   81 (183)
Q Consensus        11 ~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~   81 (183)
                      .+|.|||++++|+||||++|+||++||||+|..+..|.|..+++|.+++..++.|++|||+|||++||++|
T Consensus         1 k~C~VC~~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~c~~~~~C~~~~~~r~~Cr~CR~~KCl~~GM~~e   71 (71)
T d1lata_           1 RPCLVCSDEASGCHYGVLTCEGCKAFFKRAVEGQHNYLCKYEGKCIIDKIRRKNCPACRYRKCLQAGMNLE   71 (71)
T ss_dssp             CBCTTTCSBCCEEETTEEECHHHHHHHHHHHHSCCCCCCSSCSCCCCSTTTTTTCHHHHHHHHHHTTCCCC
T ss_pred             CcCeeCCCcCCceEcCHhhHHHHHHHHHHHHhcCcceeeecCcccccccCccccCCccchhHHhHccCCCC
Confidence            36999999999999999999999999999999999999999999999999999999999999999999875

>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=99.97  E-value=4.9e-33  Score=175.76  Aligned_cols=71  Identities=65%  Similarity=1.309  Sum_probs=68.3

Q ss_pred             CCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccc
Q psy16825         10 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLK   80 (183)
Q Consensus        10 ~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~   80 (183)
                      ...|.|||++++|+||||.+|+||++||||+|..+..|.|+.+++|.+++..++.|++|||+|||++||++
T Consensus         4 ~~~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~k   74 (74)
T d1hcqa_           4 TRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMK   74 (74)
T ss_dssp             CCBCTTTCSBCCEEETTEEECHHHHHHHHHHHSSCCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHHTCCC
T ss_pred             CCCCccCCCcCCceEcCeeehHHHHHHHHHHHHcccccccccCCCCccCCCccccchHhhHHHHHHcCCcC
Confidence            46799999999999999999999999999999999999999999999999999999999999999999974

>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=99.37  E-value=3.1e-13  Score=102.52  Aligned_cols=75  Identities=17%  Similarity=0.404  Sum_probs=69.1

Q ss_pred             CCCCCCccccccccc----------------------------------------------chhhhhhhhchhcccChhH
Q psy16825        109 NKSIPSLEDLERNTE----------------------------------------------ISCTQVIDRLEHVAVSKEE  142 (183)
Q Consensus       109 ~k~iP~f~~L~~~dq----------------------------------------------~~~~~lv~~~~~l~~~~~E  142 (183)
                      .|.+|+|.+|+.+||                                              ..+.+++.+|+.|++|.+|
T Consensus        62 AK~iP~F~~L~~~DQi~LLk~~~~El~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~l~~L~ld~~E  141 (231)
T d1osha_          62 TKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLPSGHSDLLEERIRNSGISDEYITPMFSFYKSIGELKMTQEE  141 (231)
T ss_dssp             HHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHTSSCCTTTHHHHHHHHHHHHTTCCCHHH
T ss_pred             HhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhcCccccCCCccccHHHHHhccchHHHHHHHHHHHHHHHHcCCCHHH
Confidence            489999999999999                                              3456899999999999999


Q ss_pred             HHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhcC
Q psy16825        143 YYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVLR  183 (183)
Q Consensus       143 ~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~~  183 (183)
                      |+||+||+||+||++ |.+...|+++|++++.+|.+|+...+
T Consensus       142 ~~lLkAivL~~pd~~gL~~~~~Ve~lq~~~~~aL~~y~~~~~  183 (231)
T d1osha_         142 YALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLCKIHQ  183 (231)
T ss_dssp             HHHHHHHHHTCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHhccCCCCCccHHHHHHHHHHHHHHHHHHHHHHC
Confidence            999999999999987 99999999999999999999997653

>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=99.36  E-value=1.8e-13  Score=103.92  Aligned_cols=58  Identities=16%  Similarity=0.239  Sum_probs=53.9

Q ss_pred             hhhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        125 SCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       125 ~~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      .+.+++.+|++|++|.+||+||+||+||+||++ |.+...|+++|++++.+|.+||..+
T Consensus       138 ~i~~f~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~  196 (232)
T d1xnxa_         138 SILHFHKNLKGLHLQEPEYVLMAATALFSPDRPGVTQREEIDQLQEEMALILNNHIMEQ  196 (232)
T ss_dssp             HHHHHHHHHHTTCCCHHHHHHHHHHHHTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCCCcCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            346788999999999999999999999999987 9999999999999999999999764

>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=99.36  E-value=3.7e-13  Score=103.47  Aligned_cols=59  Identities=14%  Similarity=0.231  Sum_probs=54.3

Q ss_pred             hhhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhcC
Q psy16825        125 SCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVLR  183 (183)
Q Consensus       125 ~~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~~  183 (183)
                      .+.+++.+|++|++|.+||+||+||+||+||++ |.+...|+++|++++.+|.+||...|
T Consensus       144 ~i~~f~~~l~~L~ld~~E~~lLkAiiL~~pdr~gL~~~~~Ve~lq~~~~~aL~~y~~~~~  203 (255)
T d1ie9a_         144 PLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRLSNTLQTYIRCRH  203 (255)
T ss_dssp             HHHHHHHHHHTTCCCHHHHHHHHHHHHSCSCSTTCSCHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHhcCCCcccccCHHHHHHHHHHHHHHHHHHHHHhC
Confidence            345788999999999999999999999999987 99999999999999999999997653

>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=99.36  E-value=2.2e-13  Score=104.18  Aligned_cols=74  Identities=16%  Similarity=0.260  Sum_probs=68.5

Q ss_pred             CCCCCCccccccccc-------------------------------------------------chhhhhhhhchhcccC
Q psy16825        109 NKSIPSLEDLERNTE-------------------------------------------------ISCTQVIDRLEHVAVS  139 (183)
Q Consensus       109 ~k~iP~f~~L~~~dq-------------------------------------------------~~~~~lv~~~~~l~~~  139 (183)
                      .|.+|+|.+|+.+||                                                 ..+.+++.+|++|++|
T Consensus        74 aK~lP~F~~L~~~DQi~LLk~~~~El~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~l~~L~ld  153 (246)
T d1xvpb_          74 TKDLPVFRSLPIEDQISLLKGAAVEICHIVLNTTFCLQTQNFLCGPLRYTIEDGARVGFQVEFLELLFHFHGTLRKLQLQ  153 (246)
T ss_dssp             HTTCHHHHHSCHHHHHHHHHHHHHHHHHHHHGGGEETTTTEEECSSCEECHHHHHHHTCCHHHHHHHHHHHHHHHHTCCC
T ss_pred             HHhCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHhcccCCeeecCCCccchHHHhccccchHHHHHHHHHHHHHHHhCCC
Confidence            389999999999999                                                 3456899999999999


Q ss_pred             hhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        140 KEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       140 ~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      .+||+||+||+||+||++ |.+...|+++|++++.+|.+|+...
T Consensus       154 ~~E~alLkAivL~~pD~~gL~~~~~Ve~lQ~~~~~aL~~y~~~~  197 (246)
T d1xvpb_         154 EPEYVLLAAMALFSPDRPGVTQRDEIDQLQEEMALTLQSYIKGQ  197 (246)
T ss_dssp             HHHHHHHHHHHHSCSSSTTCSCHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHhhhhhccCCCCCCCcHHHHHHHHHHHHHHHHHHHHHc
Confidence            999999999999999987 9999999999999999999999754

>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=99.34  E-value=5e-13  Score=101.81  Aligned_cols=59  Identities=14%  Similarity=0.233  Sum_probs=54.8

Q ss_pred             hhhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhcC
Q psy16825        125 SCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVLR  183 (183)
Q Consensus       125 ~~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~~  183 (183)
                      .+.+++.+|+.|++|..||++|+||+||+||.+ |.+...|+.+|++++.+|.+|+...+
T Consensus       133 ~i~~~~~~l~~L~ld~~E~alLkAivL~~pd~~gl~~~~~ve~lq~~~~~aL~~y~~~~~  192 (239)
T d1pq9a_         133 PIFEFSRAMRRLGLDDAEYALLIAINIFSADRPNVQEPGRVEALQQPYVEALLSYTRIKR  192 (239)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHHHHHHTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcCccccHHHHHHHHHHHHHHHHHHHHhcC
Confidence            456899999999999999999999999999986 99999999999999999999998653

>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=99.33  E-value=6.7e-13  Score=102.64  Aligned_cols=76  Identities=14%  Similarity=0.218  Sum_probs=69.7

Q ss_pred             CCCCCCCccccccccc--------------------------------------------------chhhhhhhhchhcc
Q psy16825        108 PNKSIPSLEDLERNTE--------------------------------------------------ISCTQVIDRLEHVA  137 (183)
Q Consensus       108 ~~k~iP~f~~L~~~dq--------------------------------------------------~~~~~lv~~~~~l~  137 (183)
                      +.|.+|+|.+|+.+||                                                  ..+.+++.+|+.|+
T Consensus        89 wAK~iPgF~~L~~~DQi~LLK~~~~Ellil~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~  168 (267)
T d2p54a1          89 FAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGMLVAYGNGFITREFLKSLRKPFCDIMEPKFDFAMKFNALE  168 (267)
T ss_dssp             HHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHGGGEETTEEEETTTTEEEEHHHHHHSCTTGGGTSHHHHHHHHHHHTTC
T ss_pred             HHhhCcChhhCCHHHHHHHHHHHHHHHHHHHHHHhccCCCCEEEeCCCccchHHHHHhcchHHHHHHHHHHHHHHHHHcC
Confidence            3488999999999999                                                  34578999999999


Q ss_pred             cChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhcC
Q psy16825        138 VSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVLR  183 (183)
Q Consensus       138 ~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~~  183 (183)
                      +|..||+||+||+|++||.+ |.+...|+++|++++.+|.+|+..++
T Consensus       169 ld~~E~alLkAIvLf~pd~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~  215 (267)
T d2p54a1         169 LDDSDISLFVAAIICCGDRPGLLNVGHIEKMQEGIVHVLRLHLQSNH  215 (267)
T ss_dssp             CCHHHHHHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHHhcCCCCCcccHHHHHHHHHHHHHHHHHHHHhcC
Confidence            99999999999999999987 99999999999999999999997653

>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=99.33  E-value=8.4e-13  Score=101.25  Aligned_cols=73  Identities=21%  Similarity=0.271  Sum_probs=68.3

Q ss_pred             CCCCCccccccccc-------------------------------------------------chhhhhhhhchhcccCh
Q psy16825        110 KSIPSLEDLERNTE-------------------------------------------------ISCTQVIDRLEHVAVSK  140 (183)
Q Consensus       110 k~iP~f~~L~~~dq-------------------------------------------------~~~~~lv~~~~~l~~~~  140 (183)
                      |.+|+|.+|+.+||                                                 ..+.+++.+|+.|++|.
T Consensus        78 K~iPgF~~L~~~DQi~LLk~~~~El~lL~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~f~~~l~~L~ld~  157 (251)
T d1n46a_          78 KKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLNGEMAVTRGQLKNGGLGVVSDAIFDLGMSLSSFNLDD  157 (251)
T ss_dssp             HTCTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTCBTTTTBEEETTTEEECHHHHHHTTTTTHHHHHHHHHHHHGGGTCCH
T ss_pred             hcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEeCCCccccHHHHhhcccHHHHHHHHHHHHHHHHcCCCH
Confidence            88999999999999                                                 34568999999999999


Q ss_pred             hHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        141 EEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       141 ~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      .||+||+||+|++||.+ |.+...|+++|++++.+|.+|+..+
T Consensus       158 ~E~alL~AivL~~pdr~gL~~~~~Ve~lQe~~~~aL~~yi~~~  200 (251)
T d1n46a_         158 TEVALLQAVLLMSSDRPGLACVERIEKYQDSFLLAFEHYINYR  200 (251)
T ss_dssp             HHHHHHHHHHHTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCCCCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999987 9999999999999999999999764

>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=99.33  E-value=5.4e-13  Score=102.57  Aligned_cols=57  Identities=25%  Similarity=0.382  Sum_probs=53.3

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|+.|++|.+||++||||+|||||.+ |++...|+++|++++.+|.+|+..+
T Consensus       147 l~~l~~~~~~L~ld~~E~~~LkaIvLfnpd~~gL~~~~~Ie~lqe~~~~aL~~y~~~~  204 (256)
T d1g2na_         147 LSELSLKMRTLRVDQAEYVALKAIILLNPDVKGLKNRQEVEVLREKMFLCLDEYCRRS  204 (256)
T ss_dssp             HHHTHHHHHHTTCCHHHHHHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHhcCccCCcccHHHHHHHHHHHHHHHHHHHHhc
Confidence            45788899999999999999999999999986 9999999999999999999999765

>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=99.32  E-value=1e-12  Score=101.79  Aligned_cols=58  Identities=9%  Similarity=0.190  Sum_probs=54.3

Q ss_pred             hhhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        125 SCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       125 ~~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      .+.+++.+|+.|++|..||++|+||+||+||.+ |.+...|+++|++++.+|.+|+..+
T Consensus       160 ~i~~f~~~~~~L~ld~~E~alLkAIvLf~pd~~gL~~~~~Ve~lQ~~~~~aL~~y~~~~  218 (271)
T d2fvja1         160 PKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLN  218 (271)
T ss_dssp             HHHHHHHHHHTTCCCHHHHHHHHHHHHTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHHcccccCCccHHHHHHHHHHHHHHHHHHHHHh
Confidence            456899999999999999999999999999987 9999999999999999999999754

>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=99.32  E-value=1.1e-12  Score=98.87  Aligned_cols=74  Identities=26%  Similarity=0.415  Sum_probs=68.5

Q ss_pred             CCCCCccccccccc-------------------------------------------------chhhhhhhhchhcccCh
Q psy16825        110 KSIPSLEDLERNTE-------------------------------------------------ISCTQVIDRLEHVAVSK  140 (183)
Q Consensus       110 k~iP~f~~L~~~dq-------------------------------------------------~~~~~lv~~~~~l~~~~  140 (183)
                      |.+|+|.+|+.+||                                                 ..+.+++.+|++|++|.
T Consensus        51 K~lp~F~~L~~~DQi~LLk~~~~el~~L~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~l~~L~ld~  130 (223)
T d2e2ra1          51 KHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEK  130 (223)
T ss_dssp             TTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTSSSCEEEETTEEECHHHHHHTTCHHHHHHHHHHHHHHHHHTCCH
T ss_pred             HhCcchhhcCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeeeecCCcccchHHhhhccHHHHHHHHHHHHHHHHHcCCCH
Confidence            89999999999999                                                 23568999999999999


Q ss_pred             hHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhcC
Q psy16825        141 EEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVLR  183 (183)
Q Consensus       141 ~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~~  183 (183)
                      +||++|+||+|++||.+ |.+...|+.+|++++.+|.+|+...+
T Consensus       131 ~E~~lLkaivL~~pd~~~L~~~~~I~~~q~~~~~aL~~y~~~~~  174 (223)
T d2e2ra1         131 EEFVTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQH  174 (223)
T ss_dssp             HHHHHHHHHHHHTCCCTTCSCHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence            99999999999999986 99999999999999999999997653

>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=99.31  E-value=1.2e-12  Score=99.50  Aligned_cols=59  Identities=20%  Similarity=0.197  Sum_probs=54.4

Q ss_pred             hhhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhcC
Q psy16825        125 SCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVLR  183 (183)
Q Consensus       125 ~~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~~  183 (183)
                      .+..++.+|+.+++|.+||++|+||+|++||.+ |.+...|+++|++++.+|.+|+...+
T Consensus       129 ~~~~~~~~l~~L~ld~~E~alL~Ai~L~~pd~~gL~~~~~Ve~lq~~~~~aL~~y~~~~~  188 (236)
T d1fcya_         129 LVFAFAGQLLPLEMDDTETGLLSAICLICGDRMDLEEPEKVDKLQEPLLEALRLYARRRR  188 (236)
T ss_dssp             HHHHHHHHHGGGCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHhhccCCCCCcccccHHHHHHHHHHHHHHHHHHHhC
Confidence            456788999999999999999999999999986 99999999999999999999997653

>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=99.29  E-value=1.5e-12  Score=100.43  Aligned_cols=58  Identities=16%  Similarity=0.355  Sum_probs=53.6

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhcC
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVLR  183 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~~  183 (183)
                      +.+++.+|+.+++|.+||++||||+||+||.+ |++...|+.+|++++.+|.+|+...+
T Consensus       153 l~~~~~~~~~L~ld~~E~~lLkaivLf~pd~~~l~~~~~Ie~lqe~~~~aL~~y~~~~~  211 (265)
T d1hg4a_         153 LSELSVKMKRLNLDRRELSCLKAIILYNPDIRGIKSRAEIEMCREKVYACLDEHCRLEH  211 (265)
T ss_dssp             HHHTHHHHHHHTCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHccccCCCCcCHHHHHHHHHHHHHHHHHHHHhhC
Confidence            34689999999999999999999999999987 99999999999999999999997653

>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=99.28  E-value=1.4e-12  Score=99.42  Aligned_cols=57  Identities=26%  Similarity=0.388  Sum_probs=53.2

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||++|+||+||+||.+ |++...|+.+|++++.+|.+|+...
T Consensus       133 ~~~l~~~l~~L~ld~~E~~lLkai~Lf~pd~~gL~~~~~v~~~q~~~~~aL~~y~~~~  190 (242)
T d1pk5a_         133 AQELVVRLRSLQFDQREFVCLKFLVLFSSDVKNLENLQLVEGVQEQVNAALLDYTVCN  190 (242)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHSCSCCSSCTTHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHhcCCCCCCchhHHHHHHHHHHHHHHHHHHHHhh
Confidence            45789999999999999999999999999986 9999999999999999999999754

>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=99.28  E-value=7.7e-13  Score=103.55  Aligned_cols=75  Identities=19%  Similarity=0.256  Sum_probs=69.0

Q ss_pred             CCCCCCccccccccc------------------------------------------------chhhhhhhhchhcccCh
Q psy16825        109 NKSIPSLEDLERNTE------------------------------------------------ISCTQVIDRLEHVAVSK  140 (183)
Q Consensus       109 ~k~iP~f~~L~~~dq------------------------------------------------~~~~~lv~~~~~l~~~~  140 (183)
                      .|.+|+|.+|+.+||                                                ..+.+++.+|+.|++|.
T Consensus       117 AK~iP~F~~L~~~DQi~LLk~~~~el~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~  196 (292)
T d1nrla_         117 AKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECGRLSYCLEDTAGGFQQLLLEPMLKFHYMLKKLQLHE  196 (292)
T ss_dssp             HHHCHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTEETTTTEEEETTEEEEECCCSSCHHHHTTSHHHHHHHHHHHTCCCH
T ss_pred             HhcCcCHhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeeeCCCccccHHHhhhhhHHHHHHHHHHHHHHHHHcCCCH
Confidence            388999999999999                                                34568999999999999


Q ss_pred             hHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhcC
Q psy16825        141 EEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVLR  183 (183)
Q Consensus       141 ~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~~  183 (183)
                      +||+||+||+|++||.+ |.+...|+++|++++.+|.+||..++
T Consensus       197 ~E~~lLkAi~L~~pd~~gL~~~~~Ve~lq~~~~~aL~~y~~~~~  240 (292)
T d1nrla_         197 EEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNR  240 (292)
T ss_dssp             HHHHHHHHHHHTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHhC
Confidence            99999999999999987 99999999999999999999997653

>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=99.27  E-value=1.7e-12  Score=99.51  Aligned_cols=59  Identities=19%  Similarity=0.226  Sum_probs=54.7

Q ss_pred             hhhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhcC
Q psy16825        125 SCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVLR  183 (183)
Q Consensus       125 ~~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~~  183 (183)
                      .+.+++.+|+.|++|.+||++|+||+|++||.+ |.+...|+++|++++.+|.+|+..++
T Consensus       142 ~~~~~~~~~~~L~ld~~E~alL~AivL~~pd~~gL~~~~~Ve~lq~~~~~aL~~~~~~~~  201 (251)
T d1n83a_         142 FVFEFGKSLCSMHLTEDEIALFSAFVLMSADRSWLQEKVKIEKLQQKIQLALQHVLQKNH  201 (251)
T ss_dssp             HHHHHHHHHHTTCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHccCccccCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence            456899999999999999999999999999986 99999999999999999999997653

>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=99.27  E-value=1.3e-12  Score=98.99  Aligned_cols=58  Identities=24%  Similarity=0.445  Sum_probs=54.2

Q ss_pred             hhhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        125 SCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       125 ~~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      .+.+++.+|+++++|.+||++||||+||+||.. +++...|+.+|++++.+|.+|+...
T Consensus       123 ~l~~~~~~~~~L~ld~~E~~lLkaiiL~~pd~~~l~~~~~i~~~q~~~~~~L~~y~~~~  181 (233)
T d1pzla_         123 ILDELVLPFQELQIDDNEYAYLKAIIFFDPDAKGLSDPGKIKRLRSQVQVSLEDYINDR  181 (233)
T ss_dssp             HHHHTHHHHHHHTCCHHHHHHHHHHHHCCTTCTTCSCHHHHHHHHHHHHHHHHHHHHSS
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHhcccccCCcccHHHHHHHHHHHHHHHHHHHHHh
Confidence            356799999999999999999999999999986 9999999999999999999999764

>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=99.27  E-value=1.5e-12  Score=98.26  Aligned_cols=58  Identities=29%  Similarity=0.456  Sum_probs=53.7

Q ss_pred             hhhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        125 SCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       125 ~~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      .+.+++.+|++|++|..||++|+||+||+||++ |++...|+.+|++++.+|.+|+..+
T Consensus       115 ~l~~~~~~~~~L~ld~~E~~lLkaivLf~pd~~gL~~~~~I~~~q~~~~~aL~~y~~~~  173 (227)
T d3d24a1         115 ALLQLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQLREALHEALLEYEAGR  173 (227)
T ss_dssp             HHHHHHHHHHTTTCCHHHHHHHHHHHHHTCCCTTCSCHHHHHHHHHHHHHHHHHHHTC-
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHhCCcCCCcccHHHHHHHHHHHHHHHHHHHHHh
Confidence            457899999999999999999999999999986 9999999999999999999998653

>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=99.26  E-value=2.8e-12  Score=97.42  Aligned_cols=74  Identities=19%  Similarity=0.335  Sum_probs=66.8

Q ss_pred             CCCCCCccccccccc------------------------------------------------chhhhhhhhchhcccCh
Q psy16825        109 NKSIPSLEDLERNTE------------------------------------------------ISCTQVIDRLEHVAVSK  140 (183)
Q Consensus       109 ~k~iP~f~~L~~~dq------------------------------------------------~~~~~lv~~~~~l~~~~  140 (183)
                      .|.+|+|.+|+.+||                                                ..+.+++.+|++|++|.
T Consensus        59 AK~iPgF~~L~~~DQi~LLk~~~~ElllL~~a~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~l~~L~ld~  138 (236)
T d1ovla_          59 AEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIFCNGVVLHRLQCVRGFGEWIDSIVEFSSNLQNMNIDI  138 (236)
T ss_dssp             HHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHSBTTTTEEECTTSBEEEHHHHTTTTTTHHHHHHHHHHHHHTTCCCH
T ss_pred             HHcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEecCCceechHhhcccHHHHHHHHHHHHHHHHHcCCCH
Confidence            388999999999999                                                34568899999999999


Q ss_pred             hHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        141 EEYYFLKALVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       141 ~E~~~lkai~L~~~d~~L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +||+||+||+|+++..+|.+...|+++|++++.+|.+|+..+
T Consensus       139 ~E~alLkAI~L~~dr~gL~~~~~Ve~lQ~~~~~aL~~~~~~~  180 (236)
T d1ovla_         139 SAFSCIAALAMVTERHGLKEPKRVEELQNKIVNCLKDHVTFN  180 (236)
T ss_dssp             HHHHHHHHHHHSSCCTTCSCHHHHHHHHHHHHHHHHHHHHGG
T ss_pred             HHHHHHHHHHHcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999844459999999999999999999999764

>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=99.25  E-value=3.4e-12  Score=97.49  Aligned_cols=58  Identities=28%  Similarity=0.339  Sum_probs=53.1

Q ss_pred             hhhhhhhhchhcccChhHHHHHHHHHhcCCC-CC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        125 SCTQVIDRLEHVAVSKEEYYFLKALVLANSD-VK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       125 ~~~~lv~~~~~l~~~~~E~~~lkai~L~~~d-~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      .+.+++.+|+++++|.+||++|+||+||||| .+ +.+...|+++|++++.+|.+|+...
T Consensus       116 ~~~~~~~~l~~L~l~~~E~~lLkaIvLfnpd~~~~l~~~~~ve~lq~~~~~aL~~y~~~~  175 (247)
T d1nhza_         116 HMLYVSSELHRLQVSYEEYLCMKTLLLLSSVPKDGLKSQELFDEIRMTYIKELGKAIVKR  175 (247)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHTSEEETTCCTTHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCcccccHHHHHHHHHHHHHHHHHHHHHh
Confidence            4568999999999999999999999999999 54 8999999999999999999999654

>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=99.25  E-value=3.8e-12  Score=96.31  Aligned_cols=74  Identities=20%  Similarity=0.245  Sum_probs=67.0

Q ss_pred             CCCCCCccccccccc------------------------------------------------chhhhhhhhchhcccCh
Q psy16825        109 NKSIPSLEDLERNTE------------------------------------------------ISCTQVIDRLEHVAVSK  140 (183)
Q Consensus       109 ~k~iP~f~~L~~~dq------------------------------------------------~~~~~lv~~~~~l~~~~  140 (183)
                      .|.+|+|.+|+.+||                                                ..+.+++.+|++|++|.
T Consensus        56 AK~iPgF~~L~~~DQi~LLk~~~~El~~L~~a~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~i~~~~~~~~~L~ld~  135 (230)
T d1pdua_          56 AEKIPGYFDLLPEDQELLFQSASLELFVLRLAYRARIDDTKLIFCNGTVLHRTQCLRSFGEWLNDIMEFSRSLHNLEIDI  135 (230)
T ss_dssp             HTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHCCSSCSEEECTTSBEEEHHHHHHHHTTHHHHHHHHHHHHHHHCCCH
T ss_pred             HHcCCChhcCCHHHHHHHHHHHHHHHHHHHHHHhccCCCCeEEecCCccccHHHHHHhHHHHHHHHHHHHHHHHHcCCCH
Confidence            489999999999999                                                34567899999999999


Q ss_pred             hHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        141 EEYYFLKALVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       141 ~E~~~lkai~L~~~d~~L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      .||++|+||+||++..+|.+...|+++|++++.+|.+|+...
T Consensus       136 ~E~alL~AivL~~d~~~L~~~~~Ve~lq~~~~~aL~~~i~~~  177 (230)
T d1pdua_         136 SAFACLCALTLITERHGLREPKKVEQLQMKIIGSLRDHVTYN  177 (230)
T ss_dssp             HHHHHHHHHHHSSCCTTCSCHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHhhheeecCcccccCHHHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999765569999999999999999999999754

>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=99.24  E-value=4.5e-12  Score=96.06  Aligned_cols=73  Identities=23%  Similarity=0.309  Sum_probs=66.4

Q ss_pred             CCCCCccccccccc------------------------------------------------chhhhhhhhchhcccChh
Q psy16825        110 KSIPSLEDLERNTE------------------------------------------------ISCTQVIDRLEHVAVSKE  141 (183)
Q Consensus       110 k~iP~f~~L~~~dq------------------------------------------------~~~~~lv~~~~~l~~~~~  141 (183)
                      |.+|+|.+|+.+||                                                ..+.+++.+|+.|++|.+
T Consensus        60 K~iPgF~~L~~~DQi~LLk~~~~el~lL~~a~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~l~~L~ld~~  139 (233)
T d2qw4a1          60 EKIPGFAELSPADQDLLLESAFLELFILRLAYRSKPGEGKLIFCSGLVLHRLQCARGFGDWIDSILAFSRSLHSLLVDVP  139 (233)
T ss_dssp             HTSTTTTTSCHHHHHHHHHHHHHHHHHHHHHHHSBGGGTEEECTTSCEEEHHHHHHHHTTHHHHHHHHHHHHHHHTCCHH
T ss_pred             HhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhCCCCCCceeecCCeeecHHhhhhhhHHHHHHHHHHHHHHHHcCCCHH
Confidence            88999999999999                                                345678999999999999


Q ss_pred             HHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        142 EYYFLKALVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       142 E~~~lkai~L~~~d~~L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      ||++|+||+|+++..+|++...|+++|++++.+|.+|+...
T Consensus       140 E~alLkAivL~~d~~gL~~~~~Ve~lq~~~~~aL~~yi~~~  180 (233)
T d2qw4a1         140 AFACLSALVLITDRHGLQEPRRVEELQNRIASCLKEHVAAV  180 (233)
T ss_dssp             HHHHHHHHHHSSCCTTCSCHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHhcCcccCccCHHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999955569999999999999999999999753

>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=99.23  E-value=2.9e-12  Score=98.20  Aligned_cols=58  Identities=24%  Similarity=0.350  Sum_probs=53.2

Q ss_pred             hhhhhhhhchhcccChhHHHHHHHHHhcCCC-CC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        125 SCTQVIDRLEHVAVSKEEYYFLKALVLANSD-VK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       125 ~~~~lv~~~~~l~~~~~E~~~lkai~L~~~d-~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      .+.+++.+|++|++|.+||++|+||+||||| .+ +++...|+++|++++.+|.+||...
T Consensus       119 ~~~~~~~~l~~L~ld~~E~~lLkAIiL~npd~~~~l~~~~~V~~lq~~~~~aL~~~~~~~  178 (251)
T d1sqna_         119 TMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELIKAIGLR  178 (251)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHHHHHHTSEECTTCCTTHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHcCCccccCCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence            4568999999999999999999999999997 55 9999999999999999999999754

>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=99.22  E-value=2.9e-12  Score=98.92  Aligned_cols=59  Identities=10%  Similarity=0.161  Sum_probs=54.6

Q ss_pred             hhhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhcC
Q psy16825        125 SCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVLR  183 (183)
Q Consensus       125 ~~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~~  183 (183)
                      .+.+++.+|+.|++|..||++|+||+||+||.. |.+...|+++|++++.+|.+|+...+
T Consensus       156 ~~~~f~~~~~~L~ld~~E~alLkAiiL~~pd~~~L~~~~~Ve~lQ~~~~~aL~~y~~~~~  215 (265)
T d2b50b1         156 PKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANH  215 (265)
T ss_dssp             HHHHHHHHHHTTCCCHHHHHHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHhhcccCccccccHHHHHHHHHHHHHHHHHHHHHhC
Confidence            356899999999999999999999999999987 99999999999999999999998653

>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=99.22  E-value=3.9e-12  Score=97.33  Aligned_cols=57  Identities=16%  Similarity=0.241  Sum_probs=52.4

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCC-C-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDV-K-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~-~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||+|||||+|||||. + |.+...|+.+|++++.+|.+|+...
T Consensus       119 ~~~~~~~~~~L~ld~~E~~lLkaIvL~npd~~~~l~~~~~i~~lq~~~~~aL~~y~~~~  177 (250)
T d1t7ra_         119 MRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFFDELRMNYIKELDRIIACK  177 (250)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHTSEEETTCCTTHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHhcCCccccCCccHHHHHHHHHHHHHHHHHHHHHh
Confidence            4679999999999999999999999999974 4 9999999999999999999999754

>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=99.22  E-value=3.2e-12  Score=97.51  Aligned_cols=59  Identities=20%  Similarity=0.225  Sum_probs=54.9

Q ss_pred             hhhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhcC
Q psy16825        125 SCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVLR  183 (183)
Q Consensus       125 ~~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~~  183 (183)
                      .+.+++.+|+++++|.+||++|+||+|++||.+ |.+...|+++|++++.+|.+|+..++
T Consensus       134 ~~~~~~~~~~~L~l~~~E~all~AivL~~pd~~~l~~~~~Ve~lq~~~~~aL~~~~~~~~  193 (244)
T d1nq7a_         134 EAFDFAKNLCSLQLTEEEIALFSSAVLISPDRAWLLEPRKVQKLQEKIYFALQHVIQKNH  193 (244)
T ss_dssp             HHHHHHHHHHTTCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCcccHHHHHHHHHHHHHHHHHHHHhcC
Confidence            457899999999999999999999999999986 99999999999999999999998754

>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=99.21  E-value=5.1e-12  Score=96.33  Aligned_cols=57  Identities=16%  Similarity=0.190  Sum_probs=51.9

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhcC
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVLR  183 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~~  183 (183)
                      +.+++.+|++|++|.+||+||+||+||+ |.+ |.+...|+++|++++.+|.+|+..+|
T Consensus       134 l~~f~~~l~~L~ld~~E~alL~AivL~s-d~~~L~~~~~ve~lq~~~~~aL~~y~~~~~  191 (243)
T d2r40d1         134 LLHFCRCMYSMMMDNVHYALLTAIVIFS-DRPGLEQPLLVEEIQRYYLNTLRVYILNQN  191 (243)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHHHHHHTS-CCTTCSCHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHhcC-CCCCCCcHHHHHHHHHHHHHHHHHHHHhhC
Confidence            4578999999999999999999999999 554 99999999999999999999997653

>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=99.19  E-value=1.1e-11  Score=93.59  Aligned_cols=57  Identities=25%  Similarity=0.367  Sum_probs=53.2

Q ss_pred             hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825        126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL  182 (183)
Q Consensus       126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~  182 (183)
                      +.+++.+|++|++|.+||++|+|++||+||.. +++...|+.+|++++.+|.+|+...
T Consensus       122 ~~~~~~~~~~L~ld~~E~~lLkaivL~~pd~~~l~~~~~i~~~q~~~~~aL~~y~~~~  179 (230)
T d2p1ta1         122 LTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHK  179 (230)
T ss_dssp             HHHTHHHHHHTTCCHHHHHHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHhccccCCcccHHHHHHHHHHHHHHHHHHHHhh
Confidence            45789999999999999999999999999986 9999999999999999999999764

>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=99.05  E-value=2.1e-11  Score=92.95  Aligned_cols=57  Identities=23%  Similarity=0.308  Sum_probs=50.0

Q ss_pred             hhhhhhhhchhcccChhHHHHHHHHHhcCCCCC---------CCchhHHHHHHHHHHHHHHHHHHh
Q psy16825        125 SCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK---------LDEFSSLKKFRNSILSSLGDCIYV  181 (183)
Q Consensus       125 ~~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~---------L~~~~~v~~~~~~~~~~L~~~~~~  181 (183)
                      .+.+++.+|+++++|.+||++|+||+|++||..         |.+.+.|+++|++++.+|.+|+..
T Consensus       121 ~~~~~~~~~~~L~ld~~E~~lLkaI~L~~pd~~~l~~~~r~~l~~~~~v~~~q~~~~~aL~~~~~~  186 (245)
T d1xpca_         121 MLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAK  186 (245)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTTTCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHcCCccccccccchhhhhHHHHHHHHHHHHHHHHHHHHHh
Confidence            456799999999999999999999999999964         345668999999999999999864

>d2j7ya1 a.123.1.1 (A:217-452) Estrogen receptor beta {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Estrogen receptor beta
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=98.91  E-value=4.2e-10  Score=84.97  Aligned_cols=57  Identities=23%  Similarity=0.306  Sum_probs=44.0

Q ss_pred             hhhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhH-------HHHHHHHHHHHHHHHHHh
Q psy16825        125 SCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSS-------LKKFRNSILSSLGDCIYV  181 (183)
Q Consensus       125 ~~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~-------v~~~~~~~~~~L~~~~~~  181 (183)
                      .+.+++.+|++|++|.+||++|+||+||+||.+ +.+...       |..+++.++.+|.+|+..
T Consensus       118 ~i~~~~~~l~~L~ld~~E~~lLkaIvLf~pd~~~l~~~~~~~~~~~~v~~~~~~~~~~l~~~~~~  182 (236)
T d2j7ya1         118 MLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLASANQEAESSRKLTHLLNAVTDALVWVIAK  182 (236)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHHHHHHTTTTCCCCC------HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHhCCcCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            356899999999999999999999999999986 665544       556677777777777653

>d1we9a_ g.50.1.2 (A:) PHD finger protein At5g26210 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein At5g26210
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=90.43  E-value=0.088  Score=30.03  Aligned_cols=53  Identities=17%  Similarity=0.547  Sum_probs=34.6

Q ss_pred             CCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhh
Q psy16825         10 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQ   71 (183)
Q Consensus        10 ~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~   71 (183)
                      ...|.||+.....-++ .+.|..|..+|...        |-.-..-.+.....+.|..|+-.
T Consensus         6 ~~~C~~C~~~~~~~~~-~I~Cd~C~~w~H~~--------C~~~~~~~~~~~~~w~C~~C~~~   58 (64)
T d1we9a_           6 SGQCGACGESYAADEF-WICCDLCEMWFHGK--------CVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             CCCCSSSCCCCCSSSC-EEECSSSCCEEETT--------TTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCcCcCcCCCCCCCCC-EEEcCCCCccCCcc--------cCCcChHHCCCCCeEECcCCcCc
Confidence            4469999987655443 35799999998776        64432223323345789888744

>d1dcqa2 g.45.1.1 (A:247-368) Pyk2-associated protein beta ARF-GAP domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: ArfGap/RecO-like zinc finger
superfamily: ArfGap/RecO-like zinc finger
family: Pyk2-associated protein beta ARF-GAP domain
domain: Pyk2-associated protein beta ARF-GAP domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.39  E-value=0.13  Score=33.39  Aligned_cols=32  Identities=19%  Similarity=0.588  Sum_probs=26.6

Q ss_pred             CCCcccccCCCCc---ccccccccccchhhhhhcc
Q psy16825          9 PRRLCLVCGDVAS---GFHYGVASCEACKAFFKRT   40 (183)
Q Consensus         9 ~~~~C~vC~~~~~---~~hyg~~~C~~C~~FFrR~   40 (183)
                      ....|.-||.+..   ..-||++.|..|++.+|-.
T Consensus        14 ~N~~CaDC~~~~p~w~s~n~GvfvC~~CsgiHR~l   48 (122)
T d1dcqa2          14 GNDVCCDCGAPDPTWLSTNLGILTCIECSGIHREL   48 (122)
T ss_dssp             TTTBCTTTCCBSCCEEETTTTEEECHHHHHHHHHH
T ss_pred             CCCccCCCCCCCCCeEEecCCEEEchhhhHHHhcC
Confidence            4568999998764   3789999999999998764