Psyllid ID: psy12688

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220--
Protein Sequence
MAYMSQIHENILDLVQRCKKRKKLKPKTPIQQLLSAATGAQTPQMQHSNNDTQSSQLSPMLGNNTSASAGGAGYNFNNMVDNSYLFQSPGGGSTNMDLSSAGISYHPFHTSTIAATPEHPDTKEGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHGVVVIWSPHSPSISENL
Secondary Structure (PSIPRED)
ccccccccHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEccccccccccccccccEEcccEEEccccccccccccccccccHHHHHHHHHHccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccEHccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEccccccEEccEEccEEccHHHHHHHHHHHHHccccccccccccccccccccccHHHHHHHHHHccccHHHHHHHHcccccccccccccccccc
Coil and Loop (DISEMBL)
MAYMSQIHENILDLVQRCKkrkklkpktpiQQLLsaatgaqtpqmqhsnndtqssqlspmlgnntsasaggagynfnnmvdnsylfqspgggstnmdlssagisyhpfhtstiaatpehpdtkegieelcpvcgdkvsgyhygllTCESCKGFFKRTVQNKKVYTCVaerschidktqrkrcpfcrfqkCLEVGMKLEVSSQSTHGVVViwsphspsisenl
Flexible Loop (DISEMBL)
MAYMSQIHENILDLVQRCKKRKKLKPKTPIQQLLSAATGAQTPQMQHSNNDTQSSQLSPMLGNNTSASAGGAGYNFNNMVDNSYLFQSPGGGSTNMDLSSAGISYHPFHTSTIAATPEHPDTKEGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAerschidktqrkrcpFCRFQKCLEVGMKLevssqsthgvvviwsphspsisenl
Low Complexity Region (SEG)
MAYMSQIHENILDLVQRCkkrkklkpkTPIQQLLSAATGAQTPQMQHSNNDTQSSQLSPMLGNNTsasaggagYNFNNMVDNSYLFQSPGGGSTNMDLSSAGISYHPFHTSTIAATPEHPDTKEGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHGVVVIWSPHSPSISENL
Disordered region (IsUnstruct)
*********NILDLVQ*********************************************************YNFNNMVDNSYLF*****************SYHPFHT**************GIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHGVVVIW***********
Disordered Region (DISOPRED)
**********************************************************************************************************************************PVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEV***********************
Disordered Region (DISEMBL)
MAYMSQIHENILDLVQRCKKRKKLKPKTPIQQLLSA********************LSPMLGNNTSASAGGAGYNFNNMVDNSYLFQSPGGGSTNMDLSSAGISYHPFHTSTIAATPEHPDTKEGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHGVVVIWSPH********
Disordered Region (DISPRO)
*AYMSQIHENILDLVQRCKKRK******************************************************************************************************GIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEV***********************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAYMSQIHENILDLVQRCKKRKKLKPKTPIQQLLSAATGAQTPQMQHSNNDTQSSQLSPMLGNNTSASAGGAGYNFNNMVDNSYLFQSPGGGSTNMDLSSAGISYHPFHTSTIAATPEHPDTKEGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHGVVVIWSPHSPSISENL
Positional Conservation
no confident homologs detected

---

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	222	2.2.26 [Sep-21-2011]
P49867	534	Nuclear hormone receptor	N/A	N/A	0.364	0.151	0.913	1e-41
P33244	1027	Nuclear hormone receptor	yes	N/A	0.387	0.083	0.855	2e-41
O00482	541	Nuclear receptor subfamil	no	N/A	0.337	0.138	0.84	3e-35
O42101	501	Nuclear receptor subfamil	yes	N/A	0.337	0.149	0.84	4e-35
P45448	560	Nuclear receptor subfamil	yes	N/A	0.337	0.133	0.813	8e-35
Q9QWM1	560	Nuclear receptor subfamil	yes	N/A	0.337	0.133	0.813	8e-35
P33242	462	Steroidogenic factor 1 OS	no	N/A	0.337	0.162	0.84	9e-34
P50569	462	Steroidogenic factor 1 OS	no	N/A	0.337	0.162	0.84	9e-34
Q04752	461	Steroidogenic factor 1 OS	no	N/A	0.337	0.162	0.84	1e-33
P79387	461	Steroidogenic factor 1 OS	yes	N/A	0.337	0.162	0.84	1e-33

>sp|P49867|FTZF1_BOMMO Nuclear hormone receptor FTZ-F1 OS=Bombyx mori GN=FTZ-F1 PE=1 SV=2

 Score =  169 bits (428), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 74/81 (91%), Positives = 78/81 (96%)

Query: 118 EHPDTKEGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKT 177
           +  DTK+ IEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAER+CHIDKT
Sbjct: 77  DQTDTKDVIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERACHIDKT 136

Query: 178 QRKRCPFCRFQKCLEVGMKLE 198
           QRKRCPFCRFQKCL+VGMKLE
Sbjct: 137 QRKRCPFCRFQKCLDVGMKLE 157

May play an important role in development.
Bombyx mori (taxid: 7091)

>sp|P33244|FTZF1_DROME Nuclear hormone receptor FTZ-F1 OS=Drosophila melanogaster GN=ftz-f1 PE=1 SV=2

 Score =  168 bits (426), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 77/90 (85%), Positives = 79/90 (87%), Gaps = 4/90 (4%)

Query: 114 AATPEHP----DTKEGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAE 169
           +ATP H     D K   EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAE
Sbjct: 488 SATPGHGGEVIDFKHLFEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAE 547

Query: 170 RSCHIDKTQRKRCPFCRFQKCLEVGMKLEV 199
           RSCHIDKTQRKRCP+CRFQKCLEVGMKLE 
Sbjct: 548 RSCHIDKTQRKRCPYCRFQKCLEVGMKLEA 577

Acts as a cofactor to fushi tarazu (ftz). Facilitates the binding of ftz to DNA. Binds the sequence element 5'-YCYYGGYCR-3' in the zebra element of ftz. Probably also functions as a receptor for a yet unknown ligand.

Drosophila melanogaster (taxid: 7227)

>sp|O00482|NR5A2_HUMAN Nuclear receptor subfamily 5 group A member 2 OS=Homo sapiens GN=NR5A2 PE=1 SV=2

 Score =  148 bits (373), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 63/75 (84%), Positives = 68/75 (90%)

Query: 124 EGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCP 183
           E +EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQN K YTC+  ++C IDKTQRKRCP
Sbjct: 80  EDLEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQNCQIDKTQRKRCP 139

Query: 184 FCRFQKCLEVGMKLE 198
           +CRFQKCL VGMKLE
Sbjct: 140 YCRFQKCLSVGMKLE 154

Binds to the sequence element 5'-AACGACCGACCTTGAG-3' of the enhancer II of hepatitis B virus genes, a critical cis-element of their expression and regulation. May be responsible for the liver-specific activity of enhancer II, probably in combination with other hepatocyte transcription factors. Key regulator of cholesterol 7-alpha-hydroxylase gene (CYP7A) expression in liver. May also contribute to the regulation of pancreas-specific genes and play important roles in embryonic development.

Homo sapiens (taxid: 9606)

>sp|O42101|NR5A2_CHICK Nuclear receptor subfamily 5 group A member 2 OS=Gallus gallus GN=NR5A2 PE=2 SV=1

 Score =  147 bits (372), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 63/75 (84%), Positives = 68/75 (90%)

Query: 124 EGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCP 183
           E +EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQN K YTC+  ++C IDKTQRKRCP
Sbjct: 40  EDLEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQNCQIDKTQRKRCP 99

Query: 184 FCRFQKCLEVGMKLE 198
           +CRFQKCL VGMKLE
Sbjct: 100 YCRFQKCLSVGMKLE 114

Transcription regulator.

Gallus gallus (taxid: 9031)

>sp|P45448|NR5A2_MOUSE Nuclear receptor subfamily 5 group A member 2 OS=Mus musculus GN=Nr5a2 PE=1 SV=3

 Score =  147 bits (370), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 61/75 (81%), Positives = 70/75 (93%)

Query: 124 EGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCP 183
           E +EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQN+K YTC+  ++C IDKTQRKRCP
Sbjct: 101 EDLEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNQKRYTCIENQNCQIDKTQRKRCP 160

Query: 184 FCRFQKCLEVGMKLE 198
           +CRF+KC++VGMKLE
Sbjct: 161 YCRFKKCIDVGMKLE 175

Binds to promoters containing the sequence element 5'-AACGACCGACCTTGAG-3'. Plays a role in the regulation of gene expression in liver and pancreas. May play a role in embryonic development.

Mus musculus (taxid: 10090)

>sp|Q9QWM1|NR5A2_RAT Nuclear receptor subfamily 5 group A member 2 OS=Rattus norvegicus GN=Nr5a2 PE=2 SV=1

 Score =  147 bits (370), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 61/75 (81%), Positives = 70/75 (93%)

Query: 124 EGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCP 183
           E +EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQN+K YTC+  ++C IDKTQRKRCP
Sbjct: 101 EDLEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNQKRYTCIENQNCQIDKTQRKRCP 160

Query: 184 FCRFQKCLEVGMKLE 198
           +CRF+KC++VGMKLE
Sbjct: 161 YCRFKKCIDVGMKLE 175

Binds to promoters containing the sequence element 5'-AACGACCGACCTTGAG-3'. Plays a role in the regulation of gene expression in liver and pancreas. May play a role in embryonic development.

Rattus norvegicus (taxid: 10116)

>sp|P33242|STF1_MOUSE Steroidogenic factor 1 OS=Mus musculus GN=Nr5a1 PE=1 SV=3

 Score =  143 bits (361), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 63/75 (84%), Positives = 67/75 (89%)

Query: 124 EGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCP 183
           E ++ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQN K YTC   +SC IDKTQRKRCP
Sbjct: 7   EDLDELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKHYTCTESQSCKIDKTQRKRCP 66

Query: 184 FCRFQKCLEVGMKLE 198
           FCRFQKCL VGM+LE
Sbjct: 67  FCRFQKCLTVGMRLE 81

Transcriptional activator. Seems to be essential for sexual differentiation and formation of the primary steroidogenic tissues. Binds to the Ad4 site found in the promoter region of steroidogenic P450 genes such as CYP11A, CYP11B and CYP21B. Also regulates the AMH/Muellerian inhibiting substance gene as well as the AHCH and STAR genes. 5'-YCAAGGYC-3' and 5'-RRAGGTCA-3' are the consensus sequences for the recognition by NR5A1. The SFPQ-NONO-NR5A1 complex binds to the CYP17 promoter and regulates basal and cAMP-dependent transcriptional avtivity (By similarity). Transcription repressor of the Moloney leukemia virus long terminal repeat in undifferentiated murine embryonal carcinoma cells. Binds phosphatidylcholine and phospholipids with a phosphatidylinositol (PI) headgroup, in particular phosphatidyl(3,4)bisphosphate, phosphatidyl(3,5)bisphosphate and phosphatidyl(3,4,5)triphosphate. Activated by the phosphorylation of NR5A1 by HIPK3 leading to increased steroidogenic gene expression upon cAMP signaling pathway stimulation.

Mus musculus (taxid: 10090)

>sp|P50569|STF1_RAT Steroidogenic factor 1 OS=Rattus norvegicus GN=Nr5a1 PE=2 SV=1

 Score =  143 bits (361), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 63/75 (84%), Positives = 67/75 (89%)

Query: 124 EGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCP 183
           E ++ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQN K YTC   +SC IDKTQRKRCP
Sbjct: 7   EDLDELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKHYTCTESQSCKIDKTQRKRCP 66

Query: 184 FCRFQKCLEVGMKLE 198
           FCRFQKCL VGM+LE
Sbjct: 67  FCRFQKCLTVGMRLE 81

Transcriptional activator. Seems to be essential for sexual differentiation and formation of the primary steroidogenic tissues. Binds to the Ad4 site found in the promoter region of steroidogenic P450 genes such as CYP11A, CYP11B and CYP21B. Also regulates the AMH/Muellerian inhibiting substance gene as well as the AHCH and STAR genes. 5'-YCAAGGYC-3' and 5'-RRAGGTCA-3' are the consensus sequences for the recognition by NR5A1. The SFPQ-NONO-NR5A1 complex binds to the CYP17 promoter and regulates basal and cAMP-dependent transcriptional avtivity. Binds phosphatidylcholine and phospholipids with a phosphatidylinositol (PI) headgroup, in particular PI(3,4)P2 and PI(3,4,5)P3. Activated by the phosphorylation of NR5A1 by HIPK3 leading to increased steroidogenic gene expression upon cAMP signaling pathway stimulation.

Rattus norvegicus (taxid: 10116)

>sp|Q04752|STF1_BOVIN Steroidogenic factor 1 OS=Bos taurus GN=NR5A1 PE=1 SV=1

 Score =  143 bits (360), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 63/75 (84%), Positives = 67/75 (89%)

Query: 124 EGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCP 183
           E ++ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQN K YTC   +SC IDKTQRKRCP
Sbjct: 7   EDLDELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKHYTCTESQSCKIDKTQRKRCP 66

Query: 184 FCRFQKCLEVGMKLE 198
           FCRFQKCL VGM+LE
Sbjct: 67  FCRFQKCLTVGMRLE 81

Transcriptional activator. Seems to be essential for sexual differentiation and formation of the primary steroidogenic tissues. Binds to the Ad4 site found in the promoter region of steroidogenic P450 genes such as CYP11A, CYP11B and CYP21B. Also regulates the AMH/Muellerian inhibiting substance gene as well as the AHCH and STAR genes. 5'-YCAAGGYC-3' and 5'-RRAGGTCA-3' are the consensus sequences for the recognition by NR5A1. The SFPQ-NONO-NR5A1 complex binds to the CYP17 promoter and regulates basal and cAMP-dependent transcriptional avtivity. Binds phospholipids with a phosphatidylinositol (PI) headgroup, in particular PI(3,4)P2 and PI(3,4,5)P3. Activated by the phosphorylation of NR5A1 by HIPK3 leading to increased steroidogenic gene expression upon cAMP signaling pathway stimulation.

Bos taurus (taxid: 9913)

>sp|P79387|STF1_PIG Steroidogenic factor 1 OS=Sus scrofa GN=NR5A1 PE=2 SV=3

 Score =  143 bits (360), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 63/75 (84%), Positives = 67/75 (89%)

Query: 124 EGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCP 183
           E ++ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQN K YTC   +SC IDKTQRKRCP
Sbjct: 7   EDLDELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKHYTCTESQSCKIDKTQRKRCP 66

Query: 184 FCRFQKCLEVGMKLE 198
           FCRFQKCL VGM+LE
Sbjct: 67  FCRFQKCLTVGMRLE 81

Transcriptional activator. Seems to be essential for sexual differentiation and formation of the primary steroidogenic tissues. Binds to the Ad4 site found in the promoter region of steroidogenic P450 genes such as CYP11A, CYP11B and CYP21B. Also regulates the AMH/Muellerian inhibiting substance gene as well as the AHCH and STAR genes. 5'-YCAAGGYC-3' and 5'-RRAGGTCA-3' are the consensus sequences for the recognition by NR5A1. The SFPQ-NONO-NR5A1 complex binds to the CYP17 promoter and regulates basal and cAMP-dependent transcriptional avtivity. Binds phosphatidylcholine and phospholipids with a phosphatidylinositol (PI) headgroup, in particular PI(3,4)P2 and PI(3,4,5)P3. Activated by the phosphorylation of NR5A1 by HIPK3 leading to increased steroidogenic gene expression upon cAMP signaling pathway stimulation.

Sus scrofa (taxid: 9823)

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	222
270004815	588	ftz transcription factor 1 [Tribolium ca	0.540	0.204	0.725	5e-46
189235773	540	PREDICTED: similar to ecdysone response	0.509	0.209	0.743	4e-44
194326123	602	nuclear receptor [Blattella germanica]	0.5	0.184	0.725	4e-44
328711947	666	PREDICTED: nuclear hormone receptor FTZ-	0.364	0.121	0.987	2e-43
242019867	253	steroidogenic factor, putative [Pediculu	0.536	0.470	0.713	4e-43
17979670	582	nuclear hormone receptor betaFTZ-F1 [Man	0.481	0.183	0.714	3e-42
357614860	514	nuclear hormone receptor betaFTZ-F1 [Dan	0.486	0.210	0.7	1e-41
341926128	541	nuclear hormone receptor [Bombyx mori]	0.504	0.207	0.68	1e-41
5306097	545	fushi tarazu-factor 1 [Metapenaeus ensis	0.450	0.183	0.726	1e-41
345494868	776	PREDICTED: nuclear hormone receptor FTZ-	0.378	0.108	0.886	3e-41

>gi|270004815|gb|EFA01263.1| ftz transcription factor 1 [Tribolium castaneum]

 Score =  189 bits (481), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 90/124 (72%), Positives = 99/124 (79%), Gaps = 4/124 (3%)

Query: 75  NFNNMVDNSYLFQSPGGGSTNMDLSSAGISYHPFHTSTIAATPEHPDTKEGIEELCPVCG 134
           N NN+ D SY+F S     + +D+   G SY     +T     + PDTK+GIEELCPVCG
Sbjct: 61  NMNNL-DASYIFSSGASAISGVDM---GASYQISGPATSLTAGDLPDTKDGIEELCPVCG 116

Query: 135 DKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVG 194
           DKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCP+CRFQKCLEVG
Sbjct: 117 DKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPYCRFQKCLEVG 176

Query: 195 MKLE 198
           MKLE
Sbjct: 177 MKLE 180

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189235773|ref|XP_970369.2| PREDICTED: similar to ecdysone response nuclear receptor Ftz-F1 [Tribolium castaneum]

 Score =  183 bits (465), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 84/113 (74%), Positives = 92/113 (81%)

Query: 86  FQSPGGGSTNMDLSSAGISYHPFHTSTIAATPEHPDTKEGIEELCPVCGDKVSGYHYGLL 145
           F +  GG++ +     G SY     +T     + PDTK+GIEELCPVCGDKVSGYHYGLL
Sbjct: 54  FAANSGGASAISGVDMGASYQISGPATSLTAGDLPDTKDGIEELCPVCGDKVSGYHYGLL 113

Query: 146 TCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLE 198
           TCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCP+CRFQKCLEVGMKLE
Sbjct: 114 TCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPYCRFQKCLEVGMKLE 166

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194326123|emb|CAQ57670.1| nuclear receptor [Blattella germanica]

 Score =  183 bits (465), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 87/120 (72%), Positives = 98/120 (81%), Gaps = 9/120 (7%)

Query: 87  QSPGGGSTNMDLSSAGISYHP---FHTSTIAATP-----EHPDTKEGIEELCPVCGDKVS 138
           +  GGG + M++++AG SY        +T+A        + PDTKEGIEELCPVCGDKVS
Sbjct: 54  EEAGGGGSTMEVAAAG-SYQASPGVSAATVAVVTGMTGGDLPDTKEGIEELCPVCGDKVS 112

Query: 139 GYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLE 198
           GYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCP+CRFQKCL+VGMKLE
Sbjct: 113 GYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPYCRFQKCLDVGMKLE 172

Source: Blattella germanica

Species: Blattella germanica

Genus: Blattella

Family: Ectobiidae

Order: Blattodea

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328711947|ref|XP_001945464.2| PREDICTED: nuclear hormone receptor FTZ-F1-like [Acyrthosiphon pisum]

 Score =  181 bits (459), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 80/81 (98%), Positives = 80/81 (98%)

Query: 118 EHPDTKEGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKT 177
           E PDTKEGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKT
Sbjct: 83  ELPDTKEGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKT 142

Query: 178 QRKRCPFCRFQKCLEVGMKLE 198
           QRKRCPFCRFQKCLEVGMKLE
Sbjct: 143 QRKRCPFCRFQKCLEVGMKLE 163

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242019867|ref|XP_002430380.1| steroidogenic factor, putative [Pediculus humanus corporis] gi|212515504|gb|EEB17642.1| steroidogenic factor, putative [Pediculus humanus corporis]

 Score =  180 bits (456), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 92/129 (71%), Positives = 104/129 (80%), Gaps = 10/129 (7%)

Query: 74  YNFNNMVDNSYLFQSPGGGSTNMDLSSAGISYHPFHTSTIAATP----EHPDTKEGIEEL 129
           YN  N +D++  F SP GG   +D+++   S  P +TS + A+     + PDTK GIEEL
Sbjct: 115 YNSGN-IDSALCFYSPPGG---IDMAAGYQS--PQNTSLVLASSRSGGDIPDTKFGIEEL 168

Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
           CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCP+CRFQK
Sbjct: 169 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPYCRFQK 228

Query: 190 CLEVGMKLE 198
           CLEVGMKLE
Sbjct: 229 CLEVGMKLE 237

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|17979670|gb|AAL50351.1| nuclear hormone receptor betaFTZ-F1 [Manduca sexta]

 Score =  177 bits (449), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 85/119 (71%), Positives = 92/119 (77%), Gaps = 12/119 (10%)

Query: 80  VDNSYLFQSPGGGSTNMDLSSAGISYHPFHTSTIAATPEHPDTKEGIEELCPVCGDKVSG 139
           +D SYLF +  GG     L +AG            A  +  DTK+ IEELCPVCGDKVSG
Sbjct: 60  LDASYLFPTGPGGEAGAYLPAAG------------AVCDQTDTKDVIEELCPVCGDKVSG 107

Query: 140 YHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLE 198
           YHYGLLTCESCKGFFKRTVQNKKVYTCVAER+CHIDKTQRKRCPFCRFQKCL+VGMKLE
Sbjct: 108 YHYGLLTCESCKGFFKRTVQNKKVYTCVAERACHIDKTQRKRCPFCRFQKCLDVGMKLE 166

Source: Manduca sexta

Species: Manduca sexta

Genus: Manduca

Family: Sphingidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357614860|gb|EHJ69333.1| nuclear hormone receptor betaFTZ-F1 [Danaus plexippus]

 Score =  175 bits (443), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 84/120 (70%), Positives = 93/120 (77%), Gaps = 12/120 (10%)

Query: 80  VDNSYLFQSPGGGSTNMDLSSAGISYHPFHTSTIAATPEHPDTKEGIEELCPVCGDKVSG 139
           +D SYLF +  G  +   L +AG         T+    +  DTK+ IEELCPVCGDKVSG
Sbjct: 58  LDASYLFPTGAGSESGAYLPAAG---------TVC---DQTDTKDVIEELCPVCGDKVSG 105

Query: 140 YHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEV 199
           YHYGLLTCESCKGFFKRTVQNKKVYTCVAER+CHIDKTQRKRCPFCRFQKCL+VGMKLE 
Sbjct: 106 YHYGLLTCESCKGFFKRTVQNKKVYTCVAERACHIDKTQRKRCPFCRFQKCLDVGMKLEA 165

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|341926128|dbj|BAK53999.1| nuclear hormone receptor [Bombyx mori]

 Score =  175 bits (443), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 85/125 (68%), Positives = 94/125 (75%), Gaps = 13/125 (10%)

Query: 74  YNFNNMVDNSYLFQSPGGGSTNMDLSSAGISYHPFHTSTIAATPEHPDTKEGIEELCPVC 133
           + + N+ D SYLF +  GG     L +AG               +  DTK+ IEELCPVC
Sbjct: 53  FGYANL-DASYLFPTGTGGEPGAYLPTAG------------TVCDQTDTKDVIEELCPVC 99

Query: 134 GDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEV 193
           GDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAER+CHIDKTQRKRCPFCRFQKCL+V
Sbjct: 100 GDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERACHIDKTQRKRCPFCRFQKCLDV 159

Query: 194 GMKLE 198
           GMKLE
Sbjct: 160 GMKLE 164

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|5306097|gb|AAD41899.1| fushi tarazu-factor 1 [Metapenaeus ensis]

 Score =  175 bits (443), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 85/117 (72%), Positives = 91/117 (77%), Gaps = 17/117 (14%)

Query: 82  NSYLFQSPGGGSTNMDLSSAGISYHPFHTSTIAATPEHPDTKEGIEELCPVCGDKVSGYH 141
           +S LF  PG  +T +D +S                 E PDTKEGIEELCPVCGDKVSGYH
Sbjct: 2   DSGLF--PGVATTTLDYTSLA---------------ELPDTKEGIEELCPVCGDKVSGYH 44

Query: 142 YGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLE 198
           YGLLTCESCKGFFKRTVQNKKVYTCVA+RSC IDKTQRKRCP+CRFQKCLEVGMKLE
Sbjct: 45  YGLLTCESCKGFFKRTVQNKKVYTCVADRSCQIDKTQRKRCPYCRFQKCLEVGMKLE 101

Source: Metapenaeus ensis

Species: Metapenaeus ensis

Genus: Metapenaeus

Family: Penaeidae

Order: Decapoda

Class: Malacostraca

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345494868|ref|XP_001600363.2| PREDICTED: nuclear hormone receptor FTZ-F1 [Nasonia vitripennis]

 Score =  174 bits (441), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 78/88 (88%), Positives = 81/88 (92%)

Query: 112 TIAATPEHPDTKEGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERS 171
           +I    + PDTK+ IEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERS
Sbjct: 276 SIPGPSDFPDTKDVIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERS 335

Query: 172 CHIDKTQRKRCPFCRFQKCLEVGMKLEV 199
           CHIDKTQRKRCPFCRFQKCLEVGMKLE 
Sbjct: 336 CHIDKTQRKRCPFCRFQKCLEVGMKLEA 363

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	222
FB|FBgn0001078	1027	ftz-f1 "ftz transcription fact	0.5	0.108	0.724	1.3e-39
UNIPROTKB|F1NVB5	501	NR5A2 "Nuclear receptor subfam	0.337	0.149	0.84	7.4e-34
UNIPROTKB|O42101	501	NR5A2 "Nuclear receptor subfam	0.337	0.149	0.84	7.4e-34
UNIPROTKB|F1PXN4	519	NR5A2 "Uncharacterized protein	0.337	0.144	0.84	7.4e-34
UNIPROTKB|B4E2P3	469	NR5A2 "cDNA FLJ52395, highly s	0.337	0.159	0.84	7.4e-34
UNIPROTKB|F1MCM4	541	NR5A2 "Uncharacterized protein	0.337	0.138	0.84	9.4e-34
UNIPROTKB|O00482	541	NR5A2 "Nuclear receptor subfam	0.337	0.138	0.84	9.4e-34
ZFIN|ZDB-GENE-990415-79	517	nr5a2 "nuclear receptor subfam	0.337	0.145	0.826	1.5e-33
UNIPROTKB|H0Y328	377	NR5A2 "Nuclear receptor subfam	0.328	0.193	0.849	2e-33
UNIPROTKB|Q04752	461	NR5A1 "Steroidogenic factor 1"	0.337	0.162	0.84	2.5e-33

FB|FBgn0001078 ftz-f1 "ftz transcription factor 1" [Drosophila melanogaster (taxid:7227)]

 Score = 422 (153.6 bits), Expect = 1.3e-39, Sum P(2) = 1.3e-39
 Identities = 84/116 (72%), Positives = 88/116 (75%)

Query:    88 SPGGGSTNMDLSSAGISYHPFHT-STIAATPEHP----DTKEGIEELCPVCGDKVSGYHY 142
             S G GS       AG +  P +     +ATP H     D K   EELCPVCGDKVSGYHY
Sbjct:   461 SVGNGSGGAGNGGAGGNSGPGNPMGGTSATPGHGGEVIDFKHLFEELCPVCGDKVSGYHY 520

Query:   143 GLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLE 198
             GLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCP+CRFQKCLEVGMKLE
Sbjct:   521 GLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPYCRFQKCLEVGMKLE 576

GO:0005634 "nucleus" evidence=ISS;NAS;IDA

GO:0003677 "DNA binding" evidence=NAS;IDA

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

GO:0007365 "periodic partitioning" evidence=IMP

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

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

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

GO:0035071 "salivary gland cell autophagic cell death" evidence=NAS

GO:0035075 "response to ecdysone" evidence=TAS

GO:0009725 "response to hormone stimulus" evidence=TAS

GO:0008219 "cell death" evidence=TAS

GO:0040034 "regulation of development, heterochronic" evidence=TAS

GO:0007552 "metamorphosis" evidence=IMP;TAS

GO:0003712 "transcription cofactor activity" evidence=NAS

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

GO:0005737 "cytoplasm" evidence=NAS

GO:0002165 "instar larval or pupal development" evidence=IMP

GO:0008270 "zinc ion binding" evidence=IEA

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

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

GO:0042048 "olfactory behavior" evidence=IMP

GO:0035074 "pupation" evidence=IMP

GO:0007480 "imaginal disc-derived leg morphogenesis" evidence=IMP

GO:0046982 "protein heterodimerization activity" evidence=IPI

GO:0008134 "transcription factor binding" evidence=IPI

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

GO:0035626 "juvenile hormone mediated signaling pathway" evidence=IMP

GO:0000976 "transcription regulatory region sequence-specific DNA binding" evidence=IDA

UNIPROTKB|F1NVB5 NR5A2 "Nuclear receptor subfamily 5 group A member 2" [Gallus gallus (taxid:9031)]

 Score = 368 (134.6 bits), Expect = 7.4e-34, P = 7.4e-34
 Identities = 63/75 (84%), Positives = 68/75 (90%)

Query:   124 EGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCP 183
             E +EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQN K YTC+  ++C IDKTQRKRCP
Sbjct:    40 EDLEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQNCQIDKTQRKRCP 99

Query:   184 FCRFQKCLEVGMKLE 198
             +CRFQKCL VGMKLE
Sbjct:   100 YCRFQKCLSVGMKLE 114

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

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

GO:0005543 "phospholipid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0008206 "bile acid metabolic process" evidence=IEA

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

GO:0042632 "cholesterol homeostasis" evidence=IEA

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

GO:0045070 "positive regulation of viral genome replication" evidence=IEA

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

UNIPROTKB|O42101 NR5A2 "Nuclear receptor subfamily 5 group A member 2" [Gallus gallus (taxid:9031)]

 Score = 368 (134.6 bits), Expect = 7.4e-34, P = 7.4e-34
 Identities = 63/75 (84%), Positives = 68/75 (90%)

Query:   124 EGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCP 183
             E +EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQN K YTC+  ++C IDKTQRKRCP
Sbjct:    40 EDLEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQNCQIDKTQRKRCP 99

Query:   184 FCRFQKCLEVGMKLE 198
             +CRFQKCL VGMKLE
Sbjct:   100 YCRFQKCLSVGMKLE 114

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|F1PXN4 NR5A2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 368 (134.6 bits), Expect = 7.4e-34, P = 7.4e-34
 Identities = 63/75 (84%), Positives = 68/75 (90%)

Query:   124 EGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCP 183
             E +EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQN K YTC+  ++C IDKTQRKRCP
Sbjct:    58 EDLEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQNCQIDKTQRKRCP 117

Query:   184 FCRFQKCLEVGMKLE 198
             +CRFQKCL VGMKLE
Sbjct:   118 YCRFQKCLSVGMKLE 132

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

GO:0005634 "nucleus" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

UNIPROTKB|B4E2P3 NR5A2 "cDNA FLJ52395, highly similar to Orphan nuclear receptor NR5A2" [Homo sapiens (taxid:9606)]

 Score = 368 (134.6 bits), Expect = 7.4e-34, P = 7.4e-34
 Identities = 63/75 (84%), Positives = 68/75 (90%)

Query:   124 EGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCP 183
             E +EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQN K YTC+  ++C IDKTQRKRCP
Sbjct:     8 EDLEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQNCQIDKTQRKRCP 67

Query:   184 FCRFQKCLEVGMKLE 198
             +CRFQKCL VGMKLE
Sbjct:    68 YCRFQKCLSVGMKLE 82

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0008206 "bile acid metabolic process" evidence=IEA

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

GO:0042632 "cholesterol homeostasis" evidence=IEA

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

UNIPROTKB|F1MCM4 NR5A2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 368 (134.6 bits), Expect = 9.4e-34, P = 9.4e-34
 Identities = 63/75 (84%), Positives = 68/75 (90%)

Query:   124 EGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCP 183
             E +EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQN K YTC+  ++C IDKTQRKRCP
Sbjct:    80 EDLEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQNCQIDKTQRKRCP 139

Query:   184 FCRFQKCLEVGMKLE 198
             +CRFQKCL VGMKLE
Sbjct:   140 YCRFQKCLSVGMKLE 154

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

GO:0045070 "positive regulation of viral genome replication" evidence=IEA

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

GO:0042632 "cholesterol homeostasis" evidence=IEA

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

GO:0008206 "bile acid metabolic process" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005543 "phospholipid binding" 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:0003707 "steroid hormone receptor activity" evidence=IEA

UNIPROTKB|O00482 NR5A2 "Nuclear receptor subfamily 5 group A member 2" [Homo sapiens (taxid:9606)]

 Score = 368 (134.6 bits), Expect = 9.4e-34, P = 9.4e-34
 Identities = 63/75 (84%), Positives = 68/75 (90%)

Query:   124 EGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCP 183
             E +EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQN K YTC+  ++C IDKTQRKRCP
Sbjct:    80 EDLEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQNCQIDKTQRKRCP 139

Query:   184 FCRFQKCLEVGMKLE 198
             +CRFQKCL VGMKLE
Sbjct:   140 YCRFQKCLSVGMKLE 154

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0008206 "bile acid metabolic process" evidence=IEA

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

GO:0042632 "cholesterol homeostasis" evidence=IEA

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

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

GO:0009790 "embryo development" evidence=TAS

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

GO:0042592 "homeostatic process" evidence=NAS

GO:0005515 "protein binding" evidence=IPI

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

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

GO:0003705 "RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity" evidence=TAS

GO:0005543 "phospholipid binding" evidence=IDA

GO:0003677 "DNA binding" evidence=IDA

GO:0005654 "nucleoplasm" evidence=TAS

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

GO:0010467 "gene expression" evidence=TAS

GO:0045070 "positive regulation of viral genome replication" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

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

GO:0005737 "cytoplasm" evidence=IDA

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

ZFIN|ZDB-GENE-990415-79 nr5a2 "nuclear receptor subfamily 5, group A, member 2" [Danio rerio (taxid:7955)]

 Score = 365 (133.5 bits), Expect = 1.5e-33, P = 1.5e-33
 Identities = 62/75 (82%), Positives = 68/75 (90%)

Query:   124 EGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCP 183
             E ++E+CPVCGDKVSGYHYGLLTCESCKGFFKRTVQN K YTC+  +SC IDKTQRKRCP
Sbjct:    40 EDLDEMCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQSCQIDKTQRKRCP 99

Query:   184 FCRFQKCLEVGMKLE 198
             +CRFQKCL VGMKLE
Sbjct:   100 YCRFQKCLTVGMKLE 114

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

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

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

GO:0005634 "nucleus" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA;NAS;IDA

GO:0051216 "cartilage development" evidence=IMP

GO:0046872 "metal ion binding" evidence=IEA

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

UNIPROTKB|H0Y328 NR5A2 "Nuclear receptor subfamily 5 group A member 2" [Homo sapiens (taxid:9606)]

 Score = 364 (133.2 bits), Expect = 2.0e-33, P = 2.0e-33
 Identities = 62/73 (84%), Positives = 67/73 (91%)

Query:   126 IEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFC 185
             +EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQN K YTC+  ++C IDKTQRKRCP+C
Sbjct:     3 LEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQNCQIDKTQRKRCPYC 62

Query:   186 RFQKCLEVGMKLE 198
             RFQKCL VGMKLE
Sbjct:    63 RFQKCLSVGMKLE 75

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

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

UNIPROTKB|Q04752 NR5A1 "Steroidogenic factor 1" [Bos taurus (taxid:9913)]

 Score = 363 (132.8 bits), Expect = 2.5e-33, P = 2.5e-33
 Identities = 63/75 (84%), Positives = 67/75 (89%)

Query:   124 EGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCP 183
             E ++ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQN K YTC   +SC IDKTQRKRCP
Sbjct:     7 EDLDELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKHYTCTESQSCKIDKTQRKRCP 66

Query:   184 FCRFQKCLEVGMKLE 198
             FCRFQKCL VGM+LE
Sbjct:    67 FCRFQKCLTVGMRLE 81

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISS;IMP

GO:0003677 "DNA binding" evidence=ISS

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

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

GO:2000195 "negative regulation of female gonad development" evidence=IEA

GO:2000020 "positive regulation of male gonad development" evidence=IEA

GO:0051457 "maintenance of protein location in nucleus" evidence=IEA

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

GO:0042445 "hormone metabolic process" evidence=IEA

GO:0030325 "adrenal gland development" evidence=IEA

GO:0030154 "cell differentiation" evidence=IEA

GO:0019899 "enzyme binding" evidence=IEA

GO:0010259 "multicellular organismal aging" evidence=IEA

GO:0009888 "tissue development" evidence=IEA

GO:0008584 "male gonad development" evidence=IEA

GO:0005543 "phospholipid binding" evidence=IEA

GO:0003705 "RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0001553 "luteinization" evidence=IEA

GO:0008270 "zinc ion binding" 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

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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	222
cd07167	93	cd07167, NR_DBD_Lrh-1_like, The DNA-binding domain	2e-51
cd06916	72	cd06916, NR_DBD_like, DNA-binding domain of nuclea	3e-41
pfam00105	70	pfam00105, zf-C4, Zinc finger, C4 type (two domain	3e-40
cd07168	90	cd07168, NR_DBD_DHR4_like, DNA-binding domain of e	2e-35
cd06969	75	cd06969, NR_DBD_NGFI-B, DNA-binding domain of the	4e-35
smart00399	70	smart00399, ZnF_C4, c4 zinc finger in nuclear horm	6e-34
cd07169	90	cd07169, NR_DBD_GCNF_like, DNA-binding domain of G	8e-32
cd06961	85	cd06961, NR_DBD_TR, DNA-binding domain of thyroid	9e-32
cd06960	76	cd06960, NR_DBD_HNF4A, DNA-binding domain of hepto	2e-31
cd07156	72	cd07156, NR_DBD_VDR_like, The DNA-binding domain o	9e-31
cd06967	87	cd06967, NR_DBD_TR2_like, DNA-binding domain of th	2e-30
cd06956	77	cd06956, NR_DBD_RXR, DNA-binding domain of retinoi	1e-29
cd07165	81	cd07165, NR_DBD_DmE78_like, DNA-binding domain of	5e-29
cd07161	91	cd07161, NR_DBD_EcR, DNA-binding domain of Ecdyson	2e-28
cd07155	75	cd07155, NR_DBD_ER_like, DNA-binding domain of est	4e-27
cd06964	85	cd06964, NR_DBD_RAR, DNA-binding domain of retinoi	4e-27
cd07170	97	cd07170, NR_DBD_ERR, DNA-binding domain of estroge	6e-27
cd06968	95	cd06968, NR_DBD_ROR, DNA-binding domain of Retinoi	3e-26
cd06959	73	cd06959, NR_DBD_EcR_like, The DNA-binding domain o	6e-26
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	3e-25
cd07171	82	cd07171, NR_DBD_ER, DNA-binding domain of estrogen	3e-25
cd06965	84	cd06965, NR_DBD_Ppar, DNA-binding domain of peroxi	5e-25
cd07158	73	cd07158, NR_DBD_Ppar_like, The DNA-binding domain	1e-24
cd07164	78	cd07164, NR_DBD_PNR_like_1, DNA-binding domain of	3e-24
cd07179	74	cd07179, 2DBD_NR_DBD2, The second DNA-binding doma	3e-24
cd06958	73	cd06958, NR_DBD_COUP_TF, DNA-binding domain of chi	3e-24
cd06963	73	cd06963, NR_DBD_GR_like, The DNA binding domain of	4e-24
cd07154	73	cd07154, NR_DBD_PNR_like, The DNA-binding domain o	7e-24
cd06962	84	cd06962, NR_DBD_FXR, DNA-binding domain of Farneso	2e-23
cd06957	82	cd06957, NR_DBD_PNR_like_2, DNA-binding domain of	3e-23
cd07173	82	cd07173, NR_DBD_AR, DNA-binding domain of androgen	4e-23
cd06955	107	cd06955, NR_DBD_VDR, DNA-binding domain of vitamin	8e-23
cd07160	101	cd07160, NR_DBD_LXR, DNA-binding domain of Liver X	3e-22
cd07162	87	cd07162, NR_DBD_PXR, DNA-binding domain of pregnan	4e-22
cd07163	92	cd07163, NR_DBD_TLX, DNA-binding domain of Tailles	6e-22
cd06966	94	cd06966, NR_DBD_CAR, DNA-binding domain of constit	1e-21
cd06970	92	cd06970, NR_DBD_PNR, DNA-binding domain of the pho	2e-19
cd07157	86	cd07157, 2DBD_NR_DBD1, The first DNA-binding domai	2e-18

>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 =  161 bits (408), Expect = 2e-51
 Identities = 60/69 (86%), Positives = 64/69 (92%)

Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
           CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKK YTC+  ++C IDKTQRKRCP+CRFQK
Sbjct: 1   CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKRYTCIENQNCQIDKTQRKRCPYCRFQK 60

Query: 190 CLEVGMKLE 198
           CL VGMKLE
Sbjct: 61  CLSVGMKLE 69

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

 Score =  134 bits (339), Expect = 3e-41
 Identities = 43/69 (62%), Positives = 50/69 (72%)

Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
           C VCGDK SGYHYG+LTCE CKGFF+R+V+    YTC A  +C IDK  R RC  CR +K
Sbjct: 1   CAVCGDKASGYHYGVLTCEGCKGFFRRSVRRNLEYTCPAGGNCVIDKRNRNRCQACRLKK 60

Query: 190 CLEVGMKLE 198
           CL VGM+ E
Sbjct: 61  CLAVGMRKE 69

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 =  131 bits (333), Expect = 3e-40
 Identities = 45/70 (64%), Positives = 52/70 (74%)

Query: 128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRF 187
           ELC VCGDK SGYHYG+LTCE CKGFF+R++Q   VYTC   + C IDK  R RC +CR 
Sbjct: 1   ELCKVCGDKASGYHYGVLTCEGCKGFFRRSIQKNIVYTCPFNKDCVIDKRNRNRCQYCRL 60

Query: 188 QKCLEVGMKL 197
           +KCLEVGM  
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|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 =  120 bits (302), Expect = 2e-35
 Identities = 44/72 (61%), Positives = 54/72 (75%)

Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
            +LC +C DK +G HYG++TCE CKGFFKRTVQNK+VYTCV +  C I K QR RC +CR
Sbjct: 6   PKLCSICEDKATGLHYGIITCEGCKGFFKRTVQNKRVYTCVGDGRCEITKAQRNRCQYCR 65

Query: 187 FQKCLEVGMKLE 198
           F+KC+  GM L 
Sbjct: 66  FRKCIRKGMMLA 77

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

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

 Score =  119 bits (299), Expect = 4e-35
 Identities = 43/72 (59%), Positives = 52/72 (72%)

Query: 128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRF 187
            LC VCGD  +  HYG+ TCE CKGFFKRTVQ    Y C+A ++C +DK +R RC +CRF
Sbjct: 1   GLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRF 60

Query: 188 QKCLEVGMKLEV 199
           QKCL+VGM  EV
Sbjct: 61  QKCLQVGMVKEV 72

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

 Score =  116 bits (292), Expect = 6e-34
 Identities = 35/70 (50%), Positives = 46/70 (65%)

Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
           LC VCGD  SG+H+G+ +C +CK FF+RTV  +  Y C  + +C I+K  R RC  CR +
Sbjct: 1   LCCVCGDHASGFHFGVCSCRACKAFFRRTVNLRYKYRCDRKNNCSINKRYRCRCRACRLK 60

Query: 189 KCLEVGMKLE 198
           KCL VGM  E
Sbjct: 61  KCLGVGMDPE 70

Length = 70

>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 =  111 bits (278), Expect = 8e-32
 Identities = 36/79 (45%), Positives = 55/79 (69%), Gaps = 2/79 (2%)

Query: 120 PDTKEGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQR 179
            D  E  +  C +CGD+ +G HYG+++CE CKGFFKR++ NK+VY C  +++C + + QR
Sbjct: 1   DDRAE--QRTCLICGDRATGLHYGIISCEGCKGFFKRSICNKRVYRCSRDKNCVMSRKQR 58

Query: 180 KRCPFCRFQKCLEVGMKLE 198
            RC +CR  KCL++GM  +
Sbjct: 59  NRCQYCRLLKCLQMGMNRK 77

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

 Score =  110 bits (277), Expect = 9e-32
 Identities = 40/70 (57%), Positives = 48/70 (68%)

Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
            C VCGDK +GYHY  +TCE CKGFF+RTVQ K  Y+C  E  C IDK  R +C  CRF+
Sbjct: 1   PCVVCGDKATGYHYRCITCEGCKGFFRRTVQKKLSYSCKGEGKCEIDKVTRNQCQECRFK 60

Query: 189 KCLEVGMKLE 198
           KC+ VGM  +
Sbjct: 61  KCIAVGMAKD 70

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

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

 Score =  109 bits (275), Expect = 2e-31
 Identities = 37/69 (53%), Positives = 50/69 (72%)

Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
           C VCGD+ +G HYG+L+C  CKGFF+R+V+  + YTC    +C +DK +R  C +CRF+K
Sbjct: 1   CAVCGDRATGKHYGVLSCNGCKGFFRRSVRKNRTYTCRFGGNCVVDKDKRNACRYCRFKK 60

Query: 190 CLEVGMKLE 198
           CLEVGM  E
Sbjct: 61  CLEVGMDPE 69

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|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 =  107 bits (270), Expect = 9e-31
 Identities = 34/69 (49%), Positives = 47/69 (68%)

Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
           C VCGD+ +GYH+  +TCE CKGFF+R+++ K  +TC     C I K  R+ C  CR +K
Sbjct: 1   CGVCGDRATGYHFNAMTCEGCKGFFRRSMKRKARFTCPFNGDCEITKDNRRHCQACRLKK 60

Query: 190 CLEVGMKLE 198
           CL++GMK E
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|143525 cd06967, NR_DBD_TR2_like, DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers

 Score =  107 bits (268), Expect = 2e-30
 Identities = 39/71 (54%), Positives = 50/71 (70%)

Query: 128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRF 187
           ELC VCGDK SG HYG ++CE CKGFFKR+++    Y+C   + C I+K  R RC +CR 
Sbjct: 4   ELCVVCGDKASGRHYGAVSCEGCKGFFKRSIRKNLGYSCRGSKDCVINKHHRNRCQYCRL 63

Query: 188 QKCLEVGMKLE 198
           QKCL +GMK +
Sbjct: 64  QKCLAMGMKSD 74

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

 Score =  105 bits (263), Expect = 1e-29
 Identities = 41/70 (58%), Positives = 51/70 (72%)

Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
           +C +CGD+ SG HYG+ +CE CKGFFKRTV+    YTC   + C IDK QR RC +CR+Q
Sbjct: 2   ICAICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQ 61

Query: 189 KCLEVGMKLE 198
           KCL +GMK E
Sbjct: 62  KCLAMGMKRE 71

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

 Score =  103 bits (259), Expect = 5e-29
 Identities = 36/66 (54%), Positives = 47/66 (71%)

Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
           C VCGDK SGYHYG+ +CE CKGFF+R++Q +  Y C+ +  C I +  R RC +CRF+K
Sbjct: 1   CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYRCLRDGKCEIIRLNRNRCQYCRFKK 60

Query: 190 CLEVGM 195
           CL  GM
Sbjct: 61  CLAAGM 66

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

 Score =  102 bits (255), Expect = 2e-28
 Identities = 41/72 (56%), Positives = 50/72 (69%)

Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
           EELC VCGD+ SGYHY  LTCE CKGFF+R+V    VY C   R+C +D   R++C  CR
Sbjct: 1   EELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYHCKYGRACEMDMYMRRKCQECR 60

Query: 187 FQKCLEVGMKLE 198
            +KCL VGM+ E
Sbjct: 61  LKKCLSVGMRPE 72

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|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 = 98.7 bits (246), Expect = 4e-27
 Identities = 39/69 (56%), Positives = 48/69 (69%)

Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
           C VCGD  SGYHYG+ +CE+CK FFKRT+Q    Y+C +   C +DK +RK C  CR QK
Sbjct: 1   CLVCGDIASGYHYGVASCEACKAFFKRTIQGNLGYSCPSTSECEVDKKRRKSCQACRLQK 60

Query: 190 CLEVGMKLE 198
           CL+VGM  E
Sbjct: 61  CLKVGMLKE 69

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

 Score = 98.8 bits (246), Expect = 4e-27
 Identities = 41/73 (56%), Positives = 51/73 (69%)

Query: 126 IEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFC 185
           I + C VC DK SGYHYG+  CE CKGFF+R++Q   VYTC  +++C I+K  R RC +C
Sbjct: 3   IYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYC 62

Query: 186 RFQKCLEVGMKLE 198
           R QKC EVGM  E
Sbjct: 63  RLQKCFEVGMSKE 75

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

 Score = 98.8 bits (246), Expect = 6e-27
 Identities = 40/67 (59%), Positives = 47/67 (70%)

Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
           LC VCGD  SGYHYG+ +CE+CK FFKRT+Q    Y+C A   C I K +RK C  CRF 
Sbjct: 6   LCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFM 65

Query: 189 KCLEVGM 195
           KCL+VGM
Sbjct: 66  KCLKVGM 72

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

 Score = 96.8 bits (241), Expect = 3e-26
 Identities = 38/66 (57%), Positives = 49/66 (74%)

Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
           C +CGDK SG HYG++TCE CKGFF+R+ QN   Y+C  +++C ID+T R RC  CR QK
Sbjct: 8   CKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVSYSCPRQKNCLIDRTNRNRCQHCRLQK 67

Query: 190 CLEVGM 195
           CL +GM
Sbjct: 68  CLALGM 73

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|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 = 95.6 bits (238), Expect = 6e-26
 Identities = 34/70 (48%), Positives = 45/70 (64%)

Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
            C VCGDK SG+HYG+L+CE CKGFF+R+V    VY C     C +D   R++C  CR +
Sbjct: 1   NCVVCGDKASGFHYGVLSCEGCKGFFRRSVTKGAVYACKFGNKCEMDMYMRRKCQECRLR 60

Query: 189 KCLEVGMKLE 198
           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|143540 cd07166, NR_DBD_REV_ERB, DNA-binding domain of REV-ERB receptor-like is composed of two C4-type zinc fingers

 Score = 95.3 bits (237), Expect = 1e-25
 Identities = 39/72 (54%), Positives = 49/72 (68%), Gaps = 1/72 (1%)

Query: 125 GIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVY-TCVAERSCHIDKTQRKRCP 183
           G+  LC VCGDK SG+HYG+  CE CKGFF+R++Q K  Y  C    +C I +  R RC 
Sbjct: 1   GMVVLCKVCGDKASGFHYGVHACEGCKGFFRRSIQQKIQYRKCTKNETCSIMRINRNRCQ 60

Query: 184 FCRFQKCLEVGM 195
           +CRF+KCL VGM
Sbjct: 61  YCRFKKCLAVGM 72

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 = 93.7 bits (233), Expect = 3e-25
 Identities = 38/72 (52%), Positives = 48/72 (66%)

Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
           +++C VC D+ SG HYG+LTC SCK FFKR V+ +  Y C     C IDK +RK CP CR
Sbjct: 2   QKICLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACR 61

Query: 187 FQKCLEVGMKLE 198
            +KCL+ GM L 
Sbjct: 62  LRKCLQAGMNLG 73

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

 Score = 93.8 bits (233), Expect = 3e-25
 Identities = 37/67 (55%), Positives = 43/67 (64%)

Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
            C VC D  SGYHYG+ +CE CK FFKR++Q    Y C A   C IDK +RK C  CR +
Sbjct: 5   FCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQACRLR 64

Query: 189 KCLEVGM 195
           KC EVGM
Sbjct: 65  KCYEVGM 71

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

 Score = 93.3 bits (232), Expect = 5e-25
 Identities = 40/68 (58%), Positives = 48/68 (70%), Gaps = 3/68 (4%)

Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVY-TCVAERSCHIDKTQRKRCPFCRF 187
            C VCGDK SG+HYG+  CE CKGFF+RT++ K VY  C  + SC I K  R +C +CRF
Sbjct: 1   ECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLVYKPC--DLSCKIHKKSRNKCQYCRF 58

Query: 188 QKCLEVGM 195
           QKCL VGM
Sbjct: 59  QKCLNVGM 66

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

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

 Score = 92.2 bits (229), Expect = 1e-24
 Identities = 37/67 (55%), Positives = 47/67 (70%), Gaps = 1/67 (1%)

Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYT-CVAERSCHIDKTQRKRCPFCRFQ 188
           C VCGDK SG+HYG+ +CE CKGFF+RT+Q+   Y  C+    C I +  R RC +CRF+
Sbjct: 1   CKVCGDKASGFHYGVHSCEGCKGFFRRTIQHNLTYRRCLNGGKCVIQRKNRNRCQYCRFK 60

Query: 189 KCLEVGM 195
           KCL VGM
Sbjct: 61  KCLSVGM 67

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|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 = 91.4 bits (227), Expect = 3e-24
 Identities = 32/67 (47%), Positives = 45/67 (67%)

Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
           C VCGD+ SG HYG+ +C+ C+GFFKR+++    Y C    SC +D  +R +C  CRF+K
Sbjct: 1   CRVCGDRASGKHYGVPSCDGCRGFFKRSIRRNLAYVCKENGSCVVDVARRNQCQACRFKK 60

Query: 190 CLEVGMK 196
           CL+V M 
Sbjct: 61  CLQVNMN 67

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|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 = 91.0 bits (226), Expect = 3e-24
 Identities = 34/66 (51%), Positives = 42/66 (63%)

Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
           C VCG K SG+H+G LTCE CKGFF+RT  +   Y C   ++C I    R  C  CRF++
Sbjct: 1   CRVCGGKSSGFHFGALTCEGCKGFFRRTELSSNSYVCPGGQNCAITPATRNACKSCRFRR 60

Query: 190 CLEVGM 195
           CL VGM
Sbjct: 61  CLAVGM 66

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|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 = 91.1 bits (226), Expect = 3e-24
 Identities = 39/71 (54%), Positives = 48/71 (67%)

Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
           C VCGDK SG HYG  TCE CK FFKR+V+    YTC   R+C ID+  R +C +CR +K
Sbjct: 1   CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRGNRNCPIDQHHRNQCQYCRLKK 60

Query: 190 CLEVGMKLEVS 200
           CL+VGM+ E  
Sbjct: 61  CLKVGMRREAV 71

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

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

 Score = 90.8 bits (225), Expect = 4e-24
 Identities = 36/69 (52%), Positives = 44/69 (63%)

Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
           C +CGD+ SG HYG+LTC SCK FFKR  + +  Y C     C IDK +RK CP CR +K
Sbjct: 1   CLICGDEASGCHYGVLTCGSCKVFFKRAAEGQHNYLCAGRNDCIIDKIRRKNCPACRLRK 60

Query: 190 CLEVGMKLE 198
           C + GM L 
Sbjct: 61  CYQAGMTLG 69

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

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

 Score = 90.3 bits (224), Expect = 7e-24
 Identities = 35/67 (52%), Positives = 46/67 (68%), Gaps = 1/67 (1%)

Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAER-SCHIDKTQRKRCPFCRFQ 188
           C VCGD+ SG HYG+  C+ C GFFKR+++   +YTC A   SC +DK +R +C  CR +
Sbjct: 1   CKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNLLYTCKAGNGSCVVDKARRNQCQACRLK 60

Query: 189 KCLEVGM 195
           KCLEV M
Sbjct: 61  KCLEVSM 67

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

 Score = 89.6 bits (222), Expect = 2e-23
 Identities = 39/72 (54%), Positives = 48/72 (66%)

Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
           EELC VCGDK SGYHY  LTCE CKGFF+R++    VY C    +C +D   R++C  CR
Sbjct: 1   EELCVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCEMDMYMRRKCQECR 60

Query: 187 FQKCLEVGMKLE 198
            +KC E+GM  E
Sbjct: 61  LRKCKEMGMLAE 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 = 88.7 bits (220), Expect = 3e-23
 Identities = 36/67 (53%), Positives = 45/67 (67%), Gaps = 1/67 (1%)

Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAER-SCHIDKTQRKRCPFCRFQ 188
           C VCGDK  G HYG+  C+ C  FFKR+V+   +YTC+A   +C +DK +R  CPFCR Q
Sbjct: 1   CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKGIIYTCIAGNGNCVVDKARRNWCPFCRLQ 60

Query: 189 KCLEVGM 195
           KC  VGM
Sbjct: 61  KCFAVGM 67

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

 Score = 88.4 bits (219), Expect = 4e-23
 Identities = 38/71 (53%), Positives = 47/71 (66%)

Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
           ++ C +CGD+ SG HYG LTC SCK FFKR  + K+ Y C +   C IDK +RK CP CR
Sbjct: 3   QKTCLICGDEASGCHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCR 62

Query: 187 FQKCLEVGMKL 197
            +KC E GM L
Sbjct: 63  LRKCFEAGMTL 73

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

 Score = 88.5 bits (219), Expect = 8e-23
 Identities = 30/74 (40%), Positives = 49/74 (66%)

Query: 125 GIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPF 184
            +  +C VCGD+ +G+H+  +TCE CKGFF+R+++ K ++TC     C I K  R+ C  
Sbjct: 4   NVPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQA 63

Query: 185 CRFQKCLEVGMKLE 198
           CR ++C+++GM  E
Sbjct: 64  CRLKRCVDIGMMKE 77

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

 Score = 86.9 bits (215), Expect = 3e-22
 Identities = 34/71 (47%), Positives = 46/71 (64%)

Query: 128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRF 187
           E+C VCGDK SG+HY +L+CE CKGFF+R+V     Y C     C +D   R++C  CR 
Sbjct: 19  EVCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAQYVCKNGGKCQMDMYMRRKCQECRL 78

Query: 188 QKCLEVGMKLE 198
           +KC E GM+ +
Sbjct: 79  RKCREAGMREQ 89

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

 Score = 86.1 bits (213), Expect = 4e-22
 Identities = 32/71 (45%), Positives = 48/71 (67%)

Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
           +C VCGD+ +GYH+  +TCE CKGFF+R ++      C  ++ C I K+ R++C  CR +
Sbjct: 1   ICRVCGDRATGYHFNAMTCEGCKGFFRRAMKRNARLCCPFQKGCVITKSNRRQCQACRLR 60

Query: 189 KCLEVGMKLEV 199
           KCL +GMK E+
Sbjct: 61  KCLSIGMKKEL 71

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

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

 Score = 85.6 bits (212), Expect = 6e-22
 Identities = 33/68 (48%), Positives = 45/68 (66%), Gaps = 2/68 (2%)

Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVA--ERSCHIDKTQRKRCPFCRF 187
           C VCGD+ SG HYG+  C+ C GFFKR+++  + Y C +  +  C +DKT R +C  CR 
Sbjct: 9   CKVCGDRSSGKHYGIYACDGCSGFFKRSIRRNRQYVCKSKGQGGCPVDKTHRNQCRACRL 68

Query: 188 QKCLEVGM 195
           +KC EVGM
Sbjct: 69  KKCFEVGM 76

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

 Score = 85.2 bits (211), Expect = 1e-21
 Identities = 32/69 (46%), Positives = 40/69 (57%)

Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
           C VCGDK  GY++  +TCESCK FF+R     K + C    SC I+   R+ C  CR  K
Sbjct: 3   CGVCGDKALGYNFNAITCESCKAFFRRNALKNKEFKCPFNESCEINVVTRRFCQKCRLDK 62

Query: 190 CLEVGMKLE 198
           C  +GMK E
Sbjct: 63  CFAIGMKKE 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|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 = 79.2 bits (195), Expect = 2e-19
 Identities = 35/68 (51%), Positives = 43/68 (63%), Gaps = 1/68 (1%)

Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERS-CHIDKTQRKRCPFCRF 187
           LC VCGD  SG HYG+  C  C GFFKR+V+ K +Y C A    C +DK  R +C  CR 
Sbjct: 8   LCRVCGDTSSGKHYGIYACNGCSGFFKRSVRRKLIYRCQAGTGMCPVDKAHRNQCQACRL 67

Query: 188 QKCLEVGM 195
           +KCL+ GM
Sbjct: 68  KKCLQAGM 75

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|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 = 76.4 bits (188), Expect = 2e-18
 Identities = 30/70 (42%), Positives = 41/70 (58%), Gaps = 2/70 (2%)

Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTV--QNKKVYTCVAERSCHIDKTQRKRCPFCRF 187
           C VCG+  +G+H+G   CE+CK FF R+    +  +  C     C IDK  R +C  CR+
Sbjct: 3   CQVCGEPAAGFHHGAYVCEACKKFFMRSSNAISFTISECPNGGKCIIDKKNRTKCQACRY 62

Query: 188 QKCLEVGMKL 197
           +KCL VGM L
Sbjct: 63  RKCLNVGMSL 72

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	222
KOG4215|consensus	432		99.96
cd06956	77	NR_DBD_RXR DNA-binding domain of retinoid X recept	99.94
cd07171	82	NR_DBD_ER DNA-binding domain of estrogen receptors	99.94
cd07160	101	NR_DBD_LXR DNA-binding domain of Liver X receptors	99.94
cd07155	75	NR_DBD_ER_like DNA-binding domain of estrogen rece	99.94
cd06961	85	NR_DBD_TR DNA-binding domain of thyroid hormone re	99.93
cd07170	97	NR_DBD_ERR DNA-binding domain of estrogen related	99.93
cd06964	85	NR_DBD_RAR DNA-binding domain of retinoic acid rec	99.93
KOG4846|consensus	538		99.93
cd06967	87	NR_DBD_TR2_like DNA-binding domain of the TR2 and	99.93
cd07164	78	NR_DBD_PNR_like_1 DNA-binding domain of the photor	99.93
cd07161	91	NR_DBD_EcR DNA-binding domain of Ecdysone receptor	99.93
cd07168	90	NR_DBD_DHR4_like DNA-binding domain of ecdysone-in	99.93
cd06970	92	NR_DBD_PNR DNA-binding domain of the photoreceptor	99.93
cd06960	76	NR_DBD_HNF4A DNA-binding domain of heptocyte nucle	99.93
cd07179	74	2DBD_NR_DBD2 The second DNA-binding domain (DBD) o	99.93
cd07173	82	NR_DBD_AR DNA-binding domain of androgen receptor	99.93
cd06959	73	NR_DBD_EcR_like The DNA-binding domain of Ecdysone	99.93
cd07163	92	NR_DBD_TLX DNA-binding domain of Tailless (TLX) is	99.93
cd06962	84	NR_DBD_FXR DNA-binding domain of Farnesoid X recep	99.93
KOG4217|consensus	605		99.93
cd07156	72	NR_DBD_VDR_like The DNA-binding domain of vitamin	99.93
cd07172	78	NR_DBD_GR_PR DNA-binding domain of glucocorticoid	99.93
cd06963	73	NR_DBD_GR_like The DNA binding domain of GR_like n	99.92
cd06969	75	NR_DBD_NGFI-B DNA-binding domain of the orphan nuc	99.92
cd07169	90	NR_DBD_GCNF_like DNA-binding domain of Germ cell n	99.92
cd06958	73	NR_DBD_COUP_TF DNA-binding domain of chicken ovalb	99.92
cd07158	73	NR_DBD_Ppar_like The DNA-binding domain of peroxis	99.92
cd07165	81	NR_DBD_DmE78_like DNA-binding domain of Drosophila	99.92
cd07162	87	NR_DBD_PXR DNA-binding domain of pregnane X recept	99.92
cd06957	82	NR_DBD_PNR_like_2 DNA-binding domain of the photor	99.92
cd07167	93	NR_DBD_Lrh-1_like The DNA-binding domain of Lrh-1	99.92
cd07166	89	NR_DBD_REV_ERB DNA-binding domain of REV-ERB recep	99.92
cd06966	94	NR_DBD_CAR DNA-binding domain of constitutive andr	99.92
cd07154	73	NR_DBD_PNR_like The DNA-binding domain of the phot	99.92
cd07157	86	2DBD_NR_DBD1 The first DNA-binding domain (DBD) of	99.92
cd06916	72	NR_DBD_like DNA-binding domain of nuclear receptor	99.92
cd06968	95	NR_DBD_ROR DNA-binding domain of Retinoid-related	99.92
cd06955	107	NR_DBD_VDR DNA-binding domain of vitamin D recepto	99.92
cd06965	84	NR_DBD_Ppar DNA-binding domain of peroxisome proli	99.91
smart00399	70	ZnF_C4 c4 zinc finger in nuclear hormone receptors	99.9
PF00105	70	zf-C4: Zinc finger, C4 type (two domains); InterPr	99.9
KOG4216|consensus	479		99.9
KOG4218|consensus	475		99.9

>KOG4215|consensus

Probab=99.96  E-value=7.3e-30  Score=235.12  Aligned_cols=87  Identities=43%  Similarity=1.018  Sum_probs=83.0

Q ss_pred             CCCccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCC
Q psy12688        125 GIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQST  204 (222)
Q Consensus       125 ~~~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r  204 (222)
                      ...+.|.||||+++|.|||+.+|.|||+||||+|.++..|.|+++.+|.|+|++|+.||||||+||+.+||++||||++|
T Consensus        17 ~~~~~CaICGDkaTGKHYGA~SCdGCKGFFRRSVrk~~~YtCRF~k~C~VDKdkRNaCRyCRfqKC~~aGMK~eAiQnER   96 (432)
T KOG4215|consen   17 GVAEFCAICGDKATGKHYGAISCDGCKGFFRRSVRKNHQYTCRFNKQCVVDKDKRNACRYCRFQKCVRAGMKREAIQNER   96 (432)
T ss_pred             cccchhheeCCcccccccceeecCcchHHHHHHHHhcceeeeeccccccccchhhhhhhHhhHHHHHHhcccHHhhhccc
Confidence            44678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcceec
Q psy12688        205 HGVVVIW  211 (222)
Q Consensus       205 ~g~~~~~  211 (222)
                      |.+..-.
T Consensus        97 DrIg~Rr  103 (432)
T KOG4215|consen   97 DRIGSRR  103 (432)
T ss_pred             ccccccC
Confidence            9998733

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

Probab=99.94  E-value=1.1e-27  Score=178.02  Aligned_cols=76  Identities=54%  Similarity=1.200  Sum_probs=73.4

Q ss_pred             cccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCC
Q psy12688        129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQST  204 (222)
Q Consensus       129 ~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r  204 (222)
                      +|.|||+.++|+||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++||.+|
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

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

Probab=99.94  E-value=2.2e-27  Score=178.73  Aligned_cols=79  Identities=48%  Similarity=1.026  Sum_probs=75.3

Q ss_pred             ccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688        128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG  206 (222)
Q Consensus       128 ~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g  206 (222)
                      ..|.|||+.++|+||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++|+.++-|
T Consensus         4 ~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~~~~   82 (82)
T cd07171           4 HFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRRERRG   82 (82)
T ss_pred             CCCeecCCcCcceEECceeehhhHHhHHHHeeCCCceeCCCCCccccCCcccccCccchhHHHhHhcCCHHHHHHhhcC
Confidence            4699999999999999999999999999999988899999999999999999999999999999999999999998764

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

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

Probab=99.94  E-value=2.7e-27  Score=184.67  Aligned_cols=80  Identities=43%  Similarity=0.970  Sum_probs=76.1

Q ss_pred             CccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688        127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG  206 (222)
Q Consensus       127 ~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g  206 (222)
                      ..+|.|||+.++|+||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++|+.+++-
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            45799999999999999999999999999999988999999999999999999999999999999999999999998864

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

>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=99.94  E-value=2.5e-27  Score=175.18  Aligned_cols=75  Identities=52%  Similarity=1.065  Sum_probs=72.5

Q ss_pred             ccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCC
Q psy12688        130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQST  204 (222)
Q Consensus       130 C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r  204 (222)
                      |.|||+.++|+||||.+|+||++||||++..+..|.|..++.|.|+...|..|++|||+|||++||++++||.+|
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            899999999999999999999999999999888999999999999999999999999999999999999999876

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

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

Probab=99.93  E-value=2.7e-27  Score=179.11  Aligned_cols=79  Identities=51%  Similarity=1.056  Sum_probs=75.9

Q ss_pred             cccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCCc
Q psy12688        129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHGV  207 (222)
Q Consensus       129 ~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g~  207 (222)
                      +|.|||+.++|+||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++|+.+++..
T Consensus         1 ~C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~   79 (85)
T cd06961           1 PCVVCGDKATGYHYRCITCEGCKGFFRRTVQKKLSYSCKGEGKCEIDKVTRNQCQECRFKKCIAVGMAKDLVLDDRKRG   79 (85)
T ss_pred             CCceeCCcCcceEEChhhhhhhhHhhHhhhccCCccccCCCCccccCccccccCccchhhhhhhccCCHHHcccccCcc
Confidence            4999999999999999999999999999999889999999999999999999999999999999999999999998875

DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TR interacts with the thyroid response element, which is a DNA site with direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pairs, upstream of target genes and modulates the rate of transcriptional initiation. Thyroid hormone receptor (TR) mediates the actions of thyroid hormones, which play critical roles in growth, development, and homeostasis in mammals. They regulate overall metabolic rate, cholesterol and triglyceride levels, and heart rate, and affect mood. TRs are expressed from two separate genes (alpha and beta) in human and each gene generates two isoforms of the receptor through differential promoter usage or splicing. TRalpha functions in the he

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

Probab=99.93  E-value=4.9e-27  Score=181.99  Aligned_cols=81  Identities=51%  Similarity=0.966  Sum_probs=75.9

Q ss_pred             ccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCCc
Q psy12688        128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHGV  207 (222)
Q Consensus       128 ~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g~  207 (222)
                      ..|.|||+.++|+||||.+|+||++||||++..+..|.|..++.|.|+...|..|++|||+|||++||++++|+.+++-.
T Consensus         5 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~vq~~r~~~   84 (97)
T cd07170           5 RLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRG   84 (97)
T ss_pred             CCCeecCCcCcceEECceeehhhhHHHHHHhccCCceeecCCCccccCcccCccCCccccchhhhcCCCHHHcccccCCC
Confidence            45999999999999999999999999999999888999999999999999999999999999999999999999987554


Q ss_pred             c
Q psy12688        208 V  208 (222)
Q Consensus       208 ~  208 (222)
                      .
T Consensus        85 ~   85 (97)
T cd07170          85 G   85 (97)
T ss_pred             C
Confidence            3

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

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

Probab=99.93  E-value=1.4e-27  Score=180.69  Aligned_cols=80  Identities=50%  Similarity=1.073  Sum_probs=76.2

Q ss_pred             CccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688        127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG  206 (222)
Q Consensus       127 ~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g  206 (222)
                      .++|.|||+.++|+||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++|+.+|+.
T Consensus         4 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~R~~   83 (85)
T cd06964           4 YKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNK   83 (85)
T ss_pred             CCCCcccCCcCcccEECcceeeeeeeEEeeeecCCCCeECCCCCccccCCcccccCccchhhhhhhhCCCHHHhhccccC
Confidence            45799999999999999999999999999999988889999999999999999999999999999999999999999986

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

>KOG4846|consensus

Probab=99.93  E-value=6.8e-27  Score=218.28  Aligned_cols=77  Identities=49%  Similarity=1.157  Sum_probs=73.3

Q ss_pred             CCCccccccCCCCcceeeccccchhhhHHHHhHhhcCcee-ccccCcccccCCCCCCCCcchHhHHHHHhcCCccccc
Q psy12688        125 GIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVY-TCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSS  201 (222)
Q Consensus       125 ~~~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~-~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr  201 (222)
                      ....+|.||||+|+||||||.+|||||+||||+|+.+..| .|-+...|.|....|++|++|||+|||.|||.++|||
T Consensus       130 ~~~~lCkVCgDkASGfHYGV~aCEGCKGFFRRSIQqkI~YrrClk~e~C~I~R~nRNRCQ~CRfKKCL~vGMSrDaVR  207 (538)
T KOG4846|consen  130 KAISLCKVCGDKASGFHYGVTACEGCKGFFRRSIQQKIDYRRCLKQEVCEIKRENRNRCQYCRFKKCLDVGMSRDAVR  207 (538)
T ss_pred             ceeEeehhhccccccceeceeecccchHHHHHHHHHhhhHHHHhhhhceehhhhccchhhhhhHHHHHhcccchhhhh
Confidence            3456899999999999999999999999999999999888 7999999999999999999999999999999999999

>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=99.93  E-value=1.8e-27  Score=180.91  Aligned_cols=82  Identities=48%  Similarity=1.037  Sum_probs=77.7

Q ss_pred             CccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688        127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG  206 (222)
Q Consensus       127 ~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g  206 (222)
                      .++|.|||+.++++||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++|+.+|+.
T Consensus         3 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~R~~   82 (87)
T cd06967           3 VELCVVCGDKASGRHYGAVSCEGCKGFFKRSIRKNLGYSCRGSKDCVINKHHRNRCQYCRLQKCLAMGMKSDSVQCERKP   82 (87)
T ss_pred             CCCCeecCCcCCcCEeCcceEeeeeeEeeeeeeCCCCcccCCCCccccCccccccCccchhhhhhHcCCCHHHhccccCC
Confidence            45699999999999999999999999999999988899999999999999999999999999999999999999999997


Q ss_pred             cc
Q psy12688        207 VV  208 (222)
Q Consensus       207 ~~  208 (222)
                      +.
T Consensus        83 ~~   84 (87)
T cd06967          83 ID   84 (87)
T ss_pred             CC
Confidence            54

DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. TR2 and TR4 interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. TR4 and TR2 are orphan nuclear receptors; the physiological ligand is as yet unidentified. TR2 is abundantly expressed in the androgen-sensitive prostate. TR4 transcripts are expressed in many tissues, including central nervous system, adrenal gland, spleen, thyroid gland, and prostate. It has been shown that human TR2 binds to a wide spectrum of natural hormone response elements (HREs) with distinct affinities suggesting that TR2 may cross-talk with other gene expression regulation systems. The genes responding to TR2 or

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

Probab=99.93  E-value=5.7e-27  Score=174.46  Aligned_cols=77  Identities=42%  Similarity=1.022  Sum_probs=74.4

Q ss_pred             ccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688        130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG  206 (222)
Q Consensus       130 C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g  206 (222)
                      |.|||+.++|+||||.+|++|++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++|+.+|+.
T Consensus         1 C~VCg~~~~g~hyG~~~C~~C~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~   77 (78)
T cd07164           1 CRVCGDRASGKHYGVPSCDGCRGFFKRSIRRNLAYVCKENGSCVVDVARRNQCQACRFKKCLQVNMNRDAVQHERAP   77 (78)
T ss_pred             CcccCccCcceEECcchhhhhhhhhhhhccCCCCccCCCCCcccccCcccccCccchhhhhhHhcCCHHHhccCCCC
Confidence            89999999999999999999999999999988899999999999999999999999999999999999999999984

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

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

Probab=99.93  E-value=7.7e-27  Score=178.91  Aligned_cols=79  Identities=51%  Similarity=1.083  Sum_probs=74.9

Q ss_pred             ccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688        128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG  206 (222)
Q Consensus       128 ~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g  206 (222)
                      ++|.|||+.++|+||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++|+.+++-
T Consensus         2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~~   80 (91)
T cd07161           2 ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYHCKYGRACEMDMYMRRKCQECRLKKCLSVGMRPECVVPESQC   80 (91)
T ss_pred             CCCeeCCCcCcceEECceeehhhHHHHHHHhccCCceecCCCCccccCccccccCccchhhHHhHcCCCHHHcCchhhh
Confidence            4599999999999999999999999999999988899999999999999999999999999999999999999988653

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

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

Probab=99.93  E-value=9.1e-27  Score=178.02  Aligned_cols=81  Identities=54%  Similarity=1.154  Sum_probs=76.7

Q ss_pred             CccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688        127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG  206 (222)
Q Consensus       127 ~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g  206 (222)
                      ...|.|||+.++++||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++|+.+|..
T Consensus         6 ~~~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R~~   85 (90)
T cd07168           6 PKLCSICEDKATGLHYGIITCEGCKGFFKRTVQNKRVYTCVGDGRCEITKAQRNRCQYCRFRKCIRKGMMLAAVREDRMP   85 (90)
T ss_pred             CCCCcccCCcCcceEECceehhhhhHhhhhhhcCCCCccCCCCCCccccccccccccccchhhhhhcCCCHHHhhcccCC
Confidence            34699999999999999999999999999999988899999999999999999999999999999999999999999876


Q ss_pred             c
Q psy12688        207 V  207 (222)
Q Consensus       207 ~  207 (222)
                      .
T Consensus        86 ~   86 (90)
T cd07168          86 G   86 (90)
T ss_pred             C
Confidence            4

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

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

Probab=99.93  E-value=3.4e-27  Score=181.22  Aligned_cols=81  Identities=43%  Similarity=0.968  Sum_probs=76.4

Q ss_pred             ccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccC-cccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688        128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAE-RSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG  206 (222)
Q Consensus       128 ~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~-~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g  206 (222)
                      .+|.|||+.++|+||||.+|+||++||||++..+..|.|..+ ++|.++...|..|++|||+|||++||++++|+.+|+.
T Consensus         7 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R~~   86 (92)
T cd06970           7 LLCRVCGDTSSGKHYGIYACNGCSGFFKRSVRRKLIYRCQAGTGMCPVDKAHRNQCQACRLKKCLQAGMNKDAVQNERQP   86 (92)
T ss_pred             CCCeecCCcCcccEECccEEeeeeeEeeeeeecCCCceeecCCCcCccCCCccccCccchhhHhhHhCCCHHHcccccCc
Confidence            359999999999999999999999999999998889999886 8999999999999999999999999999999999986


Q ss_pred             cc
Q psy12688        207 VV  208 (222)
Q Consensus       207 ~~  208 (222)
                      ..
T Consensus        87 ~~   88 (92)
T cd06970          87 RN   88 (92)
T ss_pred             cc
Confidence            54

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

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

Probab=99.93  E-value=4.3e-27  Score=174.06  Aligned_cols=76  Identities=49%  Similarity=1.154  Sum_probs=73.5

Q ss_pred             ccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCC
Q psy12688        130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTH  205 (222)
Q Consensus       130 C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~  205 (222)
                      |.|||+.++++||||.+|+||++||||++..+..|.|...+.|.|+...|..|++|||+|||++||++++|+.+||
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            8999999999999999999999999999998889999999999999999999999999999999999999999886

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

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

Probab=99.93  E-value=1.4e-26  Score=170.83  Aligned_cols=73  Identities=48%  Similarity=1.042  Sum_probs=70.5

Q ss_pred             ccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCcccccc
Q psy12688        130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQ  202 (222)
Q Consensus       130 C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~  202 (222)
                      |.|||++++++||||.+|+||++||||++..+..|.|..+++|.++...|..|++|||+|||++||++++||.
T Consensus         1 C~VCg~~~~g~hygv~sC~aC~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~   73 (74)
T cd07179           1 CRVCGGKSSGFHFGALTCEGCKGFFRRTELSSNSYVCPGGQNCAITPATRNACKSCRFRRCLAVGMSKTGSRI   73 (74)
T ss_pred             CcccCccCcceEECceeehhHHHHHHHHhhCCCcccCCCCCccccCCcccccCccchhHHHHHhCCCHhHeeC
Confidence            8999999999999999999999999999999889999999999999999999999999999999999999985

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.

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

Probab=99.93  E-value=1.8e-26  Score=173.76  Aligned_cols=79  Identities=49%  Similarity=1.042  Sum_probs=74.4

Q ss_pred             ccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688        128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG  206 (222)
Q Consensus       128 ~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g  206 (222)
                      ..|.|||+.++|+||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||+++.++.++.|
T Consensus         4 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~~~~~~~~   82 (82)
T cd07173           4 KTCLICGDEASGCHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCFEAGMTLGARKLKKLG   82 (82)
T ss_pred             CCCeecCCcCcceEECcchhhhHHHHHHHHhcCCCceecCCCCccccCCCccCcCcchhhhhhhhcCCCcChHHhhccC
Confidence            4599999999999999999999999999999988999999999999999999999999999999999999988877654

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=99.93  E-value=1.6e-26  Score=170.01  Aligned_cols=73  Identities=47%  Similarity=1.065  Sum_probs=70.0

Q ss_pred             cccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccc
Q psy12688        129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSS  201 (222)
Q Consensus       129 ~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr  201 (222)
                      +|.|||+.++++||||.+|+||++||||++..+..|.|..+++|.+++..|..|++|||+|||++||+++.|+
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            5999999999999999999999999999999888999999999999999999999999999999999999874

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

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

Probab=99.93  E-value=5e-27  Score=180.12  Aligned_cols=83  Identities=40%  Similarity=0.969  Sum_probs=76.8

Q ss_pred             CCccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccC--cccccCCCCCCCCcchHhHHHHHhcCCccccccC
Q psy12688        126 IEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAE--RSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQS  203 (222)
Q Consensus       126 ~~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~--~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~  203 (222)
                      +...|.|||+.++|+||||.+|+||++||||++..+..|.|...  +.|.++...|..|++|||+|||++||++++|+.+
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            45679999999999999999999999999999998889999873  6899999999999999999999999999999999


Q ss_pred             CCCcc
Q psy12688        204 THGVV  208 (222)
Q Consensus       204 r~g~~  208 (222)
                      |+...
T Consensus        85 r~p~~   89 (92)
T cd07163          85 RGPRN   89 (92)
T ss_pred             cCcCC
Confidence            88653

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

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

Probab=99.93  E-value=4.6e-27  Score=177.70  Aligned_cols=78  Identities=49%  Similarity=1.043  Sum_probs=74.0

Q ss_pred             ccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCC
Q psy12688        128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTH  205 (222)
Q Consensus       128 ~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~  205 (222)
                      ++|.|||+.++|+||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++|+.+.+
T Consensus         2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~   79 (84)
T cd06962           2 ELCVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCEMDMYMRRKCQECRLRKCKEMGMLAECLLTEIQ   79 (84)
T ss_pred             CCCeecCCcCcceEECcceeecceeeeeeeeccCCceecCCCCcCccCccccccCccchhhHHHHhCCChHHccCHHH
Confidence            469999999999999999999999999999998889999999999999999999999999999999999999998764

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

>KOG4217|consensus

Probab=99.93  E-value=4.8e-26  Score=215.09  Aligned_cols=79  Identities=56%  Similarity=1.141  Sum_probs=75.7

Q ss_pred             CCCccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccC
Q psy12688        125 GIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQS  203 (222)
Q Consensus       125 ~~~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~  203 (222)
                      .....|.||||.|..-||||.+|||||+||+|||+++.+|+|-.+++|.|+|..|++|+||||||||+|||-+|.||.+
T Consensus       267 ~~e~~CAVCgDnAaCqHYGvRTCEGCKGFFKRTVQKnaKYvClanKnCPVDKRrRnRCQyCRfQKCL~VGMVKEVVRtd  345 (605)
T KOG4217|consen  267 SAEGLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLAVGMVKEVVRTD  345 (605)
T ss_pred             CccceeeecCChHHhhhcCccccccchHHHHHHHhcCCeeEeecCCCCCcchhhhhhchhhhHhHHHHhhhhhhheecc
Confidence            4478899999999999999999999999999999999999999999999999999999999999999999999999954

>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=99.93  E-value=1.6e-26  Score=169.64  Aligned_cols=72  Identities=47%  Similarity=1.128  Sum_probs=69.4

Q ss_pred             ccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccc
Q psy12688        130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSS  201 (222)
Q Consensus       130 C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr  201 (222)
                      |.|||+.++|+||||.+|+||++||||++..+..|.|..+++|.++...|..|++|||+|||++||++++|+
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            899999999999999999999999999999888999999999999999999999999999999999999884

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

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

Probab=99.93  E-value=2.8e-26  Score=171.11  Aligned_cols=75  Identities=51%  Similarity=1.091  Sum_probs=71.4

Q ss_pred             ccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCcccccc
Q psy12688        128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQ  202 (222)
Q Consensus       128 ~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~  202 (222)
                      .+|.|||+.++|+||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||+..+++.
T Consensus         3 ~~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~~   77 (78)
T cd07172           3 KICLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCLQAGMNLGARKT   77 (78)
T ss_pred             CCCeecCCcCcceEECceeehhhHHhHHHHeeCCCceeCCCCCccccCCcccccCccchhHHHHHhCCCcccccC
Confidence            469999999999999999999999999999999989999999999999999999999999999999999998864

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

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

Probab=99.92  E-value=3e-26  Score=168.81  Aligned_cols=72  Identities=50%  Similarity=1.108  Sum_probs=69.5

Q ss_pred             ccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccc
Q psy12688        130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSS  201 (222)
Q Consensus       130 C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr  201 (222)
                      |.|||+.++++||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||+++||.
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            899999999999999999999999999999888999999999999999999999999999999999999885

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

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

Probab=99.92  E-value=8.4e-27  Score=172.49  Aligned_cols=73  Identities=59%  Similarity=1.229  Sum_probs=70.5

Q ss_pred             cccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccc
Q psy12688        129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSS  201 (222)
Q Consensus       129 ~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr  201 (222)
                      +|.|||+.++++||||.+|+||++||||++..+..|.|..+++|.|++..|..|++|||+|||++||++++||
T Consensus         2 ~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~   74 (75)
T cd06969           2 LCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLQVGMVKEVVR   74 (75)
T ss_pred             CCeecCCcCcceEECcceeeeeeeeeeeeeecCCcccCCcCCccccCCcccccCcccHhHHHHHhCCCHHHcc
Confidence            5999999999999999999999999999999888999999999999999999999999999999999999997

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

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

Probab=99.92  E-value=2e-26  Score=176.21  Aligned_cols=80  Identities=43%  Similarity=1.092  Sum_probs=75.6

Q ss_pred             CccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688        127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG  206 (222)
Q Consensus       127 ~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g  206 (222)
                      ..+|.|||+.++++||||.+|+||++||||++..+..|.|..++.|.|+...|..|++|||+|||++||++++||.++..
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            45699999999999999999999999999999988899999999999999999999999999999999999999998753

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).

>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=99.92  E-value=2.4e-26  Score=169.11  Aligned_cols=72  Identities=54%  Similarity=1.179  Sum_probs=69.7

Q ss_pred             ccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccc
Q psy12688        130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSS  201 (222)
Q Consensus       130 C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr  201 (222)
                      |.|||+.++|+||||.+|+||++||||++..+..|.|..+++|.++...|..|++|||+|||++||++++|+
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            899999999999999999999999999999888899999999999999999999999999999999999987

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

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

Probab=99.92  E-value=2.6e-26  Score=168.66  Aligned_cols=72  Identities=51%  Similarity=1.209  Sum_probs=69.5

Q ss_pred             ccccCCCCcceeeccccchhhhHHHHhHhhcCcee-ccccCcccccCCCCCCCCcchHhHHHHHhcCCccccc
Q psy12688        130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVY-TCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSS  201 (222)
Q Consensus       130 C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~-~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr  201 (222)
                      |.|||+.++|+||||.+|++|++||||++..+..| .|..+++|.|+...|..|++|||+|||++||++++||
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            89999999999999999999999999999988888 8999999999999999999999999999999999986

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).

>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=99.92  E-value=2.6e-26  Score=172.11  Aligned_cols=77  Identities=47%  Similarity=1.097  Sum_probs=74.2

Q ss_pred             ccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688        130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG  206 (222)
Q Consensus       130 C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g  206 (222)
                      |.|||+.++++||||.+|+||++||||++..+..|.|..+++|.|+...+..|++|||+|||++||++++||.+|..
T Consensus         1 C~VCg~~~~g~hyG~~sC~aC~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~V~~~r~~   77 (81)
T cd07165           1 CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYRCLRDGKCEIIRLNRNRCQYCRFKKCLAAGMSKDSVRYGRIP   77 (81)
T ss_pred             CCccCccCcceEECchhhhhHHHHHHhHhccCCceeCCCCCCccccccccccccchhhhhcccccCCHHHcccCCCC
Confidence            89999999999999999999999999999988899999999999999999999999999999999999999998875

DNA-binding domain of proteins similar to Drosophila ecdysone-induced protein 78 (E78) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. E78 interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Drosophila ecdysone-induced protein 78 (E78) is a transcription factor belonging to the nuclear receptor superfamily. E78 is a product of the ecdysone-inducible gene found in an early late puff locus at position 78C during the onset of Drosophila metamorphosis. An E78 orthologue from the Platyhelminth Schistosoma mansoni (SmE78) has also been identified. It is the first E78 orthologue known outside of the molting animals--the Ecdysozoa. The SmE78 may be involved in transduction of an ecdysone signal in S. mansoni,

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

Probab=99.92  E-value=2.7e-26  Score=174.24  Aligned_cols=76  Identities=42%  Similarity=1.049  Sum_probs=72.7

Q ss_pred             cccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCC
Q psy12688        129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQST  204 (222)
Q Consensus       129 ~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r  204 (222)
                      +|.|||+.++++||||.+|+||++||||++..+..|.|..+++|.++...|..|++|||+|||++||++++|+.++
T Consensus         1 ~C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~   76 (87)
T cd07162           1 ICRVCGDRATGYHFNAMTCEGCKGFFRRAMKRNARLCCPFQKGCVITKSNRRQCQACRLRKCLSIGMKKELIMSDE   76 (87)
T ss_pred             CCcccCCcCcceEECcceehhhHHHHHhhhccCceeEcCCCCceecCCcccccCccchhhHHhHhCCCHHHccCHH
Confidence            4999999999999999999999999999999888999999999999999999999999999999999999998874

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

>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=99.92  E-value=6.7e-27  Score=175.79  Aligned_cols=78  Identities=45%  Similarity=1.034  Sum_probs=73.8

Q ss_pred             ccccCCCCcceeeccccchhhhHHHHhHhhcCceeccc-cCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCCc
Q psy12688        130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCV-AERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHGV  207 (222)
Q Consensus       130 C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~-~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g~  207 (222)
                      |.|||+.++|+||||.+|+||++||||++..+..|.|. .++.|.|+...|..|++|||+|||++||++++|+.+|+..
T Consensus         1 C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~p~   79 (82)
T cd06957           1 CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKGIIYTCIAGNGNCVVDKARRNWCPFCRLQKCFAVGMNRAAVQEERGPR   79 (82)
T ss_pred             CCccCccCcceEECcceEeeeeeEEEEeecCCCceEccCccCCCccCCCccCcccCcchhhcccccCCHHHhccccCcC
Confidence            89999999999999999999999999999988899998 4689999999999999999999999999999999988764

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

>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=99.92  E-value=2.3e-26  Score=177.01  Aligned_cols=77  Identities=78%  Similarity=1.461  Sum_probs=74.2

Q ss_pred             ccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688        130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG  206 (222)
Q Consensus       130 C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g  206 (222)
                      |.|||+.++++||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++|+.++..
T Consensus         1 C~VCg~~a~g~hyGv~sC~aCk~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~Vq~~r~~   77 (93)
T cd07167           1 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMR   77 (93)
T ss_pred             CcccCccCcceEECchhhhhHHHHHHHHeeCCCccccCCCCccccCccccCcCCCcccchhhhccCCHHHhhhcccC
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999854

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

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

Probab=99.92  E-value=1.6e-26  Score=176.29  Aligned_cols=80  Identities=48%  Similarity=1.064  Sum_probs=75.3

Q ss_pred             CccccccCCCCcceeeccccchhhhHHHHhHhhcCcee-ccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCC
Q psy12688        127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVY-TCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTH  205 (222)
Q Consensus       127 ~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~-~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~  205 (222)
                      ..+|.|||+.++|+||||.+|+||++||||++..+..| .|..+++|.|+...|..|++|||+|||++||++++|+.+|.
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            34699999999999999999999999999999988888 59999999999999999999999999999999999999986


Q ss_pred             C
Q psy12688        206 G  206 (222)
Q Consensus       206 g  206 (222)
                      .
T Consensus        83 ~   83 (89)
T cd07166          83 P   83 (89)
T ss_pred             C
Confidence            5

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

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

Probab=99.92  E-value=1.6e-26  Score=178.04  Aligned_cols=79  Identities=41%  Similarity=0.899  Sum_probs=75.1

Q ss_pred             cccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCCc
Q psy12688        129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHGV  207 (222)
Q Consensus       129 ~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g~  207 (222)
                      .|.|||+.++|+||||.+|+||++||||++..+..|.|..+++|.++...+..|++|||+|||++||++++|+.+++-.
T Consensus         2 ~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~r~~~   80 (94)
T cd06966           2 ICGVCGDKALGYNFNAITCESCKAFFRRNALKNKEFKCPFNESCEINVVTRRFCQKCRLDKCFAIGMKKEWIMSEEDKS   80 (94)
T ss_pred             CCeeCCCcCcceEECcceeeeehheehhcccCCCccccCCCCccccCccccccCccchhhhCcccCCCHHHccchhhhh
Confidence            5999999999999999999999999999999888999999999999999999999999999999999999999987643

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

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

Probab=99.92  E-value=2.1e-26  Score=169.27  Aligned_cols=72  Identities=47%  Similarity=1.119  Sum_probs=68.9

Q ss_pred             ccccCCCCcceeeccccchhhhHHHHhHhhcCceeccc-cCcccccCCCCCCCCcchHhHHHHHhcCCccccc
Q psy12688        130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCV-AERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSS  201 (222)
Q Consensus       130 C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~-~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr  201 (222)
                      |.|||+.++++||||.+|+||++||||++..+..|.|. .+++|.|+...|..|++|||+|||++||++++||
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            89999999999999999999999999999988899998 6789999999999999999999999999999986

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=99.92  E-value=3e-26  Score=173.82  Aligned_cols=79  Identities=38%  Similarity=0.854  Sum_probs=73.4

Q ss_pred             cccccCCCCcceeeccccchhhhHHHHhHhhcCc--eeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688        129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKK--VYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG  206 (222)
Q Consensus       129 ~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~--~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g  206 (222)
                      .|.|||+.++|+||||.+|+||++||||++..+.  .|.|..+++|.++...|..|++|||+|||++||++++++.+|+.
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            4999999999999999999999999999988654  88999999999999999999999999999999999999988765


Q ss_pred             c
Q psy12688        207 V  207 (222)
Q Consensus       207 ~  207 (222)
                      +
T Consensus        82 ~   82 (86)
T cd07157          82 D   82 (86)
T ss_pred             c
Confidence            4

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.

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

Probab=99.92  E-value=2.1e-26  Score=168.86  Aligned_cols=72  Identities=60%  Similarity=1.233  Sum_probs=69.6

Q ss_pred             ccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccc
Q psy12688        130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSS  201 (222)
Q Consensus       130 C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr  201 (222)
                      |.|||+.++++||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++||
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            899999999999999999999999999999888899999999999999999999999999999999999886

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

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

Probab=99.92  E-value=6e-26  Score=175.21  Aligned_cols=81  Identities=47%  Similarity=1.015  Sum_probs=75.8

Q ss_pred             CccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688        127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG  206 (222)
Q Consensus       127 ~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g  206 (222)
                      ..+|.|||+.+.|+||||.+|+||++||||++..+..|.|..+++|.++...|..|++|||+|||++||++++|+.++..
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            34699999999999999999999999999999988899999999999999999999999999999999999999988754


Q ss_pred             c
Q psy12688        207 V  207 (222)
Q Consensus       207 ~  207 (222)
                      .
T Consensus        85 ~   85 (95)
T cd06968          85 K   85 (95)
T ss_pred             h
Confidence            3

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

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

Probab=99.92  E-value=5.4e-26  Score=179.08  Aligned_cols=78  Identities=38%  Similarity=1.037  Sum_probs=73.5

Q ss_pred             CCccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccC
Q psy12688        126 IEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQS  203 (222)
Q Consensus       126 ~~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~  203 (222)
                      ....|.|||+.++|+||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++|+.+
T Consensus         5 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~   82 (107)
T cd06955           5 VPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTD   82 (107)
T ss_pred             CCCCCeecCCcCcccEECcceeeeecceecceeccCCccccCCCCccccccCCccccccchhHHHHHcCCCchhccCH
Confidence            346699999999999999999999999999999988899999999999999999999999999999999999988876

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

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

Probab=99.91  E-value=1.1e-25  Score=170.07  Aligned_cols=78  Identities=51%  Similarity=1.076  Sum_probs=71.9

Q ss_pred             cccccCCCCcceeeccccchhhhHHHHhHhhcCceec-cccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCCc
Q psy12688        129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYT-CVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHGV  207 (222)
Q Consensus       129 ~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~-C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g~  207 (222)
                      +|.|||+.++|+||||.+|+||++||||++..+..|. |...  |.|+...|..|++|||+|||++||++++|+.+|...
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            4999999999999999999999999999998888884 9753  999999999999999999999999999999998764


Q ss_pred             c
Q psy12688        208 V  208 (222)
Q Consensus       208 ~  208 (222)
                      .
T Consensus        79 ~   79 (84)
T cd06965          79 V   79 (84)
T ss_pred             h
Confidence            3

DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PPAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily of ligand-activated transcription factors. PPARs play important roles in regulating cellular differentiation, development and lipid metabolism. Activated PPAR forms a heterodimer with the retinoid X receptor (RXR) that binds to the hormone response elements, which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair located upstream of the peroxisome proliferator responsive gene

>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors

Probab=99.90  E-value=5.1e-25  Score=160.39  Aligned_cols=70  Identities=50%  Similarity=1.095  Sum_probs=66.9

Q ss_pred             cccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCcc
Q psy12688        129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLE  198 (222)
Q Consensus       129 ~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~e  198 (222)
                      +|.|||+.++++||||.+|+||++||||++..+..|.|..+++|.+++..|..|++|||+|||++||+++
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            4999999999999999999999999999999888899999999999999999999999999999999874

>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=99.90  E-value=8.3e-25  Score=158.66  Aligned_cols=70  Identities=59%  Similarity=1.247  Sum_probs=62.4

Q ss_pred             ccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCc
Q psy12688        128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKL  197 (222)
Q Consensus       128 ~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~  197 (222)
                      +.|+|||++++++||||.+|++|++||+|++..+..+.|..+++|.+++..+..|++|||+|||++||++
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            3699999999999999999999999999999988889999999999999999999999999999999974

The receptors function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner. Nuclear hormone receptors consist of a highly conserved DNA-binding domain that recognises specific sequences, connected via a linker region to a C-terminal ligand-binding domain (IPR000536 from INTERPRO). In addition, certain nuclear hormone receptors have an N-terminal modulatory domain (IPR001292 from INTERPRO). The DNA-binding domain can elicit either an activating or repressing effect by binding to specific regions of the DNA known as hormone-response elements [, ]. These response elements position the receptors, and the complexes recruited by them, close to the genes of which transcription is affected. The DNA-binding domains of nuclear receptors consist of two zinc-nucleated modules and a C-terminal extension, where residues in the first zinc module determine the specificity of the DNA recognition and residues in the second zinc module are involved in dimerisation. The DNA-binding domain is furthermore involved in several other functions including nuclear localisation, and interaction with transcription factors and co-activators []. Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the two C4-type zinc finger modules involved in DNA-binding. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1DSZ_A 1LO1_A 3M9E_F 2EBL_A 1GA5_B 1A6Y_B 1HLZ_B 1HRA_A 1KB6_B 1KB4_B ....

>KOG4216|consensus

Probab=99.90  E-value=7.3e-25  Score=203.42  Aligned_cols=77  Identities=48%  Similarity=1.075  Sum_probs=73.5

Q ss_pred             ccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCC
Q psy12688        128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQST  204 (222)
Q Consensus       128 ~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r  204 (222)
                      .+|.||||+++|.||||.+|||||+||||+-+.+..|.|.+.++|.|+...|++|++|||+|||++||+.+||..-|
T Consensus        47 IPCKiCGDKSSGiHYGVITCEGCKGFFRRSQ~s~a~YsCpRqknC~iDRtnRNRCQ~CRLqKClaLGMSRDAVKFGR  123 (479)
T KOG4216|consen   47 IPCKICGDKSSGIHYGVITCEGCKGFFRRSQQSNANYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGR  123 (479)
T ss_pred             EeeeeccCCCCcceeeeEeeccchHhhhhhhhccccccCCcccCCcccccccchhhHHHHHHHHHhccchhhHHhcc
Confidence            46999999999999999999999999999999999999999999999999999999999999999999999997544

>KOG4218|consensus

Probab=99.90  E-value=7.1e-25  Score=201.41  Aligned_cols=81  Identities=79%  Similarity=1.426  Sum_probs=77.2

Q ss_pred             cCCCccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccC
Q psy12688        124 EGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQS  203 (222)
Q Consensus       124 ~~~~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~  203 (222)
                      +...++|.||||+.+|||||..+||.||+||+|+|++++.|.|....+|.|++..|++|.+|||+|||.+||+.||||.|
T Consensus        12 edl~ElCPVCGDkVSGYHYGLLTCESCKGFFKRTVQNnK~YtC~e~qnC~iDkTqRKRCP~CRFQKCLtvGMklEAVRAD   91 (475)
T KOG4218|consen   12 EDLGELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKQYTCSEEQNCHIDKTQRKRCPSCRFQKCLTVGMKLEAVRAD   91 (475)
T ss_pred             cccccccccccCccccceeeeeehhhhhhHHHHHhhcCcceecccccccccchHhhccCCchhHHHHhhhhhhHHHHHHh
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999977


Q ss_pred             C
Q psy12688        204 T  204 (222)
Q Consensus       204 r  204 (222)
                      |
T Consensus        92 R   92 (475)
T KOG4218|consen   92 R   92 (475)
T ss_pred             h
Confidence            6

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	222
2a66_A	113	Human Liver Receptor Homologue Dna-Binding Domain (		2e-34
2ff0_A	102	Solution Structure Of Steroidogenic Factor 1 Dna Bi		5e-33
3dzu_A	467	Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp		3e-23
2han_A	93	Structural Basis Of Heterodimeric Ecdysteroid Recep		2e-22
1r0o_A	86	Crystal Structure Of The Heterodimeric Ecdysone Rec		2e-21
1ynw_B	99	Crystal Structure Of Vitamin D Receptor And 9-Cis R		2e-21
1r0n_A	81	Crystal Structure Of Heterodimeric Ecdsyone Recepto		6e-21
1dsz_B	85	Structure Of The RxrRAR DNA-Binding Domain Heterodi		9e-21
1by4_A	82	Structure And Mechanism Of The Homodimeric Assembly		1e-20
1cit_A	89	Dna-Binding Mechanism Of The Monomeric Orphan Nucle		2e-20
1rxr_A	83	High Resolution Solution Structure Of The Retinoid		8e-20
2nll_A	66	Retinoid X Receptor-Thyroid Hormone Receptor Dna-Bi		8e-20
2han_B	119	Structural Basis Of Heterodimeric Ecdysteroid Recep		1e-19
1r0n_B	109	Crystal Structure Of Heterodimeric Ecdsyone Recepto		2e-19
2ebl_A	89	Solution Structure Of The Zinc Finger, C4-type Doma		3e-19
4hn5_A	117	Gr Dna Binding Domain - Tslp Ngre Complex Length =		4e-19
4hn6_A	114	Gr Dna Binding Domain R460d/d462r - Tslp Ngre Compl		5e-19
1dsz_A	86	Structure Of The RxrRAR DNA-Binding Domain Heterodi		6e-19
2gda_A	72	Refined Solution Structure Of The Glucocorticoid Re		7e-19
1gdc_A	72	Refined Solution Structure Of The Glucocorticoid Re		1e-18
1hra_A	80	The Solution Structure Of The Human Retinoic Acid R		1e-18
1rgd_A	71	Structure Refinement Of The Glucocorticoid Receptor		3e-18
3g9p_B	90	Gr Dna Binding Domain:sgk 16bp Complex-7 Length = 9		3e-18
3dzu_D	419	Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp		4e-18
1lat_A	82	Glucocorticoid Receptor MutantDNA COMPLEX Length =		5e-18
2env_A	88	Solution Sturcture Of The C4-Type Zinc Finger Domai		7e-18
1r4i_A	105	Crystal Structure Of Androgen Receptor Dna-Binding		7e-18
1r4o_A	92	Crystallographic Analysis Of The Interaction Of The		8e-18
3m9e_A	105	Thyroid Hormone Beta Dna Binding Domain Homodimer W		9e-18
1r4r_B	92	Crystallographic Analysis Of The Interaction Of The		9e-18
1glu_A	81	Crystallographic Analysis Of The Interaction Of The		1e-17
1lo1_A	98	Estrogen Related Receptor 2 Dna Binding Domain In C		2e-17
3g6t_A	91	Gr Gamma Dna-Binding Domain:fkbp5 16bp Complex-34 L		3e-17
2nll_B	103	Retinoid X Receptor-Thyroid Hormone Receptor Dna-Bi		3e-17
3cbb_A	78	Crystal Structure Of Hepatocyte Nuclear Factor 4alp		4e-17
1ynw_A	110	Crystal Structure Of Vitamin D Receptor And 9-Cis R		8e-17
1hlz_A	94	Crystal Structure Of The Orphan Nuclear Receptor Re		8e-17
1hcp_A	76	Dna Recognition By The Oestrogen Receptor: From Sol		1e-16
1hcq_A	84	The Crystal Structure Of The Estrogen Receptor Dna-		1e-16
4aa6_E	71	The Oestrogen Receptor Recognizes An Imperfectly Pa		1e-16
4aa6_A	71	The Oestrogen Receptor Recognizes An Imperfectly Pa		1e-16
2c7a_A	78	Structure Of The Progesterone Receptor-Dna Complex		3e-16
1kb2_A	110	Crystal Structure Of Vdr Dna-Binding Domain Bound T		2e-15

>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 =  142 bits (357), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 66/91 (72%), Positives = 73/91 (80%), Gaps = 1/91 (1%)
Query: 124 EGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCP 183
           E +EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQN K YTC+  ++C IDKTQRKRCP
Sbjct: 6   EDLEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQNCQIDKTQRKRCP 65
Query: 184 FCRFQKCLEVGMKLE-VSSQSTHGVVVIWSP 213
           +CRFQKCL VGMKLE V +    G    + P
Sbjct: 66  YCRFQKCLSVGMKLEAVRADRMRGGRNKFGP 96

>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 =  137 bits (344), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 65/88 (73%), Positives = 70/88 (79%), Gaps = 1/88 (1%)
Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
           +ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQN K YTC   +SC IDKTQRKRCPFCR
Sbjct: 1   DELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKHYTCTESQSCKIDKTQRKRCPFCR 60
Query: 187 FQKCLEVGMKLE-VSSQSTHGVVVIWSP 213
           FQKCL VGM+LE V +    G    + P
Sbjct: 61  FQKCLTVGMRLEAVRADRMRGGRNKFGP 88

>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 =  104 bits (260), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 45/95 (47%), Positives = 59/95 (62%), Gaps = 2/95 (2%)
Query: 107 PFHTSTIAATPEHP--DTKEGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVY 164
           P   + +   P HP  +     + +C +CGD+ SG HYG+ +CE CKGFFKRTV+    Y
Sbjct: 115 PLGLNGVLKVPAHPSGNMASFTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTY 174
Query: 165 TCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEV 199
           TC   + C IDK QR RC +CR+QKCL +GMK E 
Sbjct: 175 TCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREA 209

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

Iteration: 1
 Score =  102 bits (254), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 44/83 (53%), Positives = 55/83 (66%)
Query: 125 GIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPF 184
           G + LC +CGD+ SG HYG+ +CE CKGFFKRTV+    Y C   R+C IDK QR RC +
Sbjct: 8   GSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYACRENRNCIIDKRQRNRCQY 67
Query: 185 CRFQKCLEVGMKLEVSSQSTHGV 207
           CR+QKCL  GMK E   +   G+
Sbjct: 68  CRYQKCLTCGMKREAVQEERQGI 90

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

Iteration: 1
 Score = 99.0 bits (245), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 43/75 (57%), Positives = 52/75 (69%)
Query: 125 GIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPF 184
           G + LC +CGD+ SG HYG+ +CE CKGFFKRTV+    Y C   R+C IDK QR RC +
Sbjct: 6   GSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYACRENRNCIIDKRQRNRCQY 65
Query: 185 CRFQKCLEVGMKLEV 199
           CR+QKCL  GMK E 
Sbjct: 66  CRYQKCLTCGMKREA 80

>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 = 98.6 bits (244), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 41/71 (57%), Positives = 51/71 (71%)
Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
           +C +CGD+ SG HYG+ +CE CKGFFKRTV+    YTC   + C IDK QR RC +CR+Q
Sbjct: 5   ICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQ 64
Query: 189 KCLEVGMKLEV 199
           KCL +GMK E 
Sbjct: 65  KCLAMGMKREA 75

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

Iteration: 1
 Score = 97.4 bits (241), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 41/73 (56%), Positives = 52/73 (71%)
Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
           + +C +CGD+ SG HYG+ +CE CKGFFKRTV+    YTC   + C IDK QR RC +CR
Sbjct: 3   KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCR 62
Query: 187 FQKCLEVGMKLEV 199
           +QKCL +GMK E 
Sbjct: 63  YQKCLAMGMKREA 75

>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 = 96.7 bits (239), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 41/71 (57%), Positives = 51/71 (71%)
Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
           +C +CGD+ SG HYG+ +CE CKGFFKRTV+    YTC   + C IDK QR RC +CR+Q
Sbjct: 7   ICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQ 66
Query: 189 KCLEVGMKLEV 199
           KCL +GMK E 
Sbjct: 67  KCLAMGMKREA 77

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

Iteration: 1
 Score = 96.7 bits (239), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 41/71 (57%), Positives = 51/71 (71%)
Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
           +C +CGD+ SG HYG+ +CE CKGFFKRTV+    YTC   + C IDK QR RC +CR+Q
Sbjct: 7   ICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQ 66
Query: 189 KCLEVGMKLEV 199
           KCL +GMK E 
Sbjct: 67  KCLAMGMKREA 77

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

Iteration: 1
 Score = 95.9 bits (237), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 44/70 (62%), Positives = 49/70 (70%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
           C VCGD  S  HYG+ TCE CKGFFKRTVQ    Y C+A + C +DK +R RC FCRFQK
Sbjct: 3   CAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQK 62
Query: 190 CLEVGMKLEV 199
           CL VGM  EV
Sbjct: 63  CLAVGMVKEV 72

>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 = 93.6 bits (231), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 40/71 (56%), Positives = 50/71 (70%)
Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
           +C +CGD+ SG HYG+ +CE CKGFFKRTV+    YTC   + C IDK QR RC +CR+Q
Sbjct: 5   ICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQ 64
Query: 189 KCLEVGMKLEV 199
           K L +GMK E 
Sbjct: 65  KALAMGMKREA 75

>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 = 93.6 bits (231), Expect = 8e-20,   Method: Composition-based stats.
 Identities = 39/66 (59%), Positives = 48/66 (72%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
           C +CGD+ SG HYG+ +CE CKGFFKRTV+    YTC   + C IDK QR RC +CR+QK
Sbjct: 1   CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQK 60
Query: 190 CLEVGM 195
           CL +GM
Sbjct: 61  CLAMGM 66

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

Iteration: 1
 Score = 92.8 bits (229), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 41/72 (56%), Positives = 50/72 (69%)
Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
           EELC VCGD+ SGYHY  LTCE CKGFF+R+V    VY C   R+C +D   R++C  CR
Sbjct: 8   EELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECR 67
Query: 187 FQKCLEVGMKLE 198
            +KCL VGM+ E
Sbjct: 68  LKKCLAVGMRPE 79

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

Iteration: 1
 Score = 92.0 bits (227), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 41/72 (56%), Positives = 50/72 (69%)
Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
           EELC VCGD+ SGYHY  LTCE CKGFF+R+V    VY C   R+C +D   R++C  CR
Sbjct: 6   EELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECR 65
Query: 187 FQKCLEVGMKLE 198
            +KCL VGM+ E
Sbjct: 66  LKKCLAVGMRPE 77

>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 = 91.3 bits (225), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 43/75 (57%), Positives = 52/75 (69%), Gaps = 2/75 (2%)
Query: 125 GIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPF 184
           GIE  C VCGDK SG HYG  TCE CK FFKR+V+    YTC A R+C ID+  R +C +
Sbjct: 7   GIE--CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRANRNCPIDQHHRNQCQY 64
Query: 185 CRFQKCLEVGMKLEV 199
           CR +KCL+VGM+ E 
Sbjct: 65  CRLKKCLKVGMRREA 79

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

Iteration: 1
 Score = 90.9 bits (224), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 40/72 (55%), Positives = 49/72 (68%)
Query: 128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRF 187
           +LC VC D+ SG HYG+LTC SCK FFKR V+ +  Y C     C IDK +RK CP CR+
Sbjct: 30  KLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRY 89
Query: 188 QKCLEVGMKLEV 199
           +KCL+ GM LE 
Sbjct: 90  RKCLQAGMNLEA 101

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

Iteration: 1
 Score = 90.9 bits (224), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 40/72 (55%), Positives = 50/72 (69%)
Query: 128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRF 187
           +LC VC D+ SG HYG+LTC SCK FFKR V+ +  Y C  +  C IDK +RK CP CR+
Sbjct: 27  KLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGDNRCIIDKIRRKNCPACRY 86
Query: 188 QKCLEVGMKLEV 199
           +KCL+ GM LE 
Sbjct: 87  RKCLQAGMNLEA 98

>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 = 90.5 bits (223), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 41/73 (56%), Positives = 51/73 (69%)
Query: 126 IEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFC 185
           I + C VC DK SGYHYG+  CE CKGFF+R++Q   VYTC  +++C I+K  R RC +C
Sbjct: 3   IYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYC 62
Query: 186 RFQKCLEVGMKLE 198
           R QKC EVGM  E
Sbjct: 63  RLQKCFEVGMSKE 75

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

Iteration: 1
 Score = 90.5 bits (223), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 40/70 (57%), Positives = 48/70 (68%)
Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
           LC VC D+ SG HYG+LTC SCK FFKR V+ +  Y C     C IDK +RK CP CR++
Sbjct: 1   LCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYR 60
Query: 189 KCLEVGMKLE 198
           KCL+ GM LE
Sbjct: 61  KCLQAGMNLE 70

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

Iteration: 1
 Score = 90.1 bits (222), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 40/70 (57%), Positives = 48/70 (68%)
Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
           LC VC D+ SG HYG+LTC SCK FFKR V+ +  Y C     C IDK +RK CP CR++
Sbjct: 1   LCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYR 60
Query: 189 KCLEVGMKLE 198
           KCL+ GM LE
Sbjct: 61  KCLQAGMNLE 70

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

Iteration: 1
 Score = 89.7 bits (221), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 39/69 (56%), Positives = 49/69 (71%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
           C VC DK SGYHYG+  CE CKGFF+R++Q   +YTC  +++C I+K  R RC +CR QK
Sbjct: 8   CFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMIYTCHRDKNCVINKVTRNRCQYCRLQK 67
Query: 190 CLEVGMKLE 198
           C EVGM  E
Sbjct: 68  CFEVGMSKE 76

>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 = 88.6 bits (218), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 39/69 (56%), Positives = 47/69 (68%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
           C VC D+ SG HYG+LTC SCK FFKR V+ +  Y C     C IDK +RK CP CR++K
Sbjct: 1   CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRK 60
Query: 190 CLEVGMKLE 198
           CL+ GM LE
Sbjct: 61  CLQAGMNLE 69

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

Iteration: 1
 Score = 88.2 bits (217), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 39/71 (54%), Positives = 48/71 (67%)
Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
           +C VC D+ SG HYG+LTC SCK FFKR V+ +  Y C     C IDK +RK CP CR++
Sbjct: 4   MCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYR 63
Query: 189 KCLEVGMKLEV 199
           KCL+ GM LE 
Sbjct: 64  KCLQAGMNLEA 74

>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 = 87.8 bits (216), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 37/66 (56%), Positives = 47/66 (71%), Gaps = 1/66 (1%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
           C VCGDK SG+HYG+  CE CKGFF+RT++ K +Y    + +C I K  R +C +CRFQK
Sbjct: 53  CRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLIYD-RCDLNCRIHKKSRNKCQYCRFQK 111
Query: 190 CLEVGM 195
           CL VGM
Sbjct: 112 CLAVGM 117

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

Iteration: 1
 Score = 87.4 bits (215), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 40/72 (55%), Positives = 48/72 (66%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
           C VC D+ SG HYG+LTCE CK FFKR V+ +  Y C  E  C IDK +RK CP CR++K
Sbjct: 7   CLVCSDEASGCHYGVLTCEGCKAFFKRAVEGQHNYLCKYEGKCIIDKIRRKNCPACRYRK 66
Query: 190 CLEVGMKLEVSS 201
           CL+ GM LE   
Sbjct: 67  CLQAGMNLEARK 78

>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 = 87.0 bits (214), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 39/66 (59%), Positives = 47/66 (71%), Gaps = 1/66 (1%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
           C VCGDK SG+HYG+  CE CKGFF+RT++ K  Y    ERSC I K  R +C +CRFQK
Sbjct: 10  CRVCGDKASGFHYGVHACEGCKGFFRRTIRMKLEYE-KCERSCKIQKKNRNKCQYCRFQK 68
Query: 190 CLEVGM 195
           CL +GM
Sbjct: 69  CLALGM 74

>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 = 87.0 bits (214), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 38/71 (53%), Positives = 47/71 (66%)
Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
           ++ C +CGD+ SG HYG LTC SCK FFKR  + K+ Y C +   C IDK +RK CP CR
Sbjct: 7   QKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCR 66
Query: 187 FQKCLEVGMKL 197
            +KC E GM L
Sbjct: 67  LRKCYEAGMTL 77

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

Iteration: 1
 Score = 87.0 bits (214), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 39/70 (55%), Positives = 47/70 (67%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
           C VC D+ SG HYG+LTC SCK FFKR V+ +  Y C     C IDK +RK CP CR++K
Sbjct: 7   CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRK 66
Query: 190 CLEVGMKLEV 199
           CL+ GM LE 
Sbjct: 67  CLQAGMNLEA 76

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

Iteration: 1
 Score = 86.7 bits (213), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 41/77 (53%), Positives = 52/77 (67%), Gaps = 2/77 (2%)
Query: 125 GIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKK--VYTCVAERSCHIDKTQRKRC 182
           G +ELC VCGDK +GYHY  +TCE CKGFF+RT+Q      Y+C  E  C IDK  R +C
Sbjct: 1   GSDELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKSLHPSYSCKYEGKCIIDKVTRNQC 60
Query: 183 PFCRFQKCLEVGMKLEV 199
             CRF+KC+ VGM  ++
Sbjct: 61  QECRFKKCIYVGMATDL 77

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

Iteration: 1
 Score = 86.7 bits (213), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 39/70 (55%), Positives = 47/70 (67%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
           C VC D+ SG HYG+LTC SCK FFKR V+ +  Y C     C IDK +RK CP CR++K
Sbjct: 7   CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRK 66
Query: 190 CLEVGMKLEV 199
           CL+ GM LE 
Sbjct: 67  CLQAGMNLEA 76

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

Iteration: 1
 Score = 85.9 bits (211), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 39/70 (55%), Positives = 47/70 (67%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
           C VC D+ SG HYG+LTC SCK FFKR V+ +  Y C     C IDK +RK CP CR++K
Sbjct: 7   CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRK 66
Query: 190 CLEVGMKLEV 199
           CL+ GM LE 
Sbjct: 67  CLQAGMNLEA 76

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

Iteration: 1
 Score = 85.9 bits (211), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 39/69 (56%), Positives = 47/69 (68%)
Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
           + LC VCGD  SGYHYG+ +CE+CK FFKRT+Q    Y+C A   C I K +RK C  CR
Sbjct: 4   KRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACR 63
Query: 187 FQKCLEVGM 195
           F K L+VGM
Sbjct: 64  FMKALKVGM 72

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

Iteration: 1
 Score = 85.1 bits (209), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 39/72 (54%), Positives = 49/72 (68%), Gaps = 1/72 (1%)
Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKK-VYTCVAERSCHIDKTQRKRCPFCRF 187
           +C VC D+ SG HYG+LTC SCK FFKR V+ ++  Y C     C IDK +RK CP CR+
Sbjct: 4   MCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGRQHNYLCAGRNDCIIDKIRRKNCPACRY 63
Query: 188 QKCLEVGMKLEV 199
           +KCL+ GM LE 
Sbjct: 64  RKCLQAGMNLEA 75

>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 = 85.1 bits (209), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 40/71 (56%), Positives = 49/71 (69%), Gaps = 2/71 (2%)
Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKK--VYTCVAERSCHIDKTQRKRCPF 184
           +ELC VCGDK +GYHY  +TCE CKGFF+RT+Q      Y+C  E  C IDK  R +C  
Sbjct: 1   DELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQE 60
Query: 185 CRFQKCLEVGM 195
           CRF+KC+ VGM
Sbjct: 61  CRFKKCIYVGM 71

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

Iteration: 1
 Score = 84.7 bits (208), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 33/71 (46%), Positives = 48/71 (67%)
Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
           LC +CGD+ +G HYG  +C+ CKGFF+R+V+   +Y+C   R C +DK +R +C +CR +
Sbjct: 2   LCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLK 61
Query: 189 KCLEVGMKLEV 199
           KC   GMK E 
Sbjct: 62  KCFRAGMKKEA 72

>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 = 83.6 bits (205), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 31/73 (42%), Positives = 50/73 (68%)
Query: 126 IEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFC 185
           +  +C VCGD+ +G+H+  +TCE CKGFF+R+++ K ++TC A   C I K  R+ C  C
Sbjct: 5   VPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCAANGDCRITKDNRRACQAC 64
Query: 186 RFQKCLEVGMKLE 198
           R ++C+++GM  E
Sbjct: 65  RLKRCVDIGMMKE 77

>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 = 83.6 bits (205), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 38/72 (52%), Positives = 49/72 (68%), Gaps = 1/72 (1%)
Query: 125 GIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTV-QNKKVYTCVAERSCHIDKTQRKRCP 183
           G+  LC VCGD  SG+HYG+L CE CKGFF+R++ QN +   C+   +C I +  R RC 
Sbjct: 5   GMVLLCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQ 64
Query: 184 FCRFQKCLEVGM 195
            CRF+KCL VGM
Sbjct: 65  QCRFKKCLSVGM 76

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

Iteration: 1
 Score = 83.2 bits (204), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 37/68 (54%), Positives = 43/68 (63%)
Query: 128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRF 187
             C VC D  SGYHYG+ +CE CK FFKR++Q    Y C A   C IDK +RK C  CR 
Sbjct: 5   RYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRL 64
Query: 188 QKCLEVGM 195
           +KC EVGM
Sbjct: 65  RKCYEVGM 72

>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 = 83.2 bits (204), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 37/68 (54%), Positives = 43/68 (63%)
Query: 128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRF 187
             C VC D  SGYHYG+ +CE CK FFKR++Q    Y C A   C IDK +RK C  CR 
Sbjct: 5   RYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRL 64
Query: 188 QKCLEVGM 195
           +KC EVGM
Sbjct: 65  RKCYEVGM 72

>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 = 83.2 bits (204), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 37/68 (54%), Positives = 43/68 (63%)
Query: 128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRF 187
             C VC D  SGYHYG+ +CE CK FFKR++Q    Y C A   C IDK +RK C  CR 
Sbjct: 2   RYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRL 61
Query: 188 QKCLEVGM 195
           +KC EVGM
Sbjct: 62  RKCYEVGM 69

>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 = 83.2 bits (204), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 37/68 (54%), Positives = 43/68 (63%)
Query: 128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRF 187
             C VC D  SGYHYG+ +CE CK FFKR++Q    Y C A   C IDK +RK C  CR 
Sbjct: 2   RYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRL 61
Query: 188 QKCLEVGM 195
           +KC EVGM
Sbjct: 62  RKCYEVGM 69

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

Iteration: 1
 Score = 81.6 bits (200), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 35/71 (49%), Positives = 48/71 (67%)
Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
           +++C +CGD+ SG HYG+LTC SCK FFKR ++ +  Y C     C +DK +RK CP CR
Sbjct: 2   QKICLICGDEASGCHYGVLTCGSCKVFFKRAMEGQHNYLCAGRNDCIVDKIRRKNCPACR 61
Query: 187 FQKCLEVGMKL 197
            +KC + GM L
Sbjct: 62  LRKCCQAGMVL 72

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

Iteration: 1
 Score = 79.3 bits (194), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 30/73 (41%), Positives = 49/73 (67%)
Query: 126 IEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFC 185
           +  +C VCGD+ +G+H+  +TCE CKGFF+R+++ K ++TC     C I K  R+ C  C
Sbjct: 5   VPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQAC 64
Query: 186 RFQKCLEVGMKLE 198
           R ++C+++GM  E
Sbjct: 65  RLKRCVDIGMMKE 77

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	222
2a66_A	113	Orphan nuclear receptor NR5A2; protein-DNA complex	6e-49
1lo1_A	98	Steroid hormone receptor ERR2; estrogen related re	8e-45
1dsz_B	85	RXR-alpha, retinoic acid receptor RXR-alpha; RAR,	3e-44
1cit_A	89	NGFI-B, protein (orphan nuclear receptor NGFI-B);	3e-44
1hcq_A	84	Protein (estrogen receptor); protein-DNA complex,	3e-44
1dsz_A	86	RAR-alpha, retinoic acid receptor alpha; RAR, nucl	4e-44
3g9m_A	90	Glucocorticoid receptor; glucocorticoid, DNA-bindi	5e-44
2han_A	93	Protein ultraspiracle; transcription regulation, t	6e-44
1r4i_A	105	Androgen receptor; AR, steroid receptor, protein-D	1e-43
1kb2_A	110	Vitamin D3 receptor; VDR, nuclear receptor, protei	2e-43
1ynw_B	99	Retinoic acid receptor RXR-alpha, retinoid X recep	8e-43
2han_B	119	Ecdysone receptor; transcription regulation, trans	2e-42
2ebl_A	89	COUP transcription factor 1; DNA-binding, metal-bi	2e-42
2nll_B	103	Protein (thyroid hormone receptor); complex (trans	4e-42
1a6y_A	94	Orphan nuclear receptor NR1D1; orphan receptor, DN	8e-42
3cbb_A	78	HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DN	1e-41
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	1e-37
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	1e-31
3k1f_M	197	Transcription initiation factor IIB; RNA polymeras	8e-04

>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 =  154 bits (392), Expect = 6e-49
 Identities = 63/78 (80%), Positives = 68/78 (87%)

Query: 121 DTKEGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRK 180
              E +EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQN K YTC+  ++C IDKTQRK
Sbjct: 3   FGDEDLEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQNCQIDKTQRK 62

Query: 181 RCPFCRFQKCLEVGMKLE 198
           RCP+CRFQKCL VGMKLE
Sbjct: 63  RCPYCRFQKCLSVGMKLE 80

>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 =  144 bits (364), Expect = 8e-45
 Identities = 40/72 (55%), Positives = 48/72 (66%)

Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
           + LC VCGD  SGYHYG+ +CE+CK FFKRT+Q    Y+C A   C I K +RK C  CR
Sbjct: 4   KRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACR 63

Query: 187 FQKCLEVGMKLE 198
           F K L+VGM  E
Sbjct: 64  FMKALKVGMLKE 75

>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 =  142 bits (359), Expect = 3e-44
 Identities = 41/74 (55%), Positives = 52/74 (70%)

Query: 125 GIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPF 184
             + +C +CGD+ SG HYG+ +CE CKGFFKRTV+    YTC   + C IDK QR RC +
Sbjct: 3   FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQY 62

Query: 185 CRFQKCLEVGMKLE 198
           CR+QKCL +GMK E
Sbjct: 63  CRYQKCLAMGMKRE 76

>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 =  142 bits (359), Expect = 3e-44
 Identities = 43/69 (62%), Positives = 48/69 (69%)

Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
           C VCGD  S  HYG+ TCE CKGFFKRTVQ    Y C+A + C +DK +R RC FCRFQK
Sbjct: 3   CAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQK 62

Query: 190 CLEVGMKLE 198
           CL VGM  E
Sbjct: 63  CLAVGMVKE 71

>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 =  142 bits (359), Expect = 3e-44
 Identities = 37/72 (51%), Positives = 43/72 (59%)

Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
              C VC D  SGYHYG+ +CE CK FFKR++Q    Y C A   C IDK +RK C  CR
Sbjct: 4   TRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACR 63

Query: 187 FQKCLEVGMKLE 198
            +KC EVGM   
Sbjct: 64  LRKCYEVGMMKG 75

>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 =  142 bits (359), Expect = 4e-44
 Identities = 41/74 (55%), Positives = 51/74 (68%)

Query: 125 GIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPF 184
            I + C VC DK SGYHYG+  CE CKGFF+R++Q   VYTC  +++C I+K  R RC +
Sbjct: 2   RIYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQY 61

Query: 185 CRFQKCLEVGMKLE 198
           CR QKC EVGM  E
Sbjct: 62  CRLQKCFEVGMSKE 75

>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 =  141 bits (358), Expect = 5e-44
 Identities = 39/72 (54%), Positives = 48/72 (66%)

Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
             +C VC D+ SG HYG+LTC SCK FFKR V+ +  Y C     C IDK +RK CP CR
Sbjct: 2   SHMCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACR 61

Query: 187 FQKCLEVGMKLE 198
           ++KCL+ GM LE
Sbjct: 62  YRKCLQAGMNLE 73

>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 =  141 bits (358), Expect = 6e-44
 Identities = 43/79 (54%), Positives = 52/79 (65%)

Query: 120 PDTKEGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQR 179
                G + LC +CGD+ SG HYG+ +CE CKGFFKRTV+    Y C   R+C IDK QR
Sbjct: 3   NHPLSGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYACRENRNCIIDKRQR 62

Query: 180 KRCPFCRFQKCLEVGMKLE 198
            RC +CR+QKCL  GMK E
Sbjct: 63  NRCQYCRYQKCLTCGMKRE 81

>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 =  141 bits (356), Expect = 1e-43
 Identities = 38/72 (52%), Positives = 47/72 (65%)

Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
           ++ C +CGD+ SG HYG LTC SCK FFKR  + K+ Y C +   C IDK +RK CP CR
Sbjct: 7   QKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCR 66

Query: 187 FQKCLEVGMKLE 198
            +KC E GM L 
Sbjct: 67  LRKCYEAGMTLG 78

>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 (356), Expect = 2e-43
 Identities = 30/75 (40%), Positives = 49/75 (65%)

Query: 124 EGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCP 183
             +  +C VCGD+ +G+H+  +TCE CKGFF+R+++ K ++TC     C I K  R+ C 
Sbjct: 3   RNVPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQ 62

Query: 184 FCRFQKCLEVGMKLE 198
            CR ++C+++GM  E
Sbjct: 63  ACRLKRCVDIGMMKE 77

>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 =  139 bits (351), Expect = 8e-43
 Identities = 41/72 (56%), Positives = 52/72 (72%)

Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
           + +C +CGD+ SG HYG+ +CE CKGFFKRTV+    YTC   + C IDK QR RC +CR
Sbjct: 3   KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCR 62

Query: 187 FQKCLEVGMKLE 198
           +QKCL +GMK E
Sbjct: 63  YQKCLAMGMKRE 74

>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 =  138 bits (350), Expect = 2e-42
 Identities = 41/72 (56%), Positives = 50/72 (69%)

Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
           EELC VCGD+ SGYHY  LTCE CKGFF+R+V    VY C   R+C +D   R++C  CR
Sbjct: 8   EELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECR 67

Query: 187 FQKCLEVGMKLE 198
            +KCL VGM+ E
Sbjct: 68  LKKCLAVGMRPE 79

>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 =  137 bits (347), Expect = 2e-42
 Identities = 40/77 (51%), Positives = 50/77 (64%)

Query: 122 TKEGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKR 181
           +       C VCGDK SG HYG  TCE CK FFKR+V+    YTC A R+C ID+  R +
Sbjct: 2   SSGSSGIECVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRANRNCPIDQHHRNQ 61

Query: 182 CPFCRFQKCLEVGMKLE 198
           C +CR +KCL+VGM+ E
Sbjct: 62  CQYCRLKKCLKVGMRRE 78

>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 =  137 bits (346), Expect = 4e-42
 Identities = 40/74 (54%), Positives = 50/74 (67%), Gaps = 2/74 (2%)

Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNK--KVYTCVAERSCHIDKTQRKRCPF 184
           +ELC VCGDK +GYHY  +TCE CKGFF+RT+Q      Y+C  E  C IDK  R +C  
Sbjct: 1   DELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQE 60

Query: 185 CRFQKCLEVGMKLE 198
           CRF+KC+ VGM  +
Sbjct: 61  CRFKKCIYVGMATD 74

>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 =  136 bits (344), Expect = 8e-42
 Identities = 38/78 (48%), Positives = 49/78 (62%), Gaps = 1/78 (1%)

Query: 122 TKEGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYT-CVAERSCHIDKTQRK 180
              G+  LC VCGD  SG+HYG+L CE CKGFF+R++Q    Y  C+   +C I +  R 
Sbjct: 2   KLNGMVLLCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRN 61

Query: 181 RCPFCRFQKCLEVGMKLE 198
           RC  CRF+KCL VGM  +
Sbjct: 62  RCQQCRFKKCLSVGMSRD 79

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

 Score =  135 bits (342), Expect = 1e-41
 Identities = 33/70 (47%), Positives = 48/70 (68%)

Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
           LC +CGD+ +G HYG  +C+ CKGFF+R+V+   +Y+C   R C +DK +R +C +CR +
Sbjct: 2   LCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLK 61

Query: 189 KCLEVGMKLE 198
           KC   GMK E
Sbjct: 62  KCFRAGMKKE 71

>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 =  135 bits (341), Expect = 1e-37
 Identities = 61/168 (36%), Positives = 83/168 (49%), Gaps = 4/168 (2%)

Query: 35  SAATGAQTPQMQHSNNDTQSSQLSPML--GNNTSASAGGAGYNFNNMVDNSYLFQSPGGG 92
           S   G  +P   HS   T SS ++ M    +  S+  G    +        +   SP   
Sbjct: 41  SLGPGIGSPGQLHSPISTLSSPINGMGPPFSVISSPMGPHSMSVPTTPTLGFSTGSPQLS 100

Query: 93  STNMDLSSAGISYHPFHTSTIAATPEHPDTKE--GIEELCPVCGDKVSGYHYGLLTCESC 150
           S    +SS+     P   + +   P HP        + +C +CGD+ SG HYG+ +CE C
Sbjct: 101 SPMNPVSSSEDIKPPLGLNGVLKVPAHPSGNMASFTKHICAICGDRSSGKHYGVYSCEGC 160

Query: 151 KGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLE 198
           KGFFKRTV+    YTC   + C IDK QR RC +CR+QKCL +GMK E
Sbjct: 161 KGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKRE 208

>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 =  118 bits (296), Expect = 1e-31
 Identities = 42/112 (37%), Positives = 57/112 (50%), Gaps = 2/112 (1%)

Query: 87  QSPGGGSTNMDLSSAGISYHPFHTSTIAATPEHPDTKEGIEELCPVCGDKVSGYHYGLLT 146
                  + + +  A   Y+   T       E P     +   C VCGDK SG+HYG+  
Sbjct: 11  DDDKMYQSAIKVEPASPPYYSEKTQLYNKPHEEPSNS-LMAIECRVCGDKASGFHYGVHA 69

Query: 147 CESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLE 198
           CE CKGFF+RT++ K +Y    + +C I K  R +C +CRFQKCL VGM   
Sbjct: 70  CEGCKGFFRRTIRLKLIYDR-CDLNCRIHKKSRNKCQYCRFQKCLAVGMSHN 120

>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, transcription factor, DNA-binding, DNA-directed RNA polymerase; 4.30A {Saccharomyces cerevisiae} Length = 197

 Score = 38.1 bits (88), Expect = 8e-04
 Identities = 12/47 (25%), Positives = 15/47 (31%), Gaps = 11/47 (23%)

Query: 115 ATPEHPDTKEG-------IEELCPVCGDK----VSGYHYGLLTCESC 150
            T E  D + G       I   CP C       V  +  G + C  C
Sbjct: 2   MTRESIDKRAGRRGPNLNIVLTCPECKVYPPKIVERFSEGDVVCALC 48

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	222
3cbb_A	78	HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DN	99.96
2ebl_A	89	COUP transcription factor 1; DNA-binding, metal-bi	99.96
1hcq_A	84	Protein (estrogen receptor); protein-DNA complex,	99.96
2han_A	93	Protein ultraspiracle; transcription regulation, t	99.96
1dsz_B	85	RXR-alpha, retinoic acid receptor RXR-alpha; RAR,	99.96
1dsz_A	86	RAR-alpha, retinoic acid receptor alpha; RAR, nucl	99.96
1cit_A	89	NGFI-B, protein (orphan nuclear receptor NGFI-B);	99.96
1ynw_B	99	Retinoic acid receptor RXR-alpha, retinoid X recep	99.95
4hn5_A	117	Glucocorticoid receptor; glucocorticoid receptor,	99.95
3g9m_A	90	Glucocorticoid receptor; glucocorticoid, DNA-bindi	99.95
1a6y_A	94	Orphan nuclear receptor NR1D1; orphan receptor, DN	99.95
2a66_A	113	Orphan nuclear receptor NR5A2; protein-DNA complex	99.95
1lo1_A	98	Steroid hormone receptor ERR2; estrogen related re	99.95
2han_B	119	Ecdysone receptor; transcription regulation, trans	99.95
1kb2_A	110	Vitamin D3 receptor; VDR, nuclear receptor, protei	99.95
2nll_B	103	Protein (thyroid hormone receptor); complex (trans	99.94
1r4i_A	105	Androgen receptor; AR, steroid receptor, protein-D	99.94
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	99.92
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	99.91
2lze_A	87	A primordial catalytic fold generated by in vitro	99.67

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

Probab=99.96  E-value=2.2e-30  Score=192.33  Aligned_cols=77  Identities=43%  Similarity=1.106  Sum_probs=73.3

Q ss_pred             cccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCC
Q psy12688        129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTH  205 (222)
Q Consensus       129 ~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~  205 (222)
                      +|.||||+++|+||||.+|+||++||||++..+..|.|+.+++|.|++..|+.|++|||+|||++||++++||.+||
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            59999999999999999999999999999999999999999999999999999999999999999999999999986

>2ebl_A COUP transcription factor 1; DNA-binding, metal-binding, nuclear protein, receptor, transcription regulation, zinc, EAR3, erbal3 tfcoup1; NMR {Homo sapiens}

Probab=99.96  E-value=5.4e-30  Score=194.68  Aligned_cols=81  Identities=49%  Similarity=1.028  Sum_probs=77.0

Q ss_pred             CccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688        127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG  206 (222)
Q Consensus       127 ~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g  206 (222)
                      ...|.||||+++|+||||.+|+||++||||++..+..|.|+.+++|.|++..|+.|++|||+|||++||++++||.+|+.
T Consensus         7 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~   86 (89)
T 2ebl_A            7 GIECVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRANRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQRGSGP   86 (89)
T ss_dssp             SCBCTTTCSBCCSEETTEECCHHHHHHHHHHHTTTCCCCCSSCSCCCCCSSSSSCCSHHHHHHHHHHTCCHHHHSCSCCC
T ss_pred             CCCCcEeCCCCcceEeCchhhHHhhhhhheeeeeccceecccCccCCcCccCccccccchHHHhhhccCCHHHcccCCCC
Confidence            34699999999999999999999999999999999999999999999999999999999999999999999999999985


Q ss_pred             c
Q psy12688        207 V  207 (222)
Q Consensus       207 ~  207 (222)
                      .
T Consensus        87 ~   87 (89)
T 2ebl_A           87 S   87 (89)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1hcq_A Protein (estrogen receptor); protein-DNA complex, complexed with drug, transcription/DNA complex; HET: DNA; 2.40A {Homo sapiens} SCOP: g.39.1.2 PDB: 1hcp_A 4aa6_A

Probab=99.96  E-value=4.5e-30  Score=193.17  Aligned_cols=79  Identities=48%  Similarity=1.019  Sum_probs=68.2

Q ss_pred             ccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688        128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG  206 (222)
Q Consensus       128 ~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g  206 (222)
                      .+|.||||+++|+||||.+|+||++||||++..+..|.|..+++|.|++..|+.|++|||+|||++||++++||.+|+|
T Consensus         5 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~g   83 (84)
T 1hcq_A            5 RYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRKDRRG   83 (84)
T ss_dssp             CBCTTTCSBCCEEETTEEECHHHHHHHHHHHSSCCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHHTCCC---------
T ss_pred             CcCcEECCCCCCeeeCccchHHhhhhhhhccccccccccccCccCCcCCcCcccChhhhhHHHhHcCCCHHHhcccCCC
Confidence            5699999999999999999999999999999999999999999999999999999999999999999999999999875

>2han_A Protein ultraspiracle; transcription regulation, transcription factor, DNA-binding, nuclear protein, nuclear receptor, zinc finger; 1.95A {Drosophila melanogaster} SCOP: g.39.1.2

Probab=99.96  E-value=4.2e-30  Score=196.61  Aligned_cols=81  Identities=53%  Similarity=1.178  Sum_probs=75.4

Q ss_pred             CccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688        127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG  206 (222)
Q Consensus       127 ~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g  206 (222)
                      ..+|.||||.++|+||||.+|+||++||||++..+..|.|+.+++|.|++..|+.|++|||+|||++||++++|+.+|+.
T Consensus        10 ~~~C~VCgd~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~   89 (93)
T 2han_A           10 KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYACRENRNCIIDKRQRNRCQYCRYQKCLTCGMKREAVQEERQG   89 (93)
T ss_dssp             CCBCTTTCSBCCEEETTEEECHHHHHHHHHHHHHTCCCCCSSCSCCCCSTTTGGGCHHHHHHHHHHHTCCGGGSCCCC--
T ss_pred             CCCCcEeCCCCcCeecCcchhHHHHHHHHhhhccccCcCcCCCCcCCcCCCCCccCccccHHHHhHhCCCHHHhhhccCc
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999999985


Q ss_pred             c
Q psy12688        207 V  207 (222)
Q Consensus       207 ~  207 (222)
                      .
T Consensus        90 ~   90 (93)
T 2han_A           90 I   90 (93)
T ss_dssp             -
T ss_pred             c
Confidence            4

>1dsz_B RXR-alpha, retinoic acid receptor RXR-alpha; RAR, nuclear receptor, protein-DNA, transcription/DNA complex; HET: DNA; 1.70A {Homo sapiens} SCOP: g.39.1.2 PDB: 1by4_A* 1rxr_A 1r0n_A 1r0o_A 2nll_A*

Probab=99.96  E-value=4.5e-30  Score=193.55  Aligned_cols=80  Identities=51%  Similarity=1.143  Sum_probs=76.5

Q ss_pred             CccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688        127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG  206 (222)
Q Consensus       127 ~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g  206 (222)
                      ..+|.||||+++|+||||.+|+||++||||++..+..|.|+.+++|.|++..|+.|++|||+|||++||++++||.+|+.
T Consensus         5 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~   84 (85)
T 1dsz_B            5 KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQR   84 (85)
T ss_dssp             CEECTTTCCEESSEETTEECCHHHHHHHHHHHHHTCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCCCCC
T ss_pred             CCCCCEeCCCCCceeeCccchHHHHHHHHHhhccccceeecccccccccccccccCcchhHHHHhHcCCCHHHhhcccCC
Confidence            35699999999999999999999999999999999999999999999999999999999999999999999999999874

>1dsz_A RAR-alpha, retinoic acid receptor alpha; RAR, nuclear receptor, protein-DNA, transcription/DNA complex; HET: DNA; 1.70A {Homo sapiens} SCOP: g.39.1.2 PDB: 1hra_A

Probab=99.96  E-value=6.6e-30  Score=192.92  Aligned_cols=81  Identities=51%  Similarity=1.077  Sum_probs=73.5

Q ss_pred             CCccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCC
Q psy12688        126 IEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTH  205 (222)
Q Consensus       126 ~~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~  205 (222)
                      +..+|.||||+++|+||||.+|+||++||||++..+..|.|..+++|.|++..|+.|++|||+|||++||++++||.+|+
T Consensus         3 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~   82 (86)
T 1dsz_A            3 IYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRN   82 (86)
T ss_dssp             ---CCTTTCSCCCSEETTEECCHHHHHHHHHHHHTTCCCCCSSCSCCCCSTTTGGGCHHHHHHHHHHTTCCGGGSCCC--
T ss_pred             CCCCCcEECCCccceeeCchhHHHHHHHHHHHhhcccceeeccCCccccCccccccchhhhHHHHHHhCCCHHHhhhccc
Confidence            34579999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             C
Q psy12688        206 G  206 (222)
Q Consensus       206 g  206 (222)
                      .
T Consensus        83 ~   83 (86)
T 1dsz_A           83 K   83 (86)
T ss_dssp             -
T ss_pred             c
Confidence            5

>1cit_A NGFI-B, protein (orphan nuclear receptor NGFI-B); early immediate response gene product, transcription factor, monomeric protein-DNA complex; HET: DNA; 2.70A {Rattus norvegicus} SCOP: g.39.1.2

Probab=99.96  E-value=1.4e-29  Score=192.40  Aligned_cols=85  Identities=53%  Similarity=0.995  Sum_probs=77.6

Q ss_pred             cccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCCcc
Q psy12688        129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHGVV  208 (222)
Q Consensus       129 ~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g~~  208 (222)
                      .|.||||.++|+||||.+|+||++||||++..+..|.|..+++|.|++..|+.|++|||+|||++||++++||.++....
T Consensus         2 ~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~~~~~~   81 (89)
T 1cit_A            2 RCAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTDSLKGR   81 (89)
T ss_dssp             CCSSSCCCCCEEETTEEECHHHHHHHHHHHHHTCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHTTCCGGGSCCGGGTTC
T ss_pred             CCeEeCCCCcceEeCccchhhhhhhceeeEEecceeeeccCCccccCCCCcccChhhhhHHHhHcCCCHHHeecccccCc
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999998765544


Q ss_pred             eecCC
Q psy12688        209 VIWSP  213 (222)
Q Consensus       209 ~~~~p  213 (222)
                      --..|
T Consensus        82 r~r~p   86 (89)
T 1cit_A           82 RGRLP   86 (89)
T ss_dssp             CSCCC
T ss_pred             cccCC
Confidence            33333

>1ynw_B Retinoic acid receptor RXR-alpha, retinoid X receptor; VDR, nuclear receptor, protein-DNA complex, transcripti complex; 3.00A {Homo sapiens} SCOP: g.39.1.2

Probab=99.95  E-value=2e-29  Score=194.95  Aligned_cols=82  Identities=50%  Similarity=1.079  Sum_probs=71.6

Q ss_pred             ccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCCc
Q psy12688        128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHGV  207 (222)
Q Consensus       128 ~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g~  207 (222)
                      .+|.||||+++|+||||.+|+||++||||++..+..|.|+.+++|.|++..|+.|++|||+|||++||++++|+.+|+..
T Consensus         4 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~~   83 (99)
T 1ynw_B            4 HICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRG   83 (99)
T ss_dssp             -CBTTTBSCCCBCCTTSCBCSHHHHHHHHHHHTTCCCCCSSSSCCCCCSTTSSSCHHHHHHHHHHTTCCSTTCC------
T ss_pred             CCCceeCCCCcceeeCccchHHHHHHHHhhhccccccccCCCCcccccccCCccCccccHHHHhHcCCCHHHhhhccccc
Confidence            56999999999999999999999999999999999999999999999999999999999999999999999999998865


Q ss_pred             ce
Q psy12688        208 VV  209 (222)
Q Consensus       208 ~~  209 (222)
                      ..
T Consensus        84 ~~   85 (99)
T 1ynw_B           84 KD   85 (99)
T ss_dssp             --
T ss_pred             cc
Confidence            43

>4hn5_A Glucocorticoid receptor; glucocorticoid receptor, steroid receptors, NGRE, repre transcription; HET: DNA; 1.90A {Homo sapiens} PDB: 4hn6_A*

Probab=99.95  E-value=2.5e-29  Score=199.65  Aligned_cols=87  Identities=46%  Similarity=0.938  Sum_probs=70.3

Q ss_pred             CccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688        127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG  206 (222)
Q Consensus       127 ~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g  206 (222)
                      .++|.||||+++|+||||.+|+||++||||++..+..|.|+.+++|.|++..|..|++|||+|||++||++++|+.+++-
T Consensus        29 ~~~C~VCgd~a~G~HyGv~sC~aCk~FFRRsv~~~~~y~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~avq~kR~~  108 (117)
T 4hn5_A           29 PKLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEARKTKKKI  108 (117)
T ss_dssp             -CBCTTTCSBCCEEETTEEECHHHHHHHHHHHSSCCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHHTCCTTC-------
T ss_pred             CCcCCcCCCcCcccccCCcccchhhhhhhcceecCCceecCCCCccccCcccccCCcccchHHHhHcCCCHHHhcccccc
Confidence            45699999999999999999999999999999999999999999999999999999999999999999999999999876


Q ss_pred             cceecCC
Q psy12688        207 VVVIWSP  213 (222)
Q Consensus       207 ~~~~~~p  213 (222)
                      ....-+|
T Consensus       109 k~~~~~~  115 (117)
T 4hn5_A          109 KGIQQAT  115 (117)
T ss_dssp             -------
T ss_pred             cccCCCC
Confidence            5544444

>3g9m_A Glucocorticoid receptor; glucocorticoid, DNA-binding, allostery, lever ARM, transcription, hormone; HET: DNA; 1.61A {Rattus norvegicus} SCOP: g.39.1.2 PDB: 3g6p_A* 3g6q_B* 3g6r_B* 3g6u_A* 3g8u_A* 3g8x_A* 3g97_B* 3g99_A* 3g9i_A* 3g9j_A* 3fyl_A* 3g9o_B* 3g9p_B* 3g6t_A* 1r4o_A 1r4r_A 1glu_A* 1gdc_A 2gda_A 1rgd_A ...

Probab=99.95  E-value=1.8e-29  Score=191.77  Aligned_cols=86  Identities=45%  Similarity=0.943  Sum_probs=74.9

Q ss_pred             ccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCCc
Q psy12688        128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHGV  207 (222)
Q Consensus       128 ~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g~  207 (222)
                      .+|.||||+++|+||||.+|+||++||||++..+..|.|..+++|.|++..|..|++|||+|||++||++++|+.+++..
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            57999999999999999999999999999999999999999999999999999999999999999999999999998766


Q ss_pred             ceecCC
Q psy12688        208 VVIWSP  213 (222)
Q Consensus       208 ~~~~~p  213 (222)
                      ....++
T Consensus        83 ~~~~~~   88 (90)
T 3g9m_A           83 GIQQAT   88 (90)
T ss_dssp             ------
T ss_pred             cccCCC
Confidence            554443

>1a6y_A Orphan nuclear receptor NR1D1; orphan receptor, DNA-binding, reverb, REV- ERB, transcription regulation, transcription/DNA complex; HET: DNA 5IU; 2.30A {Homo sapiens} SCOP: g.39.1.2 PDB: 1ga5_A* 1hlz_A

Probab=99.95  E-value=4.3e-29  Score=191.35  Aligned_cols=82  Identities=45%  Similarity=1.006  Sum_probs=74.2

Q ss_pred             CCccccccCCCCcceeeccccchhhhHHHHhHhhcCcee-ccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCC
Q psy12688        126 IEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVY-TCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQST  204 (222)
Q Consensus       126 ~~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~-~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r  204 (222)
                      ...+|.||||.++|+||||.+|+||++||||++..+..| .|..+++|.|++..|+.|++|||+|||++||++++||.+|
T Consensus         6 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R   85 (94)
T 1a6y_A            6 MVLLCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGR   85 (94)
T ss_dssp             --CBCTTTSSBCCEEETTEEECHHHHHHHHHHHSSCCCCCCCSSTTCCCCCTTTTTSCHHHHHHHHTTTTCCSTTCCCCC
T ss_pred             CCCcCcEeCCCCcceEeCccchhhhhhehheeeecccceEEccCCCCCccCccccccccchhHHHhhHccCCHHHhccCc
Confidence            446799999999999999999999999999999998888 5999999999999999999999999999999999999988


Q ss_pred             CCc
Q psy12688        205 HGV  207 (222)
Q Consensus       205 ~g~  207 (222)
                      +..
T Consensus        86 ~~~   88 (94)
T 1a6y_A           86 IPK   88 (94)
T ss_dssp             ---
T ss_pred             CcC
Confidence            654

>2a66_A Orphan nuclear receptor NR5A2; protein-DNA complex, zinc finger, DNA- binding domain, transcription factor, FTZ-F1, C-terminal extension; 2.20A {Homo sapiens} PDB: 2ff0_A

Probab=99.95  E-value=7.1e-29  Score=195.95  Aligned_cols=81  Identities=77%  Similarity=1.412  Sum_probs=76.5

Q ss_pred             CccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688        127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG  206 (222)
Q Consensus       127 ~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g  206 (222)
                      ..+|.||||.++|+||||.+|+||++||||++..+..|.|..+++|.|++..|..|++|||+|||++||++++|+.+|+.
T Consensus         9 ~~~C~VCgd~a~G~HyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~R~~Cr~CR~~KCl~vGM~~~~vq~~R~~   88 (113)
T 2a66_A            9 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMR   88 (113)
T ss_dssp             -CBCTTTCCBEEEEETTEEEEHHHHHHHHHHHHTTCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCTTCCC
T ss_pred             CCCCcEeCCCCcceeeCcccHHHHHHHHhhhhhccccccccccccCCcCCCccccccchhHHHHhHhCCCHHHhcccccc
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             c
Q psy12688        207 V  207 (222)
Q Consensus       207 ~  207 (222)
                      .
T Consensus        89 ~   89 (113)
T 2a66_A           89 G   89 (113)
T ss_dssp             S
T ss_pred             C
Confidence            3

>1lo1_A Steroid hormone receptor ERR2; estrogen related receptor 2, DNA binding domain, HERR2, hormone nuclear receptor; NMR {Homo sapiens} SCOP: g.39.1.2

Probab=99.95  E-value=2.8e-29  Score=193.76  Aligned_cols=82  Identities=49%  Similarity=0.915  Sum_probs=76.9

Q ss_pred             CccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688        127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG  206 (222)
Q Consensus       127 ~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g  206 (222)
                      ..+|.||||.++|+||||.+|+||++||||++..+..|.|..+++|.|++..|..|++|||+|||++||++++|+.+|+.
T Consensus         4 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~   83 (98)
T 1lo1_A            4 KRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKALKVGMLKEGVRLDRVR   83 (98)
T ss_dssp             CCEETTTTEECSEESSSSEECHHHHHHHHHHHHTTCCCCCSSCSCCCCCHHHHHHCHHHHHHHHHHHTCCGGGSCSSCCT
T ss_pred             CCCCcEeCCCCcCeeeCccchhhhhhhheeeecccCccccCccccccccccccccccchhHHHHhHcCCCHHHeeccccc
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999998865


Q ss_pred             cc
Q psy12688        207 VV  208 (222)
Q Consensus       207 ~~  208 (222)
                      ..
T Consensus        84 ~~   85 (98)
T 1lo1_A           84 GG   85 (98)
T ss_dssp             TC
T ss_pred             Cc
Confidence            43

>2han_B Ecdysone receptor; transcription regulation, transcription factor, DNA-binding, nuclear protein, nuclear receptor, zinc finger; 1.95A {Drosophila melanogaster} SCOP: g.39.1.2 PDB: 1r0o_B 1r0n_B

Probab=99.95  E-value=1.4e-28  Score=195.62  Aligned_cols=79  Identities=52%  Similarity=1.100  Sum_probs=74.9

Q ss_pred             CccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCC
Q psy12688        127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTH  205 (222)
Q Consensus       127 ~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~  205 (222)
                      ...|.||||.++|+||||.+|+||++||||++..+..|.|..+++|.|++..|+.|++|||+|||++||++++|+.+++
T Consensus         8 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~   86 (119)
T 2han_B            8 EELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECRLKKCLAVGMRPECVVPENQ   86 (119)
T ss_dssp             SCBCTTTCSBCCEEETTEEECHHHHHHHHHHHHTTCCCCCSSCSCCCCSTTGGGTCHHHHHHHHHHTTCCGGGSSCSSH
T ss_pred             CCcCeEeCCcCCcceECchhHHhhHHhhhhheEeccccccccccccccCccccccchhhHHHHHHHhCCCHHHccchhh
Confidence            4679999999999999999999999999999999999999999999999999999999999999999999999997654

>1kb2_A Vitamin D3 receptor; VDR, nuclear receptor, protein-DNA complex, transcription/DNA complex; 2.70A {Homo sapiens} SCOP: g.39.1.2 PDB: 1kb4_A 1kb6_A 1ynw_A

Probab=99.95  E-value=1.4e-28  Score=193.37  Aligned_cols=80  Identities=38%  Similarity=0.985  Sum_probs=74.8

Q ss_pred             CccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688        127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG  206 (222)
Q Consensus       127 ~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g  206 (222)
                      ...|.||||.++|+||||.+|+||++||||++..+..|.|..+++|.|++..|..|++|||+|||++||++++|+.+++.
T Consensus         6 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~   85 (110)
T 1kb2_A            6 PRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDEEV   85 (110)
T ss_dssp             -CBCTTTCSBCCSEETTEECCHHHHHHHHHHHHTTCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCHHHH
T ss_pred             CCCCcEeCCCCCceEeCchhHhhhhhhheeeeecccceeeCCCCCccCCcccceecccccHhhhhhcCCcHHhcccHHHH
Confidence            35699999999999999999999999999999999999999999999999999999999999999999999999876643

>2nll_B Protein (thyroid hormone receptor); complex (transcription regulation/DNA), DNA-binding, nuclear protein, zinc- finger, multigene family; HET: DNA 5IU; 1.90A {Homo sapiens} SCOP: g.39.1.2 PDB: 3m9e_A*

Probab=99.94  E-value=2.6e-28  Score=189.78  Aligned_cols=78  Identities=51%  Similarity=1.096  Sum_probs=73.6

Q ss_pred             ccccccCCCCcceeeccccchhhhHHHHhHhhcCc--eeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCC
Q psy12688        128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKK--VYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTH  205 (222)
Q Consensus       128 ~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~--~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~  205 (222)
                      ++|.||||.++|+||||.+|+||++||||++..+.  .|.|...++|.|++..|..|++|||+|||++||++++|+.++.
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  7999999999999999999999999999999999999998764

>1r4i_A Androgen receptor; AR, steroid receptor, protein-DNA complex, transcription/DNA complex; 3.10A {Rattus norvegicus} SCOP: g.39.1.2

Probab=99.94  E-value=4.2e-28  Score=189.29  Aligned_cols=80  Identities=49%  Similarity=1.021  Sum_probs=70.5

Q ss_pred             CccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688        127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG  206 (222)
Q Consensus       127 ~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g  206 (222)
                      ...|.||||.++|+||||.+|+||++||||++..+..|.|..+++|.|++..|+.|++|||+|||++||++++++..+.+
T Consensus         7 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~~k~~k~~   86 (105)
T 1r4i_A            7 QKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLGARKLKKLG   86 (105)
T ss_dssp             CCBCSSSCSBEEEEETTEEEEHHHHHHHHHHHTSCCCCCCSSSSCCCCCTTTTTTCHHHHHHHHHHHTCCSCC-------
T ss_pred             CCCCcEeCCCCCceEeCCcchhhhhhhhceeEEecCceeeccCCccccCccccccchhchHHHHHhhhcccchhhhcccc
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999876643

>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_A* 3e00_A*

Probab=99.92  E-value=3.6e-26  Score=215.66  Aligned_cols=82  Identities=50%  Similarity=1.100  Sum_probs=77.4

Q ss_pred             CCccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCC
Q psy12688        126 IEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTH  205 (222)
Q Consensus       126 ~~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~  205 (222)
                      ..+.|.||||+++|+||||.+|+|||+||||++.++..|.|+.+++|.+++..|++|++|||+||+++||++++||.+|+
T Consensus       136 ~~~~C~VCg~~a~g~hygv~sC~~Ck~FFrR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~  215 (467)
T 3dzy_A          136 TKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQ  215 (467)
T ss_dssp             -CEECTTTSSEECSEETTEECCHHHHHHHHHHHHTTCCCCCSSSSCCCCCSSSSSSCHHHHHHHHHHTTCCGGGCCCCSC
T ss_pred             CCCcceeCCCCCCCCcCCCcchhhhhHhccccccCCCceeCCCCCCCCCCcccccccccchhhhhhhccccchhhhcccc
Confidence            35679999999999999999999999999999999999999999999999999999999999999999999999999887


Q ss_pred             Cc
Q psy12688        206 GV  207 (222)
Q Consensus       206 g~  207 (222)
                      ..
T Consensus       216 ~~  217 (467)
T 3dzy_A          216 RG  217 (467)
T ss_dssp             CC
T ss_pred             cc
Confidence            54

>3dzy_D Peroxisome proliferator-activated receptor gamma; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_D* 3e00_D* 2env_A

Probab=99.91  E-value=2.4e-25  Score=207.10  Aligned_cols=82  Identities=46%  Similarity=1.010  Sum_probs=73.7

Q ss_pred             CCCccccccCCCCcceeeccccchhhhHHHHhHhhcCceec-cccCcccccCCCCCCCCcchHhHHHHHhcCCccccccC
Q psy12688        125 GIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYT-CVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQS  203 (222)
Q Consensus       125 ~~~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~-C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~  203 (222)
                      .....|.||||+++|+||||.+|+|||+||||++..+..|. |  .++|.+++..|+.|++|||+||+++||++++||.+
T Consensus        48 ~~~~~C~vC~~~~~g~hygv~~C~~C~~FFrR~~~~~~~~~~c--~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~vq~~  125 (419)
T 3dzy_D           48 LMAIECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLIYDRC--DLNCRIHKKSRNKCQYCRFQKCLAVGMSHNAIRFG  125 (419)
T ss_dssp             --CCCCSSSCSCCCSBCSSSBCCHHHHHHHHHHHTTTCCCCCC--CSCCCCCTTGGGTCHHHHHHHHHHTTCCGGGCCCS
T ss_pred             CCCCcCeECCCcCCCCccCcccchhhhHHHccchhcccccccc--cCCCCcccccCccchhhhHHHHhhcccchhheecc
Confidence            44567999999999999999999999999999999888885 6  46899999999999999999999999999999998


Q ss_pred             CCCcc
Q psy12688        204 THGVV  208 (222)
Q Consensus       204 r~g~~  208 (222)
                      |....
T Consensus       126 R~~~~  130 (419)
T 3dzy_D          126 RMPQA  130 (419)
T ss_dssp             CCTTT
T ss_pred             ccccc
Confidence            87643

>2lze_A A primordial catalytic fold generated by in vitro evolution; ligase, de novo protein; NMR {Synthetic construct}

Probab=99.67  E-value=7.1e-18  Score=127.58  Aligned_cols=62  Identities=23%  Similarity=0.386  Sum_probs=51.1

Q ss_pred             cceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccc
Q psy12688        138 SGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSS  201 (222)
Q Consensus       138 sg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr  201 (222)
                      .+.||+++ |.+|++||||++ .+..|.|+.+++|.|++..|+.|++|||+|||+|||....+.
T Consensus        15 ~g~h~c~v-Cgd~asfFRRt~-~~~~y~C~~~~~C~i~~~~R~~C~~CR~qKCl~VgM~~~~~~   76 (87)
T 2lze_A           15 GGKHICAI-CGNNAEDYKHTD-MDLTYTDRDYKNCESYHKCSDLCQYCRYQKDLAIHHQHHHGG   76 (87)
T ss_dssp             CCSSSCSS-SSSSSSSCTTTT-TSCTTTSCCCCCCCCSSCCSSSCSGGGTSCCHHHHCSSCCCC
T ss_pred             CCCEEccC-CCCccceECccc-CCCeeEcCCCCccccCCCccCcCCcccChhhccCcCEeccCc
Confidence            34455543 555788999985 567899999999999999999999999999999999887543

---

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	222
d1dszb_	84	g.39.1.2 (B:) Retinoid X receptor (RXR-alpha) DNA-	3e-30
d1kb2a_	89	g.39.1.2 (A:) Vitamin D3 receptor, VDR, DNA-bindin	6e-29
d2hanb1	83	g.39.1.2 (B:5-87) Ecdysone receptor DNA-binding do	6e-29
d1lo1a_	90	g.39.1.2 (A:) Steroid hormone receptor Err2 DNA-bi	1e-27
d1r4ia_	74	g.39.1.2 (A:) Androgen receptor {Rat (Rattus norve	2e-27
d1lata_	71	g.39.1.2 (A:) Glucocorticoid receptor DNA-binding	3e-27
d1a6ya_	78	g.39.1.2 (A:) Orphan nuclear receptor reverb DNA-b	1e-26
d1dsza_	75	g.39.1.2 (A:) Retinoic acid receptor DNA-binding d	3e-26
d1cita_	89	g.39.1.2 (A:) Orphan nuclear receptor NGFI-B DNA-b	1e-25
d1hcqa_	74	g.39.1.2 (A:) Estrogen receptor DNA-binding domain	2e-25
d2nllb_	103	g.39.1.2 (B:) Thyroid hormone receptor (TR-beta) D	3e-23

>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 =  105 bits (262), Expect = 3e-30
 Identities = 41/72 (56%), Positives = 52/72 (72%)

Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
           + +C +CGD+ SG HYG+ +CE CKGFFKRTV+    YTC   + C IDK QR RC +CR
Sbjct: 5   KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCR 64

Query: 187 FQKCLEVGMKLE 198
           +QKCL +GMK E
Sbjct: 65  YQKCLAMGMKRE 76

>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 =  102 bits (254), Expect = 6e-29
 Identities = 30/70 (42%), Positives = 48/70 (68%)

Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
           +C VCGD+ +G+H+  +TCE CKGFF+R+++ K ++TC     C I K  R+ C  CR +
Sbjct: 2   ICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLK 61

Query: 189 KCLEVGMKLE 198
           +C+++GM  E
Sbjct: 62  RCVDIGMMKE 71

>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 =  101 bits (254), Expect = 6e-29
 Identities = 40/71 (56%), Positives = 49/71 (69%)

Query: 128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRF 187
           ELC VCGD+ SGYHY  LTCE CKGFF+R+V    VY C   R+C +D   R++C  CR 
Sbjct: 1   ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECRL 60

Query: 188 QKCLEVGMKLE 198
           +KCL VGM+ E
Sbjct: 61  KKCLAVGMRPE 71

>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 = 98.5 bits (245), Expect = 1e-27
 Identities = 40/72 (55%), Positives = 48/72 (66%)

Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
           + LC VCGD  SGYHYG+ +CE+CK FFKRT+Q    Y+C A   C I K +RK C  CR
Sbjct: 4   KRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACR 63

Query: 187 FQKCLEVGMKLE 198
           F K L+VGM  E
Sbjct: 64  FMKALKVGMLKE 75

>d1r4ia_ g.39.1.2 (A:) Androgen receptor {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 74

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Androgen receptor
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 97.9 bits (243), Expect = 2e-27
 Identities = 38/72 (52%), Positives = 47/72 (65%)

Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
           ++ C +CGD+ SG HYG LTC SCK FFKR  + K+ Y C +   C IDK +RK CP CR
Sbjct: 2   QKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCR 61

Query: 187 FQKCLEVGMKLE 198
            +KC E GM L 
Sbjct: 62  LRKCYEAGMTLG 73

>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 = 97.1 bits (241), Expect = 3e-27
 Identities = 40/69 (57%), Positives = 48/69 (69%)

Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
           C VC D+ SG HYG+LTCE CK FFKR V+ +  Y C  E  C IDK +RK CP CR++K
Sbjct: 3   CLVCSDEASGCHYGVLTCEGCKAFFKRAVEGQHNYLCKYEGKCIIDKIRRKNCPACRYRK 62

Query: 190 CLEVGMKLE 198
           CL+ GM LE
Sbjct: 63  CLQAGMNLE 71

>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 = 95.8 bits (238), Expect = 1e-26
 Identities = 37/71 (52%), Positives = 47/71 (66%), Gaps = 1/71 (1%)

Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYT-CVAERSCHIDKTQRKRCPFCRF 187
           LC VCGD  SG+HYG+L CE CKGFF+R++Q    Y  C+   +C I +  R RC  CRF
Sbjct: 2   LCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRF 61

Query: 188 QKCLEVGMKLE 198
           +KCL VGM  +
Sbjct: 62  KKCLSVGMSRD 72

>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 = 94.7 bits (235), Expect = 3e-26
 Identities = 40/69 (57%), Positives = 49/69 (71%)

Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
           C VC DK SGYHYG+  CE CKGFF+R++Q   VYTC  +++C I+K  R RC +CR QK
Sbjct: 2   CFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQK 61

Query: 190 CLEVGMKLE 198
           C EVGM  E
Sbjct: 62  CFEVGMSKE 70

>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 = 93.6 bits (232), Expect = 1e-25
 Identities = 43/69 (62%), Positives = 48/69 (69%)

Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
           C VCGD  S  HYG+ TCE CKGFFKRTVQ    Y C+A + C +DK +R RC FCRFQK
Sbjct: 3   CAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQK 62

Query: 190 CLEVGMKLE 198
           CL VGM  E
Sbjct: 63  CLAVGMVKE 71

>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 = 92.5 bits (229), Expect = 2e-25
 Identities = 37/70 (52%), Positives = 43/70 (61%)

Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
              C VC D  SGYHYG+ +CE CK FFKR++Q    Y C A   C IDK +RK C  CR
Sbjct: 4   TRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACR 63

Query: 187 FQKCLEVGMK 196
            +KC EVGM 
Sbjct: 64  LRKCYEVGMM 73

>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 = 87.9 bits (217), Expect = 3e-23
 Identities = 38/75 (50%), Positives = 49/75 (65%), Gaps = 2/75 (2%)

Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCV--AERSCHIDKTQRKRCPF 184
           +ELC VCGDK +GYHY  +TCE CKGFF+RT+Q     +     E  C IDK  R +C  
Sbjct: 1   DELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQE 60

Query: 185 CRFQKCLEVGMKLEV 199
           CRF+KC+ VGM  ++
Sbjct: 61  CRFKKCIYVGMATDL 75

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	222
d1dszb_	84	Retinoid X receptor (RXR-alpha) DNA-binding domain	99.95
d2hanb1	83	Ecdysone receptor DNA-binding domain {Fruit fly (D	99.95
d1dsza_	75	Retinoic acid receptor DNA-binding domain {Human (	99.95
d1kb2a_	89	Vitamin D3 receptor, VDR, DNA-binding domain {Huma	99.95
d1r4ia_	74	Androgen receptor {Rat (Rattus norvegicus) [TaxId:	99.95
d1lo1a_	90	Steroid hormone receptor Err2 DNA-binding domain {	99.94
d1a6ya_	78	Orphan nuclear receptor reverb DNA-binding domain	99.94
d1cita_	89	Orphan nuclear receptor NGFI-B DNA-binding domain	99.94
d2nllb_	103	Thyroid hormone receptor (TR-beta) DNA-binding dom	99.94
d1lata_	71	Glucocorticoid receptor DNA-binding domain {Rat (R	99.94
d1hcqa_	74	Estrogen receptor DNA-binding domain {Human and ch	99.93

>d1dszb_ g.39.1.2 (B:) Retinoid X receptor (RXR-alpha) DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Retinoid X receptor (RXR-alpha) DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=1.5e-29  Score=188.75  Aligned_cols=79  Identities=52%  Similarity=1.162  Sum_probs=76.1

Q ss_pred             CccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCC
Q psy12688        127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTH  205 (222)
Q Consensus       127 ~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~  205 (222)
                      .++|.|||+.++|+||||.+|+||++||||++.....|.|...++|.+++..|..|++|||+|||++||++++|+.+|+
T Consensus         5 ~~~C~VC~~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~c~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~Rd   83 (84)
T d1dszb_           5 KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQ   83 (84)
T ss_dssp             CEECTTTCCEESSEETTEECCHHHHHHHHHHHHHTCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCCCC
T ss_pred             CCcCccCCCcCCccCCCHHHHHHhHHHHHHHHhcCCCeeccCCCCcccCCCCCccCCCCccHHHHHcCCChHHcccccC
Confidence            4679999999999999999999999999999999999999999999999999999999999999999999999999987

>d2hanb1 g.39.1.2 (B:5-87) Ecdysone receptor DNA-binding domain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Ecdysone receptor DNA-binding domain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.95  E-value=2.9e-29  Score=186.65  Aligned_cols=78  Identities=51%  Similarity=1.099  Sum_probs=75.0

Q ss_pred             ccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCC
Q psy12688        128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTH  205 (222)
Q Consensus       128 ~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~  205 (222)
                      ++|.|||++++|+||||.+|+||++||||++..+..|.|...++|.+++..|..|++|||+|||++||++++|+.+++
T Consensus         1 e~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~c~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~   78 (83)
T d2hanb1           1 ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECRLKKCLAVGMRPECVVPENQ   78 (83)
T ss_dssp             CBCTTTCSBCCEEETTEEECHHHHHHHHHHHHTTCCCCCSSCSCCCCSTTGGGTCHHHHHHHHHHTTCCGGGSSCSSH
T ss_pred             CcCccCCCcCCccCcCHHhHhHhHHHHHHHHhcCCceeecCCCCcccCCcccccCccchHHHHHHcCCCHHHccccch
Confidence            479999999999999999999999999999999999999999999999999999999999999999999999998875

>d1dsza_ g.39.1.2 (A:) Retinoic acid receptor DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Retinoic acid receptor DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=5.9e-29  Score=181.77  Aligned_cols=75  Identities=53%  Similarity=1.152  Sum_probs=72.6

Q ss_pred             cccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccC
Q psy12688        129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQS  203 (222)
Q Consensus       129 ~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~  203 (222)
                      +|.|||+.++|+||||.+|+||++||||++..+..|.|...++|.++...+..|++|||+|||++||++++||.|
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            599999999999999999999999999999999999999999999999999999999999999999999999975

>d1kb2a_ g.39.1.2 (A:) Vitamin D3 receptor, VDR, DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Vitamin D3 receptor, VDR, DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=6.4e-29  Score=186.99  Aligned_cols=78  Identities=38%  Similarity=1.027  Sum_probs=74.6

Q ss_pred             ccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCC
Q psy12688        128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTH  205 (222)
Q Consensus       128 ~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~  205 (222)
                      ++|.|||++++|+||||.+|+||++||||++..+..|.|..+++|.++...|..|++|||+|||++||++++|+.+++
T Consensus         1 r~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~c~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~   78 (89)
T d1kb2a_           1 RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDEE   78 (89)
T ss_dssp             CBCTTTCSBCCSEETTEECCHHHHHHHHHHHHTTCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCHHH
T ss_pred             CCCeeCCCcCCccCCCHHHHHHHHHHHHHHHhcCCCeecCCCCccCCCCcCCccCchhhHHHHHHcCCCHhhccccch
Confidence            479999999999999999999999999999999999999999999999999999999999999999999999998765

>d1r4ia_ g.39.1.2 (A:) Androgen receptor {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Androgen receptor
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.95  E-value=1.1e-28  Score=179.92  Aligned_cols=73  Identities=52%  Similarity=1.104  Sum_probs=69.9

Q ss_pred             CccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccc
Q psy12688        127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEV  199 (222)
Q Consensus       127 ~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~ea  199 (222)
                      .++|.|||+.++|+||||.+|+||++||||++..+..|.|..+++|.+++..|..|++|||+|||++||+.||
T Consensus         2 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~c~~~~~C~~~~~~r~~C~~CR~~KCl~vGM~~~A   74 (74)
T d1r4ia_           2 QKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLGA   74 (74)
T ss_dssp             CCBCSSSCSBEEEEETTEEEEHHHHHHHHHHHTSCCCCCCSSSSCCCCCTTTTTTCHHHHHHHHHHHTCCSCC
T ss_pred             CCcCccCCCcCCccCCCHHhhHHHHHHHHHHHhcccceeeecCCCcccCCCCcccchhhhHHHHHHcCCcCCC
Confidence            3579999999999999999999999999999999999999999999999999999999999999999999986

>d1lo1a_ g.39.1.2 (A:) Steroid hormone receptor Err2 DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Steroid hormone receptor Err2 DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.94  E-value=3.9e-29  Score=188.53  Aligned_cols=81  Identities=49%  Similarity=0.940  Sum_probs=77.1

Q ss_pred             CccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688        127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG  206 (222)
Q Consensus       127 ~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g  206 (222)
                      .++|.|||+.++++||||.+|++|++||||++..+..+.|..+++|.++...|..|++|||+|||++||++++||.+++.
T Consensus         4 ~~~C~VCg~~~~~~hyG~~sC~aC~~FFRR~v~~~~~~~c~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~r~~   83 (90)
T d1lo1a_           4 KRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKALKVGMLKEGVRLDRVR   83 (90)
T ss_dssp             CCEETTTTEECSEESSSSEECHHHHHHHHHHHHTTCCCCCSSCSCCCCCHHHHHHCHHHHHHHHHHHTCCGGGSCSSCCT
T ss_pred             CCcCCcCCCcCCceEcCeeechhhHHHHHHHHhcCCccchhcCCCCccCCCCccccchhhHHHHHHcCCCHHHhcccccc
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999999998875


Q ss_pred             c
Q psy12688        207 V  207 (222)
Q Consensus       207 ~  207 (222)
                      .
T Consensus        84 ~   84 (90)
T d1lo1a_          84 G   84 (90)
T ss_dssp             T
T ss_pred             c
Confidence            4

>d1a6ya_ g.39.1.2 (A:) Orphan nuclear receptor reverb DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Orphan nuclear receptor reverb DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.94  E-value=1.1e-28  Score=181.46  Aligned_cols=76  Identities=49%  Similarity=1.120  Sum_probs=71.5

Q ss_pred             cccccCCCCcceeeccccchhhhHHHHhHhhcCceec-cccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCC
Q psy12688        129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYT-CVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQST  204 (222)
Q Consensus       129 ~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~-C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r  204 (222)
                      +|.|||++++|+||||.+|+||++||||++..+..|. |..+++|.+++..+..|++|||+|||++||++++||.+|
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            6999999999999999999999999999999888886 566788999999999999999999999999999999876

>d1cita_ g.39.1.2 (A:) Orphan nuclear receptor NGFI-B DNA-binding domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Orphan nuclear receptor NGFI-B DNA-binding domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.94  E-value=4.9e-28  Score=182.05  Aligned_cols=85  Identities=53%  Similarity=0.995  Sum_probs=78.0

Q ss_pred             cccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCCcc
Q psy12688        129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHGVV  208 (222)
Q Consensus       129 ~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g~~  208 (222)
                      +|+|||+.++|+||||.+|+||++||||++.....|.|...++|.++...|..|++|||+|||++||++++|+.+++...
T Consensus         2 ~C~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~c~~~~~c~~~~~~r~~Cr~CR~~KCl~~GM~~~~v~~~~~~~~   81 (89)
T d1cita_           2 RCAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTDSLKGR   81 (89)
T ss_dssp             CCSSSCCCCCEEETTEEECHHHHHHHHHHHHHTCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHTTCCGGGSCCGGGTTC
T ss_pred             CCeECCCcCCccCCCcccchhhHHHHHHHHHcCCceeecCCCCccccCCccccCchhhHHHHHHcCCCHHHhcccccccc
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999998776554


Q ss_pred             eecCC
Q psy12688        209 VIWSP  213 (222)
Q Consensus       209 ~~~~p  213 (222)
                      ....|
T Consensus        82 r~~~p   86 (89)
T d1cita_          82 RGRLP   86 (89)
T ss_dssp             CSCCC
T ss_pred             cCCCC
Confidence            44444

>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=99.94  E-value=3.9e-28  Score=186.90  Aligned_cols=78  Identities=50%  Similarity=1.045  Sum_probs=71.7

Q ss_pred             ccccccCCCCcceeeccccchhhhHHHHhHhhcCcee--ccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCC
Q psy12688        128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVY--TCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTH  205 (222)
Q Consensus       128 ~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~--~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~  205 (222)
                      ++|.|||++++|+||||.+|+||++||||++.....+  .|...+.|.++...|..|++|||+|||+|||++++|+.+++
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            5799999999999999999999999999999887655  45778899999999999999999999999999999988765

>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=99.94  E-value=6.9e-28  Score=174.40  Aligned_cols=71  Identities=56%  Similarity=1.175  Sum_probs=68.4

Q ss_pred             ccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCcc
Q psy12688        128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLE  198 (222)
Q Consensus       128 ~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~e  198 (222)
                      ++|.|||+.++|+||||.+|+||++||||++..+..+.|...++|.++...|..|++|||+|||++||++|
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            46999999999999999999999999999999999999999999999999999999999999999999976

>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=99.93  E-value=4.1e-27  Score=171.58  Aligned_cols=71  Identities=52%  Similarity=1.120  Sum_probs=68.1

Q ss_pred             CccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCc
Q psy12688        127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKL  197 (222)
Q Consensus       127 ~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~  197 (222)
                      .++|.|||++++|+||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++
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            45799999999999999999999999999999999999999999999999999999999999999999974