Psyllid ID: psy16245

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110---
Protein Sequence
MELFVGNCRQIPPRYPQYFMSRPDGRDVTSASRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccEEEccccccEEEcEEccccccccccccEEcccEEEEcccccccccccccccccccccHHHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccccccccccEEccccccEcccEccccEccHHHHHHHHHHHHcccccccccccccccccEEcHHHccHcHHHHHHHHHHcccccc
Coil and Loop (DISEMBL)
melfvgncrqipprypqyfmsrpdgrdvtsasrdrlldipckvcgdrssgkhygiyscdgcsgffkrsihrnrvytckaqgdlkghcpidkthrnqcracrlNKCFMSAMNKD
Flexible Loop (DISEMBL)
melfvgncrqipprypqyfmsrpdgRDVTSasrdrlldipckvcgdrssgkhygiysCDGCSGFFKRSIHRNRVYTCKAqgdlkghcpidkthrnqcrACRLNKCFMSAMNKD
Low Complexity Region (SEG)
MELFVGNCRQIPPRYPQYFMSRPDGRDVTSASRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD
Disordered region (IsUnstruct)
****VGNCRQIPPRYPQYF***************RLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFM******
Disordered Region (DISOPRED)
****************************************CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMN**
Disordered Region (DISEMBL)
MELFVGNCRQIPPRYPQYFMSRPDGRDVTSASRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD
Disordered Region (DISPRO)
***********************************LLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSA****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MELFVGNCRQIPPRYPQYFMSRPDGRDVTSASRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	113	2.2.26 [Sep-21-2011]
Q9YGL3	396	Nuclear receptor subfamil	N/A	N/A	0.814	0.232	0.656	2e-34
Q9Y466	385	Nuclear receptor subfamil	yes	N/A	0.761	0.223	0.691	5e-34
Q64104	385	Nuclear receptor subfamil	yes	N/A	0.761	0.223	0.691	6e-34
Q91379	385	Nuclear receptor subfamil	yes	N/A	0.761	0.223	0.691	6e-34
P70052	386	Nuclear receptor subfamil	N/A	N/A	0.761	0.222	0.691	2e-33
O16845	450	Protein tailless OS=Droso	N/A	N/A	0.725	0.182	0.678	3e-29
P18102	452	Protein tailless OS=Droso	no	N/A	0.725	0.181	0.678	3e-29
Q9XVV3	416	Nuclear hormone receptor	yes	N/A	0.690	0.187	0.670	9e-26
Q9QXZ7	395	Photoreceptor-specific nu	no	N/A	0.637	0.182	0.613	7e-25
Q9TTF0	411	Photoreceptor-specific nu	no	N/A	0.637	0.175	0.613	8e-25

>sp|Q9YGL3|NR2E1_ORYLA Nuclear receptor subfamily 2 group E member 1 OS=Oryzias latipes GN=nr2e1 PE=2 SV=1

 Score =  144 bits (363), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 65/99 (65%), Positives = 75/99 (75%), Gaps = 7/99 (7%)

Query: 20  MSRPDGR-----DVTSASRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRV 74
           MS+P G      D+ +    R+LDIPCKVCGDRSSGKHYG+Y+CDGCSGFFKRSI RNR+
Sbjct: 1   MSKPTGSTSGCLDILNVKSSRILDIPCKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNRI 60

Query: 75  YTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113
           Y CK+    +G CP+DKTHRNQCRACRL KC    MNKD
Sbjct: 61  YLCKSGS--QGGCPVDKTHRNQCRACRLKKCLEVNMNKD 97

Orphan receptor that binds DNA as a monomer to hormone response elements (HRE) containing an extended core motif half-site sequence 5'-AAGGTCA-3' in which the 5' flanking nucleotides participate in determining receptor specificity (By similarity). May be involved in the regulation of early eye development.
Oryzias latipes (taxid: 8090)

>sp|Q9Y466|NR2E1_HUMAN Nuclear receptor subfamily 2 group E member 1 OS=Homo sapiens GN=NR2E1 PE=2 SV=1

 Score =  142 bits (359), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 65/94 (69%), Positives = 72/94 (76%), Gaps = 8/94 (8%)

Query: 20  MSRPDGRDVTSASRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKA 79
           MS+P G      S  R+LDIPCKVCGDRSSGKHYG+Y+CDGCSGFFKRSI RNR Y CK+
Sbjct: 1   MSKPAG------STSRILDIPCKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNRTYVCKS 54

Query: 80  QGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113
               +G CP+DKTHRNQCRACRL KC    MNKD
Sbjct: 55  GN--QGGCPVDKTHRNQCRACRLKKCLEVNMNKD 86

Orphan receptor that binds DNA as a monomer to hormone response elements (HRE) containing an extended core motif half-site sequence 5'-AAGGTCA-3' in which the 5' flanking nucleotides participate in determining receptor specificity (By similarity). May be required to pattern anterior brain differentiation. Involved in the regulation of retinal development and essential for vision. During retinogenesis, regulates PTEN-Cyclin D expression via binding to the promoter region of PTEN and suppressing its activity (By similarity). May be involved in retinoic acic receptor (RAR) regulation in retinal cells.

Homo sapiens (taxid: 9606)

>sp|Q64104|NR2E1_MOUSE Nuclear receptor subfamily 2 group E member 1 OS=Mus musculus GN=Nr2e1 PE=1 SV=1

 Score =  142 bits (358), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 65/94 (69%), Positives = 72/94 (76%), Gaps = 8/94 (8%)

Query: 20  MSRPDGRDVTSASRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKA 79
           MS+P G      S  R+LDIPCKVCGDRSSGKHYG+Y+CDGCSGFFKRSI RNR Y CK+
Sbjct: 1   MSKPAG------STSRILDIPCKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNRTYVCKS 54

Query: 80  QGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113
               +G CP+DKTHRNQCRACRL KC    MNKD
Sbjct: 55  GN--QGGCPVDKTHRNQCRACRLKKCLEVNMNKD 86

Orphan receptor that binds DNA as a monomer to hormone response elements (HRE) containing an extended core motif half-site sequence 5'-AAGGTCA-3' in which the 5' flanking nucleotides participate in determining receptor specificity (By similarity). Regulates cell cycle progression in neural stem cells of rhe developing brain. Involved in the regulation of retinal development and essential for vision. During retinogenesis, regulates PTEN-Cyclin D expression via binding to the promoter region of PTEN and suppressing its activity. May be involved in retinoic acid receptor (RAR) regulation in retinal cells.

Mus musculus (taxid: 10090)

>sp|Q91379|NR2E1_CHICK Nuclear receptor subfamily 2 group E member 1 OS=Gallus gallus GN=NR2E1 PE=2 SV=1

 Score =  142 bits (358), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 65/94 (69%), Positives = 72/94 (76%), Gaps = 8/94 (8%)

Query: 20  MSRPDGRDVTSASRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKA 79
           MS+P G      S  R+LDIPCKVCGDRSSGKHYG+Y+CDGCSGFFKRSI RNR Y CK+
Sbjct: 1   MSKPAG------STSRILDIPCKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNRTYVCKS 54

Query: 80  QGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113
               +G CP+DKTHRNQCRACRL KC    MNKD
Sbjct: 55  GN--QGGCPVDKTHRNQCRACRLKKCLEVNMNKD 86

Orphan receptor that binds DNA as a monomer to hormone response elements (HRE) containing an extended core motif half-site sequence 5'-AAGGTCA-3' in which the 5' flanking nucleotides participate in determining receptor specificity. May be required to pattern anterior brain differentiation (By similarity). Involved in the regulation of retinal development.

Gallus gallus (taxid: 9031)

>sp|P70052|NR2E1_XENLA Nuclear receptor subfamily 2 group E member 1 OS=Xenopus laevis GN=nr2e1 PE=2 SV=1

 Score =  140 bits (354), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 65/94 (69%), Positives = 71/94 (75%), Gaps = 8/94 (8%)

Query: 20  MSRPDGRDVTSASRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKA 79
           MS P G      S  R+LDIPCKVCGDRSSGKHYG+Y+CDGCSGFFKRSI RNR Y CK+
Sbjct: 1   MSNPTG------STSRILDIPCKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNRSYVCKS 54

Query: 80  QGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113
               +G CP+DKTHRNQCRACRL KC    MNKD
Sbjct: 55  GN--QGGCPVDKTHRNQCRACRLKKCLEVNMNKD 86

Orphan receptor that binds DNA as a monomer to hormone response elements (HRE) containing an extended core motif half-site sequence 5'-AAGTCA-3' in which the 5' flanking nucleotides participate in determining receptor specificity (By similarity). Involved in the regulation of early eye development.

Xenopus laevis (taxid: 8355)

>sp|O16845|TLL_DROVI Protein tailless OS=Drosophila virilis GN=tll PE=3 SV=1

 Score =  126 bits (317), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 57/84 (67%), Positives = 65/84 (77%), Gaps = 2/84 (2%)

Query: 30  SASRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPI 89
           +AS   L  +PCKVC D SSGKHYGIY+CDGC+GFFKRSI R+R Y CK+Q   +G C +
Sbjct: 23  AASSRILYHVPCKVCRDHSSGKHYGIYACDGCAGFFKRSIRRSRQYVCKSQK--QGLCVV 80

Query: 90  DKTHRNQCRACRLNKCFMSAMNKD 113
           DKTHRNQCRACRL KCF   MNKD
Sbjct: 81  DKTHRNQCRACRLRKCFEVGMNKD 104

Orphan receptor that binds DNA as a monomer to hormone response elements (HRE) containing an extended core motif half-site sequence 5'-AAGTCA-3' in which the 5' flanking nucleotides participate in determining receptor specificity. This receptor binds to the consensus sequence [AG][AG]AAGTCAA. Plays a key role in the establishment of non-metameric domains at the anterior and posterior poles of the embryo. It may also play a role in the nervous system. The maternal terminal pathway activates the tll gene in the termini; TLL activity then represses segmentation and activates terminal-specific genes in these domains. Involved in the regulation of early eye development. In the embryonic visual system anlage drives cells to optic lobe as opposed to Bolwig's organ fate.

Drosophila virilis (taxid: 7244)

>sp|P18102|TLL_DROME Protein tailless OS=Drosophila melanogaster GN=tll PE=2 SV=1

 Score =  126 bits (317), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 57/84 (67%), Positives = 65/84 (77%), Gaps = 2/84 (2%)

Query: 30  SASRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPI 89
           +AS   L  +PCKVC D SSGKHYGIY+CDGC+GFFKRSI R+R Y CK+Q   +G C +
Sbjct: 23  AASSRILYHVPCKVCRDHSSGKHYGIYACDGCAGFFKRSIRRSRQYVCKSQK--QGLCVV 80

Query: 90  DKTHRNQCRACRLNKCFMSAMNKD 113
           DKTHRNQCRACRL KCF   MNKD
Sbjct: 81  DKTHRNQCRACRLRKCFEVGMNKD 104

Orphan receptor that binds DNA as a monomer to hormone response elements (HRE) containing an extended core motif half-site sequence 5'-AAGTCA-3' in which the 5' flanking nucleotides participate in determining receptor specificity. This receptor binds to the consensus sequence [AG][AG]AAGTCAA. Plays a key role in the establishment of non-metameric domains at the anterior and posterior poles of the embryo. It may also play a role in the nervous system. The maternal terminal pathway activates the tll gene in the termini; TLL activity then represses segmentation and activates terminal-specific genes in these domains. Involved in the regulation of early eye development. In the embryonic visual system anlage drives cells to optic lobe as opposed to Bolwig's organ fate.

Drosophila melanogaster (taxid: 7227)

>sp|Q9XVV3|NHR67_CAEEL Nuclear hormone receptor family member nhr-67 OS=Caenorhabditis elegans GN=nhr-67 PE=1 SV=1

 Score =  115 bits (288), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 53/79 (67%), Positives = 61/79 (77%), Gaps = 1/79 (1%)

Query: 36  LLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGD-LKGHCPIDKTHR 94
           LLD+ C+VC D SSGKHY I+SCDGC+GFFKRSI R+R Y CK +G   +G C +DKTHR
Sbjct: 16  LLDVDCRVCEDHSSGKHYSIFSCDGCAGFFKRSIRRHRQYVCKNKGSPSEGQCKVDKTHR 75

Query: 95  NQCRACRLNKCFMSAMNKD 113
           NQCRACRL KC    MNKD
Sbjct: 76  NQCRACRLRKCLEIGMNKD 94

Orphan nuclear receptor.

Caenorhabditis elegans (taxid: 6239)

>sp|Q9QXZ7|NR2E3_MOUSE Photoreceptor-specific nuclear receptor OS=Mus musculus GN=Nr2e3 PE=1 SV=1

 Score =  112 bits (280), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 46/75 (61%), Positives = 57/75 (76%), Gaps = 3/75 (4%)

Query: 39  IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCR 98
           + C+VCGD SSGKHYGIY+C+GCSGFFKRS+ R  +Y C+      G CP+DK HRNQC+
Sbjct: 38  LQCRVCGDSSSGKHYGIYACNGCSGFFKRSVRRRLIYRCQVGA---GMCPVDKAHRNQCQ 94

Query: 99  ACRLNKCFMSAMNKD 113
           ACRL KC  + MN+D
Sbjct: 95  ACRLKKCLQAGMNQD 109

Orphan nuclear receptor of retinal photoreceptor cells. Transcriptional factor that is an activator of rod development and repressor of cone development. Binds the promoter region of a number of rod- and cone-specific genes, including rhodopsin, M-and S-opsin and rod-specific phosphodiesterase beta subunit. Enhances rhodopsin expression. Represses M- and S-cone opsin expression.

Mus musculus (taxid: 10090)

>sp|Q9TTF0|NR2E3_BOVIN Photoreceptor-specific nuclear receptor OS=Bos taurus GN=NR2E3 PE=1 SV=2

 Score =  112 bits (279), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 46/75 (61%), Positives = 57/75 (76%), Gaps = 3/75 (4%)

Query: 39  IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCR 98
           + C+VCGD SSGKHYGIY+C+GCSGFFKRS+ R  +Y C+      G CP+DK HRNQC+
Sbjct: 37  LQCRVCGDSSSGKHYGIYACNGCSGFFKRSVRRRLIYRCQVGA---GMCPVDKAHRNQCQ 93

Query: 99  ACRLNKCFMSAMNKD 113
           ACRL KC  + MN+D
Sbjct: 94  ACRLKKCLQAGMNQD 108

Orphan nuclear receptor of retinal photoreceptor cells. Transcriptional factor that is an activator of rod development and repressor of cone development. Binds the promoter region of a number of rod- and cone-specific genes, including rhodopsin, M-and S-opsin and rod-specific phosphodiesterase beta subunit. Enhances rhodopsin expression. Represses M- and S-cone opsin expression.

Bos taurus (taxid: 9913)

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	113
242024443	438	Orphan nuclear receptor NR6A1, putative	0.725	0.187	0.951	2e-43
195434755	730	GK14705 [Drosophila willistoni] gi|19416	0.707	0.109	0.925	8e-42
195146576	819	GL19043 [Drosophila persimilis] gi|19410	0.707	0.097	0.925	2e-41
195385346	726	GJ15408 [Drosophila virilis] gi|19414782	0.707	0.110	0.925	3e-41
194760978	702	GF15588 [Drosophila ananassae] gi|190616	0.707	0.113	0.925	3e-41
195473765	691	GE25723 [Drosophila yakuba] gi|194175264	0.707	0.115	0.925	3e-41
194856940	693	GG25103 [Drosophila erecta] gi|190660727	0.707	0.115	0.925	3e-41
225581113	690	GA21482 [Drosophila miranda]	0.707	0.115	0.925	5e-41
198475944	691	GA21482 [Drosophila pseudoobscura pseudo	0.707	0.115	0.925	5e-41
195116317	736	GI17531 [Drosophila mojavensis] gi|19391	0.707	0.108	0.925	5e-41

>gi|242024443|ref|XP_002432637.1| Orphan nuclear receptor NR6A1, putative [Pediculus humanus corporis] gi|212518107|gb|EEB19899.1| Orphan nuclear receptor NR6A1, putative [Pediculus humanus corporis]

 Score =  179 bits (454), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 78/82 (95%), Positives = 81/82 (98%)

Query: 32  SRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDK 91
           +RDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKG CPIDK
Sbjct: 4   NRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGRCPIDK 63

Query: 92  THRNQCRACRLNKCFMSAMNKD 113
           THRNQCRACRLNKCF++AMNKD
Sbjct: 64  THRNQCRACRLNKCFIAAMNKD 85

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195434755|ref|XP_002065368.1| GK14705 [Drosophila willistoni] gi|194161453|gb|EDW76354.1| GK14705 [Drosophila willistoni]

 Score =  174 bits (440), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 74/80 (92%), Positives = 76/80 (95%)

Query: 34  DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTH 93
           DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNR+YTCKA GDLKG CP+DKTH
Sbjct: 6   DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRIYTCKATGDLKGRCPVDKTH 65

Query: 94  RNQCRACRLNKCFMSAMNKD 113
           RNQCRACRL KCF SAMNKD
Sbjct: 66  RNQCRACRLAKCFQSAMNKD 85

Source: Drosophila willistoni

Species: Drosophila willistoni

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195146576|ref|XP_002014260.1| GL19043 [Drosophila persimilis] gi|194106213|gb|EDW28256.1| GL19043 [Drosophila persimilis]

 Score =  172 bits (437), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 74/80 (92%), Positives = 76/80 (95%)

Query: 34  DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTH 93
           DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNR+YTCKA GDLKG CP+DKTH
Sbjct: 134 DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRIYTCKATGDLKGRCPVDKTH 193

Query: 94  RNQCRACRLNKCFMSAMNKD 113
           RNQCRACRL KCF SAMNKD
Sbjct: 194 RNQCRACRLAKCFQSAMNKD 213

Source: Drosophila persimilis

Species: Drosophila persimilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195385346|ref|XP_002051367.1| GJ15408 [Drosophila virilis] gi|194147824|gb|EDW63522.1| GJ15408 [Drosophila virilis]

 Score =  172 bits (435), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 74/80 (92%), Positives = 76/80 (95%)

Query: 34  DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTH 93
           DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNR+YTCKA GDLKG CP+DKTH
Sbjct: 6   DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRIYTCKATGDLKGRCPVDKTH 65

Query: 94  RNQCRACRLNKCFMSAMNKD 113
           RNQCRACRL KCF SAMNKD
Sbjct: 66  RNQCRACRLAKCFQSAMNKD 85

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194760978|ref|XP_001962709.1| GF15588 [Drosophila ananassae] gi|190616406|gb|EDV31930.1| GF15588 [Drosophila ananassae]

 Score =  172 bits (435), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 74/80 (92%), Positives = 76/80 (95%)

Query: 34  DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTH 93
           DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNR+YTCKA GDLKG CP+DKTH
Sbjct: 6   DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRIYTCKATGDLKGRCPVDKTH 65

Query: 94  RNQCRACRLNKCFMSAMNKD 113
           RNQCRACRL KCF SAMNKD
Sbjct: 66  RNQCRACRLAKCFQSAMNKD 85

Source: Drosophila ananassae

Species: Drosophila ananassae

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195473765|ref|XP_002089163.1| GE25723 [Drosophila yakuba] gi|194175264|gb|EDW88875.1| GE25723 [Drosophila yakuba]

 Score =  172 bits (435), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 74/80 (92%), Positives = 76/80 (95%)

Query: 34  DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTH 93
           DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNR+YTCKA GDLKG CP+DKTH
Sbjct: 6   DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRIYTCKATGDLKGRCPVDKTH 65

Query: 94  RNQCRACRLNKCFMSAMNKD 113
           RNQCRACRL KCF SAMNKD
Sbjct: 66  RNQCRACRLAKCFQSAMNKD 85

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194856940|ref|XP_001968860.1| GG25103 [Drosophila erecta] gi|190660727|gb|EDV57919.1| GG25103 [Drosophila erecta]

 Score =  172 bits (435), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 74/80 (92%), Positives = 76/80 (95%)

Query: 34  DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTH 93
           DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNR+YTCKA GDLKG CP+DKTH
Sbjct: 6   DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRIYTCKATGDLKGRCPVDKTH 65

Query: 94  RNQCRACRLNKCFMSAMNKD 113
           RNQCRACRL KCF SAMNKD
Sbjct: 66  RNQCRACRLAKCFQSAMNKD 85

Source: Drosophila erecta

Species: Drosophila erecta

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|225581113|gb|ACN94685.1| GA21482 [Drosophila miranda]

 Score =  171 bits (433), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 74/80 (92%), Positives = 76/80 (95%)

Query: 34  DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTH 93
           DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNR+YTCKA GDLKG CP+DKTH
Sbjct: 6   DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRIYTCKATGDLKGRCPVDKTH 65

Query: 94  RNQCRACRLNKCFMSAMNKD 113
           RNQCRACRL KCF SAMNKD
Sbjct: 66  RNQCRACRLAKCFQSAMNKD 85

Source: Drosophila miranda

Species: Drosophila miranda

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|198475944|ref|XP_001357213.2| GA21482 [Drosophila pseudoobscura pseudoobscura] gi|198137475|gb|EAL34282.2| GA21482 [Drosophila pseudoobscura pseudoobscura]

 Score =  171 bits (433), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 74/80 (92%), Positives = 76/80 (95%)

Query: 34  DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTH 93
           DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNR+YTCKA GDLKG CP+DKTH
Sbjct: 6   DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRIYTCKATGDLKGRCPVDKTH 65

Query: 94  RNQCRACRLNKCFMSAMNKD 113
           RNQCRACRL KCF SAMNKD
Sbjct: 66  RNQCRACRLAKCFQSAMNKD 85

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195116317|ref|XP_002002702.1| GI17531 [Drosophila mojavensis] gi|193913277|gb|EDW12144.1| GI17531 [Drosophila mojavensis]

 Score =  171 bits (433), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 74/80 (92%), Positives = 76/80 (95%)

Query: 34  DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTH 93
           DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNR+YTCKA GDLKG CP+DKTH
Sbjct: 6   DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRIYTCKATGDLKGRCPVDKTH 65

Query: 94  RNQCRACRLNKCFMSAMNKD 113
           RNQCRACRL KCF SAMNKD
Sbjct: 66  RNQCRACRLAKCFQSAMNKD 85

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	113
FB|FBgn0015381	693	dsf "dissatisfaction" [Drosoph	0.707	0.115	0.925	5.1e-40
ZFIN|ZDB-GENE-040801-127	396	nr2e1 "nuclear receptor subfam	0.814	0.232	0.666	5.2e-33
UNIPROTKB|Q91379	385	NR2E1 "Nuclear receptor subfam	0.761	0.223	0.702	1.4e-32
UNIPROTKB|F1MN68	385	NR2E1 "Uncharacterized protein	0.761	0.223	0.702	1.4e-32
UNIPROTKB|F1PD89	385	NR2E1 "Uncharacterized protein	0.761	0.223	0.702	1.4e-32
UNIPROTKB|Q9Y466	385	NR2E1 "Nuclear receptor subfam	0.761	0.223	0.702	1.4e-32
UNIPROTKB|I3LU21	385	NR2E1 "Uncharacterized protein	0.761	0.223	0.702	1.4e-32
MGI|MGI:1100526	385	Nr2e1 "nuclear receptor subfam	0.761	0.223	0.702	1.4e-32
UNIPROTKB|Q6ZMP8	422	NR2E1 "Nuclear receptor subfam	0.681	0.182	0.772	6e-32
UNIPROTKB|F1RT26	421	NR2E1 "Uncharacterized protein	0.681	0.182	0.772	6e-32

FB|FBgn0015381 dsf "dissatisfaction" [Drosophila melanogaster (taxid:7227)]

 Score = 431 (156.8 bits), Expect = 5.1e-40, P = 5.1e-40
 Identities = 74/80 (92%), Positives = 76/80 (95%)

Query:    34 DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTH 93
             DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNR+YTCKA GDLKG CP+DKTH
Sbjct:     6 DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRIYTCKATGDLKGRCPVDKTH 65

Query:    94 RNQCRACRLNKCFMSAMNKD 113
             RNQCRACRL KCF SAMNKD
Sbjct:    66 RNQCRACRLAKCFQSAMNKD 85

GO:0005634 "nucleus" evidence=IEA;ISS

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

GO:0018993 "somatic sex determination" evidence=NAS

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

GO:0007530 "sex determination" evidence=TAS

GO:0007619 "courtship behavior" evidence=NAS;TAS

GO:0007617 "mating behavior" evidence=NAS

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

GO:0007620 "copulation" evidence=NAS

GO:0018991 "oviposition" evidence=NAS;TAS

GO:0045924 "regulation of female receptivity" evidence=NAS

GO:0008049 "male courtship behavior" evidence=TAS

GO:0001078 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription" evidence=IDA

GO:0048047 "mating behavior, sex discrimination" evidence=TAS

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

GO:0035206 "regulation of hemocyte proliferation" evidence=IMP

ZFIN|ZDB-GENE-040801-127 nr2e1 "nuclear receptor subfamily 2, group E, member 1" [Danio rerio (taxid:7955)]

 Score = 360 (131.8 bits), Expect = 5.2e-33, P = 5.2e-33
 Identities = 66/99 (66%), Positives = 75/99 (75%)

Query:    20 MSRPDGR-----DVTSASRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRV 74
             MS+P G      D+ +    R+LDIPCKVCGDRSSGKHYG+Y+CDGCSGFFKRSI RNR 
Sbjct:     1 MSKPAGSTSGCLDILNVKSSRILDIPCKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNRT 60

Query:    75 YTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113
             Y CK+ G  +G CP+DKTHRNQCRACRL KC    MNKD
Sbjct:    61 YVCKS-GT-QGGCPVDKTHRNQCRACRLKKCLEVNMNKD 97

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

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

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

GO:0005634 "nucleus" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0046872 "metal ion binding" evidence=IEA

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

UNIPROTKB|Q91379 NR2E1 "Nuclear receptor subfamily 2 group E member 1" [Gallus gallus (taxid:9031)]

 Score = 356 (130.4 bits), Expect = 1.4e-32, P = 1.4e-32
 Identities = 66/94 (70%), Positives = 74/94 (78%)

Query:    20 MSRPDGRDVTSASRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKA 79
             MS+P G      S  R+LDIPCKVCGDRSSGKHYG+Y+CDGCSGFFKRSI RNR Y CK+
Sbjct:     1 MSKPAG------STSRILDIPCKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNRTYVCKS 54

Query:    80 QGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113
              G+ +G CP+DKTHRNQCRACRL KC    MNKD
Sbjct:    55 -GN-QGGCPVDKTHRNQCRACRLKKCLEVNMNKD 86

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:0007275 "multicellular organismal development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|F1MN68 NR2E1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 356 (130.4 bits), Expect = 1.4e-32, P = 1.4e-32
 Identities = 66/94 (70%), Positives = 74/94 (78%)

Query:    20 MSRPDGRDVTSASRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKA 79
             MS+P G      S  R+LDIPCKVCGDRSSGKHYG+Y+CDGCSGFFKRSI RNR Y CK+
Sbjct:     1 MSKPAG------STSRILDIPCKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNRTYVCKS 54

Query:    80 QGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113
              G+ +G CP+DKTHRNQCRACRL KC    MNKD
Sbjct:    55 -GN-QGGCPVDKTHRNQCRACRLKKCLEVNMNKD 86

GO:2000648 "positive regulation of stem cell proliferation" evidence=IEA

GO:2000179 "positive regulation of neural precursor cell proliferation" evidence=IEA

GO:2000178 "negative regulation of neural precursor cell proliferation" evidence=IEA

GO:0090049 "regulation of cell migration involved in sprouting angiogenesis" evidence=IEA

GO:0060291 "long-term synaptic potentiation" evidence=IEA

GO:0060164 "regulation of timing of neuron differentiation" evidence=IEA

GO:0060041 "retina development in camera-type eye" evidence=IEA

GO:0048814 "regulation of dendrite morphogenesis" evidence=IEA

GO:0048712 "negative regulation of astrocyte differentiation" evidence=IEA

GO:0045787 "positive regulation of cell cycle" evidence=IEA

GO:0045766 "positive regulation of angiogenesis" evidence=IEA

GO:0045665 "negative regulation of neuron differentiation" evidence=IEA

GO:0045165 "cell fate commitment" evidence=IEA

GO:0043066 "negative regulation of apoptotic process" evidence=IEA

GO:0042826 "histone deacetylase binding" evidence=IEA

GO:0035176 "social behavior" evidence=IEA

GO:0035019 "somatic stem cell maintenance" evidence=IEA

GO:0030198 "extracellular matrix organization" evidence=IEA

GO:0021960 "anterior commissure morphogenesis" evidence=IEA

GO:0021895 "cerebral cortex neuron differentiation" evidence=IEA

GO:0021872 "forebrain generation of neurons" evidence=IEA

GO:0021819 "layer formation in cerebral cortex" evidence=IEA

GO:0021772 "olfactory bulb development" evidence=IEA

GO:0021764 "amygdala development" evidence=IEA

GO:0021542 "dentate gyrus development" evidence=IEA

GO:0008347 "glial cell migration" evidence=IEA

GO:0007601 "visual perception" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0002118 "aggressive behavior" evidence=IEA

GO:0001662 "behavioral fear response" evidence=IEA

GO:0001078 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription" evidence=IEA

GO:0001077 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" 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|F1PD89 NR2E1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 356 (130.4 bits), Expect = 1.4e-32, P = 1.4e-32
 Identities = 66/94 (70%), Positives = 74/94 (78%)

Query:    20 MSRPDGRDVTSASRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKA 79
             MS+P G      S  R+LDIPCKVCGDRSSGKHYG+Y+CDGCSGFFKRSI RNR Y CK+
Sbjct:     1 MSKPAG------STSRILDIPCKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNRTYVCKS 54

Query:    80 QGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113
              G+ +G CP+DKTHRNQCRACRL KC    MNKD
Sbjct:    55 -GN-QGGCPVDKTHRNQCRACRLKKCLEVNMNKD 86

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|Q9Y466 NR2E1 "Nuclear receptor subfamily 2 group E member 1" [Homo sapiens (taxid:9606)]

 Score = 356 (130.4 bits), Expect = 1.4e-32, P = 1.4e-32
 Identities = 66/94 (70%), Positives = 74/94 (78%)

Query:    20 MSRPDGRDVTSASRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKA 79
             MS+P G      S  R+LDIPCKVCGDRSSGKHYG+Y+CDGCSGFFKRSI RNR Y CK+
Sbjct:     1 MSKPAG------STSRILDIPCKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNRTYVCKS 54

Query:    80 QGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113
              G+ +G CP+DKTHRNQCRACRL KC    MNKD
Sbjct:    55 -GN-QGGCPVDKTHRNQCRACRLKKCLEVNMNKD 86

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

GO:0001078 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription" evidence=IEA

GO:0001662 "behavioral fear response" evidence=IEA

GO:0002118 "aggressive behavior" evidence=IEA

GO:0007601 "visual perception" evidence=IEA

GO:0008347 "glial cell migration" evidence=IEA

GO:0021542 "dentate gyrus development" evidence=IEA

GO:0021764 "amygdala development" evidence=IEA

GO:0021772 "olfactory bulb development" evidence=IEA

GO:0021819 "layer formation in cerebral cortex" evidence=IEA

GO:0021872 "forebrain generation of neurons" evidence=IEA

GO:0021895 "cerebral cortex neuron differentiation" evidence=IEA

GO:0021960 "anterior commissure morphogenesis" evidence=IEA

GO:0030198 "extracellular matrix organization" evidence=IEA

GO:0035019 "somatic stem cell maintenance" evidence=IEA

GO:0035176 "social behavior" evidence=IEA

GO:0042826 "histone deacetylase binding" evidence=IEA

GO:0043066 "negative regulation of apoptotic process" evidence=IEA

GO:0045165 "cell fate commitment" evidence=IEA

GO:0045665 "negative regulation of neuron differentiation" evidence=IEA

GO:0045766 "positive regulation of angiogenesis" evidence=IEA

GO:0045787 "positive regulation of cell cycle" evidence=IEA

GO:0048712 "negative regulation of astrocyte differentiation" evidence=IEA

GO:0048814 "regulation of dendrite morphogenesis" evidence=IEA

GO:0060041 "retina development in camera-type eye" evidence=IEA

GO:0060164 "regulation of timing of neuron differentiation" evidence=IEA

GO:0060291 "long-term synaptic potentiation" evidence=IEA

GO:0090049 "regulation of cell migration involved in sprouting angiogenesis" evidence=IEA

GO:2000178 "negative regulation of neural precursor cell proliferation" evidence=IEA

GO:2000179 "positive regulation of neural precursor cell proliferation" evidence=IEA

GO:2000648 "positive regulation of stem cell proliferation" evidence=IEA

GO:0007399 "nervous system development" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

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

GO:0010467 "gene expression" evidence=TAS

UNIPROTKB|I3LU21 NR2E1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 356 (130.4 bits), Expect = 1.4e-32, P = 1.4e-32
 Identities = 66/94 (70%), Positives = 74/94 (78%)

Query:    20 MSRPDGRDVTSASRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKA 79
             MS+P G      S  R+LDIPCKVCGDRSSGKHYG+Y+CDGCSGFFKRSI RNR Y CK+
Sbjct:     1 MSKPAG------STSRILDIPCKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNRTYVCKS 54

Query:    80 QGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113
              G+ +G CP+DKTHRNQCRACRL KC    MNKD
Sbjct:    55 -GN-QGGCPVDKTHRNQCRACRLKKCLEVNMNKD 86

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

GO:0005634 "nucleus" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

MGI|MGI:1100526 Nr2e1 "nuclear receptor subfamily 2, group E, member 1" [Mus musculus (taxid:10090)]

 Score = 356 (130.4 bits), Expect = 1.4e-32, P = 1.4e-32
 Identities = 66/94 (70%), Positives = 74/94 (78%)

Query:    20 MSRPDGRDVTSASRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKA 79
             MS+P G      S  R+LDIPCKVCGDRSSGKHYG+Y+CDGCSGFFKRSI RNR Y CK+
Sbjct:     1 MSKPAG------STSRILDIPCKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNRTYVCKS 54

Query:    80 QGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113
              G+ +G CP+DKTHRNQCRACRL KC    MNKD
Sbjct:    55 -GN-QGGCPVDKTHRNQCRACRLKKCLEVNMNKD 86

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

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:0001078 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription" evidence=IDA;IMP

GO:0001662 "behavioral fear response" evidence=IMP

GO:0002118 "aggressive behavior" evidence=IMP

GO:0003677 "DNA binding" evidence=IDA

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0007420 "brain development" evidence=IMP

GO:0007601 "visual perception" evidence=IMP

GO:0007610 "behavior" evidence=IMP

GO:0008270 "zinc ion binding" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=IMP

GO:0008347 "glial cell migration" evidence=IMP

GO:0019899 "enzyme binding" evidence=IPI

GO:0021542 "dentate gyrus development" evidence=IMP

GO:0021764 "amygdala development" evidence=IMP

GO:0021772 "olfactory bulb development" evidence=IMP

GO:0021819 "layer formation in cerebral cortex" evidence=IMP

GO:0021872 "forebrain generation of neurons" evidence=IMP

GO:0021895 "cerebral cortex neuron differentiation" evidence=IMP

GO:0021960 "anterior commissure morphogenesis" evidence=IMP

GO:0021987 "cerebral cortex development" evidence=IMP

GO:0030198 "extracellular matrix organization" evidence=IMP

GO:0035019 "somatic stem cell maintenance" evidence=IMP

GO:0035176 "social behavior" evidence=IMP

GO:0042826 "histone deacetylase binding" evidence=IPI

GO:0043010 "camera-type eye development" evidence=IMP

GO:0043066 "negative regulation of apoptotic process" evidence=IMP

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

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

GO:0045165 "cell fate commitment" evidence=IGI

GO:0045665 "negative regulation of neuron differentiation" evidence=IMP

GO:0045766 "positive regulation of angiogenesis" evidence=IMP

GO:0045787 "positive regulation of cell cycle" evidence=IMP

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

GO:0046872 "metal ion binding" evidence=IEA

GO:0048712 "negative regulation of astrocyte differentiation" evidence=IMP

GO:0048814 "regulation of dendrite morphogenesis" evidence=IMP

GO:0051128 "regulation of cellular component organization" evidence=IMP

GO:0060041 "retina development in camera-type eye" evidence=IMP

GO:0060164 "regulation of timing of neuron differentiation" evidence=IMP

GO:0060291 "long-term synaptic potentiation" evidence=IMP

GO:0090049 "regulation of cell migration involved in sprouting angiogenesis" evidence=IMP

GO:2000178 "negative regulation of neural precursor cell proliferation" evidence=IMP

GO:2000179 "positive regulation of neural precursor cell proliferation" evidence=IMP

GO:2000648 "positive regulation of stem cell proliferation" evidence=IMP

UNIPROTKB|Q6ZMP8 NR2E1 "Nuclear receptor subfamily 2, group E, member 1, isoform CRA_b" [Homo sapiens (taxid:9606)]

 Score = 350 (128.3 bits), Expect = 6.0e-32, P = 6.0e-32
 Identities = 61/79 (77%), Positives = 68/79 (86%)

Query:    35 RLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHR 94
             R+LDIPCKVCGDRSSGKHYG+Y+CDGCSGFFKRSI RNR Y CK+ G+ +G CP+DKTHR
Sbjct:    47 RILDIPCKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNRTYVCKS-GN-QGGCPVDKTHR 104

Query:    95 NQCRACRLNKCFMSAMNKD 113
             NQCRACRL KC    MNKD
Sbjct:   105 NQCRACRLKKCLEVNMNKD 123

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|F1RT26 NR2E1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 350 (128.3 bits), Expect = 6.0e-32, P = 6.0e-32
 Identities = 61/79 (77%), Positives = 68/79 (86%)

Query:    35 RLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHR 94
             R+LDIPCKVCGDRSSGKHYG+Y+CDGCSGFFKRSI RNR Y CK+ G+ +G CP+DKTHR
Sbjct:    46 RILDIPCKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNRTYVCKS-GN-QGGCPVDKTHR 103

Query:    95 NQCRACRLNKCFMSAMNKD 113
             NQCRACRL KC    MNKD
Sbjct:   104 NQCRACRLKKCLEVNMNKD 122

GO:2000648 "positive regulation of stem cell proliferation" evidence=IEA

GO:2000179 "positive regulation of neural precursor cell proliferation" evidence=IEA

GO:2000178 "negative regulation of neural precursor cell proliferation" evidence=IEA

GO:0090049 "regulation of cell migration involved in sprouting angiogenesis" evidence=IEA

GO:0060291 "long-term synaptic potentiation" evidence=IEA

GO:0060164 "regulation of timing of neuron differentiation" evidence=IEA

GO:0060041 "retina development in camera-type eye" evidence=IEA

GO:0048814 "regulation of dendrite morphogenesis" evidence=IEA

GO:0048712 "negative regulation of astrocyte differentiation" evidence=IEA

GO:0045787 "positive regulation of cell cycle" evidence=IEA

GO:0045766 "positive regulation of angiogenesis" evidence=IEA

GO:0045665 "negative regulation of neuron differentiation" evidence=IEA

GO:0045165 "cell fate commitment" evidence=IEA

GO:0043066 "negative regulation of apoptotic process" evidence=IEA

GO:0042826 "histone deacetylase binding" evidence=IEA

GO:0035176 "social behavior" evidence=IEA

GO:0035019 "somatic stem cell maintenance" evidence=IEA

GO:0030198 "extracellular matrix organization" evidence=IEA

GO:0021960 "anterior commissure morphogenesis" evidence=IEA

GO:0021895 "cerebral cortex neuron differentiation" evidence=IEA

GO:0021872 "forebrain generation of neurons" evidence=IEA

GO:0021819 "layer formation in cerebral cortex" evidence=IEA

GO:0021772 "olfactory bulb development" evidence=IEA

GO:0021764 "amygdala development" evidence=IEA

GO:0021542 "dentate gyrus development" evidence=IEA

GO:0008347 "glial cell migration" evidence=IEA

GO:0007601 "visual perception" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0002118 "aggressive behavior" evidence=IEA

GO:0001662 "behavioral fear response" evidence=IEA

GO:0001078 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription" evidence=IEA

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q91379	NR2E1_CHICK	No assigned EC number	0.6914	0.7610	0.2233	yes	N/A
Q64104	NR2E1_MOUSE	No assigned EC number	0.6914	0.7610	0.2233	yes	N/A
Q9XVV3	NHR67_CAEEL	No assigned EC number	0.6708	0.6902	0.1875	yes	N/A
Q9Y466	NR2E1_HUMAN	No assigned EC number	0.6914	0.7610	0.2233	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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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	113
cd07163	92	cd07163, NR_DBD_TLX, DNA-binding domain of Tailles	2e-44
cd07154	73	cd07154, NR_DBD_PNR_like, The DNA-binding domain o	8e-32
cd06916	72	cd06916, NR_DBD_like, DNA-binding domain of nuclea	3e-31
pfam00105	70	pfam00105, zf-C4, Zinc finger, C4 type (two domain	3e-30
cd06970	92	cd06970, NR_DBD_PNR, DNA-binding domain of the pho	1e-29
cd07164	78	cd07164, NR_DBD_PNR_like_1, DNA-binding domain of	1e-28
cd06960	76	cd06960, NR_DBD_HNF4A, DNA-binding domain of hepto	8e-28
cd06957	82	cd06957, NR_DBD_PNR_like_2, DNA-binding domain of	3e-25
cd06958	73	cd06958, NR_DBD_COUP_TF, DNA-binding domain of chi	5e-24
cd06967	87	cd06967, NR_DBD_TR2_like, DNA-binding domain of th	7e-24
cd06968	95	cd06968, NR_DBD_ROR, DNA-binding domain of Retinoi	2e-23
cd06961	85	cd06961, NR_DBD_TR, DNA-binding domain of thyroid	6e-23
smart00399	70	smart00399, ZnF_C4, c4 zinc finger in nuclear horm	1e-22
cd06956	77	cd06956, NR_DBD_RXR, DNA-binding domain of retinoi	3e-21
cd06964	85	cd06964, NR_DBD_RAR, DNA-binding domain of retinoi	4e-21
cd06969	75	cd06969, NR_DBD_NGFI-B, DNA-binding domain of the	6e-21
cd07166	89	cd07166, NR_DBD_REV_ERB, DNA-binding domain of REV	3e-20
cd07167	93	cd07167, NR_DBD_Lrh-1_like, The DNA-binding domain	1e-19
cd07168	90	cd07168, NR_DBD_DHR4_like, DNA-binding domain of e	2e-19
cd07165	81	cd07165, NR_DBD_DmE78_like, DNA-binding domain of	2e-19
cd07155	75	cd07155, NR_DBD_ER_like, DNA-binding domain of est	1e-18
cd07171	82	cd07171, NR_DBD_ER, DNA-binding domain of estrogen	2e-18
cd07169	90	cd07169, NR_DBD_GCNF_like, DNA-binding domain of G	2e-18
cd07156	72	cd07156, NR_DBD_VDR_like, The DNA-binding domain o	3e-18
cd07158	73	cd07158, NR_DBD_Ppar_like, The DNA-binding domain	7e-18
cd06959	73	cd06959, NR_DBD_EcR_like, The DNA-binding domain o	1e-17
cd07179	74	cd07179, 2DBD_NR_DBD2, The second DNA-binding doma	3e-17
cd07160	101	cd07160, NR_DBD_LXR, DNA-binding domain of Liver X	3e-17
cd06965	84	cd06965, NR_DBD_Ppar, DNA-binding domain of peroxi	3e-16
cd06962	84	cd06962, NR_DBD_FXR, DNA-binding domain of Farneso	4e-16
cd07161	91	cd07161, NR_DBD_EcR, DNA-binding domain of Ecdyson	4e-16
cd07162	87	cd07162, NR_DBD_PXR, DNA-binding domain of pregnan	6e-16
cd07170	97	cd07170, NR_DBD_ERR, DNA-binding domain of estroge	8e-16
cd06955	107	cd06955, NR_DBD_VDR, DNA-binding domain of vitamin	1e-15
cd07173	82	cd07173, NR_DBD_AR, DNA-binding domain of androgen	3e-14
cd07172	78	cd07172, NR_DBD_GR_PR, DNA-binding domain of gluco	5e-14
cd06963	73	cd06963, NR_DBD_GR_like, The DNA binding domain of	3e-13
cd06966	94	cd06966, NR_DBD_CAR, DNA-binding domain of constit	6e-12
cd07157	86	cd07157, 2DBD_NR_DBD1, The first DNA-binding domai	5e-11

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

 Score =  139 bits (352), Expect = 2e-44
 Identities = 63/80 (78%), Positives = 69/80 (86%), Gaps = 2/80 (2%)

Query: 34  DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTH 93
            R+LDIPCKVCGDRSSGKHYGIY+CDGCSGFFKRSI RNR Y CK++G  +G CP+DKTH
Sbjct: 2   SRILDIPCKVCGDRSSGKHYGIYACDGCSGFFKRSIRRNRQYVCKSKG--QGGCPVDKTH 59

Query: 94  RNQCRACRLNKCFMSAMNKD 113
           RNQCRACRL KCF   MNKD
Sbjct: 60  RNQCRACRLKKCFEVGMNKD 79

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

 Score =  106 bits (266), Expect = 8e-32
 Identities = 52/73 (71%), Positives = 58/73 (79%), Gaps = 3/73 (4%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           CKVCGDRSSGKHYG+Y+CDGCSGFFKRSI RN +YTCKA     G C +DK  RNQC+AC
Sbjct: 1   CKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNLLYTCKAG---NGSCVVDKARRNQCQAC 57

Query: 101 RLNKCFMSAMNKD 113
           RL KC   +MNKD
Sbjct: 58  RLKKCLEVSMNKD 70

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

 Score =  104 bits (263), Expect = 3e-31
 Identities = 40/73 (54%), Positives = 52/73 (71%), Gaps = 4/73 (5%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C VCGD++SG HYG+ +C+GC GFF+RS+ RN  YTC A G+    C IDK +RN+C+AC
Sbjct: 1   CAVCGDKASGYHYGVLTCEGCKGFFRRSVRRNLEYTCPAGGN----CVIDKRNRNRCQAC 56

Query: 101 RLNKCFMSAMNKD 113
           RL KC    M K+
Sbjct: 57  RLKKCLAVGMRKE 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 =  102 bits (256), Expect = 3e-30
 Identities = 40/74 (54%), Positives = 51/74 (68%), Gaps = 4/74 (5%)

Query: 39  IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCR 98
             CKVCGD++SG HYG+ +C+GC GFF+RSI +N VYTC    D    C IDK +RN+C+
Sbjct: 1   ELCKVCGDKASGYHYGVLTCEGCKGFFRRSIQKNIVYTCPFNKD----CVIDKRNRNRCQ 56

Query: 99  ACRLNKCFMSAMNK 112
            CRL KC    M+K
Sbjct: 57  YCRLKKCLEVGMSK 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|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 =  101 bits (253), Expect = 1e-29
 Identities = 48/73 (65%), Positives = 57/73 (78%), Gaps = 3/73 (4%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C+VCGD SSGKHYGIY+C+GCSGFFKRS+ R  +Y C+A     G CP+DK HRNQC+AC
Sbjct: 9   CRVCGDTSSGKHYGIYACNGCSGFFKRSVRRKLIYRCQAG---TGMCPVDKAHRNQCQAC 65

Query: 101 RLNKCFMSAMNKD 113
           RL KC  + MNKD
Sbjct: 66  RLKKCLQAGMNKD 78

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|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 = 98.7 bits (246), Expect = 1e-28
 Identities = 44/73 (60%), Positives = 50/73 (68%), Gaps = 4/73 (5%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C+VCGDR+SGKHYG+ SCDGC GFFKRSI RN  Y CK  G     C +D   RNQC+AC
Sbjct: 1   CRVCGDRASGKHYGVPSCDGCRGFFKRSIRRNLAYVCKENGS----CVVDVARRNQCQAC 56

Query: 101 RLNKCFMSAMNKD 113
           R  KC    MN+D
Sbjct: 57  RFKKCLQVNMNRD 69

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

 Score = 96.5 bits (241), Expect = 8e-28
 Identities = 38/73 (52%), Positives = 50/73 (68%), Gaps = 4/73 (5%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C VCGDR++GKHYG+ SC+GC GFF+RS+ +NR YTC+  G+    C +DK  RN CR C
Sbjct: 1   CAVCGDRATGKHYGVLSCNGCKGFFRRSVRKNRTYTCRFGGN----CVVDKDKRNACRYC 56

Query: 101 RLNKCFMSAMNKD 113
           R  KC    M+ +
Sbjct: 57  RFKKCLEVGMDPE 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|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 = 90.2 bits (224), Expect = 3e-25
 Identities = 42/72 (58%), Positives = 50/72 (69%), Gaps = 3/72 (4%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           CKVCGD+S GKHYG+Y CDGCS FFKRS+ +  +YTC A     G+C +DK  RN C  C
Sbjct: 1   CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKGIIYTCIA---GNGNCVVDKARRNWCPFC 57

Query: 101 RLNKCFMSAMNK 112
           RL KCF   MN+
Sbjct: 58  RLQKCFAVGMNR 69

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|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 = 86.8 bits (215), Expect = 5e-24
 Identities = 40/73 (54%), Positives = 51/73 (69%), Gaps = 4/73 (5%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C VCGD+SSGKHYG ++C+GC  FFKRS+ RN  YTC+   +    CPID+ HRNQC+ C
Sbjct: 1   CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRGNRN----CPIDQHHRNQCQYC 56

Query: 101 RLNKCFMSAMNKD 113
           RL KC    M ++
Sbjct: 57  RLKKCLKVGMRRE 69

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|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 = 87.1 bits (216), Expect = 7e-24
 Identities = 39/73 (53%), Positives = 49/73 (67%), Gaps = 4/73 (5%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C VCGD++SG+HYG  SC+GC GFFKRSI +N  Y+C+   D    C I+K HRN+C+ C
Sbjct: 6   CVVCGDKASGRHYGAVSCEGCKGFFKRSIRKNLGYSCRGSKD----CVINKHHRNRCQYC 61

Query: 101 RLNKCFMSAMNKD 113
           RL KC    M  D
Sbjct: 62  RLQKCLAMGMKSD 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|143526 cd06968, NR_DBD_ROR, DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers

 Score = 86.0 bits (213), Expect = 2e-23
 Identities = 39/75 (52%), Positives = 53/75 (70%), Gaps = 4/75 (5%)

Query: 39  IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCR 98
           IPCK+CGD+SSG HYG+ +C+GC GFF+RS   N  Y+C  Q +    C ID+T+RN+C+
Sbjct: 6   IPCKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVSYSCPRQKN----CLIDRTNRNRCQ 61

Query: 99  ACRLNKCFMSAMNKD 113
            CRL KC    M++D
Sbjct: 62  HCRLQKCLALGMSRD 76

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

 Score = 84.4 bits (209), Expect = 6e-23
 Identities = 35/74 (47%), Positives = 47/74 (63%), Gaps = 4/74 (5%)

Query: 40  PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRA 99
           PC VCGD+++G HY   +C+GC GFF+R++ +   Y+CK +    G C IDK  RNQC+ 
Sbjct: 1   PCVVCGDKATGYHYRCITCEGCKGFFRRTVQKKLSYSCKGE----GKCEIDKVTRNQCQE 56

Query: 100 CRLNKCFMSAMNKD 113
           CR  KC    M KD
Sbjct: 57  CRFKKCIAVGMAKD 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|197701 smart00399, ZnF_C4, c4 zinc finger in nuclear hormone receptors

 Score = 83.3 bits (207), Expect = 1e-22
 Identities = 31/74 (41%), Positives = 44/74 (59%), Gaps = 4/74 (5%)

Query: 40  PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRA 99
            C VCGD +SG H+G+ SC  C  FF+R+++    Y C      K +C I+K +R +CRA
Sbjct: 1   LCCVCGDHASGFHFGVCSCRACKAFFRRTVNLRYKYRCDR----KNNCSINKRYRCRCRA 56

Query: 100 CRLNKCFMSAMNKD 113
           CRL KC    M+ +
Sbjct: 57  CRLKKCLGVGMDPE 70

Length = 70

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

 Score = 79.9 bits (197), Expect = 3e-21
 Identities = 37/73 (50%), Positives = 50/73 (68%), Gaps = 4/73 (5%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C +CGDR+SGKHYG+YSC+GC GFFKR++ ++  YTC+   D    C IDK  RN+C+ C
Sbjct: 3   CAICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKD----CLIDKRQRNRCQYC 58

Query: 101 RLNKCFMSAMNKD 113
           R  KC    M ++
Sbjct: 59  RYQKCLAMGMKRE 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|143522 cd06964, NR_DBD_RAR, DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers

 Score = 79.6 bits (196), Expect = 4e-21
 Identities = 39/74 (52%), Positives = 51/74 (68%), Gaps = 4/74 (5%)

Query: 40  PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRA 99
           PC VC D+SSG HYG+ +C+GC GFF+RSI +N VYTC    +    C I+K  RN+C+ 
Sbjct: 6   PCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKN----CIINKVTRNRCQY 61

Query: 100 CRLNKCFMSAMNKD 113
           CRL KCF   M+K+
Sbjct: 62  CRLQKCFEVGMSKE 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|143527 cd06969, NR_DBD_NGFI-B, DNA-binding domain of the orphan nuclear receptor, nerve growth factor-induced-B

 Score = 79.0 bits (195), Expect = 6e-21
 Identities = 33/74 (44%), Positives = 47/74 (63%), Gaps = 4/74 (5%)

Query: 40  PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRA 99
            C VCGD ++ +HYG+ +C+GC GFFKR++ +N  Y C A      +CP+DK  RN+C+ 
Sbjct: 2   LCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLA----NKNCPVDKRRRNRCQY 57

Query: 100 CRLNKCFMSAMNKD 113
           CR  KC    M K+
Sbjct: 58  CRFQKCLQVGMVKE 71

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

 Score = 78.0 bits (192), Expect = 3e-20
 Identities = 32/78 (41%), Positives = 50/78 (64%), Gaps = 3/78 (3%)

Query: 36  LLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRN 95
            + + CKVCGD++SG HYG+++C+GC GFF+RSI +   Y    + +    C I + +RN
Sbjct: 1   GMVVLCKVCGDKASGFHYGVHACEGCKGFFRRSIQQKIQYRKCTKNE---TCSIMRINRN 57

Query: 96  QCRACRLNKCFMSAMNKD 113
           +C+ CR  KC    M++D
Sbjct: 58  RCQYCRFKKCLAVGMSRD 75

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|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 = 76.3 bits (188), Expect = 1e-19
 Identities = 32/70 (45%), Positives = 41/70 (58%), Gaps = 4/70 (5%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C VCGD+ SG HYG+ +C+ C GFFKR++   + YTC    +    C IDKT R +C  C
Sbjct: 1   CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKRYTCIENQN----CQIDKTQRKRCPYC 56

Query: 101 RLNKCFMSAM 110
           R  KC    M
Sbjct: 57  RFQKCLSVGM 66

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|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 = 75.7 bits (186), Expect = 2e-19
 Identities = 33/70 (47%), Positives = 43/70 (61%), Gaps = 4/70 (5%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C +C D+++G HYGI +C+GC GFFKR++   RVYTC       G C I K  RN+C+ C
Sbjct: 9   CSICEDKATGLHYGIITCEGCKGFFKRTVQNKRVYTCVGD----GRCEITKAQRNRCQYC 64

Query: 101 RLNKCFMSAM 110
           R  KC    M
Sbjct: 65  RFRKCIRKGM 74

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|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 = 75.3 bits (185), Expect = 2e-19
 Identities = 36/73 (49%), Positives = 48/73 (65%), Gaps = 4/73 (5%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           CKVCGD++SG HYG+ SC+GC GFF+RSI +   Y C   G     C I + +RN+C+ C
Sbjct: 1   CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYRCLRDGK----CEIIRLNRNRCQYC 56

Query: 101 RLNKCFMSAMNKD 113
           R  KC  + M+KD
Sbjct: 57  RFKKCLAAGMSKD 69

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|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 = 72.9 bits (179), Expect = 1e-18
 Identities = 34/73 (46%), Positives = 44/73 (60%), Gaps = 4/73 (5%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C VCGD +SG HYG+ SC+ C  FFKR+I  N  Y+C +  +    C +DK  R  C+AC
Sbjct: 1   CLVCGDIASGYHYGVASCEACKAFFKRTIQGNLGYSCPSTSE----CEVDKKRRKSCQAC 56

Query: 101 RLNKCFMSAMNKD 113
           RL KC    M K+
Sbjct: 57  RLQKCLKVGMLKE 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|143545 cd07171, NR_DBD_ER, DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers

 Score = 72.6 bits (178), Expect = 2e-18
 Identities = 36/73 (49%), Positives = 43/73 (58%), Gaps = 4/73 (5%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C VC D +SG HYG++SC+GC  FFKRSI  +  Y C A       C IDK  R  C+AC
Sbjct: 6   CAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPA----TNQCTIDKNRRKSCQAC 61

Query: 101 RLNKCFMSAMNKD 113
           RL KC+   M K 
Sbjct: 62  RLRKCYEVGMMKG 74

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|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 = 73.0 bits (179), Expect = 2e-18
 Identities = 36/72 (50%), Positives = 46/72 (63%), Gaps = 4/72 (5%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C +CGDR++G HYGI SC+GC GFFKRSI   RVY C    +    C + +  RN+C+ C
Sbjct: 9   CLICGDRATGLHYGIISCEGCKGFFKRSICNKRVYRCSRDKN----CVMSRKQRNRCQYC 64

Query: 101 RLNKCFMSAMNK 112
           RL KC    MN+
Sbjct: 65  RLLKCLQMGMNR 76

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

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

 Score = 72.0 bits (177), Expect = 3e-18
 Identities = 34/73 (46%), Positives = 45/73 (61%), Gaps = 4/73 (5%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C VCGDR++G H+   +C+GC GFF+RS+ R   +TC   GD    C I K +R  C+AC
Sbjct: 1   CGVCGDRATGYHFNAMTCEGCKGFFRRSMKRKARFTCPFNGD----CEITKDNRRHCQAC 56

Query: 101 RLNKCFMSAMNKD 113
           RL KC    M K+
Sbjct: 57  RLKKCLDIGMKKE 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|143533 cd07158, NR_DBD_Ppar_like, The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family

 Score = 71.4 bits (175), Expect = 7e-18
 Identities = 33/73 (45%), Positives = 48/73 (65%), Gaps = 3/73 (4%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           CKVCGD++SG HYG++SC+GC GFF+R+I  N  Y    +    G C I + +RN+C+ C
Sbjct: 1   CKVCGDKASGFHYGVHSCEGCKGFFRRTIQHNLTYR---RCLNGGKCVIQRKNRNRCQYC 57

Query: 101 RLNKCFMSAMNKD 113
           R  KC    M+++
Sbjct: 58  RFKKCLSVGMSRN 70

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|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 = 70.6 bits (173), Expect = 1e-17
 Identities = 34/73 (46%), Positives = 45/73 (61%), Gaps = 4/73 (5%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C VCGD++SG HYG+ SC+GC GFF+RS+ +  VY CK        C +D   R +C+ C
Sbjct: 2   CVVCGDKASGFHYGVLSCEGCKGFFRRSVTKGAVYACK----FGNKCEMDMYMRRKCQEC 57

Query: 101 RLNKCFMSAMNKD 113
           RL KC  + M  D
Sbjct: 58  RLRKCKAAGMRPD 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|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 = 69.8 bits (171), Expect = 3e-17
 Identities = 28/72 (38%), Positives = 41/72 (56%), Gaps = 4/72 (5%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C+VCG +SSG H+G  +C+GC GFF+R+   +  Y C    +    C I    RN C++C
Sbjct: 1   CRVCGGKSSGFHFGALTCEGCKGFFRRTELSSNSYVCPGGQN----CAITPATRNACKSC 56

Query: 101 RLNKCFMSAMNK 112
           R  +C    M+K
Sbjct: 57  RFRRCLAVGMSK 68

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

 Score = 70.3 bits (172), Expect = 3e-17
 Identities = 32/70 (45%), Positives = 43/70 (61%), Gaps = 4/70 (5%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C VCGD++SG HY + SC+GC GFF+RS+ +   Y CK      G C +D   R +C+ C
Sbjct: 21  CSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAQYVCKNG----GKCQMDMYMRRKCQEC 76

Query: 101 RLNKCFMSAM 110
           RL KC  + M
Sbjct: 77  RLRKCREAGM 86

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

 Score = 67.5 bits (165), Expect = 3e-16
 Identities = 32/75 (42%), Positives = 45/75 (60%), Gaps = 7/75 (9%)

Query: 40  PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVY-TCKAQGDLKGHCPIDKTHRNQCR 98
            C+VCGD++SG HYG+++C+GC GFF+R+I    VY  C         C I K  RN+C+
Sbjct: 1   ECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLVYKPC------DLSCKIHKKSRNKCQ 54

Query: 99  ACRLNKCFMSAMNKD 113
            CR  KC    M+ +
Sbjct: 55  YCRFQKCLNVGMSHN 69

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

 Score = 67.3 bits (164), Expect = 4e-16
 Identities = 33/65 (50%), Positives = 43/65 (66%), Gaps = 4/65 (6%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C VCGD++SG HY   +C+GC GFF+RSI +N VY CK      G+C +D   R +C+ C
Sbjct: 4   CVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVYKCKN----GGNCEMDMYMRRKCQEC 59

Query: 101 RLNKC 105
           RL KC
Sbjct: 60  RLRKC 64

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

 Score = 67.2 bits (164), Expect = 4e-16
 Identities = 32/70 (45%), Positives = 42/70 (60%), Gaps = 4/70 (5%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C VCGDR+SG HY   +C+GC GFF+RS+ ++ VY CK        C +D   R +C+ C
Sbjct: 4   CLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYHCK----YGRACEMDMYMRRKCQEC 59

Query: 101 RLNKCFMSAM 110
           RL KC    M
Sbjct: 60  RLKKCLSVGM 69

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

 Score = 66.5 bits (162), Expect = 6e-16
 Identities = 33/73 (45%), Positives = 46/73 (63%), Gaps = 4/73 (5%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C+VCGDR++G H+   +C+GC GFF+R++ RN    C  Q      C I K++R QC+AC
Sbjct: 2   CRVCGDRATGYHFNAMTCEGCKGFFRRAMKRNARLCCPFQKG----CVITKSNRRQCQAC 57

Query: 101 RLNKCFMSAMNKD 113
           RL KC    M K+
Sbjct: 58  RLRKCLSIGMKKE 70

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

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

 Score = 66.8 bits (163), Expect = 8e-16
 Identities = 34/73 (46%), Positives = 42/73 (57%), Gaps = 4/73 (5%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C VCGD +SG HYG+ SC+ C  FFKR+I  N  Y+C A  +    C I K  R  C+AC
Sbjct: 7   CLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNE----CEITKRRRKSCQAC 62

Query: 101 RLNKCFMSAMNKD 113
           R  KC    M K+
Sbjct: 63  RFMKCLKVGMLKE 75

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

 Score = 66.5 bits (162), Expect = 1e-15
 Identities = 33/73 (45%), Positives = 46/73 (63%), Gaps = 4/73 (5%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C VCGDR++G H+   +C+GC GFF+RS+ R  ++TC   GD    C I K +R  C+AC
Sbjct: 9   CGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGD----CRITKDNRRHCQAC 64

Query: 101 RLNKCFMSAMNKD 113
           RL +C    M K+
Sbjct: 65  RLKRCVDIGMMKE 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|143547 cd07173, NR_DBD_AR, DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers

 Score = 62.2 bits (151), Expect = 3e-14
 Identities = 31/71 (43%), Positives = 40/71 (56%), Gaps = 4/71 (5%)

Query: 40  PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRA 99
            C +CGD +SG HYG  +C  C  FFKR+    + Y C ++ D    C IDK  R  C +
Sbjct: 5   TCLICGDEASGCHYGALTCGSCKVFFKRAAEGKQKYLCASRND----CTIDKFRRKNCPS 60

Query: 100 CRLNKCFMSAM 110
           CRL KCF + M
Sbjct: 61  CRLRKCFEAGM 71

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

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

 Score = 61.4 bits (149), Expect = 5e-14
 Identities = 32/72 (44%), Positives = 39/72 (54%), Gaps = 4/72 (5%)

Query: 40  PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRA 99
            C VC D +SG HYG+ +C  C  FFKR++     Y C  + D    C IDK  R  C A
Sbjct: 4   ICLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRND----CIIDKIRRKNCPA 59

Query: 100 CRLNKCFMSAMN 111
           CRL KC  + MN
Sbjct: 60  CRLRKCLQAGMN 71

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

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

 Score = 59.6 bits (144), Expect = 3e-13
 Identities = 31/71 (43%), Positives = 39/71 (54%), Gaps = 4/71 (5%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C +CGD +SG HYG+ +C  C  FFKR+      Y C  + D    C IDK  R  C AC
Sbjct: 1   CLICGDEASGCHYGVLTCGSCKVFFKRAAEGQHNYLCAGRND----CIIDKIRRKNCPAC 56

Query: 101 RLNKCFMSAMN 111
           RL KC+ + M 
Sbjct: 57  RLRKCYQAGMT 67

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

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

 Score = 56.7 bits (137), Expect = 6e-12
 Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 4/73 (5%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C VCGD++ G ++   +C+ C  FF+R+  +N+ + C         C I+   R  C+ C
Sbjct: 3   CGVCGDKALGYNFNAITCESCKAFFRRNALKNKEFKCP----FNESCEINVVTRRFCQKC 58

Query: 101 RLNKCFMSAMNKD 113
           RL+KCF   M K+
Sbjct: 59  RLDKCFAIGMKKE 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|143532 cd07157, 2DBD_NR_DBD1, The first DNA-binding domain (DBD) of the 2DBD nuclear receptors is composed of two C4-type zinc fingers

 Score = 54.0 bits (130), Expect = 5e-11
 Identities = 28/75 (37%), Positives = 39/75 (52%), Gaps = 6/75 (8%)

Query: 40  PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRV--YTCKAQGDLKGHCPIDKTHRNQC 97
            C+VCG+ ++G H+G Y C+ C  FF RS +        C       G C IDK +R +C
Sbjct: 2   TCQVCGEPAAGFHHGAYVCEACKKFFMRSSNAISFTISECP----NGGKCIIDKKNRTKC 57

Query: 98  RACRLNKCFMSAMNK 112
           +ACR  KC    M+ 
Sbjct: 58  QACRYRKCLNVGMSL 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	113
KOG4215|consensus	432		99.95
cd06959	73	NR_DBD_EcR_like The DNA-binding domain of Ecdysone	99.94
cd06956	77	NR_DBD_RXR DNA-binding domain of retinoid X recept	99.94
cd07172	78	NR_DBD_GR_PR DNA-binding domain of glucocorticoid	99.94
cd07173	82	NR_DBD_AR DNA-binding domain of androgen receptor	99.94
cd07156	72	NR_DBD_VDR_like The DNA-binding domain of vitamin	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
cd07170	97	NR_DBD_ERR DNA-binding domain of estrogen related	99.94
cd06963	73	NR_DBD_GR_like The DNA binding domain of GR_like n	99.94
cd07179	74	2DBD_NR_DBD2 The second DNA-binding domain (DBD) o	99.94
cd07161	91	NR_DBD_EcR DNA-binding domain of Ecdysone receptor	99.94
cd07155	75	NR_DBD_ER_like DNA-binding domain of estrogen rece	99.94
cd06969	75	NR_DBD_NGFI-B DNA-binding domain of the orphan nuc	99.94
cd06961	85	NR_DBD_TR DNA-binding domain of thyroid hormone re	99.94
cd07158	73	NR_DBD_Ppar_like The DNA-binding domain of peroxis	99.94
cd06958	73	NR_DBD_COUP_TF DNA-binding domain of chicken ovalb	99.94
cd06962	84	NR_DBD_FXR DNA-binding domain of Farnesoid X recep	99.94
cd07163	92	NR_DBD_TLX DNA-binding domain of Tailless (TLX) is	99.94
smart00399	70	ZnF_C4 c4 zinc finger in nuclear hormone receptors	99.93
cd07168	90	NR_DBD_DHR4_like DNA-binding domain of ecdysone-in	99.93
cd06964	85	NR_DBD_RAR DNA-binding domain of retinoic acid rec	99.93
cd06955	107	NR_DBD_VDR DNA-binding domain of vitamin D recepto	99.93
PF00105	70	zf-C4: Zinc finger, C4 type (two domains); InterPr	99.93
cd07162	87	NR_DBD_PXR DNA-binding domain of pregnane X recept	99.93
cd07154	73	NR_DBD_PNR_like The DNA-binding domain of the phot	99.93
cd06967	87	NR_DBD_TR2_like DNA-binding domain of the TR2 and	99.93
cd07169	90	NR_DBD_GCNF_like DNA-binding domain of Germ cell n	99.93
cd07164	78	NR_DBD_PNR_like_1 DNA-binding domain of the photor	99.93
cd06916	72	NR_DBD_like DNA-binding domain of nuclear receptor	99.93
cd06970	92	NR_DBD_PNR DNA-binding domain of the photoreceptor	99.93
KOG4846|consensus	538		99.93
cd06968	95	NR_DBD_ROR DNA-binding domain of Retinoid-related	99.93
KOG4217|consensus	605		99.93
cd07167	93	NR_DBD_Lrh-1_like The DNA-binding domain of Lrh-1	99.93
cd07157	86	2DBD_NR_DBD1 The first DNA-binding domain (DBD) of	99.93
cd06960	76	NR_DBD_HNF4A DNA-binding domain of heptocyte nucle	99.93
cd07165	81	NR_DBD_DmE78_like DNA-binding domain of Drosophila	99.93
cd06966	94	NR_DBD_CAR DNA-binding domain of constitutive andr	99.92
cd06957	82	NR_DBD_PNR_like_2 DNA-binding domain of the photor	99.92
cd07166	89	NR_DBD_REV_ERB DNA-binding domain of REV-ERB recep	99.92
cd06965	84	NR_DBD_Ppar DNA-binding domain of peroxisome proli	99.92
KOG4216|consensus	479		99.9
KOG4218|consensus	475		99.85

>KOG4215|consensus

Probab=99.95  E-value=1.5e-28  Score=193.02  Aligned_cols=73  Identities=48%  Similarity=1.153  Sum_probs=69.6

Q ss_pred             CCCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         37 LDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        37 ~~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      ....|.||||+++|.|||+.+|.+||+||||+|.++..|+|+.+.    +|.|+++.|+.||||||+||+.+||++|
T Consensus        18 ~~~~CaICGDkaTGKHYGA~SCdGCKGFFRRSVrk~~~YtCRF~k----~C~VDKdkRNaCRyCRfqKC~~aGMK~e   90 (432)
T KOG4215|consen   18 VAEFCAICGDKATGKHYGAISCDGCKGFFRRSVRKNHQYTCRFNK----QCVVDKDKRNACRYCRFQKCVRAGMKRE   90 (432)
T ss_pred             ccchhheeCCcccccccceeecCcchHHHHHHHHhcceeeeeccc----cccccchhhhhhhHhhHHHHHHhcccHH
Confidence            357899999999999999999999999999999999999999974    7999999999999999999999999986

>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=99.94  E-value=5.3e-28  Score=152.99  Aligned_cols=70  Identities=49%  Similarity=1.126  Sum_probs=65.6

Q ss_pred             CceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         40 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        40 ~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      +|.|||++++++||||.+|++|++||||++..+..|.|..++    +|.|+...|..|++|||+|||++||+++
T Consensus         1 ~C~vCg~~~~~~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~   70 (73)
T cd06959           1 NCVVCGDKASGFHYGVLSCEGCKGFFRRSVTKGAVYACKFGN----KCEMDMYMRRKCQECRLRKCKAAGMRPD   70 (73)
T ss_pred             CCceeCCcCcceEECceeehhhHHHHHHhhcCCCCccCCCCC----cCCcCCcccccCccchhHHHHHhCCChh
Confidence            599999999999999999999999999999988889998764    7999999999999999999999999985

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

>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=7e-28  Score=153.87  Aligned_cols=70  Identities=51%  Similarity=1.256  Sum_probs=65.6

Q ss_pred             CceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         40 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        40 ~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      +|.|||++++++||||.+|++|++||||++..+..|.|..++    +|.|+...|..|++|||+|||++||+++
T Consensus         2 ~C~VC~~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~   71 (77)
T cd06956           2 ICAICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNK----DCLIDKRQRNRCQYCRYQKCLAMGMKRE   71 (77)
T ss_pred             CCcccCCcCcceEECceeehhHHHHHHHHhhCCCccccCCCC----ccccCCCccccCccchhHHHhHhCCCHH
Confidence            599999999999999999999999999999998889998764    7999999999999999999999999864

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

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

Probab=99.94  E-value=1.1e-27  Score=153.45  Aligned_cols=72  Identities=43%  Similarity=0.959  Sum_probs=66.6

Q ss_pred             CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      +.+|.|||++++++||||.+|++|++||||++..+..|.|..++    +|.|+...|..|++|||+|||++||+.+
T Consensus         2 ~~~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~   73 (78)
T cd07172           2 QKICLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRN----DCIIDKIRRKNCPACRLRKCLQAGMNLG   73 (78)
T ss_pred             CCCCeecCCcCcceEECceeehhhHHhHHHHeeCCCceeCCCCC----ccccCCcccccCccchhHHHHHhCCCcc
Confidence            45799999999999999999999999999999999889998754    7999999999999999999999999863

DNA-binding domains of glucocorticoid receptor (GR) and progesterone receptor (PR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinate a single zinc atom. The DBD from both receptors interact with the same hormone response element (HRE), which is an imperfect palindrome GGTACAnnnTGTTCT, upstream of target genes and modulates the rate of transcriptional initiation. GR is a transcriptional regulator that mediates the biological effects of glucocorticoids and PR regulates genes controlled by progesterone. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, p

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

Probab=99.94  E-value=1.4e-27  Score=154.22  Aligned_cols=71  Identities=42%  Similarity=0.984  Sum_probs=66.3

Q ss_pred             CCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         39 IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        39 ~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      .+|.|||++++++||||.+|++|++||||++..+..|.|..++    +|.|+...+..|++|||+|||++||+++
T Consensus         4 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CRl~KCl~vGM~~~   74 (82)
T cd07173           4 KTCLICGDEASGCHYGALTCGSCKVFFKRAAEGKQKYLCASRN----DCTIDKFRRKNCPSCRLRKCFEAGMTLG   74 (82)
T ss_pred             CCCeecCCcCcceEECcchhhhHHHHHHHHhcCCCceecCCCC----ccccCCCccCcCcchhhhhhhhcCCCcC
Confidence            5799999999999999999999999999999988889998764    7999999999999999999999999874

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

>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=99.94  E-value=6.6e-28  Score=152.19  Aligned_cols=69  Identities=48%  Similarity=1.150  Sum_probs=64.8

Q ss_pred             ceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         41 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        41 C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      |.|||++++++||||.+|++|++||||++..+..|.|..++    +|.++...|..|++|||+|||++||++|
T Consensus         1 C~VC~~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~   69 (72)
T cd07156           1 CGVCGDRATGYHFNAMTCEGCKGFFRRSMKRKARFTCPFNG----DCEITKDNRRHCQACRLKKCLDIGMKKE   69 (72)
T ss_pred             CCccCccCcccEECcceehhhhhhhchhccCcCccccCCCC----ccccCCcccccCccchhHHHHHhCCCHH
Confidence            78999999999999999999999999999988889998754    7999999999999999999999999975

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

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

Probab=99.94  E-value=1e-27  Score=154.80  Aligned_cols=71  Identities=51%  Similarity=1.087  Sum_probs=66.3

Q ss_pred             CCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         39 IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        39 ~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      .+|.|||++++++||||.+|++|++||||++..+..|.|..++    +|.|+...+..|++|||+|||++||+++
T Consensus         4 ~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~   74 (82)
T cd07171           4 HFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPATN----QCTIDKNRRKSCQACRLRKCYEVGMMKG   74 (82)
T ss_pred             CCCeecCCcCcceEECceeehhhHHhHHHHeeCCCceeCCCCC----ccccCCcccccCccchhHHHhHhcCCHH
Confidence            5799999999999999999999999999999998889998754    7999999999999999999999999874

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=1.6e-27  Score=159.34  Aligned_cols=72  Identities=44%  Similarity=1.059  Sum_probs=67.1

Q ss_pred             CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      ..+|.|||++++|+||||.+|++|++||||++.....|.|..++    +|.|+...|..|++|||+|||++||+++
T Consensus        18 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~   89 (101)
T cd07160          18 NEVCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAQYVCKNGG----KCQMDMYMRRKCQECRLRKCREAGMREQ   89 (101)
T ss_pred             CCCCeecCCcCcceEECcceehhhhhhhhhcccccCccccCCCC----ccccCCcccccCccchhHHHHHhCCCHH
Confidence            46799999999999999999999999999999988889998764    7999999999999999999999999874

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

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

Probab=99.94  E-value=1.1e-27  Score=159.13  Aligned_cols=72  Identities=47%  Similarity=0.996  Sum_probs=66.7

Q ss_pred             CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      ..+|.|||++++|+||||.+|+||++||||++.....|.|..++    .|.|+...|..|++|||+|||++||+++
T Consensus         4 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CRl~KCl~vGM~~~   75 (97)
T cd07170           4 KRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATN----ECEITKRRRKSCQACRFMKCLKVGMLKE   75 (97)
T ss_pred             CCCCeecCCcCcceEECceeehhhhHHHHHHhccCCceeecCCC----ccccCcccCccCCccccchhhhcCCCHH
Confidence            45799999999999999999999999999999998889998754    7999999999999999999999999864

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

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

Probab=99.94  E-value=1.4e-27  Score=151.17  Aligned_cols=69  Identities=43%  Similarity=1.028  Sum_probs=64.9

Q ss_pred             ceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         41 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        41 C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      |.|||++++++||||.+|++|++||||++..+..|.|..++    +|.|+...|..|++|||+|||++||+++
T Consensus         1 C~VCg~~a~~~hygv~sC~aCk~FFRR~~~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~   69 (73)
T cd06963           1 CLICGDEASGCHYGVLTCGSCKVFFKRAAEGQHNYLCAGRN----DCIIDKIRRKNCPACRLRKCYQAGMTLG   69 (73)
T ss_pred             CcccCccCcceEECceeehhhhHhHHHhhcCCCceeCCCCC----ccccCCcccccCccchhhHHHHcCCChh
Confidence            78999999999999999999999999999999889998764    7999999999999999999999999875

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

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

Probab=99.94  E-value=1.6e-27  Score=151.18  Aligned_cols=69  Identities=41%  Similarity=1.068  Sum_probs=65.0

Q ss_pred             ceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         41 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        41 C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      |.|||++++++||||.+|++|++||||++..+..|.|..++    +|.++...|..|++|||+|||++||++|
T Consensus         1 C~VCg~~~~g~hygv~sC~aC~~FFRR~~~~~~~~~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~   69 (74)
T cd07179           1 CRVCGGKSSGFHFGALTCEGCKGFFRRTELSSNSYVCPGGQ----NCAITPATRNACKSCRFRRCLAVGMSKT   69 (74)
T ss_pred             CcccCccCcceEECceeehhHHHHHHHHhhCCCcccCCCCC----ccccCCcccccCccchhHHHHHhCCCHh
Confidence            78999999999999999999999999999998889998764    6999999999999999999999999975

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.

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

Probab=99.94  E-value=2.1e-27  Score=156.05  Aligned_cols=71  Identities=45%  Similarity=1.044  Sum_probs=66.3

Q ss_pred             CCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         39 IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        39 ~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      ++|.|||++++|+||||.+|++|++||||++.....|.|..++    +|.|+...|..|++|||+|||++||+++
T Consensus         2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CRl~KCl~vGM~~~   72 (91)
T cd07161           2 ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYHCKYGR----ACEMDMYMRRKCQECRLKKCLSVGMRPE   72 (91)
T ss_pred             CCCeeCCCcCcceEECceeehhhHHHHHHHhccCCceecCCCC----ccccCccccccCccchhhHHhHcCCCHH
Confidence            4699999999999999999999999999999998889998764    7999999999999999999999999874

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

>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=1.5e-27  Score=151.68  Aligned_cols=69  Identities=49%  Similarity=1.091  Sum_probs=64.7

Q ss_pred             ceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         41 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        41 C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      |.|||++++++||||.+|++|++||||++..+..|.|..++    .|.|+...+..|++|||+|||++||+++
T Consensus         1 C~VC~~~~~g~hygv~sC~aCk~FFRR~~~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~   69 (75)
T cd07155           1 CLVCGDIASGYHYGVASCEACKAFFKRTIQGNLGYSCPSTS----ECEVDKKRRKSCQACRLQKCLKVGMLKE   69 (75)
T ss_pred             CcccCccCcceEEChhhhhhhHHHHHHHhhCCCceeCCcCC----CcccCCcccccCccchhhhhhHhCCCHH
Confidence            78999999999999999999999999999988889998764    6999999999999999999999999874

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

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

Probab=99.94  E-value=5.7e-28  Score=153.61  Aligned_cols=70  Identities=47%  Similarity=1.165  Sum_probs=65.6

Q ss_pred             CceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         40 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        40 ~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      +|.|||++++++||||.+|++|++||||++.....|.|..++    +|.|+...|..|++|||+|||++||++|
T Consensus         2 ~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~   71 (75)
T cd06969           2 LCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANK----NCPVDKRRRNRCQYCRFQKCLQVGMVKE   71 (75)
T ss_pred             CCeecCCcCcceEECcceeeeeeeeeeeeeecCCcccCCcCC----ccccCCcccccCcccHhHHHHHhCCCHH
Confidence            699999999999999999999999999999988889998754    7999999999999999999999999975

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

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

Probab=99.94  E-value=1.7e-27  Score=154.70  Aligned_cols=70  Identities=50%  Similarity=1.227  Sum_probs=65.7

Q ss_pred             CceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         40 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        40 ~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      +|.|||++++++||||.+|++|++||||++..+..|.|..++    +|.|+...|..|++|||+|||++||+++
T Consensus         1 ~C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~   70 (85)
T cd06961           1 PCVVCGDKATGYHYRCITCEGCKGFFRRTVQKKLSYSCKGEG----KCEIDKVTRNQCQECRFKKCIAVGMAKD   70 (85)
T ss_pred             CCceeCCcCcceEEChhhhhhhhHhhHhhhccCCccccCCCC----ccccCccccccCccchhhhhhhccCCHH
Confidence            599999999999999999999999999999998889998764    7999999999999999999999999874

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

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

Probab=99.94  E-value=2.4e-27  Score=149.88  Aligned_cols=69  Identities=49%  Similarity=1.202  Sum_probs=64.7

Q ss_pred             ceecCCCCcceeeccccchhhHHHHHHHhhcCccc-ccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         41 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVY-TCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        41 C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~-~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      |.|||++++++||||.+|++|++||||++..+..| .|..++    +|.|+...|..|++|||+|||++||+++
T Consensus         1 C~VCg~~~~g~hyGv~~C~aC~~FFRR~v~~~~~~~~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~   70 (73)
T cd07158           1 CKVCGDKASGFHYGVHSCEGCKGFFRRTIQHNLTYRRCLNGG----KCVIQRKNRNRCQYCRFKKCLSVGMSRN   70 (73)
T ss_pred             CcccCccCcceEECcchhhHHHHHHhhhhcCCCCcccCCCCC----CcCCCccccccCccchhhhhhHccCChH
Confidence            78999999999999999999999999999998888 898764    6999999999999999999999999975

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).

>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=99.94  E-value=1.9e-27  Score=150.41  Aligned_cols=69  Identities=58%  Similarity=1.320  Sum_probs=64.6

Q ss_pred             ceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         41 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        41 C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      |.|||++++++||||.+|++|++||||++..+..|.|..++    +|.++...|..|++|||+|||++||+++
T Consensus         1 C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~   69 (73)
T cd06958           1 CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRGNR----NCPIDQHHRNQCQYCRLKKCLKVGMRRE   69 (73)
T ss_pred             CCccCccCcceEEChhhhhhhhhhhhhhhcCCCceeCCCCC----cCccCCcccccCccchhhHhhHhCCCHH
Confidence            78999999999999999999999999999998888998754    7999999999999999999999999975

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

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

Probab=99.94  E-value=9.2e-28  Score=155.70  Aligned_cols=71  Identities=48%  Similarity=1.064  Sum_probs=66.3

Q ss_pred             CCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         39 IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        39 ~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      ++|.|||++++++||||.+|++|++||||++..+..|.|..++    +|.|+...|..|++|||+|||++||+++
T Consensus         2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CRl~KCl~vGM~~~   72 (84)
T cd06962           2 ELCVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGG----NCEMDMYMRRKCQECRLRKCKEMGMLAE   72 (84)
T ss_pred             CCCeecCCcCcceEECcceeecceeeeeeeeccCCceecCCCC----cCccCccccccCccchhhHHHHhCCChH
Confidence            4699999999999999999999999999999988889998764    7999999999999999999999999874

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

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

Probab=99.94  E-value=8.5e-28  Score=158.21  Aligned_cols=76  Identities=82%  Similarity=1.585  Sum_probs=68.2

Q ss_pred             CCCCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         36 LLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        36 ~~~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      ++..+|.|||++++|+||||.+|+||++||||++..+..|.|..+.+  +.|.|+...|..|++|||+|||++||+++
T Consensus         4 ~~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~--~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~   79 (92)
T cd07163           4 ILDIPCKVCGDRSSGKHYGIYACDGCSGFFKRSIRRNRQYVCKSKGQ--GGCPVDKTHRNQCRACRLKKCFEVGMNKD   79 (92)
T ss_pred             ccCCCCcccCCcCcccEECceeeeeeeeEEeeeecCCCCcCCCCCCC--CCCccCCCccccCccchhhhhhhhcCCHH
Confidence            34678999999999999999999999999999999888899987421  37999999999999999999999999874

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).

>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors

Probab=99.93  E-value=2.7e-27  Score=148.45  Aligned_cols=70  Identities=43%  Similarity=1.019  Sum_probs=65.7

Q ss_pred             CceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         40 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        40 ~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      +|.|||++++++||||.+|++|++||||++..+..+.|..++    +|.|+...+..|++|||+|||++||++|
T Consensus         1 ~C~vC~~~~~~~hygv~~C~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~C~~CR~~KCl~~GM~~~   70 (70)
T smart00399        1 LCCVCGDHASGFHFGVCSCRACKAFFRRTVNLRYKYRCDRKN----NCSINKRYRCRCRACRLKKCLGVGMDPE   70 (70)
T ss_pred             CCeEeCCcCcccEeCCcEechhhhhhhhheeCCCCeecCCCc----ccccCCCccccCccCcChhHhhccCcCC
Confidence            499999999999999999999999999999988889998764    6999999999999999999999999986

>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=3.8e-27  Score=154.53  Aligned_cols=72  Identities=46%  Similarity=1.102  Sum_probs=66.7

Q ss_pred             CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      ..+|.|||++++++||||.+|++|++||||++..+..|.|..++    +|.|+...|..|++|||+|||++||+++
T Consensus         6 ~~~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~   77 (90)
T cd07168           6 PKLCSICEDKATGLHYGIITCEGCKGFFKRTVQNKRVYTCVGDG----RCEITKAQRNRCQYCRFRKCIRKGMMLA   77 (90)
T ss_pred             CCCCcccCCcCcceEECceehhhhhHhhhhhhcCCCCccCCCCC----CccccccccccccccchhhhhhcCCCHH
Confidence            46799999999999999999999999999999998889998754    7999999999999999999999999864

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

>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=1.1e-27  Score=155.65  Aligned_cols=72  Identities=54%  Similarity=1.168  Sum_probs=66.6

Q ss_pred             CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      ..+|.|||++++++||||.+|++|++||||++.....|.|..++    +|.|+...|..|++|||+|||++||+++
T Consensus         4 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~   75 (85)
T cd06964           4 YKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDK----NCIINKVTRNRCQYCRLQKCFEVGMSKE   75 (85)
T ss_pred             CCCCcccCCcCcccEECcceeeeeeeEEeeeecCCCCeECCCCC----ccccCCcccccCccchhhhhhhhCCCHH
Confidence            36799999999999999999999999999999988889998764    6999999999999999999999999874

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

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

Probab=99.93  E-value=2.6e-27  Score=159.70  Aligned_cols=73  Identities=44%  Similarity=1.055  Sum_probs=67.5

Q ss_pred             CCCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         37 LDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        37 ~~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      .+.+|.|||+.++++||||.+|++|++||||++..+..|.|..++    +|.|+...+..|++|||+|||++||+++
T Consensus         5 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CRl~KCl~vGM~~~   77 (107)
T cd06955           5 VPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNG----DCRITKDNRRHCQACRLKRCVDIGMMKE   77 (107)
T ss_pred             CCCCCeecCCcCcccEECcceeeeecceecceeccCCccccCCCC----ccccccCCccccccchhHHHHHcCCCch
Confidence            357899999999999999999999999999999998889998764    7999999999999999999999999874

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

>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=99.93  E-value=5.4e-27  Score=146.80  Aligned_cols=69  Identities=51%  Similarity=1.191  Sum_probs=61.3

Q ss_pred             CceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCC
Q psy16245         40 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNK  112 (113)
Q Consensus        40 ~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~  112 (113)
                      +|.|||++++++||||.+|++|++||||++.....+.|..++    +|.++...+..|++|||+|||++||++
T Consensus         2 ~C~VCg~~~~~~~ygv~sC~~C~~FFrR~~~~~~~~~C~~~~----~C~i~~~~~~~C~~CRf~KCl~~GM~k   70 (70)
T PF00105_consen    2 KCKVCGDPASGYHYGVLSCNACKMFFRRSVKKKKPYKCKKNG----NCKIDKDNRRKCRSCRFQKCLEVGMKK   70 (70)
T ss_dssp             BSTTTSSBESEEETTEEEEHHHHHHHHHHHHTTCG-STSSSS----T---STTTTTTSHHHHHHHHHHTTBSG
T ss_pred             CCeECCCccCcccccccccccceeeeeecccccccccccccc----cccccccCCCEeCcchHHHHHHHCCcC
Confidence            699999999999999999999999999999999889999865    699999999999999999999999984

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 ....

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

Probab=99.93  E-value=6.3e-27  Score=152.62  Aligned_cols=70  Identities=47%  Similarity=1.087  Sum_probs=65.4

Q ss_pred             CceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         40 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        40 ~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      +|.|||++++++||||.+|++|++||||++.....|.|..++    +|.++...+..|++|||+|||++||++|
T Consensus         1 ~C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~   70 (87)
T cd07162           1 ICRVCGDRATGYHFNAMTCEGCKGFFRRAMKRNARLCCPFQK----GCVITKSNRRQCQACRLRKCLSIGMKKE   70 (87)
T ss_pred             CCcccCCcCcceEECcceehhhHHHHHhhhccCceeEcCCCC----ceecCCcccccCccchhhHHhHhCCCHH
Confidence            499999999999999999999999999999988888998764    6999999999999999999999999975

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

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

Probab=99.93  E-value=1.8e-27  Score=150.53  Aligned_cols=70  Identities=74%  Similarity=1.453  Sum_probs=64.3

Q ss_pred             ceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         41 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        41 C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      |.|||++++++||||.+|++|++||||++..+..|.|...+   ++|.|+...|..|++|||+|||++||+++
T Consensus         1 C~vCg~~~~~~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~---~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~   70 (73)
T cd07154           1 CKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNLLYTCKAGN---GSCVVDKARRNQCQACRLKKCLEVSMNKD   70 (73)
T ss_pred             CcccCccCcceEECcceeeeeeeEeeeeecCCCCcccCCCC---CCCccCCcccccCccchhhHhhHhCCChH
Confidence            78999999999999999999999999999998889998432   37999999999999999999999999975

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

>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=2.1e-27  Score=154.90  Aligned_cols=72  Identities=53%  Similarity=1.146  Sum_probs=66.8

Q ss_pred             CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      .++|.|||++++++||||.+|++|++||||++..+..+.|..++    .|.|+...|..|++|||+|||++||+++
T Consensus         3 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~   74 (87)
T cd06967           3 VELCVVCGDKASGRHYGAVSCEGCKGFFKRSIRKNLGYSCRGSK----DCVINKHHRNRCQYCRLQKCLAMGMKSD   74 (87)
T ss_pred             CCCCeecCCcCCcCEeCcceEeeeeeEeeeeeeCCCCcccCCCC----ccccCccccccCccchhhhhhHcCCCHH
Confidence            46799999999999999999999999999999988889998754    7999999999999999999999999874

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

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

Probab=99.93  E-value=7.5e-27  Score=153.17  Aligned_cols=72  Identities=50%  Similarity=1.142  Sum_probs=66.9

Q ss_pred             CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      ..+|.|||++++++||||.+|++|++||||++..+..|.|..++    .|.|+...|..|++|||+|||++||+++
T Consensus         6 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~   77 (90)
T cd07169           6 QRTCLICGDRATGLHYGIISCEGCKGFFKRSICNKRVYRCSRDK----NCVMSRKQRNRCQYCRLLKCLQMGMNRK   77 (90)
T ss_pred             CCCCeecCCcCcceEECcceehhhHHHHHHHhcCCCceecCCCC----cccccccccccccccchhhhccccCCHH
Confidence            46799999999999999999999999999999998889998754    6999999999999999999999999874

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).

>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=8.5e-27  Score=149.16  Aligned_cols=69  Identities=64%  Similarity=1.344  Sum_probs=64.7

Q ss_pred             ceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         41 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        41 C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      |.|||++++++||||.+|++|++||||++..+..|.|..++    +|.|+...+..|++|||+|||++||+++
T Consensus         1 C~VCg~~~~g~hyG~~~C~~C~~FFRR~~~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~   69 (78)
T cd07164           1 CRVCGDRASGKHYGVPSCDGCRGFFKRSIRRNLAYVCKENG----SCVVDVARRNQCQACRFKKCLQVNMNRD   69 (78)
T ss_pred             CcccCccCcceEECcchhhhhhhhhhhhccCCCCccCCCCC----cccccCcccccCccchhhhhhHhcCCHH
Confidence            78999999999999999999999999999988889998864    7999999999999999999999999874

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

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

Probab=99.93  E-value=2e-27  Score=149.96  Aligned_cols=69  Identities=58%  Similarity=1.297  Sum_probs=64.8

Q ss_pred             ceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         41 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        41 C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      |.|||++++++||||.+|++|++||||++..+..|.|..++    .|.|+...|..|++|||+|||++||+++
T Consensus         1 C~vC~~~~~~~hygv~sC~aC~~FFRR~~~~~~~~~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~   69 (72)
T cd06916           1 CAVCGDKASGYHYGVLTCEGCKGFFRRSVRRNLEYTCPAGG----NCVIDKRNRNRCQACRLKKCLAVGMRKE   69 (72)
T ss_pred             CCccCccCcccEECcceeeeeeeeEeEeecCCCCccCCCCC----ccccCCcccccCccchhhHhhHhCCChH
Confidence            78999999999999999999999999999988889998764    6999999999999999999999999975

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

>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=2.8e-27  Score=155.73  Aligned_cols=72  Identities=67%  Similarity=1.418  Sum_probs=66.3

Q ss_pred             CCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         39 IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        39 ~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      .+|.|||++++|+||||.+|++|++||||++..+..|.|..+.   ++|.|+...|..|++|||+|||++||+++
T Consensus         7 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~---~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~   78 (92)
T cd06970           7 LLCRVCGDTSSGKHYGIYACNGCSGFFKRSVRRKLIYRCQAGT---GMCPVDKAHRNQCQACRLKKCLQAGMNKD   78 (92)
T ss_pred             CCCeecCCcCcccEECccEEeeeeeEeeeeeecCCCceeecCC---CcCccCCCccccCccchhhHhhHhCCCHH
Confidence            5799999999999999999999999999999999889998752   27999999999999999999999999874

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

>KOG4846|consensus

Probab=99.93  E-value=8e-27  Score=185.72  Aligned_cols=71  Identities=48%  Similarity=1.102  Sum_probs=66.5

Q ss_pred             CCceecCCCCcceeeccccchhhHHHHHHHhhcCccc-ccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         39 IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVY-TCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        39 ~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~-~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      ..|+||||+++|+||||.+|++||+||||+|+.+..| .|-+..    .|.|...+|++|++|||+|||.|||++|
T Consensus       133 ~lCkVCgDkASGfHYGV~aCEGCKGFFRRSIQqkI~YrrClk~e----~C~I~R~nRNRCQ~CRfKKCL~vGMSrD  204 (538)
T KOG4846|consen  133 SLCKVCGDKASGFHYGVTACEGCKGFFRRSIQQKIDYRRCLKQE----VCEIKRENRNRCQYCRFKKCLDVGMSRD  204 (538)
T ss_pred             EeehhhccccccceeceeecccchHHHHHHHHHhhhHHHHhhhh----ceehhhhccchhhhhhHHHHHhcccchh
Confidence            3699999999999999999999999999999999999 787764    7999999999999999999999999875

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

Probab=99.93  E-value=1.1e-26  Score=153.74  Aligned_cols=72  Identities=54%  Similarity=1.225  Sum_probs=66.9

Q ss_pred             CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      ..+|.|||++++++||||.+|++|++||||++..+..|.|..++    +|.++...|..|++|||+|||++||+++
T Consensus         5 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CRl~KCl~vGM~~~   76 (95)
T cd06968           5 VIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVSYSCPRQK----NCLIDRTNRNRCQHCRLQKCLALGMSRD   76 (95)
T ss_pred             ccCCcccCCcCcceEECceeehhhHHhhHHheeCCCceecCCCc----ccccccCCceeccccchhhcccccCChh
Confidence            45899999999999999999999999999999988889998754    7999999999999999999999999874

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

>KOG4217|consensus

Probab=99.93  E-value=1.6e-26  Score=186.17  Aligned_cols=73  Identities=45%  Similarity=1.105  Sum_probs=68.8

Q ss_pred             CCCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         37 LDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        37 ~~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      ....|+||||.+...||||.+|++||+||+|+|+++..|+|-.+.    +|.|++..|++|++|||+|||+|||=+|
T Consensus       268 ~e~~CAVCgDnAaCqHYGvRTCEGCKGFFKRTVQKnaKYvClanK----nCPVDKRrRnRCQyCRfQKCL~VGMVKE  340 (605)
T KOG4217|consen  268 AEGLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANK----NCPVDKRRRNRCQYCRFQKCLAVGMVKE  340 (605)
T ss_pred             ccceeeecCChHHhhhcCccccccchHHHHHHHhcCCeeEeecCC----CCCcchhhhhhchhhhHhHHHHhhhhhh
Confidence            367899999999999999999999999999999999999998874    7999999999999999999999999765

>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=99.93  E-value=1.1e-26  Score=153.17  Aligned_cols=69  Identities=46%  Similarity=1.133  Sum_probs=64.9

Q ss_pred             ceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         41 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        41 C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      |.||+++++++||||.+|++|++||||++..+..|.|..++    +|.|+...|..|++|||+|||++||+++
T Consensus         1 C~VCg~~a~g~hyGv~sC~aCk~FFRRsv~~~~~~~C~~~~----~C~i~~~~r~~Cr~CRl~KCl~vGM~~~   69 (93)
T cd07167           1 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKRYTCIENQ----NCQIDKTQRKRCPYCRFQKCLSVGMKLE   69 (93)
T ss_pred             CcccCccCcceEECchhhhhHHHHHHHHeeCCCccccCCCC----ccccCccccCcCCCcccchhhhccCCHH
Confidence            78999999999999999999999999999999999998864    7999999999999999999999999864

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

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

Probab=99.93  E-value=6.1e-27  Score=152.42  Aligned_cols=70  Identities=40%  Similarity=0.926  Sum_probs=63.9

Q ss_pred             CceecCCCCcceeeccccchhhHHHHHHHhhcCc--ccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         40 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNR--VYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        40 ~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~--~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      +|.|||++++++||||.+|++|++||||++....  .|.|..++    +|.++...|..|++|||+|||+|||+++
T Consensus         2 ~C~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~   73 (86)
T cd07157           2 TCQVCGEPAAGFHHGAYVCEACKKFFMRSSNAISFTISECPNGG----KCIIDKKNRTKCQACRYRKCLNVGMSLG   73 (86)
T ss_pred             CCcccCCcCcccEECcceeeEeeeEEecceecCCCccccCCCCC----ccccCccccccCccchhhHHhHcCCCcc
Confidence            5999999999999999999999999999998664  78898764    7999999999999999999999999864

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.

>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=6.2e-27  Score=149.06  Aligned_cols=69  Identities=55%  Similarity=1.310  Sum_probs=64.6

Q ss_pred             ceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         41 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        41 C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      |.|||++++++||||.+|++|++||||++..+..|.|..++    .|.|+...+..|++|||+|||++||+++
T Consensus         1 C~vCg~~~~~~hygv~~C~aC~~FFrR~~~~~~~~~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~   69 (76)
T cd06960           1 CAVCGDRATGKHYGVLSCNGCKGFFRRSVRKNRTYTCRFGG----NCVVDKDKRNACRYCRFKKCLEVGMDPE   69 (76)
T ss_pred             CCccCccCcccEECcceeeeehheeCccccCCCceeCCCCC----cccccCcccccCccchhhhhhhcCCCHH
Confidence            78999999999999999999999999999988889998764    7999999999999999999999999874

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

>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=99.93  E-value=2e-26  Score=148.45  Aligned_cols=69  Identities=52%  Similarity=1.210  Sum_probs=64.7

Q ss_pred             ceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         41 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        41 C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      |.|||++++++||||.+|++|++||||++.....|.|..++    +|.|+...+..|++|||+|||++||+++
T Consensus         1 C~VCg~~~~g~hyG~~sC~aC~~FFRR~~~~~~~~~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~   69 (81)
T cd07165           1 CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYRCLRDG----KCEIIRLNRNRCQYCRFKKCLAAGMSKD   69 (81)
T ss_pred             CCccCccCcceEECchhhhhHHHHHHhHhccCCceeCCCCC----CccccccccccccchhhhhcccccCCHH
Confidence            78999999999999999999999999999988889998764    7999999999999999999999999874

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,

>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=8.4e-27  Score=154.03  Aligned_cols=70  Identities=36%  Similarity=0.939  Sum_probs=65.6

Q ss_pred             CceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         40 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        40 ~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      +|.|||++++++||||.+|++|++||||++.....|.|..++    +|.++...+..|++|||+|||++||+++
T Consensus         2 ~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~   71 (94)
T cd06966           2 ICGVCGDKALGYNFNAITCESCKAFFRRNALKNKEFKCPFNE----SCEINVVTRRFCQKCRLDKCFAIGMKKE   71 (94)
T ss_pred             CCeeCCCcCcceEECcceeeeehheehhcccCCCccccCCCC----ccccCccccccCccchhhhCcccCCCHH
Confidence            699999999999999999999999999999988889998764    7999999999999999999999999874

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

>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=4.2e-27  Score=151.95  Aligned_cols=70  Identities=60%  Similarity=1.276  Sum_probs=64.4

Q ss_pred             ceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         41 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        41 C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      |.|||++++|+||||.+|++|++||||++..+..|.|...+   +.|.|+...|..|++|||+|||++||+++
T Consensus         1 C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~---~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~   70 (82)
T cd06957           1 CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKGIIYTCIAGN---GNCVVDKARRNWCPFCRLQKCFAVGMNRA   70 (82)
T ss_pred             CCccCccCcceEECcceEeeeeeEEEEeecCCCceEccCcc---CCCccCCCccCcccCcchhhcccccCCHH
Confidence            78999999999999999999999999999988889998532   37999999999999999999999999864

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

>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=1.3e-26  Score=151.75  Aligned_cols=71  Identities=46%  Similarity=1.137  Sum_probs=65.5

Q ss_pred             CCceecCCCCcceeeccccchhhHHHHHHHhhcCccc-ccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         39 IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVY-TCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        39 ~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~-~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      .+|.|||++++++||||.+|++|++||||++..+..| .|..++    +|.|+...|..|++|||+|||++||+++
T Consensus         4 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~~C~~~~----~C~i~~~~r~~Cr~CRl~KCl~vGM~~~   75 (89)
T cd07166           4 VLCKVCGDKASGFHYGVHACEGCKGFFRRSIQQKIQYRKCTKNE----TCSIMRINRNRCQYCRFKKCLAVGMSRD   75 (89)
T ss_pred             CCCcccCccCcceEEChhhhhhHhhEecceeEcCCcchhhccCC----cccccccccccccchhhhhcccccCCHH
Confidence            5799999999999999999999999999999988888 588764    7999999999999999999999999874

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

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

Probab=99.92  E-value=4.2e-26  Score=147.89  Aligned_cols=68  Identities=47%  Similarity=1.158  Sum_probs=62.5

Q ss_pred             CceecCCCCcceeeccccchhhHHHHHHHhhcCccc-ccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         40 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVY-TCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        40 ~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~-~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      +|.|||++++|+||||.+|++|++||||++..+..| .|..      .|.|+...+..|++|||+|||++||+++
T Consensus         1 ~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~~C~~------~C~i~~~~r~~Cr~CRl~KCl~vGM~~~   69 (84)
T cd06965           1 ECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLVYKPCDL------SCKIHKKSRNKCQYCRFQKCLNVGMSHN   69 (84)
T ss_pred             CCcccCccCcceEEChhhhhhhhhheeeeeecCCCcccccc------CCCcCccccccccchhhhhhhhccCCHH
Confidence            499999999999999999999999999999888878 4864      4999999999999999999999999864

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

>KOG4216|consensus

Probab=99.90  E-value=1.8e-24  Score=171.15  Aligned_cols=72  Identities=54%  Similarity=1.220  Sum_probs=67.9

Q ss_pred             CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      -.+|.||||+++|.||||.+|++||+||||+-..+..|.|.+..    +|.|+..+|++|++|||+|||++||+.|
T Consensus        46 vIPCKiCGDKSSGiHYGVITCEGCKGFFRRSQ~s~a~YsCpRqk----nC~iDRtnRNRCQ~CRLqKClaLGMSRD  117 (479)
T KOG4216|consen   46 IIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQSNANYSCPRQK----NCLIDRTNRNRCQHCRLQKCLALGMSRD  117 (479)
T ss_pred             EEeeeeccCCCCcceeeeEeeccchHhhhhhhhccccccCCccc----CCcccccccchhhHHHHHHHHHhccchh
Confidence            35799999999999999999999999999999999999998864    7999999999999999999999999875

>KOG4218|consensus

Probab=99.85  E-value=2.3e-22  Score=157.64  Aligned_cols=76  Identities=46%  Similarity=1.073  Sum_probs=70.2

Q ss_pred             CCCCCCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         34 DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        34 ~~~~~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      +....+.|.||||+.+|+|||..+|+.||+||+|+|+.++.|+|....    +|.|++..|.+|.+|||+|||.+||+-|
T Consensus        11 dedl~ElCPVCGDkVSGYHYGLLTCESCKGFFKRTVQNnK~YtC~e~q----nC~iDkTqRKRCP~CRFQKCLtvGMklE   86 (475)
T KOG4218|consen   11 DEDLGELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKQYTCSEEQ----NCHIDKTQRKRCPSCRFQKCLTVGMKLE   86 (475)
T ss_pred             ccccccccccccCccccceeeeeehhhhhhHHHHHhhcCcceeccccc----ccccchHhhccCCchhHHHHhhhhhhHH
Confidence            344568999999999999999999999999999999999999998875    7999999999999999999999999754

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	113
3dzu_A	467	Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp		8e-21
2ebl_A	89	Solution Structure Of The Zinc Finger, C4-type Doma		3e-19
3cbb_A	78	Crystal Structure Of Hepatocyte Nuclear Factor 4alp		3e-18
1ynw_B	99	Crystal Structure Of Vitamin D Receptor And 9-Cis R		9e-18
1dsz_B	85	Structure Of The RxrRAR DNA-Binding Domain Heterodi		2e-17
1r0n_A	81	Crystal Structure Of Heterodimeric Ecdsyone Recepto		2e-17
1by4_A	82	Structure And Mechanism Of The Homodimeric Assembly		2e-17
2nll_A	66	Retinoid X Receptor-Thyroid Hormone Receptor Dna-Bi		9e-17
1rxr_A	83	High Resolution Solution Structure Of The Retinoid		9e-17
1dsz_A	86	Structure Of The RxrRAR DNA-Binding Domain Heterodi		1e-16
1hra_A	80	The Solution Structure Of The Human Retinoic Acid R		2e-16
3dzu_D	419	Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp		3e-16
1r0o_A	86	Crystal Structure Of The Heterodimeric Ecdysone Rec		3e-16
2han_A	93	Structural Basis Of Heterodimeric Ecdysteroid Recep		4e-16
1cit_A	89	Dna-Binding Mechanism Of The Monomeric Orphan Nucle		1e-14
1ynw_A	110	Crystal Structure Of Vitamin D Receptor And 9-Cis R		3e-14
2a66_A	113	Human Liver Receptor Homologue Dna-Binding Domain (		5e-14
1lat_A	82	Glucocorticoid Receptor MutantDNA COMPLEX Length =		1e-13
2nll_B	103	Retinoid X Receptor-Thyroid Hormone Receptor Dna-Bi		1e-13
2ff0_A	102	Solution Structure Of Steroidogenic Factor 1 Dna Bi		1e-13
1hcp_A	76	Dna Recognition By The Oestrogen Receptor: From Sol		1e-13
4aa6_E	71	The Oestrogen Receptor Recognizes An Imperfectly Pa		1e-13
1hcq_A	84	The Crystal Structure Of The Estrogen Receptor Dna-		1e-13
4aa6_A	71	The Oestrogen Receptor Recognizes An Imperfectly Pa		1e-13
1hlz_A	94	Crystal Structure Of The Orphan Nuclear Receptor Re		2e-13
1kb2_A	110	Crystal Structure Of Vdr Dna-Binding Domain Bound T		2e-13
3m9e_A	105	Thyroid Hormone Beta Dna Binding Domain Homodimer W		4e-13
1r0n_B	109	Crystal Structure Of Heterodimeric Ecdsyone Recepto		1e-12
2han_B	119	Structural Basis Of Heterodimeric Ecdysteroid Recep		1e-12
1lo1_A	98	Estrogen Related Receptor 2 Dna Binding Domain In C		7e-12
2env_A	88	Solution Sturcture Of The C4-Type Zinc Finger Domai		8e-12
1r4o_A	92	Crystallographic Analysis Of The Interaction Of The		8e-12
1r4r_B	92	Crystallographic Analysis Of The Interaction Of The		9e-12
1glu_A	81	Crystallographic Analysis Of The Interaction Of The		9e-12
1r4i_A	105	Crystal Structure Of Androgen Receptor Dna-Binding		4e-11
4hn5_A	117	Gr Dna Binding Domain - Tslp Ngre Complex Length =		5e-11
1gdc_A	72	Refined Solution Structure Of The Glucocorticoid Re		7e-11
2gda_A	72	Refined Solution Structure Of The Glucocorticoid Re		7e-11
3g9p_B	90	Gr Dna Binding Domain:sgk 16bp Complex-7 Length = 9		8e-11
1rgd_A	71	Structure Refinement Of The Glucocorticoid Receptor		9e-11
2c7a_A	78	Structure Of The Progesterone Receptor-Dna Complex		2e-10
4hn6_A	114	Gr Dna Binding Domain R460d/d462r - Tslp Ngre Compl		2e-10
3g6t_A	91	Gr Gamma Dna-Binding Domain:fkbp5 16bp Complex-34 L		3e-10

>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 = 95.1 bits (235), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 38/73 (52%), Positives = 50/73 (68%), Gaps = 4/73 (5%)
Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C +CGDRSSGKHYG+YSC+GC GFFKR++ ++  YTC+   D    C IDK  RN+C+ C
Sbjct: 140 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKD----CLIDKRQRNRCQYC 195
Query: 101 RLNKCFMSAMNKD 113
           R  KC    M ++
Sbjct: 196 RYQKCLAMGMKRE 208

>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 = 90.1 bits (222), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 42/75 (56%), Positives = 53/75 (70%), Gaps = 4/75 (5%)
Query: 39  IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCR 98
           I C VCGD+SSGKHYG ++C+GC  FFKRS+ RN  YTC+A  +    CPID+ HRNQC+
Sbjct: 8   IECVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRANRN----CPIDQHHRNQCQ 63
Query: 99  ACRLNKCFMSAMNKD 113
            CRL KC    M ++
Sbjct: 64  YCRLKKCLKVGMRRE 78

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

Iteration: 1
 Score = 86.7 bits (213), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 39/73 (53%), Positives = 51/73 (69%), Gaps = 4/73 (5%)
Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C +CGDR++GKHYG  SCDGC GFF+RS+ +N +Y+C+        C +DK  RNQCR C
Sbjct: 3   CAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCR----FSRQCVVDKDKRNQCRYC 58
Query: 101 RLNKCFMSAMNKD 113
           RL KCF + M K+
Sbjct: 59  RLKKCFRAGMKKE 71

>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 = 85.1 bits (209), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 38/73 (52%), Positives = 50/73 (68%), Gaps = 4/73 (5%)
Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C +CGDRSSGKHYG+YSC+GC GFFKR++ ++  YTC+   D    C IDK  RN+C+ C
Sbjct: 6   CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKD----CLIDKRQRNRCQYC 61
Query: 101 RLNKCFMSAMNKD 113
           R  KC    M ++
Sbjct: 62  RYQKCLAMGMKRE 74

>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 = 84.3 bits (207), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 38/73 (52%), Positives = 50/73 (68%), Gaps = 4/73 (5%)
Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C +CGDRSSGKHYG+YSC+GC GFFKR++ ++  YTC+   D    C IDK  RN+C+ C
Sbjct: 8   CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKD----CLIDKRQRNRCQYC 63
Query: 101 RLNKCFMSAMNKD 113
           R  KC    M ++
Sbjct: 64  RYQKCLAMGMKRE 76

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

Iteration: 1
 Score = 84.3 bits (207), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 38/73 (52%), Positives = 50/73 (68%), Gaps = 4/73 (5%)
Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C +CGDRSSGKHYG+YSC+GC GFFKR++ ++  YTC+   D    C IDK  RN+C+ C
Sbjct: 6   CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKD----CLIDKRQRNRCQYC 61
Query: 101 RLNKCFMSAMNKD 113
           R  KC    M ++
Sbjct: 62  RYQKCLAMGMKRE 74

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

Iteration: 1
 Score = 84.0 bits (206), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 38/73 (52%), Positives = 50/73 (68%), Gaps = 4/73 (5%)
Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C +CGDRSSGKHYG+YSC+GC GFFKR++ ++  YTC+   D    C IDK  RN+C+ C
Sbjct: 8   CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKD----CLIDKRQRNRCQYC 63
Query: 101 RLNKCFMSAMNKD 113
           R  KC    M ++
Sbjct: 64  RYQKCLAMGMKRE 76

>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 = 81.6 bits (200), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 38/70 (54%), Positives = 48/70 (68%), Gaps = 4/70 (5%)
Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C +CGDRSSGKHYG+YSC+GC GFFKR++ ++  YTC+   D    C IDK  RN+C+ C
Sbjct: 1   CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKD----CLIDKRQRNRCQYC 56
Query: 101 RLNKCFMSAM 110
           R  KC    M
Sbjct: 57  RYQKCLAMGM 66

>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 = 81.6 bits (200), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 37/73 (50%), Positives = 49/73 (67%), Gaps = 4/73 (5%)
Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C +CGDRSSGKHYG+YSC+GC GFFKR++ ++  YTC+   D    C IDK  RN+C+ C
Sbjct: 6   CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKD----CLIDKRQRNRCQYC 61
Query: 101 RLNKCFMSAMNKD 113
           R  K     M ++
Sbjct: 62  RYQKALAMGMKRE 74

>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 = 80.9 bits (198), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 39/74 (52%), Positives = 51/74 (68%), Gaps = 4/74 (5%)
Query: 40  PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRA 99
           PC VC D+SSG HYG+ +C+GC GFF+RSI +N VYTC    +    C I+K  RN+C+ 
Sbjct: 6   PCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKN----CIINKVTRNRCQY 61
Query: 100 CRLNKCFMSAMNKD 113
           CRL KCF   M+K+
Sbjct: 62  CRLQKCFEVGMSKE 75

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

Iteration: 1
 Score = 80.9 bits (198), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 38/74 (51%), Positives = 51/74 (68%), Gaps = 4/74 (5%)
Query: 40  PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRA 99
           PC VC D+SSG HYG+ +C+GC GFF+RSI +N +YTC    +    C I+K  RN+C+ 
Sbjct: 7   PCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMIYTCHRDKN----CVINKVTRNRCQY 62
Query: 100 CRLNKCFMSAMNKD 113
           CRL KCF   M+K+
Sbjct: 63  CRLQKCFEVGMSKE 76

>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 = 80.1 bits (196), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 37/105 (35%), Positives = 60/105 (57%), Gaps = 6/105 (5%)
Query: 10  QIPPRYPQYFMSRPDGRDVT-SASRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRS 68
           ++ P  P Y+  +    +       + L+ I C+VCGD++SG HYG+++C+GC GFF+R+
Sbjct: 21  KVEPASPPYYSEKTQLYNKPHEEPSNSLMAIECRVCGDKASGFHYGVHACEGCKGFFRRT 80
Query: 69  IHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113
           I    +Y    + DL  +C I K  RN+C+ CR  KC    M+ +
Sbjct: 81  IRLKLIYD---RCDL--NCRIHKKSRNKCQYCRFQKCLAVGMSHN 120

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

Iteration: 1
 Score = 79.7 bits (195), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 35/73 (47%), Positives = 49/73 (67%), Gaps = 4/73 (5%)
Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C +CGDR+SGKHYG+YSC+GC GFFKR++ ++  Y C+   +    C IDK  RN+C+ C
Sbjct: 11  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYACRENRN----CIIDKRQRNRCQYC 66
Query: 101 RLNKCFMSAMNKD 113
           R  KC    M ++
Sbjct: 67  RYQKCLTCGMKRE 79

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

Iteration: 1
 Score = 79.3 bits (194), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 35/73 (47%), Positives = 49/73 (67%), Gaps = 4/73 (5%)
Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C +CGDR+SGKHYG+YSC+GC GFFKR++ ++  Y C+   +    C IDK  RN+C+ C
Sbjct: 13  CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYACRENRN----CIIDKRQRNRCQYC 68
Query: 101 RLNKCFMSAMNKD 113
           R  KC    M ++
Sbjct: 69  RYQKCLTCGMKRE 81

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

Iteration: 1
 Score = 75.1 bits (183), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 34/73 (46%), Positives = 47/73 (64%), Gaps = 4/73 (5%)
Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C VCGD +S +HYG+ +C+GC GFFKR++ ++  Y C A  D    CP+DK  RN+C+ C
Sbjct: 3   CAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKD----CPVDKRRRNRCQFC 58
Query: 101 RLNKCFMSAMNKD 113
           R  KC    M K+
Sbjct: 59  RFQKCLAVGMVKE 71

>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 = 73.6 bits (179), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 36/80 (45%), Positives = 50/80 (62%), Gaps = 4/80 (5%)
Query: 34  DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTH 93
           DR +   C VCGDR++G H+   +C+GC GFF+RS+ R  ++TC A GD    C I K +
Sbjct: 2   DRNVPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCAANGD----CRITKDN 57
Query: 94  RNQCRACRLNKCFMSAMNKD 113
           R  C+ACRL +C    M K+
Sbjct: 58  RRACQACRLKRCVDIGMMKE 77

>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 = 72.8 bits (177), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 35/77 (45%), Positives = 45/77 (58%), Gaps = 4/77 (5%)
Query: 34  DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTH 93
           D  L+  C VCGD+ SG HYG+ +C+ C GFFKR++  N+ YTC    +    C IDKT 
Sbjct: 5   DEDLEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQN----CQIDKTQ 60
Query: 94  RNQCRACRLNKCFMSAM 110
           R +C  CR  KC    M
Sbjct: 61  RKRCPYCRFQKCLSVGM 77

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

Iteration: 1
 Score = 71.6 bits (174), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 34/74 (45%), Positives = 43/74 (58%), Gaps = 4/74 (5%)
Query: 40  PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRA 99
           PC VC D +SG HYG+ +C+GC  FFKR++     Y CK +G     C IDK  R  C A
Sbjct: 6   PCLVCSDEASGCHYGVLTCEGCKAFFKRAVEGQHNYLCKYEGK----CIIDKIRRKNCPA 61
Query: 100 CRLNKCFMSAMNKD 113
           CR  KC  + MN +
Sbjct: 62  CRYRKCLQAGMNLE 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 = 71.6 bits (174), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 36/78 (46%), Positives = 47/78 (60%), Gaps = 6/78 (7%)
Query: 38  DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNR--VYTCKAQGDLKGHCPIDKTHRN 95
           D  C VCGD+++G HY   +C+GC GFF+R+I +N    Y+CK +    G C IDK  RN
Sbjct: 1   DELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYE----GKCVIDKVTRN 56
Query: 96  QCRACRLNKCFMSAMNKD 113
           QC+ CR  KC    M  D
Sbjct: 57  QCQECRFKKCIYVGMATD 74

>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 = 71.6 bits (174), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 34/73 (46%), Positives = 42/73 (57%), Gaps = 4/73 (5%)
Query: 38  DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQC 97
           D  C VCGD+ SG HYG+ +C+ C GFFKR++  N+ YTC         C IDKT R +C
Sbjct: 1   DELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKHYTCTESQS----CKIDKTQRKRC 56
Query: 98  RACRLNKCFMSAM 110
             CR  KC    M
Sbjct: 57  PFCRFQKCLTVGM 69

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

Iteration: 1
 Score = 71.2 bits (173), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 36/72 (50%), Positives = 43/72 (59%), Gaps = 4/72 (5%)
Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C VC D +SG HYG++SC+GC  FFKRSI  +  Y C A       C IDK  R  C+AC
Sbjct: 7   CAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPAT----NQCTIDKNRRKSCQAC 62
Query: 101 RLNKCFMSAMNK 112
           RL KC+   M K
Sbjct: 63  RLRKCYEVGMMK 74

>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 = 71.2 bits (173), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 36/72 (50%), Positives = 43/72 (59%), Gaps = 4/72 (5%)
Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C VC D +SG HYG++SC+GC  FFKRSI  +  Y C A       C IDK  R  C+AC
Sbjct: 4   CAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPAT----NQCTIDKNRRKSCQAC 59
Query: 101 RLNKCFMSAMNK 112
           RL KC+   M K
Sbjct: 60  RLRKCYEVGMMK 71

>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 = 71.2 bits (173), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 36/72 (50%), Positives = 43/72 (59%), Gaps = 4/72 (5%)
Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C VC D +SG HYG++SC+GC  FFKRSI  +  Y C A       C IDK  R  C+AC
Sbjct: 7   CAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPAT----NQCTIDKNRRKSCQAC 62
Query: 101 RLNKCFMSAMNK 112
           RL KC+   M K
Sbjct: 63  RLRKCYEVGMMK 74

>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 = 71.2 bits (173), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 36/72 (50%), Positives = 43/72 (59%), Gaps = 4/72 (5%)
Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C VC D +SG HYG++SC+GC  FFKRSI  +  Y C A       C IDK  R  C+AC
Sbjct: 4   CAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPAT----NQCTIDKNRRKSCQAC 59
Query: 101 RLNKCFMSAMNK 112
           RL KC+   M K
Sbjct: 60  RLRKCYEVGMMK 71

>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 = 70.9 bits (172), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 33/77 (42%), Positives = 50/77 (64%), Gaps = 3/77 (3%)
Query: 37  LDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQ 96
           + + CKVCGD +SG HYG+ +C+GC GFF+RSI +N  Y    + +   +C I + +RN+
Sbjct: 6   MVLLCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNE---NCSIVRINRNR 62
Query: 97  CRACRLNKCFMSAMNKD 113
           C+ CR  KC    M++D
Sbjct: 63  CQQCRFKKCLSVGMSRD 79

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

Iteration: 1
 Score = 70.5 bits (171), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 35/80 (43%), Positives = 49/80 (61%), Gaps = 4/80 (5%)
Query: 34  DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTH 93
           DR +   C VCGDR++G H+   +C+GC GFF+RS+ R  ++TC   GD    C I K +
Sbjct: 2   DRNVPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGD----CRITKDN 57
Query: 94  RNQCRACRLNKCFMSAMNKD 113
           R  C+ACRL +C    M K+
Sbjct: 58  RRHCQACRLKRCVDIGMMKE 77

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

Iteration: 1
 Score = 69.7 bits (169), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 35/78 (44%), Positives = 47/78 (60%), Gaps = 6/78 (7%)
Query: 38  DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNR--VYTCKAQGDLKGHCPIDKTHRN 95
           D  C VCGD+++G HY   +C+GC GFF+R+I ++    Y+CK +    G C IDK  RN
Sbjct: 3   DELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKSLHPSYSCKYE----GKCIIDKVTRN 58
Query: 96  QCRACRLNKCFMSAMNKD 113
           QC+ CR  KC    M  D
Sbjct: 59  QCQECRFKKCIYVGMATD 76

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

Iteration: 1
 Score = 68.2 bits (165), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 33/79 (41%), Positives = 46/79 (58%), Gaps = 4/79 (5%)
Query: 35  RLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHR 94
           R+ +  C VCGDR+SG HY   +C+GC GFF+RS+ ++ VY CK        C +D   R
Sbjct: 3   RVQEELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCK----FGRACEMDMYMR 58
Query: 95  NQCRACRLNKCFMSAMNKD 113
            +C+ CRL KC    M  +
Sbjct: 59  RKCQECRLKKCLAVGMRPE 77

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

Iteration: 1
 Score = 68.2 bits (165), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/83 (40%), Positives = 47/83 (56%), Gaps = 4/83 (4%)
Query: 31  ASRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPID 90
            S  R+ +  C VCGDR+SG HY   +C+GC GFF+RS+ ++ VY CK        C +D
Sbjct: 1   GSAPRVQEELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCK----FGRACEMD 56
Query: 91  KTHRNQCRACRLNKCFMSAMNKD 113
              R +C+ CRL KC    M  +
Sbjct: 57  MYMRRKCQECRLKKCLAVGMRPE 79

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

Iteration: 1
 Score = 65.5 bits (158), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 33/73 (45%), Positives = 41/73 (56%), Gaps = 4/73 (5%)
Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C VCGD +SG HYG+ SC+ C  FFKR+I  N  Y+C A  +    C I K  R  C+AC
Sbjct: 7   CLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNE----CEITKRRRKSCQAC 62
Query: 101 RLNKCFMSAMNKD 113
           R  K     M K+
Sbjct: 63  RFMKALKVGMLKE 75

>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 = 65.5 bits (158), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 30/75 (40%), Positives = 46/75 (61%), Gaps = 5/75 (6%)
Query: 39  IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCR 98
           + C+VCGD++SG HYG+++C+GC GFF+R+I     Y        +  C I K +RN+C+
Sbjct: 8   MECRVCGDKASGFHYGVHACEGCKGFFRRTIRMKLEYE-----KCERSCKIQKKNRNKCQ 62
Query: 99  ACRLNKCFMSAMNKD 113
            CR  KC    M+ +
Sbjct: 63  YCRFQKCLALGMSHN 77

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

Iteration: 1
 Score = 65.5 bits (158), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 32/74 (43%), Positives = 40/74 (54%), Gaps = 4/74 (5%)
Query: 40  PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRA 99
           PC VC D +SG HYG+ +C  C  FFKR++     Y C  + D    C IDK  R  C A
Sbjct: 6   PCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRND----CIIDKIRRKNCPA 61
Query: 100 CRLNKCFMSAMNKD 113
           CR  KC  + MN +
Sbjct: 62  CRYRKCLQAGMNLE 75

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

Iteration: 1
 Score = 65.1 bits (157), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 32/74 (43%), Positives = 40/74 (54%), Gaps = 4/74 (5%)
Query: 40  PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRA 99
           PC VC D +SG HYG+ +C  C  FFKR++     Y C  + D    C IDK  R  C A
Sbjct: 6   PCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRND----CIIDKIRRKNCPA 61
Query: 100 CRLNKCFMSAMNKD 113
           CR  KC  + MN +
Sbjct: 62  CRYRKCLQAGMNLE 75

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

Iteration: 1
 Score = 65.1 bits (157), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 32/74 (43%), Positives = 40/74 (54%), Gaps = 4/74 (5%)
Query: 40  PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRA 99
           PC VC D +SG HYG+ +C  C  FFKR++     Y C  + D    C IDK  R  C A
Sbjct: 6   PCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRND----CIIDKIRRKNCPA 61
Query: 100 CRLNKCFMSAMNKD 113
           CR  KC  + MN +
Sbjct: 62  CRYRKCLQAGMNLE 75

>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 = 62.8 bits (151), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 30/71 (42%), Positives = 40/71 (56%), Gaps = 4/71 (5%)
Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C +CGD +SG HYG  +C  C  FFKR+    + Y C ++ D    C IDK  R  C +C
Sbjct: 10  CLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLCASRND----CTIDKFRRKNCPSC 65
Query: 101 RLNKCFMSAMN 111
           RL KC+ + M 
Sbjct: 66  RLRKCYEAGMT 76

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

Iteration: 1
 Score = 62.8 bits (151), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 31/73 (42%), Positives = 39/73 (53%), Gaps = 4/73 (5%)
Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C VC D +SG HYG+ +C  C  FFKR++     Y C  + D    C IDK  R  C AC
Sbjct: 32  CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRND----CIIDKIRRKNCPAC 87
Query: 101 RLNKCFMSAMNKD 113
           R  KC  + MN +
Sbjct: 88  RYRKCLQAGMNLE 100

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

Iteration: 1
 Score = 62.0 bits (149), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 31/73 (42%), Positives = 39/73 (53%), Gaps = 4/73 (5%)
Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C VC D +SG HYG+ +C  C  FFKR++     Y C  + D    C IDK  R  C AC
Sbjct: 2   CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRND----CIIDKIRRKNCPAC 57
Query: 101 RLNKCFMSAMNKD 113
           R  KC  + MN +
Sbjct: 58  RYRKCLQAGMNLE 70

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

Iteration: 1
 Score = 62.0 bits (149), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 31/73 (42%), Positives = 39/73 (53%), Gaps = 4/73 (5%)
Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C VC D +SG HYG+ +C  C  FFKR++     Y C  + D    C IDK  R  C AC
Sbjct: 2   CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRND----CIIDKIRRKNCPAC 57
Query: 101 RLNKCFMSAMNKD 113
           R  KC  + MN +
Sbjct: 58  RYRKCLQAGMNLE 70

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

Iteration: 1
 Score = 62.0 bits (149), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 31/73 (42%), Positives = 39/73 (53%), Gaps = 4/73 (5%)
Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C VC D +SG HYG+ +C  C  FFKR++     Y C  + D    C IDK  R  C AC
Sbjct: 5   CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRND----CIIDKIRRKNCPAC 60
Query: 101 RLNKCFMSAMNKD 113
           R  KC  + MN +
Sbjct: 61  RYRKCLQAGMNLE 73

>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 = 62.0 bits (149), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 31/73 (42%), Positives = 39/73 (53%), Gaps = 4/73 (5%)
Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C VC D +SG HYG+ +C  C  FFKR++     Y C  + D    C IDK  R  C AC
Sbjct: 1   CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRND----CIIDKIRRKNCPAC 56
Query: 101 RLNKCFMSAMNKD 113
           R  KC  + MN +
Sbjct: 57  RYRKCLQAGMNLE 69

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

Iteration: 1
 Score = 60.8 bits (146), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 30/70 (42%), Positives = 39/70 (55%), Gaps = 4/70 (5%)
Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C +CGD +SG HYG+ +C  C  FFKR++     Y C  + D    C +DK  R  C AC
Sbjct: 5   CLICGDEASGCHYGVLTCGSCKVFFKRAMEGQHNYLCAGRND----CIVDKIRRKNCPAC 60
Query: 101 RLNKCFMSAM 110
           RL KC  + M
Sbjct: 61  RLRKCCQAGM 70

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

Iteration: 1
 Score = 60.5 bits (145), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 32/73 (43%), Positives = 39/73 (53%), Gaps = 4/73 (5%)
Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C VC D +SG HYG+ +C  C  FFKR++     Y C   GD    C IDK  R  C AC
Sbjct: 29  CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLC--AGD--NRCIIDKIRRKNCPAC 84
Query: 101 RLNKCFMSAMNKD 113
           R  KC  + MN +
Sbjct: 85  RYRKCLQAGMNLE 97

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

Iteration: 1
 Score = 60.1 bits (144), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 32/74 (43%), Positives = 40/74 (54%), Gaps = 5/74 (6%)
Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIH-RNRVYTCKAQGDLKGHCPIDKTHRNQCRA 99
           C VC D +SG HYG+ +C  C  FFKR++  R   Y C  + D    C IDK  R  C A
Sbjct: 5   CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGRQHNYLCAGRND----CIIDKIRRKNCPA 60
Query: 100 CRLNKCFMSAMNKD 113
           CR  KC  + MN +
Sbjct: 61  CRYRKCLQAGMNLE 74

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	113
2ebl_A	89	COUP transcription factor 1; DNA-binding, metal-bi	3e-36
3cbb_A	78	HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DN	2e-34
1ynw_B	99	Retinoic acid receptor RXR-alpha, retinoid X recep	4e-34
1dsz_A	86	RAR-alpha, retinoic acid receptor alpha; RAR, nucl	5e-34
2han_A	93	Protein ultraspiracle; transcription regulation, t	6e-34
1dsz_B	85	RXR-alpha, retinoic acid receptor RXR-alpha; RAR,	8e-34
1a6y_A	94	Orphan nuclear receptor NR1D1; orphan receptor, DN	2e-33
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	2e-33
1hcq_A	84	Protein (estrogen receptor); protein-DNA complex,	3e-32
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	6e-32
1cit_A	89	NGFI-B, protein (orphan nuclear receptor NGFI-B);	4e-31
3g9m_A	90	Glucocorticoid receptor; glucocorticoid, DNA-bindi	7e-31
2a66_A	113	Orphan nuclear receptor NR5A2; protein-DNA complex	1e-30
1lo1_A	98	Steroid hormone receptor ERR2; estrogen related re	3e-30
2han_B	119	Ecdysone receptor; transcription regulation, trans	3e-30
1r4i_A	105	Androgen receptor; AR, steroid receptor, protein-D	3e-29
1kb2_A	110	Vitamin D3 receptor; VDR, nuclear receptor, protei	5e-29
2nll_B	103	Protein (thyroid hormone receptor); complex (trans	8e-28

>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 =  117 bits (296), Expect = 3e-36
 Identities = 42/76 (55%), Positives = 53/76 (69%), Gaps = 4/76 (5%)

Query: 38  DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQC 97
            I C VCGD+SSGKHYG ++C+GC  FFKRS+ RN  YTC+A  +    CPID+ HRNQC
Sbjct: 7   GIECVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRANRN----CPIDQHHRNQC 62

Query: 98  RACRLNKCFMSAMNKD 113
           + CRL KC    M ++
Sbjct: 63  QYCRLKKCLKVGMRRE 78

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

 Score =  112 bits (283), Expect = 2e-34
 Identities = 39/73 (53%), Positives = 51/73 (69%), Gaps = 4/73 (5%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C +CGDR++GKHYG  SCDGC GFF+RS+ +N +Y+C+        C +DK  RNQCR C
Sbjct: 3   CAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQ----CVVDKDKRNQCRYC 58

Query: 101 RLNKCFMSAMNKD 113
           RL KCF + M K+
Sbjct: 59  RLKKCFRAGMKKE 71

>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 =  112 bits (283), Expect = 4e-34
 Identities = 38/73 (52%), Positives = 50/73 (68%), Gaps = 4/73 (5%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C +CGDRSSGKHYG+YSC+GC GFFKR++ ++  YTC+   D    C IDK  RN+C+ C
Sbjct: 6   CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKD----CLIDKRQRNRCQYC 61

Query: 101 RLNKCFMSAMNKD 113
           R  KC    M ++
Sbjct: 62  RYQKCLAMGMKRE 74

>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 =  112 bits (281), Expect = 5e-34
 Identities = 39/74 (52%), Positives = 51/74 (68%), Gaps = 4/74 (5%)

Query: 40  PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRA 99
           PC VC D+SSG HYG+ +C+GC GFF+RSI +N VYTC    +    C I+K  RN+C+ 
Sbjct: 6   PCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKN----CIINKVTRNRCQY 61

Query: 100 CRLNKCFMSAMNKD 113
           CRL KCF   M+K+
Sbjct: 62  CRLQKCFEVGMSKE 75

>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 =  112 bits (281), Expect = 6e-34
 Identities = 36/84 (42%), Positives = 50/84 (59%), Gaps = 4/84 (4%)

Query: 30  SASRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPI 89
           S          C +CGDR+SGKHYG+YSC+GC GFFKR++ ++  Y C+   +    C I
Sbjct: 2   SNHPLSGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYACRENRN----CII 57

Query: 90  DKTHRNQCRACRLNKCFMSAMNKD 113
           DK  RN+C+ CR  KC    M ++
Sbjct: 58  DKRQRNRCQYCRYQKCLTCGMKRE 81

>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 =  111 bits (279), Expect = 8e-34
 Identities = 38/78 (48%), Positives = 50/78 (64%), Gaps = 4/78 (5%)

Query: 36  LLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRN 95
                C +CGDRSSGKHYG+YSC+GC GFFKR++ ++  YTC+   D    C IDK  RN
Sbjct: 3   FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKD----CLIDKRQRN 58

Query: 96  QCRACRLNKCFMSAMNKD 113
           +C+ CR  KC    M ++
Sbjct: 59  RCQYCRYQKCLAMGMKRE 76

>1a6y_A Orphan nuclear receptor NR1D1; orphan receptor, DNA-binding, reverb, REV- ERB, transcription regulation, transcription/DNA complex; HET: DNA 5IU; 2.30A {Homo sapiens} SCOP: g.39.1.2 PDB: 1ga5_A* 1hlz_A Length = 94

 Score =  110 bits (278), Expect = 2e-33
 Identities = 33/77 (42%), Positives = 49/77 (63%), Gaps = 3/77 (3%)

Query: 37  LDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQ 96
           + + CKVCGD +SG HYG+ +C+GC GFF+RSI +N  Y    +     +C I + +RN+
Sbjct: 6   MVLLCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLK---NENCSIVRINRNR 62

Query: 97  CRACRLNKCFMSAMNKD 113
           C+ CR  KC    M++D
Sbjct: 63  CQQCRFKKCLSVGMSRD 79

>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 =  119 bits (300), Expect = 2e-33
 Identities = 40/102 (39%), Positives = 54/102 (52%), Gaps = 4/102 (3%)

Query: 12  PPRYPQYFMSRPDGRDVTSASRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHR 71
             + P             S +        C +CGDRSSGKHYG+YSC+GC GFFKR++ +
Sbjct: 111 DIKPPLGLNGVLKVPAHPSGNMASFTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRK 170

Query: 72  NRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113
           +  YTC+   D    C IDK  RN+C+ CR  KC    M ++
Sbjct: 171 DLTYTCRDNKD----CLIDKRQRNRCQYCRYQKCLAMGMKRE 208

>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 =  107 bits (269), Expect = 3e-32
 Identities = 36/76 (47%), Positives = 43/76 (56%), Gaps = 4/76 (5%)

Query: 38  DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQC 97
              C VC D +SG HYG++SC+GC  FFKRSI  +  Y C A       C IDK  R  C
Sbjct: 4   TRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQ----CTIDKNRRKSC 59

Query: 98  RACRLNKCFMSAMNKD 113
           +ACRL KC+   M K 
Sbjct: 60  QACRLRKCYEVGMMKG 75

>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 =  115 bits (288), Expect = 6e-32
 Identities = 35/108 (32%), Positives = 53/108 (49%), Gaps = 5/108 (4%)

Query: 6   GNCRQIPPRYPQYFMSRPDGRDVTSASRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFF 65
              +  P   P Y               + L+ I C+VCGD++SG HYG+++C+GC GFF
Sbjct: 18  SAIKVEPASPPYYSEKTQLYNKPHEEPSNSLMAIECRVCGDKASGFHYGVHACEGCKGFF 77

Query: 66  KRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113
           +R+I    +Y          +C I K  RN+C+ CR  KC    M+ +
Sbjct: 78  RRTIRLKLIYDRCD-----LNCRIHKKSRNKCQYCRFQKCLAVGMSHN 120

>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 =  104 bits (262), Expect = 4e-31
 Identities = 34/73 (46%), Positives = 47/73 (64%), Gaps = 4/73 (5%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C VCGD +S +HYG+ +C+GC GFFKR++ ++  Y C A  D    CP+DK  RN+C+ C
Sbjct: 3   CAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKD----CPVDKRRRNRCQFC 58

Query: 101 RLNKCFMSAMNKD 113
           R  KC    M K+
Sbjct: 59  RFQKCLAVGMVKE 71

>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 =  104 bits (260), Expect = 7e-31
 Identities = 31/74 (41%), Positives = 39/74 (52%), Gaps = 4/74 (5%)

Query: 40  PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRA 99
            C VC D +SG HYG+ +C  C  FFKR++     Y C  + D    C IDK  R  C A
Sbjct: 4   MCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRND----CIIDKIRRKNCPA 59

Query: 100 CRLNKCFMSAMNKD 113
           CR  KC  + MN +
Sbjct: 60  CRYRKCLQAGMNLE 73

>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 =  104 bits (261), Expect = 1e-30
 Identities = 35/80 (43%), Positives = 46/80 (57%), Gaps = 4/80 (5%)

Query: 34  DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTH 93
           D  L+  C VCGD+ SG HYG+ +C+ C GFFKR++  N+ YTC    +    C IDKT 
Sbjct: 5   DEDLEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQN----CQIDKTQ 60

Query: 94  RNQCRACRLNKCFMSAMNKD 113
           R +C  CR  KC    M  +
Sbjct: 61  RKRCPYCRFQKCLSVGMKLE 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 =  102 bits (257), Expect = 3e-30
 Identities = 33/74 (44%), Positives = 41/74 (55%), Gaps = 4/74 (5%)

Query: 40  PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRA 99
            C VCGD +SG HYG+ SC+ C  FFKR+I  N  Y+C A  +    C I K  R  C+A
Sbjct: 6   LCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNE----CEITKRRRKSCQA 61

Query: 100 CRLNKCFMSAMNKD 113
           CR  K     M K+
Sbjct: 62  CRFMKALKVGMLKE 75

>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 =  103 bits (258), Expect = 3e-30
 Identities = 34/82 (41%), Positives = 47/82 (57%), Gaps = 4/82 (4%)

Query: 32  SRDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDK 91
           S  R+ +  C VCGDR+SG HY   +C+GC GFF+RS+ ++ VY CK        C +D 
Sbjct: 2   SAPRVQEELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRA----CEMDM 57

Query: 92  THRNQCRACRLNKCFMSAMNKD 113
             R +C+ CRL KC    M  +
Sbjct: 58  YMRRKCQECRLKKCLAVGMRPE 79

>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 =  100 bits (251), Expect = 3e-29
 Identities = 30/74 (40%), Positives = 40/74 (54%), Gaps = 4/74 (5%)

Query: 40  PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRA 99
            C +CGD +SG HYG  +C  C  FFKR+    + Y C ++ D    C IDK  R  C +
Sbjct: 9   TCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLCASRND----CTIDKFRRKNCPS 64

Query: 100 CRLNKCFMSAMNKD 113
           CRL KC+ + M   
Sbjct: 65  CRLRKCYEAGMTLG 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 =  100 bits (250), Expect = 5e-29
 Identities = 35/80 (43%), Positives = 49/80 (61%), Gaps = 4/80 (5%)

Query: 34  DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTH 93
           DR +   C VCGDR++G H+   +C+GC GFF+RS+ R  ++TC   GD    C I K +
Sbjct: 2   DRNVPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGD----CRITKDN 57

Query: 94  RNQCRACRLNKCFMSAMNKD 113
           R  C+ACRL +C    M K+
Sbjct: 58  RRHCQACRLKRCVDIGMMKE 77

>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 = 96.7 bits (241), Expect = 8e-28
 Identities = 36/78 (46%), Positives = 47/78 (60%), Gaps = 6/78 (7%)

Query: 38  DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRN--RVYTCKAQGDLKGHCPIDKTHRN 95
           D  C VCGD+++G HY   +C+GC GFF+R+I +N    Y+CK +G     C IDK  RN
Sbjct: 1   DELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEGK----CVIDKVTRN 56

Query: 96  QCRACRLNKCFMSAMNKD 113
           QC+ CR  KC    M  D
Sbjct: 57  QCQECRFKKCIYVGMATD 74

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	113
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
1dsz_B	85	RXR-alpha, retinoic acid receptor RXR-alpha; RAR,	99.96
1hcq_A	84	Protein (estrogen receptor); protein-DNA complex,	99.96
2han_A	93	Protein ultraspiracle; transcription regulation, t	99.96
1ynw_B	99	Retinoic acid receptor RXR-alpha, retinoid X recep	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
3g9m_A	90	Glucocorticoid receptor; glucocorticoid, DNA-bindi	99.95
2han_B	119	Ecdysone receptor; transcription regulation, trans	99.95
1kb2_A	110	Vitamin D3 receptor; VDR, nuclear receptor, protei	99.95
4hn5_A	117	Glucocorticoid receptor; glucocorticoid receptor,	99.95
1r4i_A	105	Androgen receptor; AR, steroid receptor, protein-D	99.95
2nll_B	103	Protein (thyroid hormone receptor); complex (trans	99.95
2a66_A	113	Orphan nuclear receptor NR5A2; protein-DNA complex	99.95
1a6y_A	94	Orphan nuclear receptor NR1D1; orphan receptor, DN	99.95
1lo1_A	98	Steroid hormone receptor ERR2; estrogen related re	99.95
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	99.93
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	99.92
2lze_A	87	A primordial catalytic fold generated by in vitro	99.74

>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=2e-30  Score=165.15  Aligned_cols=70  Identities=56%  Similarity=1.286  Sum_probs=66.3

Q ss_pred             CceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         40 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        40 ~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      +|.|||++++|+||||.+|++|++||||++..+..|.|..++    +|.|++..|+.|++|||+|||++||++|
T Consensus         2 ~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~   71 (78)
T 3cbb_A            2 LCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSR----QCVVDKDKRNQCRYCRLKKCFRAGMKKE   71 (78)
T ss_dssp             BCTTTSSBCCSEETTEECCHHHHHHHHHHHHTTCCCCCSSCS----CCCCSTTTTTTCHHHHHHHHHHHTCCGG
T ss_pred             CCeEeCCCCCceEeCCcchhhhceeeeEEEecccCccccccc----ccCcCccccccChhhhhHHHhHcCCCHH
Confidence            699999999999999999999999999999999999998864    7999999999999999999999999975

>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=2.3e-30  Score=168.58  Aligned_cols=72  Identities=58%  Similarity=1.290  Sum_probs=67.2

Q ss_pred             CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      +.+|.|||++++|+||||.+|++|++||||++..+..|.|..++    +|.|++..|+.|++|||+|||++||++|
T Consensus         7 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~   78 (89)
T 2ebl_A            7 GIECVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRANR----NCPIDQHHRNQCQYCRLKKCLKVGMRRE   78 (89)
T ss_dssp             SCBCTTTCSBCCSEETTEECCHHHHHHHHHHHTTTCCCCCSSCS----CCCCCSSSSSCCSHHHHHHHHHHTCCHH
T ss_pred             CCCCcEeCCCCcceEeCchhhHHhhhhhheeeeeccceecccCc----cCCcCccCccccccchHHHhhhccCCHH
Confidence            46799999999999999999999999999999999999998764    7999999999999999999999999864

>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=2.3e-30  Score=167.26  Aligned_cols=72  Identities=51%  Similarity=1.218  Sum_probs=67.5

Q ss_pred             CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      +.+|.|||++++|+||||.+|++|++||||++..+..|.|..++    +|.|++..|+.|++|||+|||++||++|
T Consensus         5 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~   76 (85)
T 1dsz_B            5 KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNK----DCLIDKRQRNRCQYCRYQKCLAMGMKRE   76 (85)
T ss_dssp             CEECTTTCCEESSEETTEECCHHHHHHHHHHHHHTCCCCCSSCS----CCCCCTTTTTTCHHHHHHHHHHTTCCGG
T ss_pred             CCCCCEeCCCCCceeeCccchHHHHHHHHHhhccccceeecccc----cccccccccccCcchhHHHHhHcCCCHH
Confidence            46799999999999999999999999999999999999998864    6999999999999999999999999875

>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=165.60  Aligned_cols=72  Identities=50%  Similarity=1.074  Sum_probs=67.1

Q ss_pred             CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      ..+|.|||++++|+||||.+|++|++||||++..+..|.|..++    +|.|++..|+.|++|||+|||++||++|
T Consensus         4 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~   75 (84)
T 1hcq_A            4 TRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATN----QCTIDKNRRKSCQACRLRKCYEVGMMKG   75 (84)
T ss_dssp             CCBCTTTCSBCCEEETTEEECHHHHHHHHHHHSSCCCCCCSSSS----CCCCSTTTTTTCHHHHHHHHHHHTCCC-
T ss_pred             CCcCcEECCCCCCeeeCccchHHhhhhhhhccccccccccccCc----cCCcCCcCcccChhhhhHHHhHcCCCHH
Confidence            46899999999999999999999999999999999999998864    7999999999999999999999999975

>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=3.3e-30  Score=169.06  Aligned_cols=72  Identities=49%  Similarity=1.220  Sum_probs=67.4

Q ss_pred             CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      ..+|.|||++++|+||||.+|++|++||||++..+..|.|..++    +|.|+...|+.|++|||+|||++||++|
T Consensus        10 ~~~C~VCgd~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~   81 (93)
T 2han_A           10 KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYACRENR----NCIIDKRQRNRCQYCRYQKCLTCGMKRE   81 (93)
T ss_dssp             CCBCTTTCSBCCEEETTEEECHHHHHHHHHHHHHTCCCCCSSCS----CCCCSTTTGGGCHHHHHHHHHHHTCCGG
T ss_pred             CCCCcEeCCCCcCeecCcchhHHHHHHHHhhhccccCcCcCCCC----cCCcCCCCCccCccccHHHHhHhCCCHH
Confidence            36799999999999999999999999999999999999998864    7999999999999999999999999875

>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=99.96  E-value=6.1e-30  Score=169.48  Aligned_cols=72  Identities=51%  Similarity=1.218  Sum_probs=66.6

Q ss_pred             CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      ..+|.|||++++|+||||.+|++|++||||++..+..|.|..++    +|.|++..|+.|++|||+|||++||++|
T Consensus         3 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~   74 (99)
T 1ynw_B            3 KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNK----DCLIDKRQRNRCQYCRYQKCLAMGMKRE   74 (99)
T ss_dssp             --CBTTTBSCCCBCCTTSCBCSHHHHHHHHHHHTTCCCCCSSSS----CCCCCSTTSSSCHHHHHHHHHHTTCCST
T ss_pred             CCCCceeCCCCcceeeCccchHHHHHHHHhhhccccccccCCCC----cccccccCCccCccccHHHHhHcCCCHH
Confidence            46899999999999999999999999999999999999998864    6999999999999999999999999975

>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=165.49  Aligned_cols=72  Identities=54%  Similarity=1.168  Sum_probs=66.3

Q ss_pred             CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      ..+|.|||++++|+||||.+|++|++||||++..+..|.|..++    +|.|+...|+.|++|||+|||++||++|
T Consensus         4 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~   75 (86)
T 1dsz_A            4 YKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDK----NCIINKVTRNRCQYCRLQKCFEVGMSKE   75 (86)
T ss_dssp             --CCTTTCSCCCSEETTEECCHHHHHHHHHHHHTTCCCCCSSCS----CCCCSTTTGGGCHHHHHHHHHHTTCCGG
T ss_pred             CCCCcEECCCccceeeCchhHHHHHHHHHHHhhcccceeeccCC----ccccCccccccchhhhHHHHHHhCCCHH
Confidence            35799999999999999999999999999999999999998764    7999999999999999999999999875

>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=8.3e-30  Score=165.95  Aligned_cols=71  Identities=46%  Similarity=1.120  Sum_probs=66.6

Q ss_pred             CCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         39 IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        39 ~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      ++|.|||++++|+||||.+|++|++||||++..+..|.|..++    +|.|++..|+.|++|||+|||++||++|
T Consensus         1 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~   71 (89)
T 1cit_A            1 GRCAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANK----DCPVDKRRRNRCQFCRFQKCLAVGMVKE   71 (89)
T ss_dssp             CCCSSSCCCCCEEETTEEECHHHHHHHHHHHHHTCCCCCSSSS----CCCCSTTTTTTCHHHHHHHHHHTTCCGG
T ss_pred             CCCeEeCCCCcceEeCccchhhhhhhceeeEEecceeeeccCC----ccccCCCCcccChhhhhHHHhHcCCCHH
Confidence            3699999999999999999999999999999999999998864    7999999999999999999999999875

>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=2.9e-29  Score=163.65  Aligned_cols=71  Identities=42%  Similarity=0.962  Sum_probs=67.1

Q ss_pred             CCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         39 IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        39 ~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      .+|.|||++++|+||||.+|++|++||||++..+..|.|..++    +|.|+...|+.|++|||+|||++||++|
T Consensus         3 ~~C~VCg~~a~g~hyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~C~~CR~~KCl~~GM~~~   73 (90)
T 3g9m_A            3 HMCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRN----DCIIDKIRRKNCPACRYRKCLQAGMNLE   73 (90)
T ss_dssp             CBCTTTCSBCCEEETTEEECHHHHHHHHHHHHSCCCCCCSSSS----CCCCCTTGGGTCHHHHHHHHHHHTCCTT
T ss_pred             CcCccCCCcCcccccCCccchhHhHHhhhhhhcCCceeCCCCC----ccccCcccccCCcchhhHHHHHcCCCHH
Confidence            5799999999999999999999999999999999999998764    7999999999999999999999999975

>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=2.5e-29  Score=171.37  Aligned_cols=73  Identities=44%  Similarity=1.022  Sum_probs=68.0

Q ss_pred             CCCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         37 LDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        37 ~~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      ...+|.|||++++|+||||.+|++|++||||++..+..|.|..++    +|.|+...|+.|++|||+|||++||+++
T Consensus         7 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~   79 (119)
T 2han_B            7 QEELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGR----ACEMDMYMRRKCQECRLKKCLAVGMRPE   79 (119)
T ss_dssp             CSCBCTTTCSBCCEEETTEEECHHHHHHHHHHHHTTCCCCCSSCS----CCCCSTTGGGTCHHHHHHHHHHTTCCGG
T ss_pred             CCCcCeEeCCcCCcceECchhHHhhHHhhhhheEecccccccccc----ccccCccccccchhhHHHHHHHhCCCHH
Confidence            357899999999999999999999999999999999999998864    6999999999999999999999999874

>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=2.9e-29  Score=168.99  Aligned_cols=72  Identities=44%  Similarity=1.061  Sum_probs=67.1

Q ss_pred             CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      +.+|.|||+.++|+||||.+|++|++||||++..+..|.|..++    +|.|++..|+.|++|||+|||++||++|
T Consensus         6 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~   77 (110)
T 1kb2_A            6 PRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNG----DCRITKDNRRHCQACRLKRCVDIGMMKE   77 (110)
T ss_dssp             -CBCTTTCSBCCSEETTEECCHHHHHHHHHHHHTTCCCCCSSCS----CCCCCTTTTTTCHHHHHHHHHHTTCCGG
T ss_pred             CCCCcEeCCCCCceEeCchhHhhhhhhheeeeecccceeeCCCC----CccCCcccceecccccHhhhhhcCCcHH
Confidence            46799999999999999999999999999999999999998864    7999999999999999999999999875

>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=3.3e-29  Score=170.27  Aligned_cols=72  Identities=42%  Similarity=0.947  Sum_probs=67.2

Q ss_pred             CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      +.+|.|||++++|+||||.+|++|++||||++..+..|.|..++    +|.|+...|+.|++|||+|||++||++|
T Consensus        29 ~~~C~VCgd~a~G~HyGv~sC~aCk~FFRRsv~~~~~y~C~~~~----~C~i~~~~r~~Cr~CRl~KCl~vGM~~~  100 (117)
T 4hn5_A           29 PKLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRN----DCIIDKIRRKNCPACRYRKCLQAGMNLE  100 (117)
T ss_dssp             -CBCTTTCSBCCEEETTEEECHHHHHHHHHHHSSCCCCCCSSSS----CCCCSTTTTTTCHHHHHHHHHHHTCCTT
T ss_pred             CCcCCcCCCcCcccccCCcccchhhhhhhcceecCCceecCCCC----ccccCcccccCCcccchHHHhHcCCCHH
Confidence            46799999999999999999999999999999999999998764    7999999999999999999999999975

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

Probab=99.95  E-value=3.2e-29  Score=167.57  Aligned_cols=72  Identities=40%  Similarity=0.977  Sum_probs=67.5

Q ss_pred             CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      ..+|.|||++++|+||||.+|++|++||||++..+..|.|..++    +|.|++..|+.|++|||+|||++||+++
T Consensus         7 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~   78 (105)
T 1r4i_A            7 QKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLCASRN----DCTIDKFRRKNCPSCRLRKCYEAGMTLG   78 (105)
T ss_dssp             CCBCSSSCSBEEEEETTEEEEHHHHHHHHHHHTSCCCCCCSSSS----CCCCCTTTTTTCHHHHHHHHHHHTCCSC
T ss_pred             CCCCcEeCCCCCceEeCCcchhhhhhhhceeEEecCceeeccCC----ccccCccccccchhchHHHHHhhhcccc
Confidence            46899999999999999999999999999999999999998864    6999999999999999999999999875

>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=99.95  E-value=4.4e-29  Score=166.40  Aligned_cols=71  Identities=49%  Similarity=1.138  Sum_probs=65.9

Q ss_pred             CCceecCCCCcceeeccccchhhHHHHHHHhhcCc--ccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         39 IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNR--VYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        39 ~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~--~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      ++|.|||++++|+||||.+|++|++||||++..+.  .|.|..++    +|.|+...|+.|++|||+|||++||++|
T Consensus         2 ~~C~VCgd~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~y~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~   74 (103)
T 2nll_B            2 ELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEG----KCVIDKVTRNQCQECRFKKCIYVGMATD   74 (103)
T ss_dssp             CBCTTTCSBCCSEETTEECCHHHHHHHHHHHHTTCGGGCCCSSCT----TCCCSTTTTTSCHHHHHHHHHHTTCCGG
T ss_pred             CCCeEeCCcCcCeecCcccHHHhhhhheecccccccchhhhhccC----CcCcCccCccccchhhhHhhhHhCCCHH
Confidence            57999999999999999999999999999999875  68998764    7999999999999999999999999875

>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=2.7e-29  Score=169.79  Aligned_cols=72  Identities=46%  Similarity=1.089  Sum_probs=67.1

Q ss_pred             CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      ..+|.|||++++|+||||.+|++|++||||++..+..|.|..++    +|.|+...|+.|++|||+|||++||+++
T Consensus         9 ~~~C~VCgd~a~G~HyGv~sC~aCk~FFRR~v~~~~~y~C~~~~----~C~i~~~~R~~Cr~CR~~KCl~vGM~~~   80 (113)
T 2a66_A            9 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQ----NCQIDKTQRKRCPYCRFQKCLSVGMKLE   80 (113)
T ss_dssp             -CBCTTTCCBEEEEETTEEEEHHHHHHHHHHHHTTCCCCCSSCS----CCCCCTTTTTTCHHHHHHHHHHTTCCGG
T ss_pred             CCCCcEeCCCCcceeeCcccHHHHHHHHhhhhhccccccccccc----cCCcCCCccccccchhHHHHhHhCCCHH
Confidence            46899999999999999999999999999999999999998864    7999999999999999999999999874

>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=3.9e-29  Score=164.25  Aligned_cols=71  Identities=48%  Similarity=1.139  Sum_probs=66.3

Q ss_pred             CCceecCCCCcceeeccccchhhHHHHHHHhhcCccc-ccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         39 IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVY-TCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        39 ~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~-~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      .+|.|||++++|+||||.+|++|++||||++..+..| .|..++    +|.|+...|+.|++|||+|||++||++|
T Consensus         8 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~   79 (94)
T 1a6y_A            8 LLCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNE----NCSIVRINRNRCQQCRFKKCLSVGMSRD   79 (94)
T ss_dssp             CBCTTTSSBCCEEETTEEECHHHHHHHHHHHSSCCCCCCCSSTT----CCCCCTTTTTSCHHHHHHHHTTTTCCST
T ss_pred             CcCcEeCCCCcceEeCccchhhhhhehheeeecccceEEccCCC----CCccCccccccccchhHHHhhHccCCHH
Confidence            5799999999999999999999999999999998888 598764    7999999999999999999999999975

>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=9.4e-30  Score=168.28  Aligned_cols=72  Identities=46%  Similarity=0.945  Sum_probs=67.3

Q ss_pred             CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      ..+|.|||++++|+||||.+|++|++||||++..+..|.|..++    +|.|++..|+.|++|||+|||++||++|
T Consensus         4 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~   75 (98)
T 1lo1_A            4 KRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATN----ECEITKRRRKSCQACRFMKALKVGMLKE   75 (98)
T ss_dssp             CCEETTTTEECSEESSSSEECHHHHHHHHHHHHTTCCCCCSSCS----CCCCCHHHHHHCHHHHHHHHHHHTCCGG
T ss_pred             CCCCcEeCCCCcCeeeCccchhhhhhhheeeecccCccccCccc----cccccccccccccchhHHHHhHcCCCHH
Confidence            46899999999999999999999999999999999999998864    6999998899999999999999999875

>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=99.93  E-value=1.3e-26  Score=184.96  Aligned_cols=72  Identities=46%  Similarity=1.137  Sum_probs=64.1

Q ss_pred             CCCCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccc-cccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         36 LLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYT-CKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        36 ~~~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~-C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      .....|.|||++++|+||||.+|++|++||||++..+..|. |.      ++|.+++..|++|++|||+||+++||+++
T Consensus        48 ~~~~~C~vC~~~~~g~hygv~~C~~C~~FFrR~~~~~~~~~~c~------~~C~~~~~~r~~C~~CR~~kCl~~GM~~~  120 (419)
T 3dzy_D           48 LMAIECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLIYDRCD------LNCRIHKKSRNKCQYCRFQKCLAVGMSHN  120 (419)
T ss_dssp             --CCCCSSSCSCCCSBCSSSBCCHHHHHHHHHHHTTTCCCCCCC------SCCCCCTTGGGTCHHHHHHHHHHTTCCGG
T ss_pred             CCCCcCeECCCcCCCCccCcccchhhhHHHccchhccccccccc------CCCCcccccCccchhhhHHHHhhcccchh
Confidence            34568999999999999999999999999999999888774 53      26999999999999999999999999874

>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=1.6e-26  Score=186.83  Aligned_cols=72  Identities=51%  Similarity=1.218  Sum_probs=67.3

Q ss_pred             CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      ...|.|||++++|+||||.+|++|++||||++..+..|.|+.++    +|.+++..|++|++|||+||+++||+++
T Consensus       137 ~~~C~VCg~~a~g~hygv~sC~~Ck~FFrR~~~~~~~~~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~  208 (467)
T 3dzy_A          137 KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNK----DCLIDKRQRNRCQYCRYQKCLAMGMKRE  208 (467)
T ss_dssp             CEECTTTSSEECSEETTEECCHHHHHHHHHHHHTTCCCCCSSSS----CCCCCSSSSSSCHHHHHHHHHHTTCCGG
T ss_pred             CCcceeCCCCCCCCcCCCcchhhhhHhccccccCCCceeCCCCC----CCCCCcccccccccchhhhhhhccccch
Confidence            45699999999999999999999999999999999999998864    7999999999999999999999999864

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

Probab=99.74  E-value=2.1e-19  Score=116.27  Aligned_cols=60  Identities=20%  Similarity=0.355  Sum_probs=48.6

Q ss_pred             CcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         48 SSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        48 ~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      +.+.||+++ |.+|++||||++ .+..|.|+.++    +|.|++..|++|++|||+|||+|||+.+
T Consensus        14 ~~g~h~c~v-Cgd~asfFRRt~-~~~~y~C~~~~----~C~i~~~~R~~C~~CR~qKCl~VgM~~~   73 (87)
T 2lze_A           14 RGGKHICAI-CGNNAEDYKHTD-MDLTYTDRDYK----NCESYHKCSDLCQYCRYQKDLAIHHQHH   73 (87)
T ss_dssp             SCCSSSCSS-SSSSSSSCTTTT-TSCTTTSCCCC----CCCCSSCCSSSCSGGGTSCCHHHHCSSC
T ss_pred             CCCCEEccC-CCCccceECccc-CCCeeEcCCCC----ccccCCCccCcCCcccChhhccCcCEec
Confidence            345555553 666888999985 56778998764    7999999999999999999999999753

---

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	113
d1dszb_	84	g.39.1.2 (B:) Retinoid X receptor (RXR-alpha) DNA-	2e-18
d1kb2a_	89	g.39.1.2 (A:) Vitamin D3 receptor, VDR, DNA-bindin	3e-17
d1r4ia_	74	g.39.1.2 (A:) Androgen receptor {Rat (Rattus norve	5e-17
d1lata_	71	g.39.1.2 (A:) Glucocorticoid receptor DNA-binding	6e-17
d1dsza_	75	g.39.1.2 (A:) Retinoic acid receptor DNA-binding d	6e-17
d1a6ya_	78	g.39.1.2 (A:) Orphan nuclear receptor reverb DNA-b	8e-17
d1lo1a_	90	g.39.1.2 (A:) Steroid hormone receptor Err2 DNA-bi	8e-17
d1cita_	89	g.39.1.2 (A:) Orphan nuclear receptor NGFI-B DNA-b	1e-16
d2hanb1	83	g.39.1.2 (B:5-87) Ecdysone receptor DNA-binding do	2e-16
d2nllb_	103	g.39.1.2 (B:) Thyroid hormone receptor (TR-beta) D	1e-15
d1hcqa_	74	g.39.1.2 (A:) Estrogen receptor DNA-binding domain	2e-15

>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 = 71.1 bits (174), Expect = 2e-18
 Identities = 37/73 (50%), Positives = 49/73 (67%), Gaps = 4/73 (5%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C +CGDRSSGKHYG+YSC+GC GFFKR++ ++  YTC+        C IDK  RN+C+ C
Sbjct: 8   CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDN----KDCLIDKRQRNRCQYC 63

Query: 101 RLNKCFMSAMNKD 113
           R  KC    M ++
Sbjct: 64  RYQKCLAMGMKRE 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 = 68.5 bits (167), Expect = 3e-17
 Identities = 32/73 (43%), Positives = 45/73 (61%), Gaps = 4/73 (5%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C VCGDR++G H+   +C+GC GFF+RS+ R  ++TC       G C I K +R  C+AC
Sbjct: 3   CGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFN----GDCRITKDNRRHCQAC 58

Query: 101 RLNKCFMSAMNKD 113
           RL +C    M K+
Sbjct: 59  RLKRCVDIGMMKE 71

>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 = 67.4 bits (164), Expect = 5e-17
 Identities = 29/74 (39%), Positives = 39/74 (52%), Gaps = 4/74 (5%)

Query: 40  PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRA 99
            C +CGD +SG HYG  +C  C  FFKR+    + Y C +    +  C IDK  R  C +
Sbjct: 4   TCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLCAS----RNDCTIDKFRRKNCPS 59

Query: 100 CRLNKCFMSAMNKD 113
           CRL KC+ + M   
Sbjct: 60  CRLRKCYEAGMTLG 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 = 67.4 bits (164), Expect = 6e-17
 Identities = 34/74 (45%), Positives = 43/74 (58%), Gaps = 4/74 (5%)

Query: 40  PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRA 99
           PC VC D +SG HYG+ +C+GC  FFKR++     Y CK +    G C IDK  R  C A
Sbjct: 2   PCLVCSDEASGCHYGVLTCEGCKAFFKRAVEGQHNYLCKYE----GKCIIDKIRRKNCPA 57

Query: 100 CRLNKCFMSAMNKD 113
           CR  KC  + MN +
Sbjct: 58  CRYRKCLQAGMNLE 71

>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 = 67.4 bits (164), Expect = 6e-17
 Identities = 39/74 (52%), Positives = 51/74 (68%), Gaps = 4/74 (5%)

Query: 40  PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRA 99
           PC VC D+SSG HYG+ +C+GC GFF+RSI +N VYTC        +C I+K  RN+C+ 
Sbjct: 1   PCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRD----KNCIINKVTRNRCQY 56

Query: 100 CRLNKCFMSAMNKD 113
           CRL KCF   M+K+
Sbjct: 57  CRLQKCFEVGMSKE 70

>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 = 66.9 bits (163), Expect = 8e-17
 Identities = 33/73 (45%), Positives = 47/73 (64%), Gaps = 3/73 (4%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           CKVCGD +SG HYG+ +C+GC GFF+RSI +N  Y    +     +C I + +RN+C+ C
Sbjct: 3   CKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKN---ENCSIVRINRNRCQQC 59

Query: 101 RLNKCFMSAMNKD 113
           R  KC    M++D
Sbjct: 60  RFKKCLSVGMSRD 72

>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 = 67.3 bits (164), Expect = 8e-17
 Identities = 33/74 (44%), Positives = 41/74 (55%), Gaps = 4/74 (5%)

Query: 40  PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRA 99
            C VCGD +SG HYG+ SC+ C  FFKR+I  N  Y+C A  +    C I K  R  C+A
Sbjct: 6   LCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNE----CEITKRRRKSCQA 61

Query: 100 CRLNKCFMSAMNKD 113
           CR  K     M K+
Sbjct: 62  CRFMKALKVGMLKE 75

>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 = 66.6 bits (162), Expect = 1e-16
 Identities = 34/74 (45%), Positives = 47/74 (63%), Gaps = 4/74 (5%)

Query: 40  PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRA 99
            C VCGD +S +HYG+ +C+GC GFFKR++ ++  Y C A  D    CP+DK  RN+C+ 
Sbjct: 2   RCAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKD----CPVDKRRRNRCQF 57

Query: 100 CRLNKCFMSAMNKD 113
           CR  KC    M K+
Sbjct: 58  CRFQKCLAVGMVKE 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 = 66.5 bits (162), Expect = 2e-16
 Identities = 32/73 (43%), Positives = 43/73 (58%), Gaps = 4/73 (5%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C VCGDR+SG HY   +C+GC GFF+RS+ ++ VY CK        C +D   R +C+ C
Sbjct: 3   CLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRA----CEMDMYMRRKCQEC 58

Query: 101 RLNKCFMSAMNKD 113
           RL KC    M  +
Sbjct: 59  RLKKCLAVGMRPE 71

>d2nllb_ g.39.1.2 (B:) Thyroid hormone receptor (TR-beta) DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Length = 103

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

 Score = 64.8 bits (157), Expect = 1e-15
 Identities = 32/73 (43%), Positives = 44/73 (60%), Gaps = 2/73 (2%)

Query: 41  CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRAC 100
           C VCGD+++G HY   +C+GC GFF+R+I +N   +   + +  G C IDK  RNQC+ C
Sbjct: 4   CVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYE--GKCVIDKVTRNQCQEC 61

Query: 101 RLNKCFMSAMNKD 113
           R  KC    M  D
Sbjct: 62  RFKKCIYVGMATD 74

>d1hcqa_ g.39.1.2 (A:) Estrogen receptor DNA-binding domain {Human and chicken (Homo sapiens) and (Gallus gallus) [TaxId: 9606]} Length = 74

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Estrogen receptor DNA-binding domain
species: Human and chicken (Homo sapiens) and (Gallus gallus) [TaxId: 9606]

 Score = 63.2 bits (153), Expect = 2e-15
 Identities = 36/73 (49%), Positives = 43/73 (58%), Gaps = 4/73 (5%)

Query: 40  PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRA 99
            C VC D +SG HYG++SC+GC  FFKRSI  +  Y C A       C IDK  R  C+A
Sbjct: 6   YCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPAT----NQCTIDKNRRKSCQA 61

Query: 100 CRLNKCFMSAMNK 112
           CRL KC+   M K
Sbjct: 62  CRLRKCYEVGMMK 74

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	113
d1lata_	71	Glucocorticoid receptor DNA-binding domain {Rat (R	99.96
d1r4ia_	74	Androgen receptor {Rat (Rattus norvegicus) [TaxId:	99.96
d1dsza_	75	Retinoic acid receptor DNA-binding domain {Human (	99.96
d1dszb_	84	Retinoid X receptor (RXR-alpha) DNA-binding domain	99.96
d1hcqa_	74	Estrogen receptor DNA-binding domain {Human and ch	99.96
d2nllb_	103	Thyroid hormone receptor (TR-beta) DNA-binding dom	99.96
d1kb2a_	89	Vitamin D3 receptor, VDR, DNA-binding domain {Huma	99.95
d2hanb1	83	Ecdysone receptor DNA-binding domain {Fruit fly (D	99.95
d1a6ya_	78	Orphan nuclear receptor reverb DNA-binding domain	99.95
d1lo1a_	90	Steroid hormone receptor Err2 DNA-binding domain {	99.95
d1cita_	89	Orphan nuclear receptor NGFI-B DNA-binding domain	99.95

>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=99.96  E-value=7.3e-31  Score=163.02  Aligned_cols=71  Identities=48%  Similarity=1.102  Sum_probs=66.9

Q ss_pred             CCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         39 IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        39 ~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      .+|.||+++++|+||||.+|+||++||||++..+..+.|..++    +|.++...+..|++|||+|||++||++|
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 RPCLVCSDEASGCHYGVLTCEGCKAFFKRAVEGQHNYLCKYEG----KCIIDKIRRKNCPACRYRKCLQAGMNLE   71 (71)
T ss_dssp             CBCTTTCSBCCEEETTEEECHHHHHHHHHHHHSCCCCCCSSCS----CCCCSTTTTTTCHHHHHHHHHHTTCCCC
T ss_pred             CcCeeCCCcCCceEcCHhhHHHHHHHHHHHHhcCcceeeecCc----ccccccCccccCCccchhHHhHccCCCC
Confidence            3699999999999999999999999999999999999998764    7999999999999999999999999987

>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=99.96  E-value=6.6e-31  Score=164.37  Aligned_cols=72  Identities=40%  Similarity=0.977  Sum_probs=67.7

Q ss_pred             CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      +++|.|||++++|+||||.+|++|++||||++..+..+.|..++    +|.|+...|..|++|||+|||++||+.|
T Consensus         2 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~c~~~~----~C~~~~~~r~~C~~CR~~KCl~vGM~~~   73 (74)
T d1r4ia_           2 QKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLCASRN----DCTIDKFRRKNCPSCRLRKCYEAGMTLG   73 (74)
T ss_dssp             CCBCSSSCSBEEEEETTEEEEHHHHHHHHHHHTSCCCCCCSSSS----CCCCCTTTTTTCHHHHHHHHHHHTCCSC
T ss_pred             CCcCccCCCcCCccCCCHHhhHHHHHHHHHHHhcccceeeecCC----CcccCCCCcccchhhhHHHHHHcCCcCC
Confidence            46799999999999999999999999999999999999998864    7999999999999999999999999986

>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=99.96  E-value=3.4e-30  Score=161.48  Aligned_cols=70  Identities=56%  Similarity=1.225  Sum_probs=66.0

Q ss_pred             CceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         40 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        40 ~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      +|.|||++++|+||||.+|+||++||||++..+..+.|..++    +|.++...+..|++|||+|||++||++|
T Consensus         1 PC~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~c~~~~----~c~~~~~~r~~Cr~CR~~KCl~~GM~~~   70 (75)
T d1dsza_           1 PCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDK----NCIINKVTRNRCQYCRLQKCFEVGMSKE   70 (75)
T ss_dssp             CCTTTCSCCCSEETTEECCHHHHHHHHHHHHTTCCCCCSSCS----CCCCSTTTGGGCHHHHHHHHHHTTCCGG
T ss_pred             CCccCCCcCCccCcCHHHhhhhHHHHHHHHhcCCceecccCC----ccccCCccccccchhHHHHHHHhCCCHH
Confidence            699999999999999999999999999999999999998764    6999999999999999999999999975

>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=99.96  E-value=2.5e-30  Score=165.19  Aligned_cols=72  Identities=51%  Similarity=1.218  Sum_probs=67.2

Q ss_pred             CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      +.+|.||+++++|+||||.+|+||++||||++.....+.|..++    +|.++...|..|++|||+|||++||+++
T Consensus         5 ~~~C~VC~~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~c~~~~----~C~~~~~~r~~Cr~CR~~KCl~vGM~~~   76 (84)
T d1dszb_           5 KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNK----DCLIDKRQRNRCQYCRYQKCLAMGMKRE   76 (84)
T ss_dssp             CEECTTTCCEESSEETTEECCHHHHHHHHHHHHHTCCCCCSSCS----CCCCCTTTTTTCHHHHHHHHHHTTCCGG
T ss_pred             CCcCccCCCcCCccCCCHHHHHHhHHHHHHHHhcCCCeeccCCC----CcccCCCCCccCCCCccHHHHHcCCChH
Confidence            46899999999999999999999999999999999999998764    7999999999999999999999999875

>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=99.96  E-value=8.2e-30  Score=159.36  Aligned_cols=71  Identities=51%  Similarity=1.088  Sum_probs=66.8

Q ss_pred             CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCC
Q psy16245         38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNK  112 (113)
Q Consensus        38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~  112 (113)
                      ..+|.|||++++++||||.+|+||++||||++..+..+.|..++    +|.|+...|+.|++|||+|||++||++
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 TRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATN----QCTIDKNRRKSCQACRLRKCYEVGMMK   74 (74)
T ss_dssp             CCBCTTTCSBCCEEETTEEECHHHHHHHHHHHSSCCCCCCSSSS----CCCCSTTTTTTCHHHHHHHHHHHTCCC
T ss_pred             CCCCccCCCcCCceEcCeeehHHHHHHHHHHHHcccccccccCC----CCccCCCccccchHhhHHHHHHcCCcC
Confidence            46799999999999999999999999999999999999998764    799999999999999999999999985

>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=99.96  E-value=1e-29  Score=167.91  Aligned_cols=73  Identities=44%  Similarity=0.990  Sum_probs=64.7

Q ss_pred             CCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         39 IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        39 ~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      ++|.|||++++|+||||.+|+||++||||++..+..+.|...++  +.|.++...|..|++|||+|||+|||+++
T Consensus         2 ~~C~VCg~~a~g~HfGv~sC~aCkaFFRR~v~~~~~~~~~c~~~--~~c~~~~~~r~~Cr~CR~~KCl~vGM~~~   74 (103)
T d2nllb_           2 ELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYE--GKCVIDKVTRNQCQECRFKKCIYVGMATD   74 (103)
T ss_dssp             CBCTTTCSBCCSEETTEECCHHHHHHHHHHHHTTCGGGCCCSSC--TTCCCSTTTTTSCHHHHHHHHHHTTCCGG
T ss_pred             CcCccCCCcCCcccCchhhhHHHHHHhHHHhhccccceeecccC--CCCcCCCCccCCCccccchhHHHhhccHH
Confidence            57999999999999999999999999999999887766543322  47999999999999999999999999874

>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=8.9e-30  Score=164.23  Aligned_cols=71  Identities=45%  Similarity=1.079  Sum_probs=66.5

Q ss_pred             CCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         39 IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        39 ~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      .+|.|||++++|+||||.+|+||++||||++.....+.|..++    +|.|+...|+.|++|||+|||++||+++
T Consensus         1 r~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~c~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~   71 (89)
T d1kb2a_           1 RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNG----DCRITKDNRRHCQACRLKRCVDIGMMKE   71 (89)
T ss_dssp             CBCTTTCSBCCSEETTEECCHHHHHHHHHHHHTTCCCCCSSCS----CCCCCTTTTTTCHHHHHHHHHHTTCCGG
T ss_pred             CCCeeCCCcCCccCCCHHHHHHHHHHHHHHHhcCCCeecCCCC----ccCCCCcCCccCchhhHHHHHHcCCCHh
Confidence            3699999999999999999999999999999999999998764    7999999999999999999999999875

>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=7.5e-30  Score=162.68  Aligned_cols=71  Identities=45%  Similarity=1.046  Sum_probs=66.4

Q ss_pred             CCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         39 IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        39 ~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      ++|.|||++++|+||||.+|+||++||||++..+..|.|..++    +|.++...+..|++|||+|||++||++|
T Consensus         1 e~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~c~~~~----~C~~~~~~r~~Cr~CR~~KCl~vGM~~~   71 (83)
T d2hanb1           1 ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGR----ACEMDMYMRRKCQECRLKKCLAVGMRPE   71 (83)
T ss_dssp             CBCTTTCSBCCEEETTEEECHHHHHHHHHHHHTTCCCCCSSCS----CCCCSTTGGGTCHHHHHHHHHHTTCCGG
T ss_pred             CcCccCCCcCCccCcCHHhHhHhHHHHHHHHhcCCceeecCCC----CcccCCcccccCccchHHHHHHcCCCHH
Confidence            4799999999999999999999999999999999989888764    7999999999999999999999999875

>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=99.95  E-value=1.2e-29  Score=160.02  Aligned_cols=71  Identities=46%  Similarity=1.062  Sum_probs=64.7

Q ss_pred             CceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         40 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        40 ~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      +|.|||++++|+||||.+|+||++||||++..+..+.|...+   ++|.+++..+..|++|||+|||++||+++
T Consensus         2 iC~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~~~~~~---~~c~~~~~~r~~Cr~CR~~KCl~~GM~~~   72 (78)
T d1a6ya_           2 LCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKN---ENCSIVRINRNRCQQCRFKKCLSVGMSRD   72 (78)
T ss_dssp             BCTTTSSBCCEEETTEEECHHHHHHHHHHHSSCCCCCCCSST---TCCCCCTTTTTSCHHHHHHHHTTTTCCST
T ss_pred             CCeeCCCcCCcccCcchhhhhchhhhhhhhccCCceeeeccC---CCcccCCCCCccchhhHHHHHHHhCCCHH
Confidence            699999999999999999999999999999998888754433   37999999999999999999999999986

>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=99.95  E-value=6.4e-30  Score=165.18  Aligned_cols=72  Identities=46%  Similarity=0.945  Sum_probs=67.5

Q ss_pred             CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      ..+|.|||++++++||||.+|++|++||||++..+..+.|..++    +|.++...|..|++|||+|||++||++|
T Consensus         4 ~~~C~VCg~~~~~~hyG~~sC~aC~~FFRR~v~~~~~~~c~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~   75 (90)
T d1lo1a_           4 KRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATN----ECEITKRRRKSCQACRFMKALKVGMLKE   75 (90)
T ss_dssp             CCEETTTTEECSEESSSSEECHHHHHHHHHHHHTTCCCCCSSCS----CCCCCHHHHHHCHHHHHHHHHHHTCCGG
T ss_pred             CCcCCcCCCcCCceEcCeeechhhHHHHHHHHhcCCccchhcCC----CCccCCCCccccchhhHHHHHHcCCCHH
Confidence            46799999999999999999999999999999999999998865    6999988999999999999999999975

>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=99.95  E-value=1e-28  Score=159.24  Aligned_cols=71  Identities=46%  Similarity=1.120  Sum_probs=66.1

Q ss_pred             CCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245         39 IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD  113 (113)
Q Consensus        39 ~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~  113 (113)
                      .+|+|||++++++||||.+|++|++||||++.....|.|..++    +|.++...|..|++|||+|||++||+++
T Consensus         1 g~C~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~c~~~~----~c~~~~~~r~~Cr~CR~~KCl~~GM~~~   71 (89)
T d1cita_           1 GRCAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANK----DCPVDKRRRNRCQFCRFQKCLAVGMVKE   71 (89)
T ss_dssp             CCCSSSCCCCCEEETTEEECHHHHHHHHHHHHHTCCCCCSSSS----CCCCSTTTTTTCHHHHHHHHHHTTCCGG
T ss_pred             CCCeECCCcCCccCCCcccchhhHHHHHHHHHcCCceeecCCC----CccccCCccccCchhhHHHHHHcCCCHH
Confidence            3699999999999999999999999999999999999888764    6999999999999999999999999874