Psyllid ID: psy13208

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120
Protein Sequence
MTFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGKSM
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHccccHHHHHHHHccccccccccccccccccccHHHccccccccHHHHHHcccccccccc
Secondary Structure Prediction (SSPRO)
ccccEcEEEcccccccHHHHHHHHHHHcccEEEEEccccccccccccccccHHHHHHHHHHHccccccccHcccHHHHHHccccccccccccccccccccHHHHHHHHHHccccHHcccc
Coil and Loop (DISEMBL)
mtfrhdgmtdhptcqagtercivdkAHRNQcqacqagtgrcivdKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKClnmgmnkdgksm
Flexible Loop (DISEMBL)
mtfrhdgmtdhptcqaGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHrnqcqacrlkkclnmgmnkdgksm
Low Complexity Region (SEG)
MTFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGKSM
Disordered region (IsUnstruct)
***************AGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLN**********
Disordered Region (DISOPRED)
*TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDD*******************************CQACRLKKC*****N******
Disordered Region (DISEMBL)
**********HPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGKSM
Disordered Region (DISPRO)
**FRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMG********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MTFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGKSM
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	120	2.2.26 [Sep-21-2011]
Q9QXZ7	395	Photoreceptor-specific nu	yes	N/A	0.316	0.096	0.736	5e-11
Q9TTF0	411	Photoreceptor-specific nu	yes	N/A	0.316	0.092	0.736	6e-11
Q9Y5X4	410	Photoreceptor-specific nu	yes	N/A	0.316	0.092	0.736	6e-11
Q9YGL3	396	Nuclear receptor subfamil	N/A	N/A	0.533	0.161	0.478	2e-10
Q91379	385	Nuclear receptor subfamil	no	N/A	0.533	0.166	0.478	2e-10
Q9Y466	385	Nuclear receptor subfamil	no	N/A	0.533	0.166	0.478	3e-10
Q64104	385	Nuclear receptor subfamil	no	N/A	0.533	0.166	0.478	3e-10
P70052	386	Nuclear receptor subfamil	N/A	N/A	0.533	0.165	0.478	3e-10
O16845	450	Protein tailless OS=Droso	N/A	N/A	0.533	0.142	0.434	2e-09
P18102	452	Protein tailless OS=Droso	no	N/A	0.533	0.141	0.434	2e-09

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

 Score = 66.2 bits (160), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 28/38 (73%), Positives = 30/38 (78%)

Query: 34  CQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
           CQ G G C VDKAHRNQCQACRLKKCL  GMN+D  Q+
Sbjct: 76  CQVGAGMCPVDKAHRNQCQACRLKKCLQAGMNQDAVQN 113

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 = 66.2 bits (160), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 28/38 (73%), Positives = 30/38 (78%)

Query: 34  CQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
           CQ G G C VDKAHRNQCQACRLKKCL  GMN+D  Q+
Sbjct: 75  CQVGAGMCPVDKAHRNQCQACRLKKCLQAGMNQDAVQN 112

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)

>sp|Q9Y5X4|NR2E3_HUMAN Photoreceptor-specific nuclear receptor OS=Homo sapiens GN=NR2E3 PE=1 SV=1

 Score = 66.2 bits (160), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 28/38 (73%), Positives = 30/38 (78%)

Query: 34  CQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
           CQ G G C VDKAHRNQCQACRLKKCL  GMN+D  Q+
Sbjct: 83  CQVGAGMCPVDKAHRNQCQACRLKKCLQAGMNQDAVQN 120

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.

Homo sapiens (taxid: 9606)

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

 Score = 64.3 bits (155), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 33/69 (47%), Positives = 42/69 (60%), Gaps = 5/69 (7%)

Query: 4   RHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGT-GRCIVDKAHRNQCQACRLKKCLNM 62
           +H G+     C    +R I     RN+   C++G+ G C VDK HRNQC+ACRLKKCL +
Sbjct: 37  KHYGVYACDGCSGFFKRSI----RRNRIYLCKSGSQGGCPVDKTHRNQCRACRLKKCLEV 92

Query: 63  GMNKDDAQH 71
            MNKD  QH
Sbjct: 93  NMNKDAVQH 101

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

 Score = 64.3 bits (155), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 33/69 (47%), Positives = 41/69 (59%), Gaps = 5/69 (7%)

Query: 4  RHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGT-GRCIVDKAHRNQCQACRLKKCLNM 62
          +H G+     C    +R I     RN+   C++G  G C VDK HRNQC+ACRLKKCL +
Sbjct: 26 KHYGVYACDGCSGFFKRSI----RRNRTYVCKSGNQGGCPVDKTHRNQCRACRLKKCLEV 81

Query: 63 GMNKDDAQH 71
           MNKD  QH
Sbjct: 82 NMNKDAVQH 90

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

 Score = 63.9 bits (154), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 33/69 (47%), Positives = 41/69 (59%), Gaps = 5/69 (7%)

Query: 4  RHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGT-GRCIVDKAHRNQCQACRLKKCLNM 62
          +H G+     C    +R I     RN+   C++G  G C VDK HRNQC+ACRLKKCL +
Sbjct: 26 KHYGVYACDGCSGFFKRSI----RRNRTYVCKSGNQGGCPVDKTHRNQCRACRLKKCLEV 81

Query: 63 GMNKDDAQH 71
           MNKD  QH
Sbjct: 82 NMNKDAVQH 90

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 = 63.9 bits (154), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 33/69 (47%), Positives = 41/69 (59%), Gaps = 5/69 (7%)

Query: 4  RHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGT-GRCIVDKAHRNQCQACRLKKCLNM 62
          +H G+     C    +R I     RN+   C++G  G C VDK HRNQC+ACRLKKCL +
Sbjct: 26 KHYGVYACDGCSGFFKRSI----RRNRTYVCKSGNQGGCPVDKTHRNQCRACRLKKCLEV 81

Query: 63 GMNKDDAQH 71
           MNKD  QH
Sbjct: 82 NMNKDAVQH 90

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

 Score = 63.9 bits (154), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 33/69 (47%), Positives = 41/69 (59%), Gaps = 5/69 (7%)

Query: 4  RHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGT-GRCIVDKAHRNQCQACRLKKCLNM 62
          +H G+     C    +R I     RN+   C++G  G C VDK HRNQC+ACRLKKCL +
Sbjct: 26 KHYGVYACDGCSGFFKRSI----RRNRSYVCKSGNQGGCPVDKTHRNQCRACRLKKCLEV 81

Query: 63 GMNKDDAQH 71
           MNKD  QH
Sbjct: 82 NMNKDAVQH 90

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 = 61.2 bits (147), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 30/69 (43%), Positives = 41/69 (59%), Gaps = 5/69 (7%)

Query: 4   RHDGMTDHPTCQAGTERCIVDKAHRNQCQACQA-GTGRCIVDKAHRNQCQACRLKKCLNM 62
           +H G+     C    +R I     R++   C++   G C+VDK HRNQC+ACRL+KC  +
Sbjct: 44  KHYGIYACDGCAGFFKRSI----RRSRQYVCKSQKQGLCVVDKTHRNQCRACRLRKCFEV 99

Query: 63  GMNKDDAQH 71
           GMNKD  QH
Sbjct: 100 GMNKDAVQH 108

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 = 60.8 bits (146), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 30/69 (43%), Positives = 41/69 (59%), Gaps = 5/69 (7%)

Query: 4   RHDGMTDHPTCQAGTERCIVDKAHRNQCQACQA-GTGRCIVDKAHRNQCQACRLKKCLNM 62
           +H G+     C    +R I     R++   C++   G C+VDK HRNQC+ACRL+KC  +
Sbjct: 44  KHYGIYACDGCAGFFKRSI----RRSRQYVCKSQKQGLCVVDKTHRNQCRACRLRKCFEV 99

Query: 63  GMNKDDAQH 71
           GMNKD  QH
Sbjct: 100 GMNKDAVQH 108

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)

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	120
332023687	730	Photoreceptor-specific nuclear receptor	0.341	0.056	0.804	1e-13
340709633	540	PREDICTED: photoreceptor-specific nuclea	0.316	0.070	0.842	2e-13
328792134	538	PREDICTED: photoreceptor-specific nuclea	0.316	0.070	0.842	2e-13
383861940	537	PREDICTED: photoreceptor-specific nuclea	0.316	0.070	0.842	2e-13
345487763	551	PREDICTED: photoreceptor-specific nuclea	0.316	0.068	0.842	3e-13
307199534	538	Photoreceptor-specific nuclear receptor	0.316	0.070	0.842	3e-13
194882843	630	GG20513 [Drosophila erecta] gi|190658706	0.325	0.061	0.846	6e-13
328707384	510	PREDICTED: photoreceptor-specific nuclea	0.316	0.074	0.868	8e-13
195426545	573	GK20892 [Drosophila willistoni] gi|19415	0.316	0.066	0.894	8e-13
242004528	467	conserved hypothetical protein [Pediculu	0.316	0.081	0.868	9e-13

>gi|332023687|gb|EGI63911.1| Photoreceptor-specific nuclear receptor [Acromyrmex echinatior]

 Score = 80.5 bits (197), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 33/41 (80%), Positives = 36/41 (87%)

Query: 34  CQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKN 74
           CQAGTGRC+VDKAHRNQCQACRLKKC+ MGMNKDD    +N
Sbjct: 193 CQAGTGRCVVDKAHRNQCQACRLKKCMQMGMNKDDVCDFRN 233

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340709633|ref|XP_003393408.1| PREDICTED: photoreceptor-specific nuclear receptor-like [Bombus terrestris] gi|350422440|ref|XP_003493165.1| PREDICTED: photoreceptor-specific nuclear receptor-like [Bombus impatiens]

 Score = 80.1 bits (196), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 32/38 (84%), Positives = 35/38 (92%)

Query: 34  CQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
           CQAGTGRC+VDKAHRNQCQACRLKKC+ MGMNKD  Q+
Sbjct: 184 CQAGTGRCVVDKAHRNQCQACRLKKCMQMGMNKDAVQN 221

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328792134|ref|XP_396999.4| PREDICTED: photoreceptor-specific nuclear receptor [Apis mellifera] gi|380028656|ref|XP_003698008.1| PREDICTED: photoreceptor-specific nuclear receptor-like [Apis florea]

 Score = 79.7 bits (195), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 32/38 (84%), Positives = 35/38 (92%)

Query: 34  CQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
           CQAGTGRC+VDKAHRNQCQACRLKKC+ MGMNKD  Q+
Sbjct: 182 CQAGTGRCVVDKAHRNQCQACRLKKCMQMGMNKDAVQN 219

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383861940|ref|XP_003706442.1| PREDICTED: photoreceptor-specific nuclear receptor-like [Megachile rotundata]

 Score = 79.7 bits (195), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 32/38 (84%), Positives = 35/38 (92%)

Query: 34  CQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
           CQAGTGRC+VDKAHRNQCQACRLKKC+ MGMNKD  Q+
Sbjct: 181 CQAGTGRCVVDKAHRNQCQACRLKKCMQMGMNKDAVQN 218

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345487763|ref|XP_001606227.2| PREDICTED: photoreceptor-specific nuclear receptor [Nasonia vitripennis]

 Score = 79.0 bits (193), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 32/38 (84%), Positives = 35/38 (92%)

Query: 34  CQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
           CQAGTGRC+VDKAHRNQCQACRLKKC+ MGMNKD  Q+
Sbjct: 191 CQAGTGRCVVDKAHRNQCQACRLKKCMQMGMNKDAVQN 228

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307199534|gb|EFN80135.1| Photoreceptor-specific nuclear receptor [Harpegnathos saltator]

 Score = 79.0 bits (193), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 32/38 (84%), Positives = 35/38 (92%)

Query: 34  CQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
           CQAGTGRC+VDKAHRNQCQACRLKKC+ MGMNKD  Q+
Sbjct: 182 CQAGTGRCVVDKAHRNQCQACRLKKCMQMGMNKDAVQN 219

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194882843|ref|XP_001975519.1| GG20513 [Drosophila erecta] gi|190658706|gb|EDV55919.1| GG20513 [Drosophila erecta]

 Score = 78.2 bits (191), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 33/39 (84%), Positives = 36/39 (92%)

Query: 33  ACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
           +CQAGTGRC+VDKAHRNQCQACRLKKCL MGMNKD  Q+
Sbjct: 194 SCQAGTGRCVVDKAHRNQCQACRLKKCLQMGMNKDAVQN 232

Source: Drosophila erecta

Species: Drosophila erecta

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328707384|ref|XP_001948870.2| PREDICTED: photoreceptor-specific nuclear receptor-like [Acyrthosiphon pisum]

 Score = 77.8 bits (190), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 33/38 (86%), Positives = 35/38 (92%)

Query: 34  CQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
           CQAGTG C+VDKAHRNQCQACRLKKCLNMGMNKD  Q+
Sbjct: 141 CQAGTGSCVVDKAHRNQCQACRLKKCLNMGMNKDAVQN 178

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195426545|ref|XP_002061388.1| GK20892 [Drosophila willistoni] gi|194157473|gb|EDW72374.1| GK20892 [Drosophila willistoni]

 Score = 77.8 bits (190), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 34/38 (89%), Positives = 35/38 (92%)

Query: 34  CQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
           CQAGTGRCIVDKAHRNQCQACRLKKCL MGMNKD  Q+
Sbjct: 137 CQAGTGRCIVDKAHRNQCQACRLKKCLQMGMNKDAVQN 174

Source: Drosophila willistoni

Species: Drosophila willistoni

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242004528|ref|XP_002423135.1| conserved hypothetical protein [Pediculus humanus corporis] gi|212506081|gb|EEB10397.1| conserved hypothetical protein [Pediculus humanus corporis]

 Score = 77.8 bits (190), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 33/38 (86%), Positives = 35/38 (92%)

Query: 34  CQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
           CQAGTGRC+VDKAHRNQCQACRLKKCL MGMNKD  Q+
Sbjct: 96  CQAGTGRCVVDKAHRNQCQACRLKKCLQMGMNKDAVQN 133

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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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	120
FB|FBgn0034012	582	Hr51 "Hormone receptor 51" [Dr	0.533	0.109	0.558	3.2e-14
WB|WBGene00001400	419	fax-1 [Caenorhabditis elegans	0.533	0.152	0.544	5.6e-14
ZFIN|ZDB-GENE-041114-63	426	nr2e3 "nuclear receptor subfam	0.316	0.089	0.815	2e-12
UNIPROTKB|F1P0M4	405	NR2E3 "Uncharacterized protein	0.316	0.093	0.815	2.2e-12
ZFIN|ZDB-GENE-040801-127	396	nr2e1 "nuclear receptor subfam	0.533	0.161	0.492	2.1e-11
MGI|MGI:1346317	395	Nr2e3 "nuclear receptor subfam	0.316	0.096	0.736	4.4e-11
UNIPROTKB|Q9Y5X4	410	NR2E3 "Photoreceptor-specific	0.316	0.092	0.736	4.7e-11
UNIPROTKB|F1ML62	411	NR2E3 "Photoreceptor-specific	0.316	0.092	0.736	4.8e-11
UNIPROTKB|Q9TTF0	411	NR2E3 "Photoreceptor-specific	0.316	0.092	0.736	4.8e-11
UNIPROTKB|F1SIS0	419	F1SIS0 "Uncharacterized protei	0.316	0.090	0.736	6.4e-11

FB|FBgn0034012 Hr51 "Hormone receptor 51" [Drosophila melanogaster (taxid:7227)]

 Score = 192 (72.6 bits), Expect = 3.2e-14, P = 3.2e-14
 Identities = 38/68 (55%), Positives = 44/68 (64%)

Query:     4 RHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMG 63
             +H G+     C    +R +     R     CQAGTGRC+VDKAHRNQCQACRLKKCL MG
Sbjct:   121 KHYGILACNGCSGFFKRSV----RRKLIYRCQAGTGRCVVDKAHRNQCQACRLKKCLQMG 176

Query:    64 MNKDDAQH 71
             MNKD  Q+
Sbjct:   177 MNKDAVQN 184

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

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

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

GO:0005634 "nucleus" evidence=ISS

GO:0008270 "zinc ion binding" evidence=IEA

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

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

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

GO:0020037 "heme binding" evidence=IDA

GO:0048526 "imaginal disc-derived wing expansion" evidence=IMP

GO:0016319 "mushroom body development" evidence=IMP

GO:0022008 "neurogenesis" evidence=IMP

GO:0031103 "axon regeneration" evidence=IMP

WB|WBGene00001400 fax-1 [Caenorhabditis elegans (taxid:6239)]

 Score = 187 (70.9 bits), Expect = 5.6e-14, P = 5.6e-14
 Identities = 37/68 (54%), Positives = 43/68 (63%)

Query:     4 RHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMG 63
             +H G+     C    +R +     R     CQAGTG C+VDKAHRNQCQACRLKKCLN G
Sbjct:   112 KHYGILACNGCSGFFKRSV----RRRLIYRCQAGTGNCVVDKAHRNQCQACRLKKCLNKG 167

Query:    64 MNKDDAQH 71
             MNKD  Q+
Sbjct:   168 MNKDAVQN 175

GO:0005634 "nucleus" evidence=IEA;IDA

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

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

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

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

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0043059 "regulation of forward locomotion" evidence=IMP

GO:0043058 "regulation of backward locomotion" evidence=IMP

GO:0007626 "locomotory behavior" evidence=IMP

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

GO:0048665 "neuron fate specification" evidence=IMP

ZFIN|ZDB-GENE-041114-63 nr2e3 "nuclear receptor subfamily 2, group E, member 3" [Danio rerio (taxid:7955)]

 Score = 173 (66.0 bits), Expect = 2.0e-12, P = 2.0e-12
 Identities = 31/38 (81%), Positives = 32/38 (84%)

Query:    34 CQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
             CQAGTG C VDKAHRNQCQACRLKKCL  GMNKD  Q+
Sbjct:    82 CQAGTGMCPVDKAHRNQCQACRLKKCLQAGMNKDAVQN 119

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

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IEA;IDA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

GO:0046872 "metal ion binding" evidence=IEA

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

UNIPROTKB|F1P0M4 NR2E3 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 172 (65.6 bits), Expect = 2.2e-12, P = 2.2e-12
 Identities = 31/38 (81%), Positives = 32/38 (84%)

Query:    34 CQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
             CQAGTG C VDKAHRNQCQACRLKKCL  GMNKD  Q+
Sbjct:    71 CQAGTGLCPVDKAHRNQCQACRLKKCLQAGMNKDAVQN 108

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IEA

GO:0008285 "negative regulation of cell proliferation" evidence=IEA

GO:0042462 "eye photoreceptor cell development" evidence=IEA

GO:0045872 "positive regulation of rhodopsin gene expression" evidence=IEA

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

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

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

 Score = 163 (62.4 bits), Expect = 2.1e-11, P = 2.1e-11
 Identities = 34/69 (49%), Positives = 42/69 (60%)

Query:     4 RHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGT-GRCIVDKAHRNQCQACRLKKCLNM 62
             +H G+     C    +R I     RN+   C++GT G C VDK HRNQC+ACRLKKCL +
Sbjct:    37 KHYGVYACDGCSGFFKRSI----RRNRTYVCKSGTQGGCPVDKTHRNQCRACRLKKCLEV 92

Query:    63 GMNKDDAQH 71
              MNKD  QH
Sbjct:    93 NMNKDAVQH 101

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

MGI|MGI:1346317 Nr2e3 "nuclear receptor subfamily 2, group E, member 3" [Mus musculus (taxid:10090)]

 Score = 160 (61.4 bits), Expect = 4.4e-11, P = 4.4e-11
 Identities = 28/38 (73%), Positives = 30/38 (78%)

Query:    34 CQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
             CQ G G C VDKAHRNQCQACRLKKCL  GMN+D  Q+
Sbjct:    76 CQVGAGMCPVDKAHRNQCQACRLKKCLQAGMNQDAVQN 113

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IGI

GO:0003677 "DNA binding" evidence=IEA

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

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005667 "transcription factor complex" evidence=IDA

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

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0008285 "negative regulation of cell proliferation" evidence=IMP

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

GO:0042462 "eye photoreceptor cell development" evidence=IMP

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

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

GO:0045872 "positive regulation of rhodopsin gene expression" evidence=IGI

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

GO:0046872 "metal ion binding" evidence=IEA

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

UNIPROTKB|Q9Y5X4 NR2E3 "Photoreceptor-specific nuclear receptor" [Homo sapiens (taxid:9606)]

 Score = 160 (61.4 bits), Expect = 4.7e-11, P = 4.7e-11
 Identities = 28/38 (73%), Positives = 30/38 (78%)

Query:    34 CQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
             CQ G G C VDKAHRNQCQACRLKKCL  GMN+D  Q+
Sbjct:    83 CQVGAGMCPVDKAHRNQCQACRLKKCLQAGMNQDAVQN 120

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0007601 "visual perception" evidence=IEA

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

GO:0005634 "nucleus" evidence=TAS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=TAS

GO:0007165 "signal transduction" evidence=TAS

GO:0007602 "phototransduction" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

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

GO:0010467 "gene expression" evidence=TAS

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

UNIPROTKB|F1ML62 NR2E3 "Photoreceptor-specific nuclear receptor" [Bos taurus (taxid:9913)]

 Score = 160 (61.4 bits), Expect = 4.8e-11, P = 4.8e-11
 Identities = 28/38 (73%), Positives = 30/38 (78%)

Query:    34 CQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
             CQ G G C VDKAHRNQCQACRLKKCL  GMN+D  Q+
Sbjct:    75 CQVGAGMCPVDKAHRNQCQACRLKKCLQAGMNQDAVQN 112

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

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

GO:0045872 "positive regulation of rhodopsin gene expression" evidence=IEA

GO:0042462 "eye photoreceptor cell development" evidence=IEA

GO:0008285 "negative regulation of cell proliferation" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IEA

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

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

UNIPROTKB|Q9TTF0 NR2E3 "Photoreceptor-specific nuclear receptor" [Bos taurus (taxid:9913)]

 Score = 160 (61.4 bits), Expect = 4.8e-11, P = 4.8e-11
 Identities = 28/38 (73%), Positives = 30/38 (78%)

Query:    34 CQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
             CQ G G C VDKAHRNQCQACRLKKCL  GMN+D  Q+
Sbjct:    75 CQVGAGMCPVDKAHRNQCQACRLKKCLQAGMNQDAVQN 112

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

UNIPROTKB|F1SIS0 F1SIS0 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 159 (61.0 bits), Expect = 6.4e-11, P = 6.4e-11
 Identities = 28/38 (73%), Positives = 30/38 (78%)

Query:    34 CQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
             CQ G G C VDKAHRNQCQACRLKKCL  GMN+D  Q+
Sbjct:    83 CQMGAGMCPVDKAHRNQCQACRLKKCLQAGMNQDAVQN 120

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

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

GO:0045872 "positive regulation of rhodopsin gene expression" evidence=IEA

GO:0042462 "eye photoreceptor cell development" evidence=IEA

GO:0008285 "negative regulation of cell proliferation" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IEA

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

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	120
cd06970	92	cd06970, NR_DBD_PNR, DNA-binding domain of the pho	4e-15
cd07163	92	cd07163, NR_DBD_TLX, DNA-binding domain of Tailles	7e-13
cd07154	73	cd07154, NR_DBD_PNR_like, The DNA-binding domain o	6e-12
cd06970	92	cd06970, NR_DBD_PNR, DNA-binding domain of the pho	2e-10
cd06916	72	cd06916, NR_DBD_like, DNA-binding domain of nuclea	4e-10
cd07163	92	cd07163, NR_DBD_TLX, DNA-binding domain of Tailles	6e-10
cd07164	78	cd07164, NR_DBD_PNR_like_1, DNA-binding domain of	1e-09
cd06916	72	cd06916, NR_DBD_like, DNA-binding domain of nuclea	2e-09
cd06957	82	cd06957, NR_DBD_PNR_like_2, DNA-binding domain of	2e-08
pfam00105	70	pfam00105, zf-C4, Zinc finger, C4 type (two domain	2e-08
cd07154	73	cd07154, NR_DBD_PNR_like, The DNA-binding domain o	3e-08
pfam00105	70	pfam00105, zf-C4, Zinc finger, C4 type (two domain	6e-08
cd07164	78	cd07164, NR_DBD_PNR_like_1, DNA-binding domain of	7e-08
cd06967	87	cd06967, NR_DBD_TR2_like, DNA-binding domain of th	3e-07
cd06960	76	cd06960, NR_DBD_HNF4A, DNA-binding domain of hepto	3e-07
cd06960	76	cd06960, NR_DBD_HNF4A, DNA-binding domain of hepto	8e-07
smart00399	70	smart00399, ZnF_C4, c4 zinc finger in nuclear horm	2e-06
smart00399	70	smart00399, ZnF_C4, c4 zinc finger in nuclear horm	3e-06
cd06961	85	cd06961, NR_DBD_TR, DNA-binding domain of thyroid	3e-06
cd06968	95	cd06968, NR_DBD_ROR, DNA-binding domain of Retinoi	5e-06
cd06958	73	cd06958, NR_DBD_COUP_TF, DNA-binding domain of chi	6e-06
cd06967	87	cd06967, NR_DBD_TR2_like, DNA-binding domain of th	8e-06
cd06968	95	cd06968, NR_DBD_ROR, DNA-binding domain of Retinoi	8e-06
cd07156	72	cd07156, NR_DBD_VDR_like, The DNA-binding domain o	1e-05
cd07157	86	cd07157, 2DBD_NR_DBD1, The first DNA-binding domai	1e-05
cd07155	75	cd07155, NR_DBD_ER_like, DNA-binding domain of est	1e-05
cd06957	82	cd06957, NR_DBD_PNR_like_2, DNA-binding domain of	2e-05
cd06961	85	cd06961, NR_DBD_TR, DNA-binding domain of thyroid	2e-05
cd06958	73	cd06958, NR_DBD_COUP_TF, DNA-binding domain of chi	2e-05
cd07155	75	cd07155, NR_DBD_ER_like, DNA-binding domain of est	3e-05
cd07165	81	cd07165, NR_DBD_DmE78_like, DNA-binding domain of	3e-05
cd07157	86	cd07157, 2DBD_NR_DBD1, The first DNA-binding domai	4e-05
cd07156	72	cd07156, NR_DBD_VDR_like, The DNA-binding domain o	5e-05
cd07171	82	cd07171, NR_DBD_ER, DNA-binding domain of estrogen	6e-05
cd07168	90	cd07168, NR_DBD_DHR4_like, DNA-binding domain of e	7e-05
cd06969	75	cd06969, NR_DBD_NGFI-B, DNA-binding domain of the	8e-05
cd07158	73	cd07158, NR_DBD_Ppar_like, The DNA-binding domain	9e-05
cd07165	81	cd07165, NR_DBD_DmE78_like, DNA-binding domain of	1e-04
cd07171	82	cd07171, NR_DBD_ER, DNA-binding domain of estrogen	1e-04
cd06965	84	cd06965, NR_DBD_Ppar, DNA-binding domain of peroxi	1e-04
cd06965	84	cd06965, NR_DBD_Ppar, DNA-binding domain of peroxi	1e-04
cd06956	77	cd06956, NR_DBD_RXR, DNA-binding domain of retinoi	1e-04
cd07162	87	cd07162, NR_DBD_PXR, DNA-binding domain of pregnan	2e-04
cd07158	73	cd07158, NR_DBD_Ppar_like, The DNA-binding domain	3e-04
cd07167	93	cd07167, NR_DBD_Lrh-1_like, The DNA-binding domain	3e-04
cd07172	78	cd07172, NR_DBD_GR_PR, DNA-binding domain of gluco	3e-04
cd06964	85	cd06964, NR_DBD_RAR, DNA-binding domain of retinoi	3e-04
cd07168	90	cd07168, NR_DBD_DHR4_like, DNA-binding domain of e	4e-04
cd06956	77	cd06956, NR_DBD_RXR, DNA-binding domain of retinoi	4e-04
cd07162	87	cd07162, NR_DBD_PXR, DNA-binding domain of pregnan	7e-04
cd07166	89	cd07166, NR_DBD_REV_ERB, DNA-binding domain of REV	7e-04
cd07166	89	cd07166, NR_DBD_REV_ERB, DNA-binding domain of REV	7e-04
cd07167	93	cd07167, NR_DBD_Lrh-1_like, The DNA-binding domain	8e-04
cd07172	78	cd07172, NR_DBD_GR_PR, DNA-binding domain of gluco	8e-04
cd06969	75	cd06969, NR_DBD_NGFI-B, DNA-binding domain of the	0.001
cd07169	90	cd07169, NR_DBD_GCNF_like, DNA-binding domain of G	0.001
cd07169	90	cd07169, NR_DBD_GCNF_like, DNA-binding domain of G	0.001
cd06955	107	cd06955, NR_DBD_VDR, DNA-binding domain of vitamin	0.001
cd06964	85	cd06964, NR_DBD_RAR, DNA-binding domain of retinoi	0.002
cd07179	74	cd07179, 2DBD_NR_DBD2, The second DNA-binding doma	0.004

>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 = 65.0 bits (158), Expect = 4e-15
 Identities = 31/38 (81%), Positives = 32/38 (84%)

Query: 34 CQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
          CQAGTG C VDKAHRNQCQACRLKKCL  GMNKD  Q+
Sbjct: 45 CQAGTGMCPVDKAHRNQCQACRLKKCLQAGMNKDAVQN 82

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

 Score = 59.4 bits (144), Expect = 7e-13
 Identities = 28/46 (60%), Positives = 33/46 (71%), Gaps = 1/46 (2%)

Query: 27 HRNQCQACQA-GTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
           RN+   C++ G G C VDK HRNQC+ACRLKKC  +GMNKD  QH
Sbjct: 38 RRNRQYVCKSKGQGGCPVDKTHRNQCRACRLKKCFEVGMNKDAVQH 83

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 = 56.4 bits (136), Expect = 6e-12
 Identities = 29/43 (67%), Positives = 32/43 (74%)

Query: 28 RNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQ 70
          RN    C+AG G C+VDKA RNQCQACRLKKCL + MNKD  Q
Sbjct: 31 RNLLYTCKAGNGSCVVDKARRNQCQACRLKKCLEVSMNKDAVQ 73

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

>gnl|CDD|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 = 52.6 bits (126), Expect = 2e-10
 Identities = 24/28 (85%), Positives = 24/28 (85%)

Query: 89  RCIVDKAHRNQCQACRLKKCLNMGMNKD 116
            C VDKAHRNQCQACRLKKCL  GMNKD
Sbjct: 51  MCPVDKAHRNQCQACRLKKCLQAGMNKD 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|143512 cd06916, NR_DBD_like, DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers

 Score = 51.4 bits (124), Expect = 4e-10
 Identities = 19/31 (61%), Positives = 25/31 (80%)

Query: 37 GTGRCIVDKAHRNQCQACRLKKCLNMGMNKD 67
            G C++DK +RN+CQACRLKKCL +GM K+
Sbjct: 39 AGGNCVIDKRNRNRCQACRLKKCLAVGMRKE 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|143537 cd07163, NR_DBD_TLX, DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers

 Score = 51.7 bits (124), Expect = 6e-10
 Identities = 22/37 (59%), Positives = 27/37 (72%)

Query: 80  FACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKD 116
           + C +  +  C VDK HRNQC+ACRLKKC  +GMNKD
Sbjct: 43  YVCKSKGQGGCPVDKTHRNQCRACRLKKCFEVGMNKD 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|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 = 50.5 bits (121), Expect = 1e-09
 Identities = 25/44 (56%), Positives = 29/44 (65%), Gaps = 1/44 (2%)

Query: 28 RNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
          RN    C+   G C+VD A RNQCQACR KKCL + MN+D  QH
Sbjct: 31 RNLAYVCKEN-GSCVVDVARRNQCQACRFKKCLQVNMNRDAVQH 73

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

 Score = 49.9 bits (120), Expect = 2e-09
 Identities = 18/29 (62%), Positives = 24/29 (82%)

Query: 89  RCIVDKAHRNQCQACRLKKCLNMGMNKDG 117
            C++DK +RN+CQACRLKKCL +GM K+ 
Sbjct: 42  NCVIDKRNRNRCQACRLKKCLAVGMRKEA 70

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|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 = 47.5 bits (113), Expect = 2e-08
 Identities = 21/43 (48%), Positives = 26/43 (60%)

Query: 28 RNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQ 70
          +     C AG G C+VDKA RN C  CRL+KC  +GMN+   Q
Sbjct: 31 KGIIYTCIAGNGNCVVDKARRNWCPFCRLQKCFAVGMNRAAVQ 73

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

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

 Score = 47.2 bits (113), Expect = 2e-08
 Identities = 17/39 (43%), Positives = 24/39 (61%)

Query: 28 RNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNK 66
          +            C++DK +RN+CQ CRLKKCL +GM+K
Sbjct: 32 QKNIVYTCPFNKDCVIDKRNRNRCQYCRLKKCLEVGMSK 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|143529 cd07154, NR_DBD_PNR_like, The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family

 Score = 47.2 bits (112), Expect = 3e-08
 Identities = 22/28 (78%), Positives = 24/28 (85%)

Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKDG 117
           C+VDKA RNQCQACRLKKCL + MNKD 
Sbjct: 44  CVVDKARRNQCQACRLKKCLEVSMNKDA 71

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

 Score = 45.7 bits (109), Expect = 6e-08
 Identities = 17/26 (65%), Positives = 23/26 (88%)

Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNK 115
           C++DK +RN+CQ CRLKKCL +GM+K
Sbjct: 45  CVIDKRNRNRCQYCRLKKCLEVGMSK 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|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 = 45.9 bits (109), Expect = 7e-08
 Identities = 19/29 (65%), Positives = 22/29 (75%)

Query: 89  RCIVDKAHRNQCQACRLKKCLNMGMNKDG 117
            C+VD A RNQCQACR KKCL + MN+D 
Sbjct: 42  SCVVDVARRNQCQACRFKKCLQVNMNRDA 70

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|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 = 44.8 bits (106), Expect = 3e-07
 Identities = 19/35 (54%), Positives = 25/35 (71%)

Query: 37 GTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
          G+  C+++K HRN+CQ CRL+KCL MGM  D  Q 
Sbjct: 44 GSKDCVINKHHRNRCQYCRLQKCLAMGMKSDSVQC 78

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

 Score = 44.5 bits (106), Expect = 3e-07
 Identities = 17/34 (50%), Positives = 23/34 (67%)

Query: 38 TGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
           G C+VDK  RN C+ CR KKCL +GM+ +  Q+
Sbjct: 40 GGNCVVDKDKRNACRYCRFKKCLEVGMDPEAVQN 73

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

 Score = 43.3 bits (103), Expect = 8e-07
 Identities = 15/28 (53%), Positives = 20/28 (71%)

Query: 89  RCIVDKAHRNQCQACRLKKCLNMGMNKD 116
            C+VDK  RN C+ CR KKCL +GM+ +
Sbjct: 42  NCVVDKDKRNACRYCRFKKCLEVGMDPE 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|197701 smart00399, ZnF_C4, c4 zinc finger in nuclear hormone receptors

 Score = 42.1 bits (100), Expect = 2e-06
 Identities = 14/29 (48%), Positives = 22/29 (75%)

Query: 39 GRCIVDKAHRNQCQACRLKKCLNMGMNKD 67
            C ++K +R +C+ACRLKKCL +GM+ +
Sbjct: 42 NNCSINKRYRCRCRACRLKKCLGVGMDPE 70

Length = 70

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

 Score = 41.4 bits (98), Expect = 3e-06
 Identities = 14/27 (51%), Positives = 22/27 (81%)

Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKD 116
           C ++K +R +C+ACRLKKCL +GM+ +
Sbjct: 44  CSINKRYRCRCRACRLKKCLGVGMDPE 70

Length = 70

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

 Score = 42.0 bits (99), Expect = 3e-06
 Identities = 19/31 (61%), Positives = 23/31 (74%)

Query: 37 GTGRCIVDKAHRNQCQACRLKKCLNMGMNKD 67
          G G+C +DK  RNQCQ CR KKC+ +GM KD
Sbjct: 40 GEGKCEIDKVTRNQCQECRFKKCIAVGMAKD 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|143526 cd06968, NR_DBD_ROR, DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers

 Score = 41.8 bits (98), Expect = 5e-06
 Identities = 15/28 (53%), Positives = 24/28 (85%)

Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKDG 117
           C++D+ +RN+CQ CRL+KCL +GM++D 
Sbjct: 50  CLIDRTNRNRCQHCRLQKCLALGMSRDA 77

DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ROR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RORS are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma, which differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum particularly in the regulation of the maturation and survival of Purkinje cells. RORbeta expression is largely restricted to several regions of the brain, the retina, and pineal gland. RORgamma is essential for lymph node organogenesis. Recently, it has been suggested that cholesterol or a cholesterol derivative are the natural ligands of RORalpha. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, retinoid-related orphan receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). Length = 95

>gnl|CDD|143516 cd06958, NR_DBD_COUP_TF, DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers

 Score = 41.0 bits (96), Expect = 6e-06
 Identities = 19/34 (55%), Positives = 24/34 (70%)

Query: 37 GTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQ 70
          G   C +D+ HRNQCQ CRLKKCL +GM ++  Q
Sbjct: 39 GNRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQ 72

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

>gnl|CDD|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 = 40.9 bits (96), Expect = 8e-06
 Identities = 17/27 (62%), Positives = 22/27 (81%)

Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKD 116
           C+++K HRN+CQ CRL+KCL MGM  D
Sbjct: 48  CVINKHHRNRCQYCRLQKCLAMGMKSD 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 = 41.0 bits (96), Expect = 8e-06
 Identities = 15/27 (55%), Positives = 24/27 (88%)

Query: 41 CIVDKAHRNQCQACRLKKCLNMGMNKD 67
          C++D+ +RN+CQ CRL+KCL +GM++D
Sbjct: 50 CLIDRTNRNRCQHCRLQKCLALGMSRD 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|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 = 40.1 bits (94), Expect = 1e-05
 Identities = 17/30 (56%), Positives = 22/30 (73%)

Query: 38 TGRCIVDKAHRNQCQACRLKKCLNMGMNKD 67
           G C + K +R  CQACRLKKCL++GM K+
Sbjct: 40 NGDCEITKDNRRHCQACRLKKCLDIGMKKE 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|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 = 40.2 bits (94), Expect = 1e-05
 Identities = 17/31 (54%), Positives = 24/31 (77%)

Query: 39 GRCIVDKAHRNQCQACRLKKCLNMGMNKDDA 69
          G+CI+DK +R +CQACR +KCLN+GM+    
Sbjct: 45 GKCIIDKKNRTKCQACRYRKCLNVGMSLGGP 75

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

>gnl|CDD|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 = 39.8 bits (93), Expect = 1e-05
 Identities = 18/31 (58%), Positives = 21/31 (67%)

Query: 37 GTGRCIVDKAHRNQCQACRLKKCLNMGMNKD 67
           T  C VDK  R  CQACRL+KCL +GM K+
Sbjct: 39 STSECEVDKKRRKSCQACRLQKCLKVGMLKE 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|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 = 39.8 bits (93), Expect = 2e-05
 Identities = 16/27 (59%), Positives = 20/27 (74%)

Query: 89  RCIVDKAHRNQCQACRLKKCLNMGMNK 115
            C+VDKA RN C  CRL+KC  +GMN+
Sbjct: 43  NCVVDKARRNWCPFCRLQKCFAVGMNR 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|143519 cd06961, NR_DBD_TR, DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers

 Score = 39.7 bits (93), Expect = 2e-05
 Identities = 17/28 (60%), Positives = 21/28 (75%)

Query: 89  RCIVDKAHRNQCQACRLKKCLNMGMNKD 116
           +C +DK  RNQCQ CR KKC+ +GM KD
Sbjct: 43  KCEIDKVTRNQCQECRFKKCIAVGMAKD 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|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 = 39.4 bits (92), Expect = 2e-05
 Identities = 17/27 (62%), Positives = 22/27 (81%)

Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKD 116
           C +D+ HRNQCQ CRLKKCL +GM ++
Sbjct: 43  CPIDQHHRNQCQYCRLKKCLKVGMRRE 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|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 = 39.0 bits (91), Expect = 3e-05
 Identities = 18/29 (62%), Positives = 21/29 (72%)

Query: 89  RCIVDKAHRNQCQACRLKKCLNMGMNKDG 117
            C VDK  R  CQACRL+KCL +GM K+G
Sbjct: 42  ECEVDKKRRKSCQACRLQKCLKVGMLKEG 70

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

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

 Score = 39.5 bits (92), Expect = 3e-05
 Identities = 16/35 (45%), Positives = 25/35 (71%)

Query: 39 GRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLK 73
          G+C + + +RN+CQ CR KKCL  GM+KD  ++ +
Sbjct: 41 GKCEIIRLNRNRCQYCRFKKCLAAGMSKDSVRYGR 75

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|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 = 39.0 bits (91), Expect = 4e-05
 Identities = 19/48 (39%), Positives = 27/48 (56%), Gaps = 2/48 (4%)

Query: 70  QHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDG 117
           +           C N    +CI+DK +R +CQACR +KCLN+GM+  G
Sbjct: 29  RSSNAISFTISECPN--GGKCIIDKKNRTKCQACRYRKCLNVGMSLGG 74

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

>gnl|CDD|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 = 38.5 bits (90), Expect = 5e-05
 Identities = 16/28 (57%), Positives = 21/28 (75%)

Query: 89  RCIVDKAHRNQCQACRLKKCLNMGMNKD 116
            C + K +R  CQACRLKKCL++GM K+
Sbjct: 42  DCEITKDNRRHCQACRLKKCLDIGMKKE 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|143545 cd07171, NR_DBD_ER, DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers

 Score = 38.3 bits (89), Expect = 6e-05
 Identities = 16/31 (51%), Positives = 20/31 (64%)

Query: 37 GTGRCIVDKAHRNQCQACRLKKCLNMGMNKD 67
           T +C +DK  R  CQACRL+KC  +GM K 
Sbjct: 44 ATNQCTIDKNRRKSCQACRLRKCYEVGMMKG 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|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 = 38.3 bits (89), Expect = 7e-05
 Identities = 16/28 (57%), Positives = 20/28 (71%)

Query: 37 GTGRCIVDKAHRNQCQACRLKKCLNMGM 64
          G GRC + KA RN+CQ CR +KC+  GM
Sbjct: 47 GDGRCEITKAQRNRCQYCRFRKCIRKGM 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|143527 cd06969, NR_DBD_NGFI-B, DNA-binding domain of the orphan nuclear receptor, nerve growth factor-induced-B

 Score = 37.8 bits (88), Expect = 8e-05
 Identities = 16/36 (44%), Positives = 21/36 (58%)

Query: 36 AGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
               C VDK  RN+CQ CR +KCL +GM K+  + 
Sbjct: 40 LANKNCPVDKRRRNRCQYCRFQKCLQVGMVKEVVRT 75

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

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

 Score = 37.9 bits (88), Expect = 9e-05
 Identities = 14/29 (48%), Positives = 25/29 (86%)

Query: 39 GRCIVDKAHRNQCQACRLKKCLNMGMNKD 67
          G+C++ + +RN+CQ CR KKCL++GM+++
Sbjct: 42 GKCVIQRKNRNRCQYCRFKKCLSVGMSRN 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|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 = 37.5 bits (87), Expect = 1e-04
 Identities = 15/28 (53%), Positives = 21/28 (75%)

Query: 89  RCIVDKAHRNQCQACRLKKCLNMGMNKD 116
           +C + + +RN+CQ CR KKCL  GM+KD
Sbjct: 42  KCEIIRLNRNRCQYCRFKKCLAAGMSKD 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|143545 cd07171, NR_DBD_ER, DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers

 Score = 37.9 bits (88), Expect = 1e-04
 Identities = 16/28 (57%), Positives = 19/28 (67%)

Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKDG 117
           C +DK  R  CQACRL+KC  +GM K G
Sbjct: 48  CTIDKNRRKSCQACRLRKCYEVGMMKGG 75

DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ER interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Estrogen receptor is a transcription regulator that mediates the biological effects of hormone estrogen. The binding of estrogen to the receptor triggers the dimerization and the binding of the receptor dimer to estrogen response element, which is a palindromic inverted repeat: 5'GGTCAnnnTGACC-3', of target genes. Through ER, estrogen regulates development, reproduction and homeostasis. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER has a central well-conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). Length = 82

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

 Score = 37.8 bits (88), Expect = 1e-04
 Identities = 15/30 (50%), Positives = 22/30 (73%)

Query: 87  ELRCIVDKAHRNQCQACRLKKCLNMGMNKD 116
           +L C + K  RN+CQ CR +KCLN+GM+ +
Sbjct: 40  DLSCKIHKKSRNKCQYCRFQKCLNVGMSHN 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|143523 cd06965, NR_DBD_Ppar, DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers

 Score = 37.8 bits (88), Expect = 1e-04
 Identities = 14/27 (51%), Positives = 20/27 (74%)

Query: 41 CIVDKAHRNQCQACRLKKCLNMGMNKD 67
          C + K  RN+CQ CR +KCLN+GM+ +
Sbjct: 43 CKIHKKSRNKCQYCRFQKCLNVGMSHN 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|143514 cd06956, NR_DBD_RXR, DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers

 Score = 37.5 bits (87), Expect = 1e-04
 Identities = 16/32 (50%), Positives = 22/32 (68%)

Query: 39 GRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQ 70
            C++DK  RN+CQ CR +KCL MGM ++  Q
Sbjct: 43 KDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQ 74

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

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

 Score = 36.8 bits (85), Expect = 2e-04
 Identities = 18/43 (41%), Positives = 29/43 (67%)

Query: 25 KAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKD 67
          +A +   + C      C++ K++R QCQACRL+KCL++GM K+
Sbjct: 28 RAMKRNARLCCPFQKGCVITKSNRRQCQACRLRKCLSIGMKKE 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|143533 cd07158, NR_DBD_Ppar_like, The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family

 Score = 36.4 bits (84), Expect = 3e-04
 Identities = 13/28 (46%), Positives = 24/28 (85%)

Query: 89  RCIVDKAHRNQCQACRLKKCLNMGMNKD 116
           +C++ + +RN+CQ CR KKCL++GM+++
Sbjct: 43  KCVIQRKNRNRCQYCRFKKCLSVGMSRN 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|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 = 36.7 bits (85), Expect = 3e-04
 Identities = 12/27 (44%), Positives = 17/27 (62%)

Query: 38 TGRCIVDKAHRNQCQACRLKKCLNMGM 64
             C +DK  R +C  CR +KCL++GM
Sbjct: 40 NQNCQIDKTQRKRCPYCRFQKCLSVGM 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|143546 cd07172, NR_DBD_GR_PR, DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers

 Score = 36.3 bits (84), Expect = 3e-04
 Identities = 18/30 (60%), Positives = 20/30 (66%)

Query: 36 AGTGRCIVDKAHRNQCQACRLKKCLNMGMN 65
          AG   CI+DK  R  C ACRL+KCL  GMN
Sbjct: 42 AGRNDCIIDKIRRKNCPACRLRKCLQAGMN 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|143522 cd06964, NR_DBD_RAR, DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers

 Score = 36.8 bits (85), Expect = 3e-04
 Identities = 18/48 (37%), Positives = 29/48 (60%), Gaps = 1/48 (2%)

Query: 27 HRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKN 74
           +N    C      CI++K  RN+CQ CRL+KC  +GM+K+  ++ +N
Sbjct: 36 QKNMVYTC-HRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRN 82

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|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 = 36.4 bits (84), Expect = 4e-04
 Identities = 14/25 (56%), Positives = 18/25 (72%)

Query: 89  RCIVDKAHRNQCQACRLKKCLNMGM 113
           RC + KA RN+CQ CR +KC+  GM
Sbjct: 50  RCEITKAQRNRCQYCRFRKCIRKGM 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|143514 cd06956, NR_DBD_RXR, DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers

 Score = 36.4 bits (84), Expect = 4e-04
 Identities = 15/27 (55%), Positives = 21/27 (77%)

Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKD 116
           C++DK  RN+CQ CR +KCL MGM ++
Sbjct: 45  CLIDKRQRNRCQYCRYQKCLAMGMKRE 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|143536 cd07162, NR_DBD_PXR, DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers

 Score = 35.7 bits (82), Expect = 7e-04
 Identities = 16/27 (59%), Positives = 24/27 (88%)

Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKD 116
           C++ K++R QCQACRL+KCL++GM K+
Sbjct: 44  CVITKSNRRQCQACRLRKCLSIGMKKE 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|143540 cd07166, NR_DBD_REV_ERB, DNA-binding domain of REV-ERB receptor-like is composed of two C4-type zinc fingers

 Score = 35.6 bits (82), Expect = 7e-04
 Identities = 14/27 (51%), Positives = 21/27 (77%)

Query: 41 CIVDKAHRNQCQACRLKKCLNMGMNKD 67
          C + + +RN+CQ CR KKCL +GM++D
Sbjct: 49 CSIMRINRNRCQYCRFKKCLAVGMSRD 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|143540 cd07166, NR_DBD_REV_ERB, DNA-binding domain of REV-ERB receptor-like is composed of two C4-type zinc fingers

 Score = 35.6 bits (82), Expect = 7e-04
 Identities = 14/27 (51%), Positives = 21/27 (77%)

Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKD 116
           C + + +RN+CQ CR KKCL +GM++D
Sbjct: 49  CSIMRINRNRCQYCRFKKCLAVGMSRD 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 = 35.9 bits (83), Expect = 8e-04
 Identities = 12/25 (48%), Positives = 17/25 (68%)

Query: 89  RCIVDKAHRNQCQACRLKKCLNMGM 113
            C +DK  R +C  CR +KCL++GM
Sbjct: 42  NCQIDKTQRKRCPYCRFQKCLSVGM 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|143546 cd07172, NR_DBD_GR_PR, DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers

 Score = 35.6 bits (82), Expect = 8e-04
 Identities = 16/31 (51%), Positives = 19/31 (61%)

Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKDGKSM 120
           CI+DK  R  C ACRL+KCL  GMN   +  
Sbjct: 47  CIIDKIRRKNCPACRLRKCLQAGMNLGARKT 77

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

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

 Score = 35.1 bits (81), Expect = 0.001
 Identities = 16/27 (59%), Positives = 20/27 (74%)

Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKD 116
           C VDK  RN+CQ CR +KCL +GM K+
Sbjct: 45  CPVDKRRRNRCQYCRFQKCLQVGMVKE 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|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 = 35.2 bits (81), Expect = 0.001
 Identities = 15/26 (57%), Positives = 20/26 (76%)

Query: 41 CIVDKAHRNQCQACRLKKCLNMGMNK 66
          C++ +  RN+CQ CRL KCL MGMN+
Sbjct: 51 CVMSRKQRNRCQYCRLLKCLQMGMNR 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|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 = 35.2 bits (81), Expect = 0.001
 Identities = 15/26 (57%), Positives = 20/26 (76%)

Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNK 115
           C++ +  RN+CQ CRL KCL MGMN+
Sbjct: 51  CVMSRKQRNRCQYCRLLKCLQMGMNR 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|143513 cd06955, NR_DBD_VDR, DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers

 Score = 35.3 bits (81), Expect = 0.001
 Identities = 15/29 (51%), Positives = 22/29 (75%)

Query: 39 GRCIVDKAHRNQCQACRLKKCLNMGMNKD 67
          G C + K +R  CQACRLK+C+++GM K+
Sbjct: 49 GDCRITKDNRRHCQACRLKRCVDIGMMKE 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|143522 cd06964, NR_DBD_RAR, DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers

 Score = 34.9 bits (80), Expect = 0.002
 Identities = 15/28 (53%), Positives = 22/28 (78%)

Query: 89  RCIVDKAHRNQCQACRLKKCLNMGMNKD 116
            CI++K  RN+CQ CRL+KC  +GM+K+
Sbjct: 48  NCIINKVTRNRCQYCRLQKCFEVGMSKE 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|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 = 33.2 bits (76), Expect = 0.004
 Identities = 13/28 (46%), Positives = 20/28 (71%)

Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKDG 117
           C +  A RN C++CR ++CL +GM+K G
Sbjct: 43  CAITPATRNACKSCRFRRCLAVGMSKTG 70

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	120
cd06957	82	NR_DBD_PNR_like_2 DNA-binding domain of the photor	99.88
cd07164	78	NR_DBD_PNR_like_1 DNA-binding domain of the photor	99.86
cd07163	92	NR_DBD_TLX DNA-binding domain of Tailless (TLX) is	99.86
cd06964	85	NR_DBD_RAR DNA-binding domain of retinoic acid rec	99.86
cd06970	92	NR_DBD_PNR DNA-binding domain of the photoreceptor	99.86
cd06961	85	NR_DBD_TR DNA-binding domain of thyroid hormone re	99.86
cd06956	77	NR_DBD_RXR DNA-binding domain of retinoid X recept	99.86
cd07165	81	NR_DBD_DmE78_like DNA-binding domain of Drosophila	99.85
cd06967	87	NR_DBD_TR2_like DNA-binding domain of the TR2 and	99.85
cd07155	75	NR_DBD_ER_like DNA-binding domain of estrogen rece	99.85
cd07166	89	NR_DBD_REV_ERB DNA-binding domain of REV-ERB recep	99.85
cd06960	76	NR_DBD_HNF4A DNA-binding domain of heptocyte nucle	99.85
cd07168	90	NR_DBD_DHR4_like DNA-binding domain of ecdysone-in	99.85
cd07160	101	NR_DBD_LXR DNA-binding domain of Liver X receptors	99.84
cd07170	97	NR_DBD_ERR DNA-binding domain of estrogen related	99.84
cd07154	73	NR_DBD_PNR_like The DNA-binding domain of the phot	99.84
cd06962	84	NR_DBD_FXR DNA-binding domain of Farnesoid X recep	99.84
cd07171	82	NR_DBD_ER DNA-binding domain of estrogen receptors	99.84
cd07169	90	NR_DBD_GCNF_like DNA-binding domain of Germ cell n	99.84
cd07167	93	NR_DBD_Lrh-1_like The DNA-binding domain of Lrh-1	99.84
cd07161	91	NR_DBD_EcR DNA-binding domain of Ecdysone receptor	99.84
cd06968	95	NR_DBD_ROR DNA-binding domain of Retinoid-related	99.83
cd06969	75	NR_DBD_NGFI-B DNA-binding domain of the orphan nuc	99.83
cd06966	94	NR_DBD_CAR DNA-binding domain of constitutive andr	99.83
cd06916	72	NR_DBD_like DNA-binding domain of nuclear receptor	99.83
cd06958	73	NR_DBD_COUP_TF DNA-binding domain of chicken ovalb	99.83
KOG4215|consensus	432		99.83
cd07156	72	NR_DBD_VDR_like The DNA-binding domain of vitamin	99.83
cd07179	74	2DBD_NR_DBD2 The second DNA-binding domain (DBD) o	99.83
cd07157	86	2DBD_NR_DBD1 The first DNA-binding domain (DBD) of	99.82
cd06963	73	NR_DBD_GR_like The DNA binding domain of GR_like n	99.82
cd07158	73	NR_DBD_Ppar_like The DNA-binding domain of peroxis	99.82
cd06965	84	NR_DBD_Ppar DNA-binding domain of peroxisome proli	99.82
cd07162	87	NR_DBD_PXR DNA-binding domain of pregnane X recept	99.82
cd06959	73	NR_DBD_EcR_like The DNA-binding domain of Ecdysone	99.82
cd07172	78	NR_DBD_GR_PR DNA-binding domain of glucocorticoid	99.81
cd07173	82	NR_DBD_AR DNA-binding domain of androgen receptor	99.81
KOG4216|consensus	479		99.81
cd06955	107	NR_DBD_VDR DNA-binding domain of vitamin D recepto	99.81
KOG4217|consensus	605		99.78
smart00399	70	ZnF_C4 c4 zinc finger in nuclear hormone receptors	99.78
KOG4846|consensus	538		99.77
PF00105	70	zf-C4: Zinc finger, C4 type (two domains); InterPr	99.74
KOG4218|consensus	475		99.69
cd07156	72	NR_DBD_VDR_like The DNA-binding domain of vitamin	99.16
cd06963	73	NR_DBD_GR_like The DNA binding domain of GR_like n	99.14
KOG4216|consensus	479		99.14
cd07154	73	NR_DBD_PNR_like The DNA-binding domain of the phot	99.13
cd06969	75	NR_DBD_NGFI-B DNA-binding domain of the orphan nuc	99.12
cd07179	74	2DBD_NR_DBD2 The second DNA-binding domain (DBD) o	99.11
cd07158	73	NR_DBD_Ppar_like The DNA-binding domain of peroxis	99.11
cd06958	73	NR_DBD_COUP_TF DNA-binding domain of chicken ovalb	99.11
cd06959	73	NR_DBD_EcR_like The DNA-binding domain of Ecdysone	99.1
cd06916	72	NR_DBD_like DNA-binding domain of nuclear receptor	99.1
cd06956	77	NR_DBD_RXR DNA-binding domain of retinoid X recept	99.07
cd07171	82	NR_DBD_ER DNA-binding domain of estrogen receptors	99.06
cd07170	97	NR_DBD_ERR DNA-binding domain of estrogen related	99.06
cd06962	84	NR_DBD_FXR DNA-binding domain of Farnesoid X recep	99.06
KOG4215|consensus	432		99.06
cd07163	92	NR_DBD_TLX DNA-binding domain of Tailless (TLX) is	99.06
cd06960	76	NR_DBD_HNF4A DNA-binding domain of heptocyte nucle	99.06
cd07172	78	NR_DBD_GR_PR DNA-binding domain of glucocorticoid	99.06
cd07155	75	NR_DBD_ER_like DNA-binding domain of estrogen rece	99.05
cd06961	85	NR_DBD_TR DNA-binding domain of thyroid hormone re	99.05
cd07164	78	NR_DBD_PNR_like_1 DNA-binding domain of the photor	99.05
cd07160	101	NR_DBD_LXR DNA-binding domain of Liver X receptors	99.04
cd07161	91	NR_DBD_EcR DNA-binding domain of Ecdysone receptor	99.03
cd06964	85	NR_DBD_RAR DNA-binding domain of retinoic acid rec	99.03
KOG4846|consensus	538		99.02
cd07162	87	NR_DBD_PXR DNA-binding domain of pregnane X recept	99.02
cd06967	87	NR_DBD_TR2_like DNA-binding domain of the TR2 and	99.01
cd06955	107	NR_DBD_VDR DNA-binding domain of vitamin D recepto	99.01
cd06970	92	NR_DBD_PNR DNA-binding domain of the photoreceptor	98.99
cd06957	82	NR_DBD_PNR_like_2 DNA-binding domain of the photor	98.98
cd07173	82	NR_DBD_AR DNA-binding domain of androgen receptor	98.97
cd07165	81	NR_DBD_DmE78_like DNA-binding domain of Drosophila	98.97
KOG4217|consensus	605		98.97
cd07168	90	NR_DBD_DHR4_like DNA-binding domain of ecdysone-in	98.97
cd07157	86	2DBD_NR_DBD1 The first DNA-binding domain (DBD) of	98.96
cd07169	90	NR_DBD_GCNF_like DNA-binding domain of Germ cell n	98.96
cd06968	95	NR_DBD_ROR DNA-binding domain of Retinoid-related	98.96
cd07167	93	NR_DBD_Lrh-1_like The DNA-binding domain of Lrh-1	98.95
cd06966	94	NR_DBD_CAR DNA-binding domain of constitutive andr	98.95
KOG4218|consensus	475		98.93
smart00399	70	ZnF_C4 c4 zinc finger in nuclear hormone receptors	98.93
cd07166	89	NR_DBD_REV_ERB DNA-binding domain of REV-ERB recep	98.93
cd06965	84	NR_DBD_Ppar DNA-binding domain of peroxisome proli	98.88
PF00105	70	zf-C4: Zinc finger, C4 type (two domains); InterPr	98.77

>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=99.88  E-value=1.5e-23  Score=129.91  Aligned_cols=72  Identities=33%  Similarity=0.624  Sum_probs=65.5

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhccc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLL   77 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~   77 (120)
                      +-+||||.+|+||++    ||+|++..+..|.|..++++|.|+...+..|++|||+||+++||++++|+.+|+|+.
T Consensus         9 ~g~hyGv~sC~aCk~----FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~p~~   80 (82)
T cd06957           9 YGKHYGVYCCDGCSC----FFKRSVRKGIIYTCIAGNGNCVVDKARRNWCPFCRLQKCFAVGMNRAAVQEERGPRK   80 (82)
T ss_pred             cceEECcceEeeeee----EEEEeecCCCceEccCccCCCccCCCccCcccCcchhhcccccCCHHHhccccCcCC
Confidence            458999999999987    888999888999998546899999999999999999999999999999999998754

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

>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=99.86  E-value=6.5e-23  Score=126.03  Aligned_cols=69  Identities=41%  Similarity=0.791  Sum_probs=63.6

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNS   75 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~   75 (120)
                      +.+||||.+|+||++    ||+|++..+..+.|.. +++|.|+...+..|++|||+|||++||++++||.+|+|
T Consensus         9 ~g~hyG~~~C~~C~~----FFRR~~~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~   77 (78)
T cd07164           9 SGKHYGVPSCDGCRG----FFKRSIRRNLAYVCKE-NGSCVVDVARRNQCQACRFKKCLQVNMNRDAVQHERAP   77 (78)
T ss_pred             cceEECcchhhhhhh----hhhhhccCCCCccCCC-CCcccccCcccccCccchhhhhhHhcCCHHHhccCCCC
Confidence            458999999999987    7888888888899996 69999999999999999999999999999999999986

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

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

Probab=99.86  E-value=9.9e-23  Score=128.73  Aligned_cols=72  Identities=42%  Similarity=0.757  Sum_probs=64.6

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCC-CCCccccCcccccccccccchhhhcccCchhhhhhhhccc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAG-TGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLL   77 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g-~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~   77 (120)
                      +-+||||.+|+||++    ||+|++..+..|.|..+ +++|.++...+..|++|||+||+++||++++||.+|+|+.
T Consensus        17 ~g~hyGv~sC~aCk~----FFRR~v~~~~~~~C~~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~r~p~~   89 (92)
T cd07163          17 SGKHYGIYACDGCSG----FFKRSIRRNRQYVCKSKGQGGCPVDKTHRNQCRACRLKKCFEVGMNKDAVQHERGPRN   89 (92)
T ss_pred             cccEECceeeeeeee----EEeeeecCCCCcCCCCCCCCCCccCCCccccCccchhhhhhhhcCCHHHhhcccCcCC
Confidence            458999999999987    78899988888999863 3699999999999999999999999999999999999754

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).

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

Probab=99.86  E-value=1e-22  Score=126.90  Aligned_cols=70  Identities=30%  Similarity=0.667  Sum_probs=63.9

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhcc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSL   76 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~   76 (120)
                      +.+||||.+|+||++    ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||++++||.+|+++
T Consensus        15 ~g~hyGv~sC~aC~~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~R~~~   84 (85)
T cd06964          15 SGYHYGVSACEGCKG----FFRRSIQKNMVYTCHR-DKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNKK   84 (85)
T ss_pred             cccEECcceeeeeee----EEeeeecCCCCeECCC-CCccccCCcccccCccchhhhhhhhCCCHHHhhccccCC
Confidence            468999999999987    7888988888899986 689999999999999999999999999999999999853

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

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

Probab=99.86  E-value=8.6e-23  Score=128.88  Aligned_cols=71  Identities=49%  Similarity=0.806  Sum_probs=64.4

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhcc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSL   76 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~   76 (120)
                      +-+||||.+|+||++    ||+|++..+..|.|..++++|.++...+..|++|||+|||++||++++|+.+|++.
T Consensus        17 ~g~hyGv~sC~aCk~----FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R~~~   87 (92)
T cd06970          17 SGKHYGIYACNGCSG----FFKRSVRRKLIYRCQAGTGMCPVDKAHRNQCQACRLKKCLQAGMNKDAVQNERQPR   87 (92)
T ss_pred             cccEECccEEeeeee----EeeeeeecCCCceeecCCCcCccCCCccccCccchhhHhhHhCCCHHHcccccCcc
Confidence            358999999999987    78899988889999864489999999999999999999999999999999999864

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

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

Probab=99.86  E-value=9.1e-23  Score=127.21  Aligned_cols=70  Identities=31%  Similarity=0.590  Sum_probs=64.3

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhcc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSL   76 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~   76 (120)
                      +-+||||.+|+||++    ||+|++..+..|.|.. +++|.++...+..|++|||+|||++||++++||.++++.
T Consensus        10 ~g~hygv~sC~aC~~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~   79 (85)
T cd06961          10 TGYHYRCITCEGCKG----FFRRTVQKKLSYSCKG-EGKCEIDKVTRNQCQECRFKKCIAVGMAKDLVLDDRKRG   79 (85)
T ss_pred             cceEEChhhhhhhhH----hhHhhhccCCccccCC-CCccccCccccccCccchhhhhhhccCCHHHcccccCcc
Confidence            468999999999988    7888998888999996 699999999999999999999999999999999999864

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

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

Probab=99.86  E-value=7.7e-23  Score=125.41  Aligned_cols=67  Identities=30%  Similarity=0.698  Sum_probs=61.5

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhh
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLK   73 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r   73 (120)
                      +-+||||.+|+||++    ||+|++..+..|.|.. +++|.++...+..|++|||+|||++||++++||.+|
T Consensus        11 ~g~hygv~sC~aC~~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r   77 (77)
T cd06956          11 SGKHYGVYSCEGCKG----FFKRTVRKDLTYTCRD-NKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER   77 (77)
T ss_pred             cceEECceeehhHHH----HHHHHhhCCCccccCC-CCccccCCCccccCccchhHHHhHhCCCHHHhccCC
Confidence            458999999999988    7888998888999996 799999999999999999999999999999999875

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

>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=99.85  E-value=1.1e-22  Score=125.74  Aligned_cols=71  Identities=30%  Similarity=0.540  Sum_probs=64.6

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhccc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLL   77 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~   77 (120)
                      +.+||||.+|+||++    ||+|++.....+.|.. +++|.|+...+..|++|||+|||++||++++||.+|+|+.
T Consensus         9 ~g~hyG~~sC~aC~~----FFRR~~~~~~~~~C~~-~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~V~~~r~~~~   79 (81)
T cd07165           9 SGYHYGVTSCEGCKG----FFRRSIQKQIEYRCLR-DGKCEIIRLNRNRCQYCRFKKCLAAGMSKDSVRYGRIPNR   79 (81)
T ss_pred             cceEECchhhhhHHH----HHHhHhccCCceeCCC-CCCccccccccccccchhhhhcccccCCHHHcccCCCCcc
Confidence            468999999999988    6778888888899996 6899999999999999999999999999999999998753

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,

>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=99.85  E-value=1.5e-22  Score=126.71  Aligned_cols=70  Identities=34%  Similarity=0.725  Sum_probs=64.5

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhcc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSL   76 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~   76 (120)
                      +-+||||.+|+||++    ||+|++..+..+.|.. +++|.|+...+..|++|||+|||++||++++||.+|++.
T Consensus        14 ~g~hyGv~sC~aC~~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~R~~~   83 (87)
T cd06967          14 SGRHYGAVSCEGCKG----FFKRSIRKNLGYSCRG-SKDCVINKHHRNRCQYCRLQKCLAMGMKSDSVQCERKPI   83 (87)
T ss_pred             CcCEeCcceEeeeee----EeeeeeeCCCCcccCC-CCccccCccccccCccchhhhhhHcCCCHHHhccccCCC
Confidence            458999999999987    7889998888999995 799999999999999999999999999999999999973

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

>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=99.85  E-value=1.3e-22  Score=123.87  Aligned_cols=67  Identities=36%  Similarity=0.657  Sum_probs=61.3

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhh
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLK   73 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r   73 (120)
                      +-+||||.+|+||++    ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||++++||.+|
T Consensus         9 ~g~hygv~sC~aCk~----FFRR~~~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r   75 (75)
T cd07155           9 SGYHYGVASCEACKA----FFKRTIQGNLGYSCPS-TSECEVDKKRRKSCQACRLQKCLKVGMLKEGVRLDR   75 (75)
T ss_pred             cceEEChhhhhhhHH----HHHHHhhCCCceeCCc-CCCcccCCcccccCccchhhhhhHhCCCHHHcccCC
Confidence            458999999999988    7888988888899996 799999999999999999999999999999999875

DNA-binding domains of estrogen receptor (ER) and estrogen related receptors (ERR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. ER and ERR interact with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulate the rate of transcriptional initiation. ERR and ER are closely related and share sequence similarity, target genes, co-regulators and promoters. While ER is activated by endogenous estrogen, ERR lacks the ability to bind to estrogen. Estrogen receptor mediates the biological effects of hormone estrogen by the binding of the receptor dimer to estrogen response element of target genes. However, ERRs seem to interfere with the classic ER-mediated estrogen responsive signaling by targeting the same set of genes. E

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

Probab=99.85  E-value=2.4e-22  Score=126.22  Aligned_cols=71  Identities=25%  Similarity=0.506  Sum_probs=63.9

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcce-eccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhccc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQ-ACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLL   77 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~-~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~   77 (120)
                      +-+||||.+|+||++    ||+|++..+..| .|.. +++|.|+...+..|++|||+|||++||++++||.+|+|+.
T Consensus        14 ~g~hyGv~sC~aCk~----FFRR~v~~~~~~~~C~~-~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~~~~   85 (89)
T cd07166          14 SGFHYGVHACEGCKG----FFRRSIQQKIQYRKCTK-NETCSIMRINRNRCQYCRFKKCLAVGMSRDAVRFGRIPKR   85 (89)
T ss_pred             cceEEChhhhhhHhh----EecceeEcCCcchhhcc-CCcccccccccccccchhhhhcccccCCHHHhcCCCCCCc
Confidence            458999999999988    788888877888 5985 7999999999999999999999999999999999998754

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

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

Probab=99.85  E-value=3.1e-22  Score=122.48  Aligned_cols=68  Identities=34%  Similarity=0.742  Sum_probs=62.0

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhh
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKN   74 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~   74 (120)
                      +-+||||.+|+||++    ||+|++..+..+.|.. +++|.|+...+..|++|||+|||++||++++|+.+|+
T Consensus         9 ~~~hygv~~C~aC~~----FFrR~~~~~~~~~C~~-~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~   76 (76)
T cd06960           9 TGKHYGVLSCNGCKG----FFRRSVRKNRTYTCRF-GGNCVVDKDKRNACRYCRFKKCLEVGMDPEAVQNERD   76 (76)
T ss_pred             cccEECcceeeeehh----eeCccccCCCceeCCC-CCcccccCcccccCccchhhhhhhcCCCHHHcccCCC
Confidence            358999999999987    7888988888899996 6899999999999999999999999999999998874

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

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

Probab=99.85  E-value=3e-22  Score=126.05  Aligned_cols=70  Identities=29%  Similarity=0.566  Sum_probs=64.0

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhcc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSL   76 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~   76 (120)
                      +-+||||.+|+||++    ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||++++|+.+|+|.
T Consensus        17 ~g~hyGv~sC~aCk~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R~~~   86 (90)
T cd07168          17 TGLHYGIITCEGCKG----FFKRTVQNKRVYTCVG-DGRCEITKAQRNRCQYCRFRKCIRKGMMLAAVREDRMPG   86 (90)
T ss_pred             cceEECceehhhhhH----hhhhhhcCCCCccCCC-CCCccccccccccccccchhhhhhcCCCHHHhhcccCCC
Confidence            458999999999988    7788888888899995 799999999999999999999999999999999999874

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

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

Probab=99.84  E-value=3.2e-22  Score=128.17  Aligned_cols=70  Identities=23%  Similarity=0.451  Sum_probs=63.9

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhcc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSL   76 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~   76 (120)
                      +-+||||.+|+||++    ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||++++||+++++.
T Consensus        29 ~g~hyGv~sC~aCk~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~~~~   98 (101)
T cd07160          29 SGFHYNVLSCEGCKG----FFRRSVIKGAQYVCKN-GGKCQMDMYMRRKCQECRLRKCREAGMREQCVLSEEQIR   98 (101)
T ss_pred             cceEECcceehhhhh----hhhhcccccCccccCC-CCccccCCcccccCccchhHHHHHhCCCHHHhcChhhhh
Confidence            458999999999987    7888888888999996 699999999999999999999999999999999998853

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=99.84  E-value=3.7e-22  Score=127.05  Aligned_cols=69  Identities=32%  Similarity=0.577  Sum_probs=63.1

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNS   75 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~   75 (120)
                      +-+||||.+|+||++    ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||++++||.+++.
T Consensus        15 ~g~hyGv~sC~aCk~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~vq~~r~~   83 (97)
T cd07170          15 SGYHYGVASCEACKA----FFKRTIQGNIEYSCPA-TNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVR   83 (97)
T ss_pred             cceEECceeehhhhH----HHHHHhccCCceeecC-CCccccCcccCccCCccccchhhhcCCCHHHcccccCC
Confidence            458999999999988    7788888888899995 79999999999999999999999999999999998874

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

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

Probab=99.84  E-value=4.1e-22  Score=121.06  Aligned_cols=65  Identities=49%  Similarity=0.865  Sum_probs=59.1

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhh
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQ   70 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~   70 (120)
                      +.+||||.+|+||++    ||+|++..+..|.|..++++|.|+...+..|++|||+|||++||++++||
T Consensus         9 ~~~hyGv~sC~aC~~----FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~vq   73 (73)
T cd07154           9 SGKHYGVYACDGCSG----FFKRSIRRNLLYTCKAGNGSCVVDKARRNQCQACRLKKCLEVSMNKDAVQ   73 (73)
T ss_pred             cceEECcceeeeeee----EeeeeecCCCCcccCCCCCCCccCCcccccCccchhhHhhHhCCChHHCC
Confidence            458999999999987    88899988889999855789999999999999999999999999998875

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

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

Probab=99.84  E-value=6.2e-22  Score=123.12  Aligned_cols=68  Identities=26%  Similarity=0.479  Sum_probs=62.5

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhh
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKN   74 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~   74 (120)
                      +-+||||.+|+||++    ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||+.++|+++.+
T Consensus        12 ~g~hyGv~sC~aCk~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~   79 (84)
T cd06962          12 SGYHYNALTCEGCKG----FFRRSITKNAVYKCKN-GGNCEMDMYMRRKCQECRLRKCKEMGMLAECLLTEIQ   79 (84)
T ss_pred             cceEECcceeeccee----eeeeeeccCCceecCC-CCcCccCccccccCccchhhHHHHhCCChHHccCHHH
Confidence            458999999999987    7889998888999996 6999999999999999999999999999999998876

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

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

Probab=99.84  E-value=6e-22  Score=122.69  Aligned_cols=68  Identities=32%  Similarity=0.616  Sum_probs=61.6

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhh
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKN   74 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~   74 (120)
                      +-+||||.+|+||++    ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||++++|+.++.
T Consensus        14 ~g~hyGv~sC~aC~~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~~~   81 (82)
T cd07171          14 SGYHYGVWSCEGCKA----FFKRSIQGHNDYICPA-TNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRRERR   81 (82)
T ss_pred             cceEECceeehhhHH----hHHHHeeCCCceeCCC-CCccccCCcccccCccchhHHHhHhcCCHHHHHHhhc
Confidence            458999999999988    6778888788899985 7999999999999999999999999999999998763

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

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

Probab=99.84  E-value=5.2e-22  Score=124.93  Aligned_cols=69  Identities=29%  Similarity=0.583  Sum_probs=63.2

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNS   75 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~   75 (120)
                      +-+||||.+|+||++    ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||++++|+.++++
T Consensus        17 ~g~hyGv~sC~aCk~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~   85 (90)
T cd07169          17 TGLHYGIISCEGCKG----FFKRSICNKRVYRCSR-DKNCVMSRKQRNRCQYCRLLKCLQMGMNRKAIREDGMP   85 (90)
T ss_pred             cceEECcceehhhHH----HHHHHhcCCCceecCC-CCcccccccccccccccchhhhccccCCHHHhccccCC
Confidence            458999999999988    7788888888899996 68999999999999999999999999999999999875

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

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

Probab=99.84  E-value=5.2e-22  Score=125.50  Aligned_cols=69  Identities=23%  Similarity=0.560  Sum_probs=63.3

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNS   75 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~   75 (120)
                      +-+||||.+|+||++    ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||++++||.+|+.
T Consensus         9 ~g~hyGv~sC~aCk~----FFRRsv~~~~~~~C~~-~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~Vq~~r~~   77 (93)
T cd07167           9 SGYHYGLLTCESCKG----FFKRTVQNKKRYTCIE-NQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMR   77 (93)
T ss_pred             cceEECchhhhhHHH----HHHHHeeCCCccccCC-CCccccCccccCcCCCcccchhhhccCCHHHhhhcccC
Confidence            358999999999988    7788988888999996 69999999999999999999999999999999999874

The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This nuclear receptor family includes at least three subgroups of receptors that function in embryo development and differentiation, and other processes. FTZ-F1 interacts with the cis-acting DNA motif of ftz gene, which is required at several stages of development. Particularly, FTZ-F1 regulated genes are strongly linked to steroid biosynthesis and sex-determination; LRH-1 is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development; SF-1 is an essential regu

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

Probab=99.84  E-value=6.2e-22  Score=124.77  Aligned_cols=68  Identities=25%  Similarity=0.465  Sum_probs=62.6

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhh
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKN   74 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~   74 (120)
                      +-+||||.+|+||++    ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||++++|+++++
T Consensus        12 ~g~hyGv~sC~aCk~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~   79 (91)
T cd07161          12 SGYHYNALTCEGCKG----FFRRSVTKSAVYHCKY-GRACEMDMYMRRKCQECRLKKCLSVGMRPECVVPESQ   79 (91)
T ss_pred             cceEECceeehhhHH----HHHHHhccCCceecCC-CCccccCccccccCccchhhHHhHcCCCHHHcCchhh
Confidence            458999999999988    7788988888999996 6899999999999999999999999999999999976

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

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

Probab=99.83  E-value=7.6e-22  Score=125.29  Aligned_cols=72  Identities=29%  Similarity=0.612  Sum_probs=65.2

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhccch
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLY   78 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~   78 (120)
                      +.+||||.+|+||++    ||+|++..+..+.|.. +++|.++...+..|++|||+||+++||++++|+.++.++..
T Consensus        16 ~g~hyGv~sC~aC~~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~V~~~r~~~~~   87 (95)
T cd06968          16 SGIHYGVITCEGCKG----FFRRSQQNNVSYSCPR-QKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQ   87 (95)
T ss_pred             cceEECceeehhhHH----hhHHheeCCCceecCC-CcccccccCCceeccccchhhcccccCChhhcccCcCChhh
Confidence            468999999999988    7788888888899996 68999999999999999999999999999999999887544

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

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

Probab=99.83  E-value=1e-21  Score=119.89  Aligned_cols=65  Identities=34%  Similarity=0.680  Sum_probs=59.2

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhh
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH   71 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~   71 (120)
                      +-+||||.+|+||++    ||+|++..+..|.|.. +++|.++...+..|++|||+|||++||++++||.
T Consensus        11 ~g~hyGv~sC~aC~~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~   75 (75)
T cd06969          11 ACQHYGVRTCEGCKG----FFKRTVQKNAKYVCLA-NKNCPVDKRRRNRCQYCRFQKCLQVGMVKEVVRT   75 (75)
T ss_pred             cceEECcceeeeeee----eeeeeeecCCcccCCc-CCccccCCcccccCcccHhHHHHHhCCCHHHccC
Confidence            458999999999987    7888988888899996 7999999999999999999999999999999873

DNA-binding domain (DBD) of the orphan nuclear receptor, nerve growth factor-induced-B (NGFI-B) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NGFI-B interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. NGFI-B is a member of the nuclear-steroid receptor superfamily. NGFI-B is classified as an orphan receptor because no ligand has yet been identified. NGFI-B is an early immediate gene product of embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as neuronal differentiation and function. NGFI-B regulates transcription by binding to a specific DNA target upstream of its target genes and regulating the rate of transcrip

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

Probab=99.83  E-value=1.1e-21  Score=124.45  Aligned_cols=69  Identities=25%  Similarity=0.443  Sum_probs=63.4

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNS   75 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~   75 (120)
                      +-+||||.+|+||++    ||+|++..+..|.|.. +++|.++...+..|++|||+|||++||++++|+++++.
T Consensus        11 ~g~hyGv~sC~aC~~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~r~~   79 (94)
T cd06966          11 LGYNFNAITCESCKA----FFRRNALKNKEFKCPF-NESCEINVVTRRFCQKCRLDKCFAIGMKKEWIMSEEDK   79 (94)
T ss_pred             cceEECcceeeeehh----eehhcccCCCccccCC-CCccccCccccccCccchhhhCcccCCCHHHccchhhh
Confidence            468999999999987    7888998888899996 69999999999999999999999999999999999874

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

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

Probab=99.83  E-value=1.1e-21  Score=118.81  Aligned_cols=64  Identities=41%  Similarity=0.785  Sum_probs=58.6

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhh
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQ   70 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~   70 (120)
                      +.+||||.+|+||++    ||+|++..+..+.|.. +++|.++...+..|++|||+|||++||++++||
T Consensus         9 ~~~hygv~sC~aC~~----FFRR~~~~~~~~~C~~-~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   72 (72)
T cd06916           9 SGYHYGVLTCEGCKG----FFRRSVRRNLEYTCPA-GGNCVIDKRNRNRCQACRLKKCLAVGMRKEAVR   72 (72)
T ss_pred             cccEECcceeeeeee----eEeEeecCCCCccCCC-CCccccCCcccccCccchhhHhhHhCCChHHcC
Confidence            458999999999987    8889998888899996 699999999999999999999999999998875

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

>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=99.83  E-value=1.3e-21  Score=118.90  Aligned_cols=64  Identities=38%  Similarity=0.753  Sum_probs=58.5

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhh
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQ   70 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~   70 (120)
                      +-+||||.+|+||++    ||+|++..+..+.|.. +++|.++...+..|++|||+|||++||++++||
T Consensus         9 ~g~hygv~sC~aC~~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   72 (73)
T cd06958           9 SGKHYGQFTCEGCKS----FFKRSVRRNLTYTCRG-NRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQ   72 (73)
T ss_pred             cceEEChhhhhhhhh----hhhhhhcCCCceeCCC-CCcCccCCcccccCccchhhHhhHhCCCHHHcc
Confidence            458999999999988    7788888888899995 799999999999999999999999999999887

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

>KOG4215|consensus

Probab=99.83  E-value=3.7e-22  Score=150.16  Aligned_cols=71  Identities=28%  Similarity=0.628  Sum_probs=66.6

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhccc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLL   77 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~   77 (120)
                      |-+|||+.+|+|||    +||||||.++..|.|+. +.+|.||+..|+.|++|||+||+.+||.+++||++|++..
T Consensus        30 TGKHYGA~SCdGCK----GFFRRSVrk~~~YtCRF-~k~C~VDKdkRNaCRyCRfqKC~~aGMK~eAiQnERDrIg  100 (432)
T KOG4215|consen   30 TGKHYGAISCDGCK----GFFRRSVRKNHQYTCRF-NKQCVVDKDKRNACRYCRFQKCVRAGMKREAIQNERDRIG  100 (432)
T ss_pred             cccccceeecCcch----HHHHHHHHhcceeeeec-cccccccchhhhhhhHhhHHHHHHhcccHHhhhccccccc
Confidence            67899999999995    69999999999999997 7999999999999999999999999999999999998643

>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=99.83  E-value=1.6e-21  Score=118.19  Aligned_cols=63  Identities=35%  Similarity=0.640  Sum_probs=57.6

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhh
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDA   69 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v   69 (120)
                      +-+||||.+|+||++    ||+|++..+..+.|.. +++|.++...+..|++|||+|||++||++++|
T Consensus         9 ~g~hygv~sC~aC~~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v   71 (72)
T cd07156           9 TGYHFNAMTCEGCKG----FFRRSMKRKARFTCPF-NGDCEITKDNRRHCQACRLKKCLDIGMKKEMI   71 (72)
T ss_pred             cccEECcceehhhhh----hhchhccCcCccccCC-CCccccCCcccccCccchhHHHHHhCCCHHHc
Confidence            458999999999988    7788888888899996 69999999999999999999999999999876

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

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

Probab=99.83  E-value=1.1e-21  Score=119.49  Aligned_cols=65  Identities=25%  Similarity=0.562  Sum_probs=59.2

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhh
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH   71 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~   71 (120)
                      +-+||||.+|+||++    ||+|++..+..+.|.. +++|.++...+..|++|||+|||++||++++|+.
T Consensus         9 ~g~hygv~sC~aC~~----FFRR~~~~~~~~~C~~-~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~   73 (74)
T cd07179           9 SGFHFGALTCEGCKG----FFRRTELSSNSYVCPG-GQNCAITPATRNACKSCRFRRCLAVGMSKTGSRI   73 (74)
T ss_pred             cceEECceeehhHHH----HHHHHhhCCCcccCCC-CCccccCCcccccCccchhHHHHHhCCCHhHeeC
Confidence            458999999999988    7788888888999996 6889999999999999999999999999999875

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

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

Probab=99.82  E-value=1.9e-21  Score=121.43  Aligned_cols=70  Identities=31%  Similarity=0.619  Sum_probs=62.0

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCc--ceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhcc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQ--CQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSL   76 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~--~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~   76 (120)
                      +-+||||.+|+||++    ||+|++....  .|.|.. +++|.++...+..|++|||+|||++||+.++++.+|+..
T Consensus        11 ~g~hyGv~sC~aCk~----FFRR~~~~~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~~~~~~~   82 (86)
T cd07157          11 AGFHHGAYVCEACKK----FFMRSSNAISFTISECPN-GGKCIIDKKNRTKCQACRYRKCLNVGMSLGGPRYGRRSD   82 (86)
T ss_pred             cccEECcceeeEeee----EEecceecCCCccccCCC-CCccccCccccccCccchhhHHhHcCCCccccccccccc
Confidence            458999999999987    7888887654  789996 699999999999999999999999999999999888743

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.

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

Probab=99.82  E-value=2.1e-21  Score=117.86  Aligned_cols=64  Identities=30%  Similarity=0.616  Sum_probs=58.1

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhh
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQ   70 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~   70 (120)
                      +-+||||.+|+||++    ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||+++++.
T Consensus         9 ~~~hygv~sC~aCk~----FFRR~~~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~a~~   72 (73)
T cd06963           9 SGCHYGVLTCGSCKV----FFKRAAEGQHNYLCAG-RNDCIIDKIRRKNCPACRLRKCYQAGMTLGARK   72 (73)
T ss_pred             cceEECceeehhhhH----hHHHhhcCCCceeCCC-CCccccCCcccccCccchhhHHHHcCCChhhcc
Confidence            468999999999987    7888998888899985 799999999999999999999999999998764

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

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

Probab=99.82  E-value=2.5e-21  Score=117.59  Aligned_cols=64  Identities=30%  Similarity=0.709  Sum_probs=57.9

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcce-eccCCCCCccccCcccccccccccchhhhcccCchhhh
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQ-ACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQ   70 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~-~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~   70 (120)
                      +-+||||.+|+||++    ||+|++..+..+ .|.. +++|.++...+..|++|||+|||++||++++|+
T Consensus         9 ~g~hyGv~~C~aC~~----FFRR~v~~~~~~~~C~~-~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   73 (73)
T cd07158           9 SGFHYGVHSCEGCKG----FFRRTIQHNLTYRRCLN-GGKCVIQRKNRNRCQYCRFKKCLSVGMSRNAVR   73 (73)
T ss_pred             cceEECcchhhHHHH----HHhhhhcCCCCcccCCC-CCCcCCCccccccCccchhhhhhHccCChHHcC
Confidence            458999999999988    778888888888 8985 699999999999999999999999999998875

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

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

Probab=99.82  E-value=2.5e-21  Score=120.45  Aligned_cols=70  Identities=26%  Similarity=0.514  Sum_probs=61.5

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCccee-ccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhccch
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQA-CQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLY   78 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~-C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~   78 (120)
                      +-+||||.+|+||++    ||+|++..+..|. |..   +|.|+...+..|++|||+||+++||++++|+.+|+|+..
T Consensus        10 ~g~hyGv~sC~aCk~----FFRR~v~~~~~~~~C~~---~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~~~~~   80 (84)
T cd06965          10 SGFHYGVHACEGCKG----FFRRTIRLKLVYKPCDL---SCKIHKKSRNKCQYCRFQKCLNVGMSHNAIRFGRMPRVE   80 (84)
T ss_pred             cceEEChhhhhhhhh----heeeeeecCCCcccccc---CCCcCccccccccchhhhhhhhccCCHHHcccCCCCchh
Confidence            458999999999987    7888888777884 973   399999999999999999999999999999999997543

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

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

Probab=99.82  E-value=2.3e-21  Score=121.38  Aligned_cols=68  Identities=32%  Similarity=0.574  Sum_probs=61.3

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhh
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKN   74 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~   74 (120)
                      +-+||||.+|+||++    ||+|++..+..|.|.. +++|.++...+..|++|||+|||++||++++|++++.
T Consensus        10 ~g~hygv~sC~aC~~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~~   77 (87)
T cd07162          10 TGYHFNAMTCEGCKG----FFRRAMKRNARLCCPF-QKGCVITKSNRRQCQACRLRKCLSIGMKKELIMSDEA   77 (87)
T ss_pred             cceEECcceehhhHH----HHHhhhccCceeEcCC-CCceecCCcccccCccchhhHHhHhCCCHHHccCHHH
Confidence            468999999999988    6778888888899996 6899999999999999999999999999999888754

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

>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=99.82  E-value=2.1e-21  Score=117.94  Aligned_cols=63  Identities=29%  Similarity=0.555  Sum_probs=57.5

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhh
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDA   69 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v   69 (120)
                      +-+||||.+|+||++    ||||++..+..|.|.. +++|.++...+..|++|||+|||++||+++.|
T Consensus        10 ~~~hygv~sC~aC~~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v   72 (73)
T cd06959          10 SGFHYGVLSCEGCKG----FFRRSVTKGAVYACKF-GNKCEMDMYMRRKCQECRLRKCKAAGMRPDCL   72 (73)
T ss_pred             cceEECceeehhhHH----HHHHhhcCCCCccCCC-CCcCCcCCcccccCccchhHHHHHhCCChhhc
Confidence            468999999999988    7788888888999996 69999999999999999999999999999876

The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: Ecdysone receptor (EcR), Liver X receptor (LXR) and Farnesoid X receptor (FXR). The DNA binding activity is regulated by their corresponding ligands. The ligands for EcR are ecdysteroids; LXR is regulated by oxidized cholesterol derivatives or oxysterols; and bile acids control FXR's activities. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcR-like receptors have a central well conserved DNA binding domai

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

Probab=99.81  E-value=5.3e-21  Score=117.43  Aligned_cols=64  Identities=31%  Similarity=0.642  Sum_probs=57.9

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhh
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQ   70 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~   70 (120)
                      +-+||||.+|+||++    ||||++..+..|.|.. +++|.|+...+..|++|||+|||++||+..++.
T Consensus        13 ~g~hyGv~sC~aC~~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~   76 (78)
T cd07172          13 SGCHYGVLTCGSCKV----FFKRAVEGQHNYLCAG-RNDCIIDKIRRKNCPACRLRKCLQAGMNLGARK   76 (78)
T ss_pred             cceEECceeehhhHH----hHHHHeeCCCceeCCC-CCccccCCcccccCccchhHHHHHhCCCccccc
Confidence            458999999999988    7788888888899985 799999999999999999999999999987765

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=99.81  E-value=7.7e-21  Score=117.69  Aligned_cols=66  Identities=27%  Similarity=0.546  Sum_probs=58.9

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhh
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHL   72 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~   72 (120)
                      +-+||||.+|+||++    ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||++.....+
T Consensus        14 ~g~hyGv~sC~aCk~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~~~~~   79 (82)
T cd07173          14 SGCHYGALTCGSCKV----FFKRAAEGKQKYLCAS-RNDCTIDKFRRKNCPSCRLRKCFEAGMTLGARKLK   79 (82)
T ss_pred             cceEECcchhhhHHH----HHHHHhcCCCceecCC-CCccccCCCccCcCcchhhhhhhhcCCCcChHHhh
Confidence            358999999999988    7788888888899996 79999999999999999999999999998776654

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

>KOG4216|consensus

Probab=99.81  E-value=2.9e-21  Score=146.31  Aligned_cols=70  Identities=30%  Similarity=0.618  Sum_probs=65.3

Q ss_pred             CccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhccc
Q psy13208          3 FRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLL   77 (120)
Q Consensus         3 ~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~   77 (120)
                      -.||||.+|||||    +|||||-+.+..|.|++ ..+|.||...|+.|+.|||+|||++||++++|..+|++++
T Consensus        58 GiHYGVITCEGCK----GFFRRSQ~s~a~YsCpR-qknC~iDRtnRNRCQ~CRLqKClaLGMSRDAVKFGRMSKK  127 (479)
T KOG4216|consen   58 GIHYGVITCEGCK----GFFRRSQQSNANYSCPR-QKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSKK  127 (479)
T ss_pred             cceeeeEeeccch----HhhhhhhhccccccCCc-ccCCcccccccchhhHHHHHHHHHhccchhhHHhccccHh
Confidence            3799999999995    68999999999999996 8999999999999999999999999999999999998764

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

Probab=99.81  E-value=7.7e-21  Score=122.88  Aligned_cols=66  Identities=30%  Similarity=0.543  Sum_probs=59.5

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhh
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHL   72 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~   72 (120)
                      +-+||||.+|+||++    ||+|++..+..|.|.. +++|.++...+..|++|||+|||++||++++|+++
T Consensus        17 ~g~hyGv~sC~aCk~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~   82 (107)
T cd06955          17 TGFHFNAMTCEGCKG----FFRRSMKRKALFTCPF-NGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTD   82 (107)
T ss_pred             cccEECcceeeeecc----eecceeccCCccccCC-CCccccccCCccccccchhHHHHHcCCCchhccCH
Confidence            458999999999987    7888998888899986 79999999999999999999999999998777765

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

>KOG4217|consensus

Probab=99.78  E-value=1.2e-20  Score=145.85  Aligned_cols=64  Identities=34%  Similarity=0.658  Sum_probs=59.4

Q ss_pred             ccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhh
Q psy13208          4 RHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHL   72 (120)
Q Consensus         4 ~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~   72 (120)
                      -||||.+|||||    +||+|+++++..|+|.+ +.+|+||+..|+.|++|||+|||+|||-.+.|+.+
T Consensus       282 qHYGvRTCEGCK----GFFKRTVQKnaKYvCla-nKnCPVDKRrRnRCQyCRfQKCL~VGMVKEVVRtd  345 (605)
T KOG4217|consen  282 QHYGVRTCEGCK----GFFKRTVQKNAKYVCLA-NKNCPVDKRRRNRCQYCRFQKCLAVGMVKEVVRTD  345 (605)
T ss_pred             hhcCccccccch----HHHHHHHhcCCeeEeec-CCCCCcchhhhhhchhhhHhHHHHhhhhhhheecc
Confidence            399999999995    69999999999999995 89999999999999999999999999998888754

>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors

Probab=99.78  E-value=5.9e-20  Score=110.70  Aligned_cols=61  Identities=31%  Similarity=0.625  Sum_probs=55.0

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCch
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKD   67 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~   67 (120)
                      +.+||||.+|+||++    ||+|++..+..+.|.. +++|.++...+..|++|||+|||++||+++
T Consensus        10 ~~~hygv~~C~aC~~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~   70 (70)
T smart00399       10 SGFHFGVCSCRACKA----FFRRTVNLRYKYRCDR-KNNCSINKRYRCRCRACRLKKCLGVGMDPE   70 (70)
T ss_pred             cccEeCCcEechhhh----hhhhheeCCCCeecCC-CcccccCCCccccCccCcChhHhhccCcCC
Confidence            468999999999987    7888988888899996 688999999999999999999999999863

>KOG4846|consensus

Probab=99.77  E-value=2.1e-20  Score=142.69  Aligned_cols=69  Identities=28%  Similarity=0.547  Sum_probs=63.4

Q ss_pred             CccCCccCChhhhhcccceeeeccccCcce-eccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhcc
Q psy13208          3 FRHDGMTDHPTCQAGTERCIVDKAHRNQCQ-ACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSL   76 (120)
Q Consensus         3 ~~hygv~~C~~C~~ff~~ff~rsi~~~~~~-~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~   76 (120)
                      -|||||.+|||||    +||||+|+.+..| .|- ++.+|.|....|+.|+.|||+|||.+||++++|+.++++.
T Consensus       144 GfHYGV~aCEGCK----GFFRRSIQqkI~YrrCl-k~e~C~I~R~nRNRCQ~CRfKKCL~vGMSrDaVRFG~m~~  213 (538)
T KOG4846|consen  144 GFHYGVTACEGCK----GFFRRSIQQKIDYRRCL-KQEVCEIKRENRNRCQYCRFKKCLDVGMSRDAVRFGQMKF  213 (538)
T ss_pred             cceeceeecccch----HHHHHHHHHhhhHHHHh-hhhceehhhhccchhhhhhHHHHHhcccchhhhhhccccc
Confidence            4899999999995    6999999999988 798 4899999999999999999999999999999999887754

>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=99.74  E-value=2.2e-19  Score=108.19  Aligned_cols=60  Identities=30%  Similarity=0.733  Sum_probs=50.4

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNK   66 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~   66 (120)
                      +.+||||.+|++|++    ||+|++.....+.|.. +++|.++...+..|++|||+|||++||..
T Consensus        11 ~~~~ygv~sC~~C~~----FFrR~~~~~~~~~C~~-~~~C~i~~~~~~~C~~CRf~KCl~~GM~k   70 (70)
T PF00105_consen   11 SGYHYGVLSCNACKM----FFRRSVKKKKPYKCKK-NGNCKIDKDNRRKCRSCRFQKCLEVGMKK   70 (70)
T ss_dssp             SEEETTEEEEHHHHH----HHHHHHHTTCG-STSS-SST---STTTTTTSHHHHHHHHHHTTBSG
T ss_pred             Cccccccccccccee----eeeecccccccccccc-cccccccccCCCEeCcchHHHHHHHCCcC
Confidence            458999999999987    7788888888899995 79999999999999999999999999973

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 ....

>KOG4218|consensus

Probab=99.69  E-value=3.6e-18  Score=128.18  Aligned_cols=67  Identities=25%  Similarity=0.597  Sum_probs=63.3

Q ss_pred             CccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhh
Q psy13208          3 FRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKN   74 (120)
Q Consensus         3 ~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~   74 (120)
                      -||||-++||.||    +||+|+++.++.|.|.. +.+|.||+..|..|++|||+|||.+||..++|+-+|+
T Consensus        27 GYHYGLLTCESCK----GFFKRTVQNnK~YtC~e-~qnC~iDkTqRKRCP~CRFQKCLtvGMklEAVRADRM   93 (475)
T KOG4218|consen   27 GYHYGLLTCESCK----GFFKRTVQNNKQYTCSE-EQNCHIDKTQRKRCPSCRFQKCLTVGMKLEAVRADRM   93 (475)
T ss_pred             cceeeeeehhhhh----hHHHHHhhcCcceeccc-ccccccchHhhccCCchhHHHHhhhhhhHHHHHHhhh
Confidence            5899999999995    68999999999999995 8999999999999999999999999999999998886

>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=99.16  E-value=1e-11  Score=75.10  Aligned_cols=59  Identities=36%  Similarity=0.797  Sum_probs=50.0

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       +++++.+..+..     |.|..  +++|.|+...+..|++|||+|||++||++++|
T Consensus        13 ygv~sC~aC~-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v   71 (72)
T cd07156          13 FNAMTCEGCK-------GFFRRSMKRKAR-----FTCPF--NGDCEITKDNRRHCQACRLKKCLDIGMKKEMI   71 (72)
T ss_pred             ECcceehhhh-------hhhchhccCcCc-----cccCC--CCccccCCcccccCccchhHHHHHhCCCHHHc
Confidence            3456899999       898888875543     77874  57899999999999999999999999999876

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

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

Probab=99.14  E-value=1.4e-11  Score=74.70  Aligned_cols=60  Identities=33%  Similarity=0.725  Sum_probs=50.6

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCcc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGKS  119 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~~  119 (120)
                      .+...|.+|.       +++++.++.+..     |.|..  +++|.|+...++.|++|||+|||++||+++++-
T Consensus        13 ygv~sC~aCk-------~FFRR~~~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~a~~   72 (73)
T cd06963          13 YGVLTCGSCK-------VFFKRAAEGQHN-----YLCAG--RNDCIIDKIRRKNCPACRLRKCYQAGMTLGARK   72 (73)
T ss_pred             ECceeehhhh-------HhHHHhhcCCCc-----eeCCC--CCccccCCcccccCccchhhHHHHcCCChhhcc
Confidence            3456899999       888888876644     77864  578999999999999999999999999998873

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

>KOG4216|consensus

Probab=99.14  E-value=1.3e-11  Score=94.28  Aligned_cols=59  Identities=36%  Similarity=0.898  Sum_probs=52.8

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+..-|..|+       |+++++-++.-.     |.|+.  ..+|+||+.+||.|++|||+|||++||+.+||
T Consensus        61 YGVITCEGCK-------GFFRRSQ~s~a~-----YsCpR--qknC~iDRtnRNRCQ~CRLqKClaLGMSRDAV  119 (479)
T KOG4216|consen   61 YGVITCEGCK-------GFFRRSQQSNAN-----YSCPR--QKNCLIDRTNRNRCQHCRLQKCLALGMSRDAV  119 (479)
T ss_pred             eeeEeeccch-------Hhhhhhhhcccc-----ccCCc--ccCCcccccccchhhHHHHHHHHHhccchhhH
Confidence            4457899999       999887777766     99985  69999999999999999999999999999998

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

Probab=99.13  E-value=1.5e-11  Score=74.48  Aligned_cols=60  Identities=45%  Similarity=0.806  Sum_probs=50.3

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+-..|.+|.       +++++.++.+..     |.|.. ..++|.|+...+..|++|||+|||++||++++|
T Consensus        13 yGv~sC~aC~-------~FFRR~v~~~~~-----~~C~~-~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v   72 (73)
T cd07154          13 YGVYACDGCS-------GFFKRSIRRNLL-----YTCKA-GNGSCVVDKARRNQCQACRLKKCLEVSMNKDAV   72 (73)
T ss_pred             ECcceeeeee-------eEeeeeecCCCC-----cccCC-CCCCCccCCcccccCccchhhHhhHhCCChHHC
Confidence            4457899999       999888876644     77863 246899999999999999999999999999876

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

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

Probab=99.12  E-value=1.5e-11  Score=74.89  Aligned_cols=59  Identities=37%  Similarity=0.780  Sum_probs=50.1

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       ++++++++.+..     |.|..  +++|.|+...+..|++|||+|||++||++++|
T Consensus        15 yGv~sC~aC~-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V   73 (75)
T cd06969          15 YGVRTCEGCK-------GFFKRTVQKNAK-----YVCLA--NKNCPVDKRRRNRCQYCRFQKCLQVGMVKEVV   73 (75)
T ss_pred             ECcceeeeee-------eeeeeeeecCCc-----ccCCc--CCccccCCcccccCcccHhHHHHHhCCCHHHc
Confidence            4457899999       999888875543     77874  57899999999999999999999999999876

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

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

Probab=99.11  E-value=1.5e-11  Score=74.71  Aligned_cols=59  Identities=29%  Similarity=0.795  Sum_probs=49.7

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       ++++++++....     |.|..  +++|.|+...+..|++|||+|||++||++++|
T Consensus        13 ygv~sC~aC~-------~FFRR~~~~~~~-----~~C~~--~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v   71 (74)
T cd07179          13 FGALTCEGCK-------GFFRRTELSSNS-----YVCPG--GQNCAITPATRNACKSCRFRRCLAVGMSKTGS   71 (74)
T ss_pred             ECceeehhHH-------HHHHHHhhCCCc-----ccCCC--CCccccCCcccccCccchhHHHHHhCCCHhHe
Confidence            3456899998       888888876544     77875  46799999999999999999999999999887

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.

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

Probab=99.11  E-value=1.5e-11  Score=74.56  Aligned_cols=59  Identities=34%  Similarity=0.862  Sum_probs=49.5

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhc-ccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEF-ACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~-~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       +++++.++.+..     | .|..  +++|.|+...+..|++|||+|||++||++++|
T Consensus        13 yGv~~C~aC~-------~FFRR~v~~~~~-----~~~C~~--~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v   72 (73)
T cd07158          13 YGVHSCEGCK-------GFFRRTIQHNLT-----YRRCLN--GGKCVIQRKNRNRCQYCRFKKCLSVGMSRNAV   72 (73)
T ss_pred             ECcchhhHHH-------HHHhhhhcCCCC-----cccCCC--CCCcCCCccccccCccchhhhhhHccCChHHc
Confidence            3456899999       888888876644     6 6764  47899999999999999999999999999876

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=99.11  E-value=2e-11  Score=73.97  Aligned_cols=59  Identities=36%  Similarity=0.822  Sum_probs=49.7

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       +++++++..+..     |.|..  +++|.|+...+..|++|||+|||++||++++|
T Consensus        13 ygv~sC~aC~-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v   71 (73)
T cd06958          13 YGQFTCEGCK-------SFFKRSVRRNLT-----YTCRG--NRNCPIDQHHRNQCQYCRLKKCLKVGMRREAV   71 (73)
T ss_pred             EChhhhhhhh-------hhhhhhhcCCCc-----eeCCC--CCcCccCCcccccCccchhhHhhHhCCCHHHc
Confidence            3456899999       888888876543     77864  57899999999999999999999999999876

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

>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=99.10  E-value=2.4e-11  Score=73.65  Aligned_cols=59  Identities=31%  Similarity=0.637  Sum_probs=49.2

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       ++++++++.+..     |.|..  +++|.|+...+..|++|||+|||++||+++.|
T Consensus        14 ygv~sC~aC~-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v   72 (73)
T cd06959          14 YGVLSCEGCK-------GFFRRSVTKGAV-----YACKF--GNKCEMDMYMRRKCQECRLRKCKAAGMRPDCL   72 (73)
T ss_pred             ECceeehhhH-------HHHHHhhcCCCC-----ccCCC--CCcCCcCCcccccCccchhHHHHHhCCChhhc
Confidence            3456899999       888888875533     77874  47899999999999999999999999998765

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

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

Probab=99.10  E-value=2.4e-11  Score=73.47  Aligned_cols=59  Identities=37%  Similarity=0.844  Sum_probs=50.1

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+-..|.+|.       +++++++..+..     |.|..  ++.|.|+...+..|++|||+|||++||++++|
T Consensus        13 ygv~sC~aC~-------~FFRR~~~~~~~-----~~C~~--~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v   71 (72)
T cd06916          13 YGVLTCEGCK-------GFFRRSVRRNLE-----YTCPA--GGNCVIDKRNRNRCQACRLKKCLAVGMRKEAV   71 (72)
T ss_pred             ECcceeeeee-------eeEeEeecCCCC-----ccCCC--CCccccCCcccccCccchhhHhhHhCCChHHc
Confidence            3456899999       999888886644     77874  47899999999999999999999999998875

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

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

Probab=99.07  E-value=2e-11  Score=74.71  Aligned_cols=59  Identities=34%  Similarity=0.834  Sum_probs=49.6

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       +++++.++.+..     |.|..  +++|.|+...++.|++|||+|||++||++++|
T Consensus        15 ygv~sC~aC~-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v   73 (77)
T cd06956          15 YGVYSCEGCK-------GFFKRTVRKDLT-----YTCRD--NKDCLIDKRQRNRCQYCRYQKCLAMGMKREAV   73 (77)
T ss_pred             ECceeehhHH-------HHHHHHhhCCCc-----cccCC--CCccccCCCccccCccchhHHHhHhCCCHHHh
Confidence            3456899998       888888875543     78874  57899999999999999999999999998876

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

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

Probab=99.06  E-value=2.4e-11  Score=75.21  Aligned_cols=59  Identities=36%  Similarity=0.782  Sum_probs=49.7

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+-..|.+|.       +++++++....     +|.|..  +++|.|+...+..|++|||+|||++||++++|
T Consensus        18 yGv~sC~aC~-------~FFRR~v~~~~-----~~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v   76 (82)
T cd07171          18 YGVWSCEGCK-------AFFKRSIQGHN-----DYICPA--TNQCTIDKNRRKSCQACRLRKCYEVGMMKGGI   76 (82)
T ss_pred             ECceeehhhH-------HhHHHHeeCCC-----ceeCCC--CCccccCCcccccCccchhHHHhHhcCCHHHH
Confidence            3456899999       88888887654     377874  58899999999999999999999999999876

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

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

Probab=99.06  E-value=4e-11  Score=76.36  Aligned_cols=60  Identities=35%  Similarity=0.732  Sum_probs=50.6

Q ss_pred             CcccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         45 KAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        45 ~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      ..+...|.+|.       ++++++++....     |.|..  .+.|.|+...+..|++|||+|||++||++++|
T Consensus        18 hyGv~sC~aCk-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v   77 (97)
T cd07170          18 HYGVASCEACK-------AFFKRTIQGNIE-----YSCPA--TNECEITKRRRKSCQACRFMKCLKVGMLKEGV   77 (97)
T ss_pred             EECceeehhhh-------HHHHHHhccCCc-----eeecC--CCccccCcccCccCCccccchhhhcCCCHHHc
Confidence            34557899999       999888876543     77874  57899999999999999999999999998776

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

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

Probab=99.06  E-value=4.3e-11  Score=74.37  Aligned_cols=59  Identities=31%  Similarity=0.669  Sum_probs=49.9

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       +++++++.....     |.|..  +++|.|+...+..|++|||+|||++||++++|
T Consensus        16 yGv~sC~aCk-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v   74 (84)
T cd06962          16 YNALTCEGCK-------GFFRRSITKNAV-----YKCKN--GGNCEMDMYMRRKCQECRLRKCKEMGMLAECL   74 (84)
T ss_pred             ECcceeecce-------eeeeeeeccCCc-----eecCC--CCcCccCccccccCccchhhHHHHhCCChHHc
Confidence            4457899999       999888875433     78874  47899999999999999999999999998876

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

>KOG4215|consensus

Probab=99.06  E-value=4e-11  Score=91.03  Aligned_cols=59  Identities=29%  Similarity=0.789  Sum_probs=53.7

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      ++-.+|..|+       |++++.|+.+.+     |+|.-  ..+|+||+..||.|++|||+||+.+||.++||
T Consensus        34 YGA~SCdGCK-------GFFRRSVrk~~~-----YtCRF--~k~C~VDKdkRNaCRyCRfqKC~~aGMK~eAi   92 (432)
T KOG4215|consen   34 YGAISCDGCK-------GFFRRSVRKNHQ-----YTCRF--NKQCVVDKDKRNACRYCRFQKCVRAGMKREAI   92 (432)
T ss_pred             cceeecCcch-------HHHHHHHHhcce-----eeeec--cccccccchhhhhhhHhhHHHHHHhcccHHhh
Confidence            4457999999       999999998888     99974  68999999999999999999999999999876

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

Probab=99.06  E-value=3.4e-11  Score=76.07  Aligned_cols=61  Identities=43%  Similarity=0.835  Sum_probs=50.6

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+-..|.+|.       +++++++..+..     |.|.....+.|.|+...+..|++|||+|||++||++++|
T Consensus        21 yGv~sC~aCk-------~FFRR~v~~~~~-----~~C~~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V   81 (92)
T cd07163          21 YGIYACDGCS-------GFFKRSIRRNRQ-----YVCKSKGQGGCPVDKTHRNQCRACRLKKCFEVGMNKDAV   81 (92)
T ss_pred             ECceeeeeee-------eEEeeeecCCCC-----cCCCCCCCCCCccCCCccccCccchhhhhhhhcCCHHHh
Confidence            4457899999       999888876654     778652246899999999999999999999999998776

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).

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

Probab=99.06  E-value=3.6e-11  Score=73.41  Aligned_cols=59  Identities=32%  Similarity=0.790  Sum_probs=49.9

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       +++++.+..+..     |.|..  ++.|.|+..++..|++|||+|||++||++++|
T Consensus        13 ygv~~C~aC~-------~FFrR~~~~~~~-----~~C~~--~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v   71 (76)
T cd06960          13 YGVLSCNGCK-------GFFRRSVRKNRT-----YTCRF--GGNCVVDKDKRNACRYCRFKKCLEVGMDPEAV   71 (76)
T ss_pred             ECcceeeeeh-------heeCccccCCCc-----eeCCC--CCcccccCcccccCccchhhhhhhcCCCHHHc
Confidence            4457899999       898888876654     77874  47899999999999999999999999998776

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

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

Probab=99.06  E-value=5.8e-11  Score=72.83  Aligned_cols=61  Identities=34%  Similarity=0.737  Sum_probs=51.1

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCccC
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGKSM  120 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~~~  120 (120)
                      .+-..|.+|.       +++++.++.+..     |.|..  +++|.|+..+++.|++|||+|||++||+..++-|
T Consensus        17 yGv~sC~aC~-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~~   77 (78)
T cd07172          17 YGVLTCGSCK-------VFFKRAVEGQHN-----YLCAG--RNDCIIDKIRRKNCPACRLRKCLQAGMNLGARKT   77 (78)
T ss_pred             ECceeehhhH-------HhHHHHeeCCCc-----eeCCC--CCccccCCcccccCccchhHHHHHhCCCcccccC
Confidence            3456899999       888888876554     77874  5889999999999999999999999999987643

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

>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=99.05  E-value=2.7e-11  Score=73.78  Aligned_cols=59  Identities=41%  Similarity=0.807  Sum_probs=49.6

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       ++++++++.+..     |.|..  ++.|.|+...+..|++|||+|||++||++++|
T Consensus        13 ygv~sC~aCk-------~FFRR~~~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v   71 (75)
T cd07155          13 YGVASCEACK-------AFFKRTIQGNLG-----YSCPS--TSECEVDKKRRKSCQACRLQKCLKVGMLKEGV   71 (75)
T ss_pred             EChhhhhhhH-------HHHHHHhhCCCc-----eeCCc--CCCcccCCcccccCccchhhhhhHhCCCHHHc
Confidence            3456899998       888888876644     77874  57899999999999999999999999998876

DNA-binding domains of estrogen receptor (ER) and estrogen related receptors (ERR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. ER and ERR interact with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulate the rate of transcriptional initiation. ERR and ER are closely related and share sequence similarity, target genes, co-regulators and promoters. While ER is activated by endogenous estrogen, ERR lacks the ability to bind to estrogen. Estrogen receptor mediates the biological effects of hormone estrogen by the binding of the receptor dimer to estrogen response element of target genes. However, ERRs seem to interfere with the classic ER-mediated estrogen responsive signaling by targeting the same set of genes. E

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

Probab=99.05  E-value=3.1e-11  Score=75.17  Aligned_cols=59  Identities=39%  Similarity=0.828  Sum_probs=49.9

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       +++++++..+..     |.|..  +++|.|+...++.|++|||+|||++||++++|
T Consensus        14 ygv~sC~aC~-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v   72 (85)
T cd06961          14 YRCITCEGCK-------GFFRRTVQKKLS-----YSCKG--EGKCEIDKVTRNQCQECRFKKCIAVGMAKDLV   72 (85)
T ss_pred             EChhhhhhhh-------HhhHhhhccCCc-----cccCC--CCccccCccccccCccchhhhhhhccCCHHHc
Confidence            3456899999       898888876543     88875  47899999999999999999999999998776

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

>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=99.05  E-value=4.4e-11  Score=73.37  Aligned_cols=59  Identities=42%  Similarity=0.848  Sum_probs=49.7

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       ++++++++....     |.|..  +++|.|+...++.|++|||+|||++||++++|
T Consensus        13 yG~~~C~~C~-------~FFRR~~~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v   71 (78)
T cd07164          13 YGVPSCDGCR-------GFFKRSIRRNLA-----YVCKE--NGSCVVDVARRNQCQACRFKKCLQVNMNRDAV   71 (78)
T ss_pred             ECcchhhhhh-------hhhhhhccCCCC-----ccCCC--CCcccccCcccccCccchhhhhhHhcCCHHHh
Confidence            4456899999       888888876543     77875  57899999999999999999999999998776

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

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

Probab=99.04  E-value=6.6e-11  Score=75.86  Aligned_cols=59  Identities=29%  Similarity=0.677  Sum_probs=50.4

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+-..|.+|.       ++++++++....     |.|..  +++|.|+...+..|++|||+|||++||++++|
T Consensus        33 yGv~sC~aCk-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V   91 (101)
T cd07160          33 YNVLSCEGCK-------GFFRRSVIKGAQ-----YVCKN--GGKCQMDMYMRRKCQECRLRKCREAGMREQCV   91 (101)
T ss_pred             ECcceehhhh-------hhhhhcccccCc-----cccCC--CCccccCCcccccCccchhHHHHHhCCCHHHh
Confidence            4457899999       999888876543     88875  47899999999999999999999999999876

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

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

Probab=99.03  E-value=5.7e-11  Score=74.87  Aligned_cols=59  Identities=31%  Similarity=0.697  Sum_probs=49.8

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       ++++++++....     |.|..  .++|.|+...+..|++|||+|||++||++++|
T Consensus        16 yGv~sC~aCk-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v   74 (91)
T cd07161          16 YNALTCEGCK-------GFFRRSVTKSAV-----YHCKY--GRACEMDMYMRRKCQECRLKKCLSVGMRPECV   74 (91)
T ss_pred             ECceeehhhH-------HHHHHHhccCCc-----eecCC--CCccccCccccccCccchhhHHhHcCCCHHHc
Confidence            3456899999       888888875544     78875  47899999999999999999999999998876

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

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

Probab=99.03  E-value=5.3e-11  Score=74.14  Aligned_cols=59  Identities=34%  Similarity=0.836  Sum_probs=49.8

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       +++++.+.....     |.|..  +++|.|+...+..|++|||+|||++||++++|
T Consensus        19 yGv~sC~aC~-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v   77 (85)
T cd06964          19 YGVSACEGCK-------GFFRRSIQKNMV-----YTCHR--DKNCIINKVTRNRCQYCRLQKCFEVGMSKESV   77 (85)
T ss_pred             ECcceeeeee-------eEEeeeecCCCC-----eECCC--CCccccCCcccccCccchhhhhhhhCCCHHHh
Confidence            4557899999       898888875433     77874  47899999999999999999999999998776

DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RARs mediate the biological effect of retinoids, including both natural dietary vitamin A (retinol) metabolites and active synthetic analogs. Retinoids play key roles in a wide variety of essential biological processes, such as vertebrate embryonic morphogenesis and organogenesis, differentiation and apoptosis, and homeostasis. RAR function as a heterodimer with retinoic X receptor by binding to specific RAR response elements (RAREs), which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair and found in the promoter reg

>KOG4846|consensus

Probab=99.02  E-value=6.3e-11  Score=91.20  Aligned_cols=60  Identities=32%  Similarity=0.787  Sum_probs=53.5

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhc-ccccccccceeccccccccChhhhHHHHHHhcCCcCCcc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEF-ACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGKS  119 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~-~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~~  119 (120)
                      ++...|..|+       |++++.+|.+-+     | .|.  +..+|.|-+.+||.|++||++|||++||+.|+|-
T Consensus       147 YGV~aCEGCK-------GFFRRSIQqkI~-----YrrCl--k~e~C~I~R~nRNRCQ~CRfKKCL~vGMSrDaVR  207 (538)
T KOG4846|consen  147 YGVTACEGCK-------GFFRRSIQQKID-----YRRCL--KQEVCEIKRENRNRCQYCRFKKCLDVGMSRDAVR  207 (538)
T ss_pred             eceeecccch-------HHHHHHHHHhhh-----HHHHh--hhhceehhhhccchhhhhhHHHHHhcccchhhhh
Confidence            4567999999       999999998877     6 676  4689999999999999999999999999999983

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

Probab=99.02  E-value=6e-11  Score=74.19  Aligned_cols=59  Identities=34%  Similarity=0.807  Sum_probs=49.2

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       +++++.+..+.     .|.|..  .++|.|+...++.|++|||+|||++||++++|
T Consensus        14 ygv~sC~aC~-------~FFRR~v~~~~-----~~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V   72 (87)
T cd07162          14 FNAMTCEGCK-------GFFRRAMKRNA-----RLCCPF--QKGCVITKSNRRQCQACRLRKCLSIGMKKELI   72 (87)
T ss_pred             ECcceehhhH-------HHHHhhhccCc-----eeEcCC--CCceecCCcccccCccchhhHHhHhCCCHHHc
Confidence            3457899999       88888887553     377875  47899999999999999999999999999765

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

>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=99.01  E-value=6.3e-11  Score=74.09  Aligned_cols=59  Identities=37%  Similarity=0.861  Sum_probs=49.8

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+-..|.+|.       ++++++++.+..     +.|..  ++.|.|+...+..|++|||+|||++||++++|
T Consensus        18 yGv~sC~aC~-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V   76 (87)
T cd06967          18 YGAVSCEGCK-------GFFKRSIRKNLG-----YSCRG--SKDCVINKHHRNRCQYCRLQKCLAMGMKSDSV   76 (87)
T ss_pred             eCcceEeeee-------eEeeeeeeCCCC-----cccCC--CCccccCccccccCccchhhhhhHcCCCHHHh
Confidence            4557899999       999888875543     77864  57899999999999999999999999998776

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

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

Probab=99.01  E-value=1.4e-10  Score=75.11  Aligned_cols=60  Identities=32%  Similarity=0.729  Sum_probs=50.7

Q ss_pred             CcccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         45 KAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        45 ~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      ..+...|.+|.       +++++.+.....     |.|..  +++|.|+...+..|++|||+|||++||++++|
T Consensus        20 hyGv~sC~aCk-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v   79 (107)
T cd06955          20 HFNAMTCEGCK-------GFFRRSMKRKAL-----FTCPF--NGDCRITKDNRRHCQACRLKRCVDIGMMKEFI   79 (107)
T ss_pred             EECcceeeeec-------ceecceeccCCc-----cccCC--CCccccccCCccccccchhHHHHHcCCCchhc
Confidence            34457899999       999988876644     77864  58899999999999999999999999998765

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

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

Probab=98.99  E-value=9.2e-11  Score=74.04  Aligned_cols=61  Identities=48%  Similarity=0.796  Sum_probs=50.4

Q ss_pred             CcccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         45 KAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        45 ~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      ..+-..|.+|.       +++++.++.+..     |.|... .++|.|+...+..|++|||+|||++||++++|
T Consensus        20 hyGv~sC~aCk-------~FFRR~v~~~~~-----~~C~~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V   80 (92)
T cd06970          20 HYGIYACNGCS-------GFFKRSVRRKLI-----YRCQAG-TGMCPVDKAHRNQCQACRLKKCLQAGMNKDAV   80 (92)
T ss_pred             EECccEEeeee-------eEeeeeeecCCC-----ceeecC-CCcCccCCCccccCccchhhHhhHhCCCHHHc
Confidence            34457899999       999888886544     788642 36899999999999999999999999998765

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

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

Probab=98.98  E-value=6.1e-11  Score=73.39  Aligned_cols=60  Identities=33%  Similarity=0.643  Sum_probs=50.0

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       ++++++++.+..     |.|... .+.|.|+...+..|++|||+|||++||++++|
T Consensus        13 yGv~sC~aCk-------~FFRR~v~~~~~-----~~C~~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v   72 (82)
T cd06957          13 YGVYCCDGCS-------CFFKRSVRKGII-----YTCIAG-NGNCVVDKARRNWCPFCRLQKCFAVGMNRAAV   72 (82)
T ss_pred             ECcceEeeee-------eEEEEeecCCCc-----eEccCc-cCCCccCCCccCcccCcchhhcccccCCHHHh
Confidence            3457899999       999888876544     888732 46899999999999999999999999998776

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

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

Probab=98.97  E-value=1.1e-10  Score=72.15  Aligned_cols=59  Identities=29%  Similarity=0.704  Sum_probs=49.5

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       +++++++..+..     |.|..  +++|.|+...++.|++|||+|||++||++.+.
T Consensus        18 yGv~sC~aCk-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~~   76 (82)
T cd07173          18 YGALTCGSCK-------VFFKRAAEGKQK-----YLCAS--RNDCTIDKFRRKNCPSCRLRKCFEAGMTLGAR   76 (82)
T ss_pred             ECcchhhhHH-------HHHHHHhcCCCc-----eecCC--CCccccCCCccCcCcchhhhhhhhcCCCcChH
Confidence            4457899999       888888876544     78874  58899999999999999999999999998764

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

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

Probab=98.97  E-value=7e-11  Score=72.96  Aligned_cols=60  Identities=35%  Similarity=0.775  Sum_probs=49.6

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCcc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGKS  119 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~~  119 (120)
                      .+...|.+|.       ++++..+....     .|.|..  +++|.|+...+..|++|||+|||++||++++|-
T Consensus        13 yG~~sC~aC~-------~FFRR~~~~~~-----~~~C~~--~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~V~   72 (81)
T cd07165          13 YGVTSCEGCK-------GFFRRSIQKQI-----EYRCLR--DGKCEIIRLNRNRCQYCRFKKCLAAGMSKDSVR   72 (81)
T ss_pred             ECchhhhhHH-------HHHHhHhccCC-----ceeCCC--CCCccccccccccccchhhhhcccccCCHHHcc
Confidence            4456899999       88888776543     377875  478999999999999999999999999998763

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,

>KOG4217|consensus

Probab=98.97  E-value=1.4e-10  Score=90.55  Aligned_cols=71  Identities=35%  Similarity=0.812  Sum_probs=59.5

Q ss_pred             CcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHH
Q psy13208         29 NQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKC  108 (120)
Q Consensus        29 ~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kc  108 (120)
                      ++.-+|.+ +.-|.  ..+..-|..|+       |++.+.||.+-.     |.|..  .++|.||+..||.|++||++||
T Consensus       270 ~~CAVCgD-nAaCq--HYGvRTCEGCK-------GFFKRTVQKnaK-----YvCla--nKnCPVDKRrRnRCQyCRfQKC  332 (605)
T KOG4217|consen  270 GLCAVCGD-NAACQ--HYGVRTCEGCK-------GFFKRTVQKNAK-----YVCLA--NKNCPVDKRRRNRCQYCRFQKC  332 (605)
T ss_pred             ceeeecCC-hHHhh--hcCccccccch-------HHHHHHHhcCCe-----eEeec--CCCCCcchhhhhhchhhhHhHH
Confidence            34557763 55665  56678999999       999999998877     99974  6899999999999999999999


Q ss_pred             HHhcCCcC
Q psy13208        109 LNMGMNKD  116 (120)
Q Consensus       109 l~~gm~~~  116 (120)
                      |+|||-.+
T Consensus       333 L~VGMVKE  340 (605)
T KOG4217|consen  333 LAVGMVKE  340 (605)
T ss_pred             HHhhhhhh
Confidence            99999753

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

Probab=98.97  E-value=1.1e-10  Score=73.49  Aligned_cols=59  Identities=34%  Similarity=0.753  Sum_probs=49.8

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       +++++.++....     |.|..  +++|.|+..++..|++|||+|||++||++++|
T Consensus        21 yGv~sC~aCk-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V   79 (90)
T cd07168          21 YGIITCEGCK-------GFFKRTVQNKRV-----YTCVG--DGRCEITKAQRNRCQYCRFRKCIRKGMMLAAV   79 (90)
T ss_pred             ECceehhhhh-------HhhhhhhcCCCC-----ccCCC--CCCccccccccccccccchhhhhhcCCCHHHh
Confidence            4457899999       888888876544     77873  57899999999999999999999999998765

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

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

Probab=98.96  E-value=2.5e-10  Score=71.24  Aligned_cols=61  Identities=36%  Similarity=0.743  Sum_probs=49.2

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+-..|.+|.       ++++++++....   ..|.|..  +++|.|+...+..|++|||+|||++||+++++
T Consensus        15 yGv~sC~aCk-------~FFRR~~~~~~~---~~~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~   75 (86)
T cd07157          15 HGAYVCEACK-------KFFMRSSNAISF---TISECPN--GGKCIIDKKNRTKCQACRYRKCLNVGMSLGGP   75 (86)
T ss_pred             ECcceeeEee-------eEEecceecCCC---ccccCCC--CCccccCccccccCccchhhHHhHcCCCcccc
Confidence            4456899999       888887765431   1377874  47899999999999999999999999998765

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.

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

Probab=98.96  E-value=8.6e-11  Score=73.91  Aligned_cols=59  Identities=34%  Similarity=0.809  Sum_probs=49.9

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       +++++++.....     |.|..  ++.|.|+...+..|++|||+|||++||++++|
T Consensus        21 yGv~sC~aCk-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v   79 (90)
T cd07169          21 YGIISCEGCK-------GFFKRSICNKRV-----YRCSR--DKNCVMSRKQRNRCQYCRLLKCLQMGMNRKAI   79 (90)
T ss_pred             ECcceehhhH-------HHHHHHhcCCCc-----eecCC--CCcccccccccccccccchhhhccccCCHHHh
Confidence            4557899999       888888876544     77874  47899999999999999999999999998776

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).

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

Probab=98.96  E-value=1e-10  Score=74.25  Aligned_cols=60  Identities=33%  Similarity=0.868  Sum_probs=50.1

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCcc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGKS  119 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~~  119 (120)
                      .+...|.+|.       +++++++.....     |.|..  +++|.|+...+..|++|||+|||++||++++|-
T Consensus        20 yGv~sC~aC~-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~V~   79 (95)
T cd06968          20 YGVITCEGCK-------GFFRRSQQNNVS-----YSCPR--QKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVK   79 (95)
T ss_pred             ECceeehhhH-------HhhHHheeCCCc-----eecCC--CcccccccCCceeccccchhhcccccCChhhcc
Confidence            4457899999       888888875533     77875  478999999999999999999999999988763

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

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

Probab=98.95  E-value=6.2e-11  Score=74.93  Aligned_cols=59  Identities=32%  Similarity=0.795  Sum_probs=49.6

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       +++++++..+..     |.|..  +++|.|+...++.|++|||+|||++||++++|
T Consensus        13 yGv~sC~aCk-------~FFRRsv~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~V   71 (93)
T cd07167          13 YGLLTCESCK-------GFFKRTVQNKKR-----YTCIE--NQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAV   71 (93)
T ss_pred             ECchhhhhHH-------HHHHHHeeCCCc-----cccCC--CCccccCccccCcCCCcccchhhhccCCHHHh
Confidence            3456899998       888888876554     78875  48899999999999999999999999998765

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

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

Probab=98.95  E-value=1.1e-10  Score=73.90  Aligned_cols=59  Identities=31%  Similarity=0.693  Sum_probs=50.0

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       ++++..+.....     |.|..  +++|.|+...+..|++|||+|||++||++++|
T Consensus        15 yGv~sC~aC~-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V   73 (94)
T cd06966          15 FNAITCESCK-------AFFRRNALKNKE-----FKCPF--NESCEINVVTRRFCQKCRLDKCFAIGMKKEWI   73 (94)
T ss_pred             ECcceeeeeh-------heehhcccCCCc-----cccCC--CCccccCccccccCccchhhhCcccCCCHHHc
Confidence            4457899999       999888875544     77874  58899999999999999999999999998765

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

>KOG4218|consensus

Probab=98.93  E-value=1.5e-10  Score=87.44  Aligned_cols=57  Identities=35%  Similarity=0.884  Sum_probs=52.9

Q ss_pred             cccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         48 RNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        48 r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      -.-|.+|.       |++.+.||++.+     |+|.+  +.+|.||+..|..|++||++|||.+||..+||
T Consensus        32 LLTCESCK-------GFFKRTVQNnK~-----YtC~e--~qnC~iDkTqRKRCP~CRFQKCLtvGMklEAV   88 (475)
T KOG4218|consen   32 LLTCESCK-------GFFKRTVQNNKQ-----YTCSE--EQNCHIDKTQRKRCPSCRFQKCLTVGMKLEAV   88 (475)
T ss_pred             eeehhhhh-------hHHHHHhhcCcc-----eeccc--ccccccchHhhccCCchhHHHHhhhhhhHHHH
Confidence            46899999       999999999988     99985  68999999999999999999999999998776

>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors

Probab=98.93  E-value=3.4e-10  Score=67.98  Aligned_cols=57  Identities=32%  Similarity=0.751  Sum_probs=47.7

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcC
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKD  116 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~  116 (120)
                      .+-..|.+|.       ++++++++.+..     +.|..  +++|.|+...+..|++|||+|||++||+++
T Consensus        14 ygv~~C~aC~-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~   70 (70)
T smart00399       14 FGVCSCRACK-------AFFRRTVNLRYK-----YRCDR--KNNCSINKRYRCRCRACRLKKCLGVGMDPE   70 (70)
T ss_pred             eCCcEechhh-------hhhhhheeCCCC-----eecCC--CcccccCCCccccCccCcChhHhhccCcCC
Confidence            3456899999       888888876654     77874  467999999999999999999999999864

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

Probab=98.93  E-value=1.2e-10  Score=73.06  Aligned_cols=59  Identities=34%  Similarity=0.805  Sum_probs=49.3

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhc-ccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEF-ACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~-~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       ++++..++....     | .|..  +++|.|+..++..|++|||+|||++||++++|
T Consensus        18 yGv~sC~aCk-------~FFRR~v~~~~~-----~~~C~~--~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v   77 (89)
T cd07166          18 YGVHACEGCK-------GFFRRSIQQKIQ-----YRKCTK--NETCSIMRINRNRCQYCRFKKCLAVGMSRDAV   77 (89)
T ss_pred             EChhhhhhHh-------hEecceeEcCCc-----chhhcc--CCcccccccccccccchhhhhcccccCCHHHh
Confidence            4457899999       888888876644     6 4764  47899999999999999999999999998776

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=98.88  E-value=3.6e-10  Score=70.23  Aligned_cols=57  Identities=32%  Similarity=0.767  Sum_probs=47.2

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhc-ccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEF-ACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~-~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       +++++++.....     | .|..    .|.|+..+++.|++|||+|||++||++++|
T Consensus        14 yGv~sC~aCk-------~FFRR~v~~~~~-----~~~C~~----~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v   71 (84)
T cd06965          14 YGVHACEGCK-------GFFRRTIRLKLV-----YKPCDL----SCKIHKKSRNKCQYCRFQKCLNVGMSHNAI   71 (84)
T ss_pred             EChhhhhhhh-------hheeeeeecCCC-----cccccc----CCCcCccccccccchhhhhhhhccCCHHHc
Confidence            4457899999       898888876544     6 3753    399999999999999999999999998876

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

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

Probab=98.77  E-value=2e-09  Score=64.53  Aligned_cols=55  Identities=31%  Similarity=0.782  Sum_probs=41.2

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCC
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMN  114 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~  114 (120)
                      .+...|.+|+       .++.+.+.....     +.|..  +++|.|+...+..|++|||+|||++||+
T Consensus        15 ygv~sC~~C~-------~FFrR~~~~~~~-----~~C~~--~~~C~i~~~~~~~C~~CRf~KCl~~GM~   69 (70)
T PF00105_consen   15 YGVLSCNACK-------MFFRRSVKKKKP-----YKCKK--NGNCKIDKDNRRKCRSCRFQKCLEVGMK   69 (70)
T ss_dssp             TTEEEEHHHH-------HHHHHHHHTTCG------STSS--SST---STTTTTTSHHHHHHHHHHTTBS
T ss_pred             ccccccccce-------eeeeeccccccc-----ccccc--cccccccccCCCEeCcchHHHHHHHCCc
Confidence            4456888888       667666665544     78864  5889999999999999999999999996

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 ....

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Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	120
3dzu_A	467	Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp		9e-06
3dzu_A	467	Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp		2e-05
3m9e_A	105	Thyroid Hormone Beta Dna Binding Domain Homodimer W		1e-05
3m9e_A	105	Thyroid Hormone Beta Dna Binding Domain Homodimer W		2e-05
2nll_B	103	Retinoid X Receptor-Thyroid Hormone Receptor Dna-Bi		3e-05
2nll_B	103	Retinoid X Receptor-Thyroid Hormone Receptor Dna-Bi		9e-05
2ebl_A	89	Solution Structure Of The Zinc Finger, C4-type Doma		3e-05
2ebl_A	89	Solution Structure Of The Zinc Finger, C4-type Doma		7e-05
3cbb_A	78	Crystal Structure Of Hepatocyte Nuclear Factor 4alp		4e-05
3cbb_A	78	Crystal Structure Of Hepatocyte Nuclear Factor 4alp		5e-04
4hn6_A	114	Gr Dna Binding Domain R460d/d462r - Tslp Ngre Compl		1e-04
3g6t_A	91	Gr Gamma Dna-Binding Domain:fkbp5 16bp Complex-34 L		1e-04
1dsz_A	86	Structure Of The RxrRAR DNA-Binding Domain Heterodi		2e-04
1dsz_A	86	Structure Of The RxrRAR DNA-Binding Domain Heterodi		8e-04
1lat_A	82	Glucocorticoid Receptor MutantDNA COMPLEX Length =		3e-04
1dsz_B	85	Structure Of The RxrRAR DNA-Binding Domain Heterodi		4e-04
1by4_A	82	Structure And Mechanism Of The Homodimeric Assembly		4e-04
1ynw_B	99	Crystal Structure Of Vitamin D Receptor And 9-Cis R		4e-04
1ynw_B	99	Crystal Structure Of Vitamin D Receptor And 9-Cis R		9e-04
1r0n_A	81	Crystal Structure Of Heterodimeric Ecdsyone Recepto		4e-04
1hra_A	80	The Solution Structure Of The Human Retinoic Acid R		6e-04
1gdc_A	72	Refined Solution Structure Of The Glucocorticoid Re		6e-04
2gda_A	72	Refined Solution Structure Of The Glucocorticoid Re		6e-04
2han_A	93	Structural Basis Of Heterodimeric Ecdysteroid Recep		7e-04
1rgd_A	71	Structure Refinement Of The Glucocorticoid Receptor		7e-04
1glu_A	81	Crystallographic Analysis Of The Interaction Of The		8e-04
4hn5_A	117	Gr Dna Binding Domain - Tslp Ngre Complex Length =		8e-04

>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 = 45.1 bits (105), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 16/30 (53%), Positives = 22/30 (73%)
Query: 41  CIVDKAHRNQCQACRLKKCLNMGMNKDDAQ 70
           C++DK  RN+CQ CR +KCL MGM ++  Q
Sbjct: 182 CLIDKRQRNRCQYCRYQKCLAMGMKREAVQ 211

>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 = 43.9 bits (102), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 15/28 (53%), Positives = 21/28 (75%)
Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKDG 117
           C++DK  RN+CQ CR +KCL MGM ++ 
Sbjct: 182 CLIDKRQRNRCQYCRYQKCLAMGMKREA 209

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 18/29 (62%), Positives = 22/29 (75%)
Query: 39 GRCIVDKAHRNQCQACRLKKCLNMGMNKD 67
          G+CI+DK  RNQCQ CR KKC+ +GM  D
Sbjct: 48 GKCIIDKVTRNQCQECRFKKCIYVGMATD 76

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/45 (46%), Positives = 29/45 (64%), Gaps = 2/45 (4%)
Query: 72  LKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKD 116
           ++ SL   ++C    E +CI+DK  RNQCQ CR KKC+ +GM  D
Sbjct: 34  IQKSLHPSYSCK--YEGKCIIDKVTRNQCQECRFKKCIYVGMATD 76

>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 = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 17/29 (58%), Positives = 22/29 (75%)
Query: 39 GRCIVDKAHRNQCQACRLKKCLNMGMNKD 67
          G+C++DK  RNQCQ CR KKC+ +GM  D
Sbjct: 46 GKCVIDKVTRNQCQECRFKKCIYVGMATD 74

>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 = 42.0 bits (97), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 17/30 (56%), Positives = 22/30 (73%)
Query: 87  ELRCIVDKAHRNQCQACRLKKCLNMGMNKD 116
           E +C++DK  RNQCQ CR KKC+ +GM  D
Sbjct: 45  EGKCVIDKVTRNQCQECRFKKCIYVGMATD 74

>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 = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 18/30 (60%), Positives = 23/30 (76%)
Query: 41 CIVDKAHRNQCQACRLKKCLNMGMNKDDAQ 70
          C +D+ HRNQCQ CRLKKCL +GM ++  Q
Sbjct: 52 CPIDQHHRNQCQYCRLKKCLKVGMRREAVQ 81

>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 = 42.4 bits (98), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 20/45 (44%), Positives = 26/45 (57%)
Query: 72  LKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKD 116
            K S+      T      C +D+ HRNQCQ CRLKKCL +GM ++
Sbjct: 34  FKRSVRRNLTYTCRANRNCPIDQHHRNQCQYCRLKKCLKVGMRRE 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 = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 28/73 (38%), Positives = 40/73 (54%), Gaps = 5/73 (6%)
Query: 2  TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLN 61
          T +H G +    C+ G  R  V K H   C+     + +C+VDK  RNQC+ CRLKKC  
Sbjct: 11 TGKHYGASSCDGCK-GFFRRSVRKNHMYSCRF----SRQCVVDKDKRNQCRYCRLKKCFR 65
Query: 62 MGMNKDDAQHLKN 74
           GM K+  Q+ ++
Sbjct: 66 AGMKKEAVQNERD 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 = 39.7 bits (91), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 17/28 (60%), Positives = 20/28 (71%)
Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKDG 117
           C+VDK  RNQC+ CRLKKC   GM K+ 
Sbjct: 45  CVVDKDKRNQCRYCRLKKCFRAGMKKEA 72

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/61 (40%), Positives = 32/61 (52%), Gaps = 5/61 (8%)
Query: 5  HDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGM 64
          H G+    +C+   +R  V+  H   C    AG  RCI+DK  R  C ACR +KCL  GM
Sbjct: 40 HYGVLTCGSCKVFFKR-AVEGQHNYLC----AGDNRCIIDKIRRKNCPACRYRKCLQAGM 94
Query: 65 N 65
          N
Sbjct: 95 N 95

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/61 (37%), Positives = 31/61 (50%), Gaps = 4/61 (6%)
Query: 5  HDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGM 64
          H G+    +C+   +R +  + H   C    AG   CI+DK  R  C ACR +KCL  GM
Sbjct: 16 HYGVLTCGSCKVFFKRAVEGRQHNYLC----AGRNDCIIDKIRRKNCPACRYRKCLQAGM 71
Query: 65 N 65
          N
Sbjct: 72 N 72

>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 = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 16/34 (47%), Positives = 26/34 (76%)
Query: 41 CIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKN 74
          CI++K  RN+CQ CRL+KC  +GM+K+  ++ +N
Sbjct: 49 CIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRN 82

>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 = 38.9 bits (89), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 15/28 (53%), Positives = 22/28 (78%)
Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKDG 117
           CI++K  RN+CQ CRL+KC  +GM+K+ 
Sbjct: 49  CIINKVTRNRCQYCRLQKCFEVGMSKES 76

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

Iteration: 1
 Score = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/61 (39%), Positives = 32/61 (52%), Gaps = 5/61 (8%)
Query: 5  HDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGM 64
          H G+     C+A  +R  V+  H   C+      G+CI+DK  R  C ACR +KCL  GM
Sbjct: 18 HYGVLTCEGCKAFFKR-AVEGQHNYLCKY----EGKCIIDKIRRKNCPACRYRKCLQAGM 72
Query: 65 N 65
          N
Sbjct: 73 N 73

>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 = 40.0 bits (92), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 16/31 (51%), Positives = 22/31 (70%)
Query: 41 CIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
          C++DK  RN+CQ CR +KCL MGM ++  Q 
Sbjct: 50 CLIDKRQRNRCQYCRYQKCLAMGMKREAVQE 80

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

Iteration: 1
 Score = 40.0 bits (92), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 16/31 (51%), Positives = 22/31 (70%)
Query: 41 CIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
          C++DK  RN+CQ CR +KCL MGM ++  Q 
Sbjct: 50 CLIDKRQRNRCQYCRYQKCLAMGMKREAVQE 80

>pdb|1YNW|B Chain B, Crystal Structure Of Vitamin D Receptor And 9-Cis Retinoic Acid Receptor Dna-Binding Domains Bound To A Dr3 Response Element Length = 99

Iteration: 1
 Score = 40.0 bits (92), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 16/31 (51%), Positives = 22/31 (70%)
Query: 41 CIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
          C++DK  RN+CQ CR +KCL MGM ++  Q 
Sbjct: 48 CLIDKRQRNRCQYCRYQKCLAMGMKREAVQE 78

>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 = 38.5 bits (88), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 15/28 (53%), Positives = 21/28 (75%)
Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKDG 117
           C++DK  RN+CQ CR +KCL MGM ++ 
Sbjct: 48  CLIDKRQRNRCQYCRYQKCLAMGMKREA 75

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

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 16/30 (53%), Positives = 22/30 (73%)
Query: 41 CIVDKAHRNQCQACRLKKCLNMGMNKDDAQ 70
          C++DK  RN+CQ CR +KCL MGM ++  Q
Sbjct: 48 CLIDKRQRNRCQYCRYQKCLAMGMKREAVQ 77

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

Iteration: 1
 Score = 39.3 bits (90), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 14/31 (45%), Positives = 24/31 (77%)
Query: 41 CIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
          C+++K  RN+CQ CRL+KC  +GM+K+  ++
Sbjct: 50 CVINKVTRNRCQYCRLQKCFEVGMSKESVRN 80

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

Iteration: 1
 Score = 39.3 bits (90), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 24/63 (38%), Positives = 32/63 (50%), Gaps = 5/63 (7%)
Query: 5  HDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGM 64
          H G+    +C+   +R  V+  H   C    AG   CI+DK  R  C ACR +KCL  GM
Sbjct: 13 HYGVLTCGSCKVFFKR-AVEGQHNYLC----AGRNDCIIDKIRRKNCPACRYRKCLQAGM 67
Query: 65 NKD 67
          N +
Sbjct: 68 NLE 70

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

Iteration: 1
 Score = 39.3 bits (90), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 24/61 (39%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 5  HDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGM 64
          H G+    +C+   +R  V+  H   C    AG   CI+DK  R  C ACR +KCL  GM
Sbjct: 13 HYGVLTCGSCKVFFKR-AVEGQHNYLC----AGRNDCIIDKIRRKNCPACRYRKCLQAGM 67
Query: 65 N 65
          N
Sbjct: 68 N 68

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

Iteration: 1
 Score = 38.9 bits (89), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 16/36 (44%), Positives = 23/36 (63%)
Query: 41 CIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSL 76
          CI+DK  RN+CQ CR +KCL  GM ++  Q  +  +
Sbjct: 55 CIIDKRQRNRCQYCRYQKCLTCGMKREAVQEERQGI 90

>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 = 38.9 bits (89), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 24/61 (39%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 5  HDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGM 64
          H G+    +C+   +R  V+  H   C    AG   CI+DK  R  C ACR +KCL  GM
Sbjct: 12 HYGVLTCGSCKVFFKR-AVEGQHNYLC----AGRNDCIIDKIRRKNCPACRYRKCLQAGM 66
Query: 65 N 65
          N
Sbjct: 67 N 67

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

Iteration: 1
 Score = 38.9 bits (89), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 24/61 (39%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 5  HDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGM 64
          H G+    +C+   +R  V+  H   C    AG   CI+DK  R  C ACR +KCL  GM
Sbjct: 18 HYGVLTCGSCKVFFKR-AVEGQHNYLC----AGRNDCIIDKIRRKNCPACRYRKCLQAGM 72
Query: 65 N 65
          N
Sbjct: 73 N 73

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

Iteration: 1
 Score = 38.9 bits (89), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 24/61 (39%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 5  HDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGM 64
          H G+    +C+   +R  V+  H   C    AG   CI+DK  R  C ACR +KCL  GM
Sbjct: 43 HYGVLTCGSCKVFFKR-AVEGQHNYLC----AGRNDCIIDKIRRKNCPACRYRKCLQAGM 97
Query: 65 N 65
          N
Sbjct: 98 N 98

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	120
2ebl_A	89	COUP transcription factor 1; DNA-binding, metal-bi	7e-12
2ebl_A	89	COUP transcription factor 1; DNA-binding, metal-bi	9e-11
3cbb_A	78	HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DN	2e-11
3cbb_A	78	HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DN	4e-10
1a6y_A	94	Orphan nuclear receptor NR1D1; orphan receptor, DN	2e-11
1a6y_A	94	Orphan nuclear receptor NR1D1; orphan receptor, DN	6e-10
2han_A	93	Protein ultraspiracle; transcription regulation, t	6e-11
2han_A	93	Protein ultraspiracle; transcription regulation, t	5e-10
1dsz_A	86	RAR-alpha, retinoic acid receptor alpha; RAR, nucl	7e-11
1dsz_A	86	RAR-alpha, retinoic acid receptor alpha; RAR, nucl	8e-10
1ynw_B	99	Retinoic acid receptor RXR-alpha, retinoid X recep	1e-10
1ynw_B	99	Retinoic acid receptor RXR-alpha, retinoid X recep	8e-10
1dsz_B	85	RXR-alpha, retinoic acid receptor RXR-alpha; RAR,	1e-10
1dsz_B	85	RXR-alpha, retinoic acid receptor RXR-alpha; RAR,	1e-09
1hcq_A	84	Protein (estrogen receptor); protein-DNA complex,	2e-10
1hcq_A	84	Protein (estrogen receptor); protein-DNA complex,	1e-09
3g9m_A	90	Glucocorticoid receptor; glucocorticoid, DNA-bindi	2e-10
3g9m_A	90	Glucocorticoid receptor; glucocorticoid, DNA-bindi	2e-09
1cit_A	89	NGFI-B, protein (orphan nuclear receptor NGFI-B);	6e-10
1cit_A	89	NGFI-B, protein (orphan nuclear receptor NGFI-B);	2e-09
1lo1_A	98	Steroid hormone receptor ERR2; estrogen related re	7e-10
1lo1_A	98	Steroid hormone receptor ERR2; estrogen related re	3e-09
2a66_A	113	Orphan nuclear receptor NR5A2; protein-DNA complex	2e-09
2a66_A	113	Orphan nuclear receptor NR5A2; protein-DNA complex	4e-09
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	3e-09
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	5e-09
1r4i_A	105	Androgen receptor; AR, steroid receptor, protein-D	3e-09
1r4i_A	105	Androgen receptor; AR, steroid receptor, protein-D	1e-08
2han_B	119	Ecdysone receptor; transcription regulation, trans	4e-09
2han_B	119	Ecdysone receptor; transcription regulation, trans	1e-08
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	7e-09
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	5e-08
1kb2_A	110	Vitamin D3 receptor; VDR, nuclear receptor, protei	1e-08
1kb2_A	110	Vitamin D3 receptor; VDR, nuclear receptor, protei	4e-08
2nll_B	103	Protein (thyroid hormone receptor); complex (trans	2e-08
2nll_B	103	Protein (thyroid hormone receptor); complex (trans	5e-08
1lbd_A	282	RXR_LBD, retinoid X receptor; transcription factor	3e-04
1lbd_A	282	RXR_LBD, retinoid X receptor; transcription factor	4e-04

>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 = 56.2 bits (136), Expect = 7e-12
 Identities = 18/35 (51%), Positives = 23/35 (65%)

Query: 37 GTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
              C +D+ HRNQCQ CRLKKCL +GM ++  Q 
Sbjct: 48 ANRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQR 82

>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 = 53.1 bits (128), Expect = 9e-11
 Identities = 17/28 (60%), Positives = 22/28 (78%)

Query: 89  RCIVDKAHRNQCQACRLKKCLNMGMNKD 116
            C +D+ HRNQCQ CRLKKCL +GM ++
Sbjct: 51  NCPIDQHHRNQCQYCRLKKCLKVGMRRE 78

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

 Score = 54.6 bits (132), Expect = 2e-11
 Identities = 20/45 (44%), Positives = 28/45 (62%), Gaps = 1/45 (2%)

Query: 27 HRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
           +N   +C+    +C+VDK  RNQC+ CRLKKC   GM K+  Q+
Sbjct: 32 RKNHMYSCRFS-RQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQN 75

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

 Score = 51.1 bits (123), Expect = 4e-10
 Identities = 17/28 (60%), Positives = 21/28 (75%)

Query: 89  RCIVDKAHRNQCQACRLKKCLNMGMNKD 116
           +C+VDK  RNQC+ CRLKKC   GM K+
Sbjct: 44  QCVVDKDKRNQCRYCRLKKCFRAGMKKE 71

>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 = 55.1 bits (133), Expect = 2e-11
 Identities = 15/45 (33%), Positives = 25/45 (55%)

Query: 27 HRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
           +N           C + + +RN+CQ CR KKCL++GM++D  + 
Sbjct: 39 QQNIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRF 83

>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 = 51.2 bits (123), Expect = 6e-10
 Identities = 14/28 (50%), Positives = 22/28 (78%)

Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKDG 117
           C + + +RN+CQ CR KKCL++GM++D 
Sbjct: 53  CSIVRINRNRCQQCRFKKCLSVGMSRDA 80

>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 = 53.9 bits (130), Expect = 6e-11
 Identities = 16/35 (45%), Positives = 21/35 (60%)

Query: 37 GTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
              CI+DK  RN+CQ CR +KCL  GM ++  Q 
Sbjct: 51 ENRNCIIDKRQRNRCQYCRYQKCLTCGMKREAVQE 85

>2han_A Protein ultraspiracle; transcription regulation, transcription factor, DNA-binding, nuclear protein, nuclear receptor, zinc finger; 1.95A {Drosophila melanogaster} SCOP: g.39.1.2 Length = 93

 Score = 51.6 bits (124), Expect = 5e-10
 Identities = 15/28 (53%), Positives = 20/28 (71%)

Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKDG 117
           CI+DK  RN+CQ CR +KCL  GM ++ 
Sbjct: 55  CIIDKRQRNRCQYCRYQKCLTCGMKREA 82

>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 = 53.5 bits (129), Expect = 7e-11
 Identities = 15/35 (42%), Positives = 24/35 (68%)

Query: 37 GTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
              CI++K  RN+CQ CRL+KC  +GM+K+  ++
Sbjct: 45 RDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRN 79

>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 = 50.8 bits (122), Expect = 8e-10
 Identities = 15/29 (51%), Positives = 22/29 (75%)

Query: 89  RCIVDKAHRNQCQACRLKKCLNMGMNKDG 117
            CI++K  RN+CQ CRL+KC  +GM+K+ 
Sbjct: 48  NCIINKVTRNRCQYCRLQKCFEVGMSKES 76

>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 = 53.2 bits (128), Expect = 1e-10
 Identities = 16/35 (45%), Positives = 22/35 (62%)

Query: 37 GTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
              C++DK  RN+CQ CR +KCL MGM ++  Q 
Sbjct: 44 DNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQE 78

>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 = 50.9 bits (122), Expect = 8e-10
 Identities = 15/29 (51%), Positives = 21/29 (72%)

Query: 89  RCIVDKAHRNQCQACRLKKCLNMGMNKDG 117
            C++DK  RN+CQ CR +KCL MGM ++ 
Sbjct: 47  DCLIDKRQRNRCQYCRYQKCLAMGMKREA 75

>1dsz_B RXR-alpha, retinoic acid receptor RXR-alpha; RAR, nuclear receptor, protein-DNA, transcription/DNA complex; HET: DNA; 1.70A {Homo sapiens} SCOP: g.39.1.2 PDB: 1by4_A* 1rxr_A 1r0n_A 1r0o_A 2nll_A* Length = 85

 Score = 52.7 bits (127), Expect = 1e-10
 Identities = 16/35 (45%), Positives = 22/35 (62%)

Query: 37 GTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
              C++DK  RN+CQ CR +KCL MGM ++  Q 
Sbjct: 46 DNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQE 80

>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 = 50.4 bits (121), Expect = 1e-09
 Identities = 15/28 (53%), Positives = 21/28 (75%)

Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKDG 117
           C++DK  RN+CQ CR +KCL MGM ++ 
Sbjct: 50  CLIDKRQRNRCQYCRYQKCLAMGMKREA 77

>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 = 52.4 bits (126), Expect = 2e-10
 Identities = 16/36 (44%), Positives = 21/36 (58%)

Query: 36 AGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
            T +C +DK  R  CQACRL+KC  +GM K   + 
Sbjct: 44 PATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRK 79

>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 = 50.1 bits (120), Expect = 1e-09
 Identities = 16/28 (57%), Positives = 19/28 (67%)

Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKDG 117
           C +DK  R  CQACRL+KC  +GM K G
Sbjct: 49  CTIDKNRRKSCQACRLRKCYEVGMMKGG 76

>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 = 52.0 bits (125), Expect = 2e-10
 Identities = 17/36 (47%), Positives = 21/36 (58%)

Query: 36 AGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
          AG   CI+DK  R  C ACR +KCL  GMN +  + 
Sbjct: 42 AGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEARKT 77

>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 = 49.7 bits (119), Expect = 2e-09
 Identities = 15/29 (51%), Positives = 18/29 (62%)

Query: 89  RCIVDKAHRNQCQACRLKKCLNMGMNKDG 117
            CI+DK  R  C ACR +KCL  GMN + 
Sbjct: 46  DCIIDKIRRKNCPACRYRKCLQAGMNLEA 74

>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 = 51.2 bits (123), Expect = 6e-10
 Identities = 16/35 (45%), Positives = 21/35 (60%)

Query: 37 GTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
              C VDK  RN+CQ CR +KCL +GM K+  + 
Sbjct: 41 ANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRT 75

>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 = 49.6 bits (119), Expect = 2e-09
 Identities = 16/28 (57%), Positives = 20/28 (71%)

Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKDG 117
           C VDK  RN+CQ CR +KCL +GM K+ 
Sbjct: 45  CPVDKRRRNRCQFCRFQKCLAVGMVKEV 72

>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 = 51.3 bits (123), Expect = 7e-10
 Identities = 14/35 (40%), Positives = 18/35 (51%)

Query: 37 GTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
           T  C + K  R  CQACR  K L +GM K+  + 
Sbjct: 45 ATNECEITKRRRKSCQACRFMKALKVGMLKEGVRL 79

>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 = 49.3 bits (118), Expect = 3e-09
 Identities = 14/28 (50%), Positives = 17/28 (60%)

Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKDG 117
           C + K  R  CQACR  K L +GM K+G
Sbjct: 49  CEITKRRRKSCQACRFMKALKVGMLKEG 76

>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 = 50.5 bits (121), Expect = 2e-09
 Identities = 12/35 (34%), Positives = 19/35 (54%)

Query: 37 GTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
              C +DK  R +C  CR +KCL++GM  +  + 
Sbjct: 50 ENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRA 84

>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 = 49.4 bits (118), Expect = 4e-09
 Identities = 12/28 (42%), Positives = 18/28 (64%)

Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKDG 117
           C +DK  R +C  CR +KCL++GM  + 
Sbjct: 54  CQIDKTQRKRCPYCRFQKCLSVGMKLEA 81

>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 = 52.4 bits (125), Expect = 3e-09
 Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 6/63 (9%)

Query: 5   HDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGM 64
           H G+     C+    R I  K   ++C         C + K  RN+CQ CR +KCL +GM
Sbjct: 64  HYGVHACEGCKGFFRRTIRLKLIYDRCD------LNCRIHKKSRNKCQYCRFQKCLAVGM 117

Query: 65  NKD 67
           + +
Sbjct: 118 SHN 120

>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 = 51.6 bits (123), Expect = 5e-09
 Identities = 13/28 (46%), Positives = 19/28 (67%)

Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKDG 117
           C + K  RN+CQ CR +KCL +GM+ + 
Sbjct: 94  CRIHKKSRNKCQYCRFQKCLAVGMSHNA 121

>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 = 49.4 bits (118), Expect = 3e-09
 Identities = 13/36 (36%), Positives = 17/36 (47%)

Query: 36 AGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
          A    C +DK  R  C +CRL+KC   GM     + 
Sbjct: 47 ASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLGARKL 82

>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 = 48.2 bits (115), Expect = 1e-08
 Identities = 12/28 (42%), Positives = 15/28 (53%)

Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKDG 117
           C +DK  R  C +CRL+KC   GM    
Sbjct: 52  CTIDKFRRKNCPSCRLRKCYEAGMTLGA 79

>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 = 49.5 bits (118), Expect = 4e-09
 Identities = 14/35 (40%), Positives = 18/35 (51%)

Query: 37 GTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
              C +D   R +CQ CRLKKCL +GM  +    
Sbjct: 49 FGRACEMDMYMRRKCQECRLKKCLAVGMRPECVVP 83

>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 = 48.3 bits (115), Expect = 1e-08
 Identities = 14/27 (51%), Positives = 18/27 (66%)

Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKD 116
           C +D   R +CQ CRLKKCL +GM  +
Sbjct: 53  CEMDMYMRRKCQECRLKKCLAVGMRPE 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 = 51.3 bits (122), Expect = 7e-09
 Identities = 17/44 (38%), Positives = 26/44 (59%), Gaps = 1/44 (2%)

Query: 28  RNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
           ++    C+     C++DK  RN+CQ CR +KCL MGM ++  Q 
Sbjct: 170 KDLTYTCRDN-KDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQE 212

>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 = 48.6 bits (115), Expect = 5e-08
 Identities = 15/28 (53%), Positives = 21/28 (75%)

Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKDG 117
           C++DK  RN+CQ CR +KCL MGM ++ 
Sbjct: 182 CLIDKRQRNRCQYCRYQKCLAMGMKREA 209

>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 = 47.9 bits (114), Expect = 1e-08
 Identities = 15/31 (48%), Positives = 22/31 (70%)

Query: 37 GTGRCIVDKAHRNQCQACRLKKCLNMGMNKD 67
            G C + K +R  CQACRLK+C+++GM K+
Sbjct: 47 FNGDCRITKDNRRHCQACRLKRCVDIGMMKE 77

>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 = 46.7 bits (111), Expect = 4e-08
 Identities = 14/28 (50%), Positives = 21/28 (75%)

Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKDG 117
           C + K +R  CQACRLK+C+++GM K+ 
Sbjct: 51  CRITKDNRRHCQACRLKRCVDIGMMKEF 78

>2nll_B Protein (thyroid hormone receptor); complex (transcription regulation/DNA), DNA-binding, nuclear protein, zinc- finger, multigene family; HET: DNA 5IU; 1.90A {Homo sapiens} SCOP: g.39.1.2 PDB: 3m9e_A* Length = 103

 Score = 47.4 bits (113), Expect = 2e-08
 Identities = 17/31 (54%), Positives = 22/31 (70%)

Query: 37 GTGRCIVDKAHRNQCQACRLKKCLNMGMNKD 67
            G+C++DK  RNQCQ CR KKC+ +GM  D
Sbjct: 44 YEGKCVIDKVTRNQCQECRFKKCIYVGMATD 74

>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 = 46.3 bits (110), Expect = 5e-08
 Identities = 16/28 (57%), Positives = 21/28 (75%)

Query: 89  RCIVDKAHRNQCQACRLKKCLNMGMNKD 116
           +C++DK  RNQCQ CR KKC+ +GM  D
Sbjct: 47  KCVIDKVTRNQCQECRFKKCIYVGMATD 74

>1lbd_A RXR_LBD, retinoid X receptor; transcription factor, nuclear receptor, structural proteomic europe, spine, structural genomics; 2.70A {Homo sapiens} SCOP: a.123.1.1 PDB: 1z5x_U* 2q60_A Length = 282

 Score = 37.9 bits (88), Expect = 3e-04
 Identities = 1/26 (3%), Positives = 7/26 (26%), Gaps = 3/26 (11%)

Query: 92  VDKAHRNQCQACRLKKCLNMGMNKDG 117
               H +   +  + +       ++ 
Sbjct: 2   GSSHHHHHHSSGLVPRG---SHKREA 24

>1lbd_A RXR_LBD, retinoid X receptor; transcription factor, nuclear receptor, structural proteomic europe, spine, structural genomics; 2.70A {Homo sapiens} SCOP: a.123.1.1 PDB: 1z5x_U* 2q60_A Length = 282

 Score = 37.5 bits (87), Expect = 4e-04
 Identities = 1/25 (4%), Positives = 7/25 (28%), Gaps = 3/25 (12%)

Query: 43 VDKAHRNQCQACRLKKCLNMGMNKD 67
              H +   +  + +       ++
Sbjct: 2  GSSHHHHHHSSGLVPRG---SHKRE 23

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	120
3cbb_A	78	HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DN	99.89
2ebl_A	89	COUP transcription factor 1; DNA-binding, metal-bi	99.89
1dsz_A	86	RAR-alpha, retinoic acid receptor alpha; RAR, nucl	99.89
1dsz_B	85	RXR-alpha, retinoic acid receptor RXR-alpha; RAR,	99.89
2han_A	93	Protein ultraspiracle; transcription regulation, t	99.88
1hcq_A	84	Protein (estrogen receptor); protein-DNA complex,	99.88
1ynw_B	99	Retinoic acid receptor RXR-alpha, retinoid X recep	99.88
1a6y_A	94	Orphan nuclear receptor NR1D1; orphan receptor, DN	99.88
3g9m_A	90	Glucocorticoid receptor; glucocorticoid, DNA-bindi	99.87
1cit_A	89	NGFI-B, protein (orphan nuclear receptor NGFI-B);	99.87
1lo1_A	98	Steroid hormone receptor ERR2; estrogen related re	99.86
2a66_A	113	Orphan nuclear receptor NR5A2; protein-DNA complex	99.86
4hn5_A	117	Glucocorticoid receptor; glucocorticoid receptor,	99.86
1kb2_A	110	Vitamin D3 receptor; VDR, nuclear receptor, protei	99.85
2nll_B	103	Protein (thyroid hormone receptor); complex (trans	99.85
2han_B	119	Ecdysone receptor; transcription regulation, trans	99.84
1r4i_A	105	Androgen receptor; AR, steroid receptor, protein-D	99.84
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	99.75
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	99.71
2lze_A	87	A primordial catalytic fold generated by in vitro	99.61
3cbb_A	78	HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DN	99.26
1dsz_B	85	RXR-alpha, retinoic acid receptor RXR-alpha; RAR,	99.23
1ynw_B	99	Retinoic acid receptor RXR-alpha, retinoid X recep	99.21
1hcq_A	84	Protein (estrogen receptor); protein-DNA complex,	99.2
1cit_A	89	NGFI-B, protein (orphan nuclear receptor NGFI-B);	99.2
1dsz_A	86	RAR-alpha, retinoic acid receptor alpha; RAR, nucl	99.2
2han_A	93	Protein ultraspiracle; transcription regulation, t	99.18
2ebl_A	89	COUP transcription factor 1; DNA-binding, metal-bi	99.16
3g9m_A	90	Glucocorticoid receptor; glucocorticoid, DNA-bindi	99.13
4hn5_A	117	Glucocorticoid receptor; glucocorticoid receptor,	99.13
1lo1_A	98	Steroid hormone receptor ERR2; estrogen related re	99.13
1kb2_A	110	Vitamin D3 receptor; VDR, nuclear receptor, protei	99.13
1a6y_A	94	Orphan nuclear receptor NR1D1; orphan receptor, DN	99.12
2a66_A	113	Orphan nuclear receptor NR5A2; protein-DNA complex	99.11
1r4i_A	105	Androgen receptor; AR, steroid receptor, protein-D	99.11
2nll_B	103	Protein (thyroid hormone receptor); complex (trans	99.1
2han_B	119	Ecdysone receptor; transcription regulation, trans	99.08
2lze_A	87	A primordial catalytic fold generated by in vitro	98.84
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	98.81
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	98.65
1lbd_A	282	RXR_LBD, retinoid X receptor; transcription factor	93.25

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

Probab=99.89  E-value=5e-25  Score=134.36  Aligned_cols=68  Identities=35%  Similarity=0.737  Sum_probs=61.5

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhh
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKN   74 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~   74 (120)
                      +-+||||+||+||++    ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||++++||.+|+
T Consensus        11 ~g~hyGv~sC~aCk~----FFRR~v~~~~~y~C~~-~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~Rd   78 (78)
T 3cbb_A           11 TGKHYGASSCDGCKG----FFRRSVRKNHMYSCRF-SRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNERD   78 (78)
T ss_dssp             CSEETTEECCHHHHH----HHHHHHHTTCCCCCSS-CSCCCCSTTTTTTCHHHHHHHHHHHTCCGGGCCCC--
T ss_pred             CceEeCCcchhhhce----eeeEEEecccCccccc-ccccCcCccccccChhhhhHHHhHcCCCHHHccccCC
Confidence            358999999999988    7889999889999995 7999999999999999999999999999999998875

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

Probab=99.89  E-value=5.7e-25  Score=137.09  Aligned_cols=70  Identities=36%  Similarity=0.674  Sum_probs=64.6

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhcc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSL   76 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~   76 (120)
                      +-+||||++|+||++    ||||++..+..|.|.. +++|.|+...+..|++|||+|||++||.+++||.+|++.
T Consensus        18 ~g~hyGv~sC~aCk~----FFRR~v~~~~~y~C~~-~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~~   87 (89)
T 2ebl_A           18 SGKHYGQFTCEGCKS----FFKRSVRRNLTYTCRA-NRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQRGSGPS   87 (89)
T ss_dssp             CSEETTEECCHHHHH----HHHHHHTTTCCCCCSS-CSCCCCCSSSSSCCSHHHHHHHHHHTCCHHHHSCSCCCC
T ss_pred             cceEeCchhhHHhhh----hhheeeeeccceeccc-CccCCcCccCccccccchHHHhhhccCCHHHcccCCCCC
Confidence            358999999999988    7889999889999995 799999999999999999999999999999999999864

>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=99.89  E-value=9.2e-25  Score=135.46  Aligned_cols=70  Identities=30%  Similarity=0.667  Sum_probs=61.7

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhcc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSL   76 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~   76 (120)
                      +-+||||+||+||++    ||+|+++.+..|.|.. +++|.|+...+..|++|||+|||++||++++||.+|+++
T Consensus        15 ~g~hyGv~sC~aCk~----FFRR~v~~~~~y~C~~-~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~~   84 (86)
T 1dsz_A           15 SGYHYGVSACEGCKG----FFRRSIQKNMVYTCHR-DKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNKK   84 (86)
T ss_dssp             CSEETTEECCHHHHH----HHHHHHHTTCCCCCSS-CSCCCCSTTTGGGCHHHHHHHHHHTTCCGGGSCCC----
T ss_pred             cceeeCchhHHHHHH----HHHHHhhcccceeecc-CCccccCccccccchhhhHHHHHHhCCCHHHhhhccccc
Confidence            458999999999988    7889999888999985 799999999999999999999999999999999999864

>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=99.89  E-value=9.1e-25  Score=135.16  Aligned_cols=69  Identities=29%  Similarity=0.680  Sum_probs=63.6

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNS   75 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~   75 (120)
                      +-+||||.||+||++    ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||++++||.+|++
T Consensus        16 ~g~hyGv~sC~aCk~----FFRR~v~~~~~y~C~~-~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~   84 (85)
T 1dsz_B           16 SGKHYGVYSCEGCKG----FFKRTVRKDLTYTCRD-NKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQR   84 (85)
T ss_dssp             SSEETTEECCHHHHH----HHHHHHHHTCCCCCSS-CSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCCCCC
T ss_pred             CceeeCccchHHHHH----HHHHhhccccceeecc-cccccccccccccCcchhHHHHhHcCCCHHHhhcccCC
Confidence            358999999999988    7889998889999995 78999999999999999999999999999999999874

>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=99.88  E-value=1.3e-24  Score=136.60  Aligned_cols=69  Identities=30%  Similarity=0.688  Sum_probs=61.9

Q ss_pred             CccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhcc
Q psy13208          3 FRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSL   76 (120)
Q Consensus         3 ~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~   76 (120)
                      -+||||.+|+||++    ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||++++||.+|++.
T Consensus        22 g~hyGv~sC~aCk~----FFRR~v~~~~~y~C~~-~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~~   90 (93)
T 2han_A           22 GKHYGVYSCEGCKG----FFKRTVRKDLTYACRE-NRNCIIDKRQRNRCQYCRYQKCLTCGMKREAVQEERQGI   90 (93)
T ss_dssp             EEETTEEECHHHHH----HHHHHHHHTCCCCCSS-CSCCCCSTTTGGGCHHHHHHHHHHHTCCGGGSCCCC---
T ss_pred             CeecCcchhHHHHH----HHHhhhccccCcCcCC-CCcCCcCCCCCccCccccHHHHhHhCCCHHHhhhccCcc
Confidence            57999999999988    7889998888999995 799999999999999999999999999999999999854

>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=99.88  E-value=2.3e-24  Score=133.08  Aligned_cols=68  Identities=32%  Similarity=0.611  Sum_probs=55.9

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhh
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKN   74 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~   74 (120)
                      +-+||||+||+||++    ||||+++.+..|.|.. +++|.|+...+..|++|||+|||++||++++||.+|.
T Consensus        15 ~g~hyGv~sC~aCk~----FFRR~v~~~~~y~C~~-~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~   82 (84)
T 1hcq_A           15 SGYHYGVWSCEGCKA----FFKRSIQGHNDYMCPA-TNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRKDRR   82 (84)
T ss_dssp             CEEETTEEECHHHHH----HHHHHHSSCCCCCCSS-SSCCCCSTTTTTTCHHHHHHHHHHHTCCC--------
T ss_pred             CCeeeCccchHHhhh----hhhhcccccccccccc-CccCCcCCcCcccChhhhhHHHhHcCCCHHHhcccCC
Confidence            358999999999988    7889999899999995 7999999999999999999999999999999998874

>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=99.88  E-value=3e-24  Score=136.25  Aligned_cols=71  Identities=28%  Similarity=0.631  Sum_probs=59.8

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhccc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLL   77 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~   77 (120)
                      +-+||||.+|+||++    ||||++..+..|.|.. +++|.|+...+..|++|||+|||++||.+++||.+|++..
T Consensus        14 ~g~hyGv~sC~aCk~----FFRR~v~~~~~y~C~~-~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~~~   84 (99)
T 1ynw_B           14 SGKHYGVYSCEGCKG----FFKRTVRKDLTYTCRD-NKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRGK   84 (99)
T ss_dssp             CBCCTTSCBCSHHHH----HHHHHHHTTCCCCCSS-SSCCCCCSTTSSSCHHHHHHHHHHTTCCSTTCC-------
T ss_pred             cceeeCccchHHHHH----HHHhhhccccccccCC-CCcccccccCCccCccccHHHHhHcCCCHHHhhhcccccc
Confidence            358999999999988    7889999889999995 7899999999999999999999999999999999998643

>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=99.88  E-value=2.7e-24  Score=135.34  Aligned_cols=71  Identities=27%  Similarity=0.525  Sum_probs=61.7

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcce-eccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhccc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQ-ACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLL   77 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~-~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~   77 (120)
                      +-+||||+||+||++    ||+|++..+..| .|.. +++|.|+...+..|++|||+|||++||++++||.+|+|..
T Consensus        18 ~g~hyGv~sC~aCk~----FFRR~v~~~~~y~~C~~-~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~~~   89 (94)
T 1a6y_A           18 SGFHYGVLACEGCKG----FFRRSIQQNIQYKRCLK-NENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGRIPKR   89 (94)
T ss_dssp             CEEETTEEECHHHHH----HHHHHHSSCCCCCCCSS-TTCCCCCTTTTTSCHHHHHHHHTTTTCCSTTCCCCC----
T ss_pred             cceEeCccchhhhhh----ehheeeecccceEEccC-CCCCccCccccccccchhHHHhhHccCCHHHhccCcCcCc
Confidence            358999999999988    788999888888 5985 7999999999999999999999999999999999998654

>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=99.87  E-value=6.6e-24  Score=132.75  Aligned_cols=71  Identities=28%  Similarity=0.541  Sum_probs=62.5

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhccc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLL   77 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~   77 (120)
                      +-+||||.+|+||++    ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||++++||.+++.+.
T Consensus        13 ~g~hyGv~sC~~Ck~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~avq~~r~~~~   83 (90)
T 3g9m_A           13 SGCHYGVLTCGSCKV----FFKRAVEGQHNYLCAG-RNDCIIDKIRRKNCPACRYRKCLQAGMNLEARKTKKKIKG   83 (90)
T ss_dssp             CEEETTEEECHHHHH----HHHHHHHSCCCCCCSS-SSCCCCCTTGGGTCHHHHHHHHHHHTCCTTHHHHHC----
T ss_pred             cccccCCccchhHhH----HhhhhhhcCCceeCCC-CCccccCcccccCCcchhhHHHHHcCCCHHHhcccccccc
Confidence            358999999999988    7889999999999985 7999999999999999999999999999999999987543

>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=99.87  E-value=7.4e-24  Score=132.10  Aligned_cols=68  Identities=31%  Similarity=0.594  Sum_probs=62.4

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhh
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKN   74 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~   74 (120)
                      +-+||||.||+||++    ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||++++||.++.
T Consensus        11 ~g~hyGv~sC~aCk~----FFRR~v~~~~~y~C~~-~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~~~   78 (89)
T 1cit_A           11 SCQHYGVRTCEGCKG----FFKRTVQKSAKYICLA-NKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTDSL   78 (89)
T ss_dssp             CEEETTEEECHHHHH----HHHHHHHHTCCCCCSS-SSCCCCSTTTTTTCHHHHHHHHHHTTCCGGGSCCGGG
T ss_pred             cceEeCccchhhhhh----hceeeEEecceeeecc-CCccccCCCCcccChhhhhHHHhHcCCCHHHeecccc
Confidence            358999999999988    7889998888999995 7999999999999999999999999999999998765

>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=99.86  E-value=6.1e-24  Score=134.57  Aligned_cols=69  Identities=30%  Similarity=0.524  Sum_probs=63.4

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNS   75 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~   75 (120)
                      +-+||||++|+||++    ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||++++||.+|++
T Consensus        15 ~g~hyGv~sC~aCk~----FFRR~v~~~~~y~C~~-~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~   83 (98)
T 1lo1_A           15 SGYHYGVASCEACKA----FFKRTIQGNIEYSCPA-TNECEITKRRRKSCQACRFMKALKVGMLKEGVRLDRVR   83 (98)
T ss_dssp             SEESSSSEECHHHHH----HHHHHHHTTCCCCCSS-CSCCCCCHHHHHHCHHHHHHHHHHHTCCGGGSCSSCCT
T ss_pred             cCeeeCccchhhhhh----hheeeecccCccccCc-cccccccccccccccchhHHHHhHcCCCHHHeeccccc
Confidence            358999999999988    7889999889999995 78999999999999999999999999999999998874

>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=99.86  E-value=2e-23  Score=135.17  Aligned_cols=68  Identities=25%  Similarity=0.576  Sum_probs=63.2

Q ss_pred             CccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhc
Q psy13208          3 FRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNS   75 (120)
Q Consensus         3 ~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~   75 (120)
                      -+||||.||+||++    ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||++++||.+|++
T Consensus        21 G~HyGv~sC~aCk~----FFRR~v~~~~~y~C~~-~~~C~i~~~~R~~Cr~CR~~KCl~vGM~~~~vq~~R~~   88 (113)
T 2a66_A           21 GYHYGLLTCESCKG----FFKRTVQNNKRYTCIE-NQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMR   88 (113)
T ss_dssp             EEETTEEEEHHHHH----HHHHHHHTTCCCCCSS-CSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCTTCCC
T ss_pred             ceeeCcccHHHHHH----HHhhhhhccccccccc-cccCCcCCCccccccchhHHHHhHhCCCHHHhcccccc
Confidence            47999999999988    7889999889999995 79999999999999999999999999999999999874

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

Probab=99.86  E-value=2.9e-23  Score=135.09  Aligned_cols=71  Identities=28%  Similarity=0.541  Sum_probs=57.7

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhccc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLL   77 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~   77 (120)
                      +-+||||.+|+||++    ||||++..+..|.|.. +++|.|+...+..|++|||+|||++||.+++||.+++.+.
T Consensus        40 ~G~HyGv~sC~aCk~----FFRRsv~~~~~y~C~~-~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~avq~kR~~k~  110 (117)
T 4hn5_A           40 SGCHYGVLTCGSCKV----FFKRAVEGQHNYLCAG-RNDCIIDKIRRKNCPACRYRKCLQAGMNLEARKTKKKIKG  110 (117)
T ss_dssp             CEEETTEEECHHHHH----HHHHHHSSCCCCCCSS-SSCCCCSTTTTTTCHHHHHHHHHHHTCCTTC---------
T ss_pred             cccccCCcccchhhh----hhhcceecCCceecCC-CCccccCcccccCCcccchHHHhHcCCCHHHhcccccccc
Confidence            358999999999988    7889999999999985 7999999999999999999999999999999999987543

>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=99.85  E-value=5.6e-23  Score=132.63  Aligned_cols=69  Identities=29%  Similarity=0.525  Sum_probs=62.6

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNS   75 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~   75 (120)
                      +-+||||.+|+||++    ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||.+++|+.++..
T Consensus        17 ~g~hyGv~sC~aCk~----FFRR~v~~~~~y~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~   85 (110)
T 1kb2_A           17 TGFHFNAMTCEGCKG----FFRRSMKRKALFTCPF-NGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDEEV   85 (110)
T ss_dssp             CSEETTEECCHHHHH----HHHHHHHTTCCCCCSS-CSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCHHHH
T ss_pred             CceEeCchhHhhhhh----hheeeeecccceeeCC-CCCccCCcccceecccccHhhhhhcCCcHHhcccHHHH
Confidence            358999999999988    7889998889999995 79999999999999999999999999999988877764

>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=99.85  E-value=5.9e-23  Score=131.18  Aligned_cols=70  Identities=33%  Similarity=0.622  Sum_probs=62.9

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCc--ceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhcc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQ--CQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSL   76 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~--~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~   76 (120)
                      +-+||||+||+||++    ||+|++..+.  .|.|.. +++|.|+...+..|++|||+|||++||.+++|+.++++.
T Consensus        12 ~g~hyGv~sC~aCk~----FFRR~v~~~~~~~y~C~~-~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~~~~~   83 (103)
T 2nll_B           12 TGYHYRCITCEGCKG----FFRRTIQKNLHPSYSCKY-EGKCVIDKVTRNQCQECRFKKCIYVGMATDLVLDDSKRL   83 (103)
T ss_dssp             CSEETTEECCHHHHH----HHHHHHHTTCGGGCCCSS-CTTCCCSTTTTTSCHHHHHHHHHHTTCCGGGSCCHHHHH
T ss_pred             cCeecCcccHHHhhh----hheecccccccchhhhhc-cCCcCcCccCccccchhhhHhhhHhCCCHHHhhhhhhhH
Confidence            458999999999988    7888988765  799985 799999999999999999999999999999999988753

>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=99.84  E-value=7.9e-23  Score=133.64  Aligned_cols=69  Identities=25%  Similarity=0.462  Sum_probs=62.9

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNS   75 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~   75 (120)
                      +-+||||.+|+||++    ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||++++|+.+++.
T Consensus        19 ~g~hyGv~sC~aCk~----FFRR~v~~~~~y~C~~-~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~   87 (119)
T 2han_B           19 SGYHYNALTCEGCKG----FFRRSVTKSAVYCCKF-GRACEMDMYMRRKCQECRLKKCLAVGMRPECVVPENQC   87 (119)
T ss_dssp             CEEETTEEECHHHHH----HHHHHHHTTCCCCCSS-CSCCCCSTTGGGTCHHHHHHHHHHTTCCGGGSSCSSHH
T ss_pred             CcceECchhHHhhHH----hhhhheEecccccccc-ccccccCccccccchhhHHHHHHHhCCCHHHccchhhh
Confidence            358999999999988    7889998888999995 68999999999999999999999999999999987763

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

Probab=99.84  E-value=1.4e-22  Score=129.72  Aligned_cols=68  Identities=28%  Similarity=0.523  Sum_probs=57.1

Q ss_pred             CccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhc
Q psy13208          3 FRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNS   75 (120)
Q Consensus         3 ~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~   75 (120)
                      -+||||.+|+||++    ||||++..+..|.|.. +++|.|+...+..|++|||+|||++||++++++..+.+
T Consensus        19 g~hyGv~sC~aCk~----FFRR~v~~~~~y~C~~-~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~~k~~k~~   86 (105)
T 1r4i_A           19 GAHYGALTCGSCKV----FFKRAAEGKQKYLCAS-RNDCTIDKFRRKNCPSCRLRKCYEAGMTLGARKLKKLG   86 (105)
T ss_dssp             EEETTEEEEHHHHH----HHHHHHTSCCCCCCSS-SSCCCCCTTTTTTCHHHHHHHHHHHTCCSCC-------
T ss_pred             ceEeCCcchhhhhh----hhceeEEecCceeecc-CCccccCccccccchhchHHHHHhhhcccchhhhcccc
Confidence            47999999999988    7889999889999985 78999999999999999999999999999998877653

>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=99.75  E-value=8.7e-20  Score=142.80  Aligned_cols=69  Identities=29%  Similarity=0.652  Sum_probs=63.7

Q ss_pred             CccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhcc
Q psy13208          3 FRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSL   76 (120)
Q Consensus         3 ~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~   76 (120)
                      -+||||.+|+|||+    ||||+++++..|.|.. +++|.+++..|+.|++|||+||+++||..++||.+|++.
T Consensus       149 g~hygv~sC~~Ck~----FFrR~~~~~~~~~C~~-~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~~  217 (467)
T 3dzy_A          149 GKHYGVYSCEGCKG----FFKRTVRKDLTYTCRD-NKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRG  217 (467)
T ss_dssp             SEETTEECCHHHHH----HHHHHHHTTCCCCCSS-SSCCCCCSSSSSSCHHHHHHHHHHTTCCGGGCCCCSCCC
T ss_pred             CCcCCCcchhhhhH----hccccccCCCceeCCC-CCCCCCCcccccccccchhhhhhhccccchhhhcccccc
Confidence            58999999999987    7889999999999995 799999999999999999999999999999999988754

>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=99.71  E-value=7.8e-19  Score=135.79  Aligned_cols=69  Identities=25%  Similarity=0.484  Sum_probs=61.0

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCccee-ccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhccc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQA-CQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLL   77 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~-C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~   77 (120)
                      .-+||||.+|+|||+    ||||++..+..|. |.   ++|.+++..++.|++|||+||+++||++++||.+|++..
T Consensus        61 ~g~hygv~~C~~C~~----FFrR~~~~~~~~~~c~---~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~vq~~R~~~~  130 (419)
T 3dzy_D           61 SGFHYGVHACEGCKG----FFRRTIRLKLIYDRCD---LNCRIHKKSRNKCQYCRFQKCLAVGMSHNAIRFGRMPQA  130 (419)
T ss_dssp             CSBCSSSBCCHHHHH----HHHHHHTTTCCCCCCC---SCCCCCTTGGGTCHHHHHHHHHHTTCCGGGCCCSCCTTT
T ss_pred             CCCccCcccchhhhH----HHccchhccccccccc---CCCCcccccCccchhhhHHHHhhcccchhheeccccccc
Confidence            358999999999987    7888998888775 53   689999999999999999999999999999999997654

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

Probab=99.61  E-value=9.6e-17  Score=99.21  Aligned_cols=61  Identities=13%  Similarity=0.102  Sum_probs=51.9

Q ss_pred             CccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhh
Q psy13208          3 FRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQ   70 (120)
Q Consensus         3 ~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~   70 (120)
                      ..||++. |.+|++    ||+|++ ++..|.|+. +++|.|++..++.|++|||+|||+|||....+.
T Consensus        16 g~h~c~v-Cgd~as----fFRRt~-~~~~y~C~~-~~~C~i~~~~R~~C~~CR~qKCl~VgM~~~~~~   76 (87)
T 2lze_A           16 GKHICAI-CGNNAE----DYKHTD-MDLTYTDRD-YKNCESYHKCSDLCQYCRYQKDLAIHHQHHHGG   76 (87)
T ss_dssp             CSSSCSS-SSSSSS----SCTTTT-TSCTTTSCC-CCCCCCSSCCSSSCSGGGTSCCHHHHCSSCCCC
T ss_pred             CCEEccC-CCCccc----eECccc-CCCeeEcCC-CCccccCCCccCcCCcccChhhccCcCEeccCc
Confidence            4689987 999988    556664 567899985 799999999999999999999999999876544

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

Probab=99.26  E-value=1e-12  Score=79.75  Aligned_cols=59  Identities=36%  Similarity=0.835  Sum_probs=51.2

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       ++++++++....     |.|..  .++|.|+...++.|++|||+|||++||++++|
T Consensus        15 yGv~sC~aCk-------~FFRR~v~~~~~-----y~C~~--~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v   73 (78)
T 3cbb_A           15 YGASSCDGCK-------GFFRRSVRKNHM-----YSCRF--SRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAV   73 (78)
T ss_dssp             TTEECCHHHH-------HHHHHHHHTTCC-----CCCSS--CSCCCCSTTTTTTCHHHHHHHHHHHTCCGGGC
T ss_pred             eCCcchhhhc-------eeeeEEEecccC-----ccccc--ccccCcCccccccChhhhhHHHhHcCCCHHHc
Confidence            4457899999       999988886544     88874  57899999999999999999999999999876

>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=99.23  E-value=1.8e-12  Score=79.80  Aligned_cols=59  Identities=34%  Similarity=0.834  Sum_probs=51.3

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       +++++.++.+..     |.|..  .++|.|+...++.|++|||+|||++||++++|
T Consensus        20 yGv~sC~aCk-------~FFRR~v~~~~~-----y~C~~--~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v   78 (85)
T 1dsz_B           20 YGVYSCEGCK-------GFFKRTVRKDLT-----YTCRD--NKDCLIDKRQRNRCQYCRYQKCLAMGMKREAV   78 (85)
T ss_dssp             TTEECCHHHH-------HHHHHHHHHTCC-----CCCSS--CSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGS
T ss_pred             eCccchHHHH-------HHHHHhhccccc-----eeecc--cccccccccccccCcchhHHHHhHcCCCHHHh
Confidence            4457899999       999999886654     88975  57899999999999999999999999999876

>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=99.21  E-value=4.4e-12  Score=80.14  Aligned_cols=60  Identities=33%  Similarity=0.823  Sum_probs=52.0

Q ss_pred             CcccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         45 KAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        45 ~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      ..+...|.+|.       +++++.++.+..     |.|..  .++|.|+...++.|++|||+|||++||++++|
T Consensus        17 hyGv~sC~aCk-------~FFRR~v~~~~~-----y~C~~--~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v   76 (99)
T 1ynw_B           17 HYGVYSCEGCK-------GFFKRTVRKDLT-----YTCRD--NKDCLIDKRQRNRCQYCRYQKCLAMGMKREAV   76 (99)
T ss_dssp             CTTSCBCSHHH-------HHHHHHHHTTCC-----CCCSS--SSCCCCCSTTSSSCHHHHHHHHHHTTCCSTTC
T ss_pred             eeCccchHHHH-------HHHHhhhccccc-----cccCC--CCcccccccCCccCccccHHHHhHcCCCHHHh
Confidence            34567999999       999999886654     88975  57899999999999999999999999999876

>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=99.20  E-value=2.1e-12  Score=79.37  Aligned_cols=59  Identities=36%  Similarity=0.780  Sum_probs=48.8

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       ++++++++....     |.|..  .++|.|+...++.|++|||+|||++||++++|
T Consensus        19 yGv~sC~aCk-------~FFRR~v~~~~~-----y~C~~--~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v   77 (84)
T 1hcq_A           19 YGVWSCEGCK-------AFFKRSIQGHND-----YMCPA--TNQCTIDKNRRKSCQACRLRKCYEVGMMKGGI   77 (84)
T ss_dssp             TTEEECHHHH-------HHHHHHHSSCCC-----CCCSS--SSCCCCSTTTTTTCHHHHHHHHHHHTCCC---
T ss_pred             eCccchHHhh-------hhhhhccccccc-----ccccc--CccCCcCCcCcccChhhhhHHHhHcCCCHHHh
Confidence            3457899999       999988887654     88875  57899999999999999999999999999876

>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=99.20  E-value=3.1e-12  Score=79.36  Aligned_cols=59  Identities=37%  Similarity=0.771  Sum_probs=51.2

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       ++++++++....     |.|..  .++|.|+...++.|++|||+|||++||++++|
T Consensus        15 yGv~sC~aCk-------~FFRR~v~~~~~-----y~C~~--~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v   73 (89)
T 1cit_A           15 YGVRTCEGCK-------GFFKRTVQKSAK-----YICLA--NKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVV   73 (89)
T ss_dssp             TTEEECHHHH-------HHHHHHHHHTCC-----CCCSS--SSCCCCSTTTTTTCHHHHHHHHHHTTCCGGGS
T ss_pred             eCccchhhhh-------hhceeeEEecce-----eeecc--CCccccCCCCcccChhhhhHHHhHcCCCHHHe
Confidence            4457899999       999999887654     88874  57899999999999999999999999998876

>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=99.20  E-value=3.1e-12  Score=78.93  Aligned_cols=59  Identities=34%  Similarity=0.836  Sum_probs=51.2

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       ++++++++....     |.|..  .++|.|+...++.|++|||+|||++||++++|
T Consensus        19 yGv~sC~aCk-------~FFRR~v~~~~~-----y~C~~--~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v   77 (86)
T 1dsz_A           19 YGVSACEGCK-------GFFRRSIQKNMV-----YTCHR--DKNCIINKVTRNRCQYCRLQKCFEVGMSKESV   77 (86)
T ss_dssp             TTEECCHHHH-------HHHHHHHHTTCC-----CCCSS--CSCCCCSTTTGGGCHHHHHHHHHHTTCCGGGS
T ss_pred             eCchhHHHHH-------HHHHHHhhcccc-----eeecc--CCccccCccccccchhhhHHHHHHhCCCHHHh
Confidence            4457899999       999988886654     88874  57899999999999999999999999999876

>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=99.18  E-value=3.8e-12  Score=79.58  Aligned_cols=59  Identities=36%  Similarity=0.821  Sum_probs=51.2

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       +++++.++.+..     |.|..  .++|.|+...++.|++|||+|||++||++++|
T Consensus        25 yGv~sC~aCk-------~FFRR~v~~~~~-----y~C~~--~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v   83 (93)
T 2han_A           25 YGVYSCEGCK-------GFFKRTVRKDLT-----YACRE--NRNCIIDKRQRNRCQYCRYQKCLTCGMKREAV   83 (93)
T ss_dssp             TTEEECHHHH-------HHHHHHHHHTCC-----CCCSS--CSCCCCSTTTGGGCHHHHHHHHHHHTCCGGGS
T ss_pred             cCcchhHHHH-------HHHHhhhccccC-----cCcCC--CCcCCcCCCCCccCccccHHHHhHhCCCHHHh
Confidence            4457899999       999988886654     88975  57899999999999999999999999999876

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

Probab=99.16  E-value=2.5e-12  Score=79.81  Aligned_cols=59  Identities=36%  Similarity=0.818  Sum_probs=50.5

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       +++++.++....     |.|..  .++|.|+...++.|++|||+|||++||++++|
T Consensus        22 yGv~sC~aCk-------~FFRR~v~~~~~-----y~C~~--~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v   80 (89)
T 2ebl_A           22 YGQFTCEGCK-------SFFKRSVRRNLT-----YTCRA--NRNCPIDQHHRNQCQYCRLKKCLKVGMRREAV   80 (89)
T ss_dssp             TTEECCHHHH-------HHHHHHHTTTCC-----CCCSS--CSCCCCCSSSSSCCSHHHHHHHHHHTCCHHHH
T ss_pred             eCchhhHHhh-------hhhheeeeeccc-----eeccc--CccCCcCccCccccccchHHHhhhccCCHHHc
Confidence            4457899999       999888876544     88874  57899999999999999999999999998765

>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=99.13  E-value=5.9e-12  Score=78.33  Aligned_cols=59  Identities=34%  Similarity=0.757  Sum_probs=50.2

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       ++++++++....     |.|..  .++|.|+...++.|++|||+|||++||++++|
T Consensus        17 yGv~sC~~Ck-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~av   75 (90)
T 3g9m_A           17 YGVLTCGSCK-------VFFKRAVEGQHN-----YLCAG--RNDCIIDKIRRKNCPACRYRKCLQAGMNLEAR   75 (90)
T ss_dssp             TTEEECHHHH-------HHHHHHHHSCCC-----CCCSS--SSCCCCCTTGGGTCHHHHHHHHHHHTCCTTHH
T ss_pred             cCCccchhHh-------HHhhhhhhcCCc-----eeCCC--CCccccCcccccCCcchhhHHHHHcCCCHHHh
Confidence            3456899998       888888876655     78874  57899999999999999999999999999876

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

Probab=99.13  E-value=1.2e-11  Score=80.28  Aligned_cols=59  Identities=34%  Similarity=0.757  Sum_probs=49.9

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       ++++++++....     |.|..  .++|.|+...++.|++|||+|||++||++++|
T Consensus        44 yGv~sC~aCk-------~FFRRsv~~~~~-----y~C~~--~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~av  102 (117)
T 4hn5_A           44 YGVLTCGSCK-------VFFKRAVEGQHN-----YLCAG--RNDCIIDKIRRKNCPACRYRKCLQAGMNLEAR  102 (117)
T ss_dssp             TTEEECHHHH-------HHHHHHHSSCCC-----CCCSS--SSCCCCSTTTTTTCHHHHHHHHHHHTCCTTC-
T ss_pred             cCCcccchhh-------hhhhcceecCCc-----eecCC--CCccccCcccccCCcccchHHHhHcCCCHHHh
Confidence            4456899999       888888876655     78874  57899999999999999999999999999886

>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=99.13  E-value=5.2e-12  Score=79.67  Aligned_cols=60  Identities=33%  Similarity=0.671  Sum_probs=52.0

Q ss_pred             CcccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         45 KAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        45 ~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      ..+...|.+|.       ++++++++....     |.|..  .++|.|+...++.|++|||+|||++||++++|
T Consensus        18 hyGv~sC~aCk-------~FFRR~v~~~~~-----y~C~~--~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v   77 (98)
T 1lo1_A           18 HYGVASCEACK-------AFFKRTIQGNIE-----YSCPA--TNECEITKRRRKSCQACRFMKALKVGMLKEGV   77 (98)
T ss_dssp             SSSSEECHHHH-------HHHHHHHHTTCC-----CCCSS--CSCCCCCHHHHHHCHHHHHHHHHHHTCCGGGS
T ss_pred             eeCccchhhhh-------hhheeeecccCc-----cccCc--cccccccccccccccchhHHHHhHcCCCHHHe
Confidence            34567899999       999999887654     88975  57899999999999999999999999999876

>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=99.13  E-value=1.1e-11  Score=79.73  Aligned_cols=59  Identities=32%  Similarity=0.738  Sum_probs=51.1

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       +++++.++....     |.|..  .++|.|+...++.|++|||+|||++||++++|
T Consensus        21 yGv~sC~aCk-------~FFRR~v~~~~~-----y~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v   79 (110)
T 1kb2_A           21 FNAMTCEGCK-------GFFRRSMKRKAL-----FTCPF--NGDCRITKDNRRHCQACRLKRCVDIGMMKEFI   79 (110)
T ss_dssp             TTEECCHHHH-------HHHHHHHHTTCC-----CCCSS--CSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGS
T ss_pred             eCchhHhhhh-------hhheeeeecccc-----eeeCC--CCCccCCcccceecccccHhhhhhcCCcHHhc
Confidence            4457899999       999998886654     88975  57899999999999999999999999998865

>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=99.12  E-value=7.4e-12  Score=78.42  Aligned_cols=59  Identities=32%  Similarity=0.776  Sum_probs=50.4

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhc-ccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEF-ACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~-~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       ++++++++....     | .|..  .++|.|+...++.|++|||+|||++||++++|
T Consensus        22 yGv~sC~aCk-------~FFRR~v~~~~~-----y~~C~~--~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v   81 (94)
T 1a6y_A           22 YGVLACEGCK-------GFFRRSIQQNIQ-----YKRCLK--NENCSIVRINRNRCQQCRFKKCLSVGMSRDAV   81 (94)
T ss_dssp             TTEEECHHHH-------HHHHHHHSSCCC-----CCCCSS--TTCCCCCTTTTTSCHHHHHHHHTTTTCCSTTC
T ss_pred             eCccchhhhh-------hehheeeecccc-----eEEccC--CCCCccCccccccccchhHHHhhHccCCHHHh
Confidence            4457899999       999888876654     6 4864  57899999999999999999999999999887

>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=99.11  E-value=1.1e-11  Score=80.01  Aligned_cols=59  Identities=32%  Similarity=0.790  Sum_probs=51.4

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       +++++.++....     |.|..  .++|.|+...++.|++|||+|||++||++++|
T Consensus        24 yGv~sC~aCk-------~FFRR~v~~~~~-----y~C~~--~~~C~i~~~~R~~Cr~CR~~KCl~vGM~~~~v   82 (113)
T 2a66_A           24 YGLLTCESCK-------GFFKRTVQNNKR-----YTCIE--NQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAV   82 (113)
T ss_dssp             TTEEEEHHHH-------HHHHHHHHTTCC-----CCCSS--CSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGS
T ss_pred             eCcccHHHHH-------HHHhhhhhcccc-----ccccc--cccCCcCCCccccccchhHHHHhHhCCCHHHh
Confidence            4457899999       999998887654     88975  57899999999999999999999999999876

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

Probab=99.11  E-value=1.1e-11  Score=79.04  Aligned_cols=59  Identities=29%  Similarity=0.692  Sum_probs=50.3

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       +++++.++....     |.|..  .++|.|+...++.|++|||+|||++||+++++
T Consensus        22 yGv~sC~aCk-------~FFRR~v~~~~~-----y~C~~--~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~~   80 (105)
T 1r4i_A           22 YGALTCGSCK-------VFFKRAAEGKQK-----YLCAS--RNDCTIDKFRRKNCPSCRLRKCYEAGMTLGAR   80 (105)
T ss_dssp             TTEEEEHHHH-------HHHHHHHTSCCC-----CCCSS--SSCCCCCTTTTTTCHHHHHHHHHHHTCCSCC-
T ss_pred             eCCcchhhhh-------hhhceeEEecCc-----eeecc--CCccccCccccccchhchHHHHHhhhcccchh
Confidence            4457899999       999888877654     88975  57899999999999999999999999998775

>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=99.10  E-value=1.7e-11  Score=77.91  Aligned_cols=62  Identities=35%  Similarity=0.736  Sum_probs=51.6

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCcc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGKS  119 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~~  119 (120)
                      .+...|.+|.       ++++++++...   ...|.|..  .++|.|+...++.|++|||+|||++||++++|-
T Consensus        16 yGv~sC~aCk-------~FFRR~v~~~~---~~~y~C~~--~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   77 (103)
T 2nll_B           16 YRCITCEGCK-------GFFRRTIQKNL---HPSYSCKY--EGKCVIDKVTRNQCQECRFKKCIYVGMATDLVL   77 (103)
T ss_dssp             TTEECCHHHH-------HHHHHHHHTTC---GGGCCCSS--CTTCCCSTTTTTSCHHHHHHHHHHTTCCGGGSC
T ss_pred             cCcccHHHhh-------hhheecccccc---cchhhhhc--cCCcCcCccCccccchhhhHhhhHhCCCHHHhh
Confidence            4457899999       99988887653   12488975  588999999999999999999999999998873

>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=99.08  E-value=2.2e-11  Score=79.35  Aligned_cols=60  Identities=30%  Similarity=0.671  Sum_probs=51.5

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCcc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGKS  119 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~~  119 (120)
                      .+...|.+|.       +++++.++....     |.|..  .++|.|+...++.|++|||+|||++||++++|.
T Consensus        23 yGv~sC~aCk-------~FFRR~v~~~~~-----y~C~~--~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   82 (119)
T 2han_B           23 YNALTCEGCK-------GFFRRSVTKSAV-----YCCKF--GRACEMDMYMRRKCQECRLKKCLAVGMRPECVV   82 (119)
T ss_dssp             TTEEECHHHH-------HHHHHHHHTTCC-----CCCSS--CSCCCCSTTGGGTCHHHHHHHHHHTTCCGGGSS
T ss_pred             ECchhHHhhH-------HhhhhheEeccc-----ccccc--ccccccCccccccchhhHHHHHHHhCCCHHHcc
Confidence            4457899999       999988886544     88975  478999999999999999999999999998774

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

Probab=98.84  E-value=7.7e-10  Score=68.16  Aligned_cols=38  Identities=18%  Similarity=0.332  Sum_probs=33.5

Q ss_pred             hhcccccccccceeccccccccChhhhHHHHHHhcCCcCC
Q psy13208         78 YEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDG  117 (120)
Q Consensus        78 ~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~  117 (120)
                      .+|.|..  +++|.|+...|+.|++|||+|||+|||.++.
T Consensus        37 ~~y~C~~--~~~C~i~~~~R~~C~~CR~qKCl~VgM~~~~   74 (87)
T 2lze_A           37 LTYTDRD--YKNCESYHKCSDLCQYCRYQKDLAIHHQHHH   74 (87)
T ss_dssp             CTTTSCC--CCCCCCSSCCSSSCSGGGTSCCHHHHCSSCC
T ss_pred             CeeEcCC--CCccccCCCccCcCCcccChhhccCcCEecc
Confidence            3588974  5899999999999999999999999998754

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

Probab=98.81  E-value=9e-10  Score=86.15  Aligned_cols=59  Identities=34%  Similarity=0.834  Sum_probs=51.0

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       |+++++++.+..     |.|..  .++|.|++..|+.|++|||+||+++||++++|
T Consensus       152 ygv~sC~~Ck-------~FFrR~~~~~~~-----~~C~~--~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v  210 (467)
T 3dzy_A          152 YGVYSCEGCK-------GFFKRTVRKDLT-----YTCRD--NKDCLIDKRQRNRCQYCRYQKCLAMGMKREAV  210 (467)
T ss_dssp             TTEECCHHHH-------HHHHHHHHTTCC-----CCCSS--SSCCCCCSSSSSSCHHHHHHHHHHTTCCGGGC
T ss_pred             CCCcchhhhh-------HhccccccCCCc-----eeCCC--CCCCCCCcccccccccchhhhhhhccccchhh
Confidence            4456899999       999988876655     88975  57899999999999999999999999998776

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

Probab=98.65  E-value=5.4e-09  Score=80.71  Aligned_cols=58  Identities=31%  Similarity=0.767  Sum_probs=48.8

Q ss_pred             CcccccccccccchhhhcccCchhhhhhhhccchhc-ccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         45 KAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEF-ACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        45 ~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~-~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      ..+...|.+|.       |++++.++.+..     | .|.    ++|.|++..|+.|++|||+||+++||++++|
T Consensus        64 hygv~~C~~C~-------~FFrR~~~~~~~-----~~~c~----~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v  122 (419)
T 3dzy_D           64 HYGVHACEGCK-------GFFRRTIRLKLI-----YDRCD----LNCRIHKKSRNKCQYCRFQKCLAVGMSHNAI  122 (419)
T ss_dssp             CSSSBCCHHHH-------HHHHHHHTTTCC-----CCCCC----SCCCCCTTGGGTCHHHHHHHHHHTTCCGGGC
T ss_pred             ccCcccchhhh-------HHHccchhcccc-----ccccc----CCCCcccccCccchhhhHHHHhhcccchhhe
Confidence            35567999999       999888876654     4 352    6899999999999999999999999999876

>1lbd_A RXR_LBD, retinoid X receptor; transcription factor, nuclear receptor, structural proteomic europe, spine, structural genomics; 2.70A {Homo sapiens} SCOP: a.123.1.1 PDB: 1z5x_U* 2q60_A

Probab=93.25  E-value=0.015  Score=41.94  Aligned_cols=22  Identities=5%  Similarity=-0.129  Sum_probs=0.0

Q ss_pred             cchhhhcccCchhhhhhhhccc
Q psy13208         56 LKKCLNMGMNKDDAQHLKNSLL   77 (120)
Q Consensus        56 ~~kCl~~gm~~~~v~~~r~~~~   77 (120)
                      -.||+++||.+++||.+|++..
T Consensus        12 ~~kCl~vGMkkeaVq~~R~~~~   33 (282)
T 1lbd_A           12 SGLVPRGSHKREAVQEERQRGK   33 (282)
T ss_dssp             ----------------------
T ss_pred             CCCcCccCCcHHhhcCCCCCCC
Confidence            4699999999999999998654

---

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	120
d1a6ya_	78	g.39.1.2 (A:) Orphan nuclear receptor reverb DNA-b	8e-06
d1a6ya_	78	g.39.1.2 (A:) Orphan nuclear receptor reverb DNA-b	7e-04
d1dszb_	84	g.39.1.2 (B:) Retinoid X receptor (RXR-alpha) DNA-	1e-05
d1dszb_	84	g.39.1.2 (B:) Retinoid X receptor (RXR-alpha) DNA-	3e-04
d1r4ia_	74	g.39.1.2 (A:) Androgen receptor {Rat (Rattus norve	2e-05
d1r4ia_	74	g.39.1.2 (A:) Androgen receptor {Rat (Rattus norve	1e-04
d1lo1a_	90	g.39.1.2 (A:) Steroid hormone receptor Err2 DNA-bi	2e-05
d1lo1a_	90	g.39.1.2 (A:) Steroid hormone receptor Err2 DNA-bi	2e-04
d1hcqa_	74	g.39.1.2 (A:) Estrogen receptor DNA-binding domain	5e-05
d1hcqa_	74	g.39.1.2 (A:) Estrogen receptor DNA-binding domain	5e-04
d2nllb_	103	g.39.1.2 (B:) Thyroid hormone receptor (TR-beta) D	7e-05
d1dsza_	75	g.39.1.2 (A:) Retinoic acid receptor DNA-binding d	8e-05
d1dsza_	75	g.39.1.2 (A:) Retinoic acid receptor DNA-binding d	0.002
d2hanb1	83	g.39.1.2 (B:5-87) Ecdysone receptor DNA-binding do	1e-04
d2hanb1	83	g.39.1.2 (B:5-87) Ecdysone receptor DNA-binding do	0.002
d1lata_	71	g.39.1.2 (A:) Glucocorticoid receptor DNA-binding	2e-04
d1lata_	71	g.39.1.2 (A:) Glucocorticoid receptor DNA-binding	4e-04
d1kb2a_	89	g.39.1.2 (A:) Vitamin D3 receptor, VDR, DNA-bindin	3e-04
d1kb2a_	89	g.39.1.2 (A:) Vitamin D3 receptor, VDR, DNA-bindin	0.002
d1cita_	89	g.39.1.2 (A:) Orphan nuclear receptor NGFI-B DNA-b	0.001

>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 = 38.8 bits (90), Expect = 8e-06
 Identities = 16/55 (29%), Positives = 27/55 (49%)

Query: 17 GTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
          G +        +N           C + + +RN+CQ CR KKCL++GM++D  + 
Sbjct: 22 GCKGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRF 76

>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 = 33.8 bits (77), Expect = 7e-04
 Identities = 14/29 (48%), Positives = 22/29 (75%)

Query: 89  RCIVDKAHRNQCQACRLKKCLNMGMNKDG 117
            C + + +RN+CQ CR KKCL++GM++D 
Sbjct: 45  NCSIVRINRNRCQQCRFKKCLSVGMSRDA 73

>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 = 38.4 bits (89), Expect = 1e-05
 Identities = 17/47 (36%), Positives = 24/47 (51%)

Query: 25 KAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
          +  R            C++DK  RN+CQ CR +KCL MGM ++  Q 
Sbjct: 34 RTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQE 80

>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 = 34.9 bits (80), Expect = 3e-04
 Identities = 15/27 (55%), Positives = 21/27 (77%)

Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKD 116
           C++DK  RN+CQ CR +KCL MGM ++
Sbjct: 50  CLIDKRQRNRCQYCRYQKCLAMGMKRE 76

>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 = 37.8 bits (87), Expect = 2e-05
 Identities = 14/42 (33%), Positives = 19/42 (45%)

Query: 26 AHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKD 67
          A   + +   A    C +DK  R  C +CRL+KC   GM   
Sbjct: 32 AAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLG 73

>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 = 35.4 bits (81), Expect = 1e-04
 Identities = 12/27 (44%), Positives = 15/27 (55%)

Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKD 116
           C +DK  R  C +CRL+KC   GM   
Sbjct: 47  CTIDKFRRKNCPSCRLRKCYEAGMTLG 73

>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 = 38.1 bits (88), Expect = 2e-05
 Identities = 14/47 (29%), Positives = 21/47 (44%)

Query: 25 KAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
          +  +   +     T  C + K  R  CQACR  K L +GM K+  + 
Sbjct: 33 RTIQGNIEYSCPATNECEITKRRRKSCQACRFMKALKVGMLKEGVRL 79

>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 = 35.4 bits (81), Expect = 2e-04
 Identities = 14/29 (48%), Positives = 17/29 (58%)

Query: 89  RCIVDKAHRNQCQACRLKKCLNMGMNKDG 117
            C + K  R  CQACR  K L +GM K+G
Sbjct: 48  ECEITKRRRKSCQACRFMKALKVGMLKEG 76

>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 = 36.6 bits (84), Expect = 5e-05
 Identities = 16/42 (38%), Positives = 23/42 (54%)

Query: 25 KAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNK 66
          ++ +         T +C +DK  R  CQACRL+KC  +GM K
Sbjct: 33 RSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMK 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 = 34.0 bits (77), Expect = 5e-04
 Identities = 15/27 (55%), Positives = 19/27 (70%)

Query: 89  RCIVDKAHRNQCQACRLKKCLNMGMNK 115
           +C +DK  R  CQACRL+KC  +GM K
Sbjct: 48  QCTIDKNRRKSCQACRLRKCYEVGMMK 74

>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 = 37.1 bits (85), Expect = 7e-05
 Identities = 19/60 (31%), Positives = 25/60 (41%)

Query: 12 PTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
           TC+                       G+C++DK  RNQCQ CR KKC+ +GM  D    
Sbjct: 19 ITCEGCKGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQECRFKKCIYVGMATDLVLD 78

>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 = 36.2 bits (83), Expect = 8e-05
 Identities = 15/47 (31%), Positives = 27/47 (57%)

Query: 25 KAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
          ++ +            CI++K  RN+CQ CRL+KC  +GM+K+  ++
Sbjct: 28 RSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRN 74

>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 = 32.7 bits (74), Expect = 0.002
 Identities = 15/28 (53%), Positives = 22/28 (78%)

Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKDG 117
           CI++K  RN+CQ CRL+KC  +GM+K+ 
Sbjct: 44  CIINKVTRNRCQYCRLQKCFEVGMSKES 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 = 35.7 bits (82), Expect = 1e-04
 Identities = 15/47 (31%), Positives = 21/47 (44%)

Query: 25 KAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
          ++       C      C +D   R +CQ CRLKKCL +GM  +    
Sbjct: 29 RSVTKSAVYCCKFGRACEMDMYMRRKCQECRLKKCLAVGMRPECVVP 75

>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 = 33.0 bits (75), Expect = 0.002
 Identities = 14/27 (51%), Positives = 18/27 (66%)

Query: 90  CIVDKAHRNQCQACRLKKCLNMGMNKD 116
           C +D   R +CQ CRLKKCL +GM  +
Sbjct: 45  CEMDMYMRRKCQECRLKKCLAVGMRPE 71

>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 = 35.4 bits (81), Expect = 2e-04
 Identities = 18/43 (41%), Positives = 23/43 (53%)

Query: 25 KAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKD 67
          +A   Q        G+CI+DK  R  C ACR +KCL  GMN +
Sbjct: 29 RAVEGQHNYLCKYEGKCIIDKIRRKNCPACRYRKCLQAGMNLE 71

>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 = 34.3 bits (78), Expect = 4e-04
 Identities = 15/28 (53%), Positives = 19/28 (67%)

Query: 89  RCIVDKAHRNQCQACRLKKCLNMGMNKD 116
           +CI+DK  R  C ACR +KCL  GMN +
Sbjct: 44  KCIIDKIRRKNCPACRYRKCLQAGMNLE 71

>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 = 35.0 bits (80), Expect = 3e-04
 Identities = 15/46 (32%), Positives = 25/46 (54%)

Query: 26 AHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
          + + +        G C + K +R  CQACRLK+C+++GM K+    
Sbjct: 30 SMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILT 75

>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 = 33.1 bits (75), Expect = 0.002
 Identities = 14/28 (50%), Positives = 21/28 (75%)

Query: 89  RCIVDKAHRNQCQACRLKKCLNMGMNKD 116
            C + K +R  CQACRLK+C+++GM K+
Sbjct: 44  DCRITKDNRRHCQACRLKRCVDIGMMKE 71

>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 = 33.9 bits (77), Expect = 0.001
 Identities = 16/47 (34%), Positives = 24/47 (51%)

Query: 25 KAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
          +  +   +        C VDK  RN+CQ CR +KCL +GM K+  + 
Sbjct: 29 RTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRT 75

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	120
d1dszb_	84	Retinoid X receptor (RXR-alpha) DNA-binding domain	99.87
d1a6ya_	78	Orphan nuclear receptor reverb DNA-binding domain	99.86
d1kb2a_	89	Vitamin D3 receptor, VDR, DNA-binding domain {Huma	99.86
d2hanb1	83	Ecdysone receptor DNA-binding domain {Fruit fly (D	99.86
d1dsza_	75	Retinoic acid receptor DNA-binding domain {Human (	99.85
d1lo1a_	90	Steroid hormone receptor Err2 DNA-binding domain {	99.84
d2nllb_	103	Thyroid hormone receptor (TR-beta) DNA-binding dom	99.83
d1r4ia_	74	Androgen receptor {Rat (Rattus norvegicus) [TaxId:	99.83
d1cita_	89	Orphan nuclear receptor NGFI-B DNA-binding domain	99.83
d1lata_	71	Glucocorticoid receptor DNA-binding domain {Rat (R	99.82
d1hcqa_	74	Estrogen receptor DNA-binding domain {Human and ch	99.8
d1dszb_	84	Retinoid X receptor (RXR-alpha) DNA-binding domain	99.13
d1kb2a_	89	Vitamin D3 receptor, VDR, DNA-binding domain {Huma	99.12
d1r4ia_	74	Androgen receptor {Rat (Rattus norvegicus) [TaxId:	99.12
d1dsza_	75	Retinoic acid receptor DNA-binding domain {Human (	99.11
d1lo1a_	90	Steroid hormone receptor Err2 DNA-binding domain {	99.11
d2hanb1	83	Ecdysone receptor DNA-binding domain {Fruit fly (D	99.09
d1a6ya_	78	Orphan nuclear receptor reverb DNA-binding domain	99.07
d2nllb_	103	Thyroid hormone receptor (TR-beta) DNA-binding dom	99.06
d1cita_	89	Orphan nuclear receptor NGFI-B DNA-binding domain	99.03
d1lata_	71	Glucocorticoid receptor DNA-binding domain {Rat (R	99.01
d1hcqa_	74	Estrogen receptor DNA-binding domain {Human and ch	98.96

>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=99.87  E-value=3.3e-24  Score=130.75  Aligned_cols=68  Identities=29%  Similarity=0.691  Sum_probs=62.6

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhh
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKN   74 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~   74 (120)
                      +-+||||++|+||++    ||+|++.....+.|.. +++|.++...+..|++|||+|||++||.+++||.+|+
T Consensus        16 ~g~hyGv~sC~aCk~----FFRR~v~~~~~~~c~~-~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~Rd   83 (84)
T d1dszb_          16 SGKHYGVYSCEGCKG----FFKRTVRKDLTYTCRD-NKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQ   83 (84)
T ss_dssp             SSEETTEECCHHHHH----HHHHHHHHTCCCCCSS-CSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCCCC
T ss_pred             CccCCCHHHHHHhHH----HHHHHHhcCCCeeccC-CCCcccCCCCCccCCCCccHHHHHcCCChHHcccccC
Confidence            357999999999998    7888999888999985 7999999999999999999999999999999998876

>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=99.86  E-value=5.2e-24  Score=128.30  Aligned_cols=68  Identities=26%  Similarity=0.502  Sum_probs=60.0

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhh
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLK   73 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r   73 (120)
                      +-+||||++|+||++    ||+|++..+..+.|...+++|.+++..+..|++|||+|||++||.+++||.+|
T Consensus        11 ~g~hyGv~sC~aCk~----FFRR~~~~~~~~~~~~~~~~c~~~~~~r~~Cr~CR~~KCl~~GM~~~~vq~~R   78 (78)
T d1a6ya_          11 SGFHYGVLACEGCKG----FFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGR   78 (78)
T ss_dssp             CEEETTEEECHHHHH----HHHHHHSSCCCCCCCSSTTCCCCCTTTTTSCHHHHHHHHTTTTCCSTTCCCCC
T ss_pred             CcccCcchhhhhchh----hhhhhhccCCceeeeccCCCcccCCCCCccchhhHHHHHHHhCCCHHHhcCCC
Confidence            458999999999998    78889888888875435789999999999999999999999999999999765

>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=99.86  E-value=8.9e-24  Score=130.13  Aligned_cols=70  Identities=29%  Similarity=0.510  Sum_probs=63.7

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhcc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSL   76 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~   76 (120)
                      .-+||||++|+||++    ||+|++.....+.|.. +++|.++...+..|++|||+|||++||.+++||.+++..
T Consensus        11 ~g~hyGv~sC~aC~~----FFRR~v~~~~~~~c~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~   80 (89)
T d1kb2a_          11 TGFHFNAMTCEGCKG----FFRRSMKRKALFTCPF-NGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDEEVQ   80 (89)
T ss_dssp             CSEETTEECCHHHHH----HHHHHHHTTCCCCCSS-CSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCHHHHH
T ss_pred             CccCCCHHHHHHHHH----HHHHHHhcCCCeecCC-CCccCCCCcCCccCchhhHHHHHHcCCCHhhccccchhc
Confidence            358999999999998    7889998888899985 799999999999999999999999999999999988753

>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=99.86  E-value=9.4e-24  Score=128.47  Aligned_cols=68  Identities=25%  Similarity=0.461  Sum_probs=62.6

Q ss_pred             CccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhc
Q psy13208          3 FRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNS   75 (120)
Q Consensus         3 ~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~   75 (120)
                      -+||||.+|+||++    ||+|++..+..|.|.. +++|.++...+..|++|||+|||++||.+++||++++.
T Consensus        12 g~hyGv~sC~aCk~----FFRR~v~~~~~~~c~~-~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~   79 (83)
T d2hanb1          12 GYHYNALTCEGCKG----FFRRSVTKSAVYCCKF-GRACEMDMYMRRKCQECRLKKCLAVGMRPECVVPENQC   79 (83)
T ss_dssp             EEETTEEECHHHHH----HHHHHHHTTCCCCCSS-CSCCCCSTTGGGTCHHHHHHHHHHTTCCGGGSSCSSHH
T ss_pred             ccCcCHHhHhHhHH----HHHHHHhcCCceeecC-CCCcccCCcccccCccchHHHHHHcCCCHHHccccchh
Confidence            47999999999998    7889998888999985 79999999999999999999999999999999988873

>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=99.85  E-value=2.7e-23  Score=124.22  Aligned_cols=66  Identities=30%  Similarity=0.684  Sum_probs=60.4

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhh
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHL   72 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~   72 (120)
                      +-+||||.+|+||++    ||||++..+..+.|.. +++|.++...+..|++|||+|||++||++++||++
T Consensus        10 ~g~hyGv~sC~aC~~----FFRR~v~~~~~~~c~~-~~~c~~~~~~r~~Cr~CR~~KCl~~GM~~~~vq~d   75 (75)
T d1dsza_          10 SGYHYGVSACEGCKG----FFRRSIQKNMVYTCHR-DKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRND   75 (75)
T ss_dssp             CSEETTEECCHHHHH----HHHHHHHTTCCCCCSS-CSCCCCSTTTGGGCHHHHHHHHHHTTCCGGGSCCC
T ss_pred             CccCcCHHHhhhhHH----HHHHHHhcCCceeccc-CCccccCCccccccchhHHHHHHHhCCCHHHccCC
Confidence            358999999999998    7889998889999985 79999999999999999999999999999999864

>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=99.84  E-value=1.7e-23  Score=129.03  Aligned_cols=69  Identities=30%  Similarity=0.524  Sum_probs=63.4

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNS   75 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~   75 (120)
                      +.+||||.+|+||++    ||+|++..+..+.|.. +++|.++...+..|++|||+|||++||++++||.++++
T Consensus        15 ~~~hyG~~sC~aC~~----FFRR~v~~~~~~~c~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~r~~   83 (90)
T d1lo1a_          15 SGYHYGVASCEACKA----FFKRTIQGNIEYSCPA-TNECEITKRRRKSCQACRFMKALKVGMLKEGVRLDRVR   83 (90)
T ss_dssp             SEESSSSEECHHHHH----HHHHHHHTTCCCCCSS-CSCCCCCHHHHHHCHHHHHHHHHHHTCCGGGSCSSCCT
T ss_pred             CceEcCeeechhhHH----HHHHHHhcCCccchhc-CCCCccCCCCccccchhhHHHHHHcCCCHHHhcccccc
Confidence            357999999999998    7888998889999995 79999999999999999999999999999999998874

>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=99.83  E-value=1.2e-22  Score=128.23  Aligned_cols=71  Identities=32%  Similarity=0.593  Sum_probs=61.1

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcc--eeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhccc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQC--QACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLL   77 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~--~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~   77 (120)
                      +-+||||+||+||++    ||+|++.....  +.|. ++++|.++...+..|++|||+|||++||.+++|+.++++..
T Consensus        12 ~g~HfGv~sC~aCka----FFRR~v~~~~~~~~~c~-~~~~c~~~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~~   84 (103)
T d2nllb_          12 TGYHYRCITCEGCKG----FFRRTIQKNLHPSYSCK-YEGKCVIDKVTRNQCQECRFKKCIYVGMATDLVLDDSKRLA   84 (103)
T ss_dssp             CSEETTEECCHHHHH----HHHHHHHTTCGGGCCCS-SCTTCCCSTTTTTSCHHHHHHHHHHTTCCGGGSCCHHHHHH
T ss_pred             CcccCchhhhHHHHH----HhHHHhhccccceeecc-cCCCCcCCCCccCCCccccchhHHHhhccHHhhhccccchh
Confidence            468999999999998    78888877654  4556 47899999999999999999999999999999999887543

>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=99.83  E-value=1.2e-22  Score=121.11  Aligned_cols=61  Identities=30%  Similarity=0.597  Sum_probs=55.8

Q ss_pred             CccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchh
Q psy13208          3 FRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDD   68 (120)
Q Consensus         3 ~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~   68 (120)
                      -+||||.||+||++    ||||++..+..+.|.. +++|.++...+..|++|||+|||++||+.+|
T Consensus        14 g~hyGv~sC~aCk~----FFRR~~~~~~~~~c~~-~~~C~~~~~~r~~C~~CR~~KCl~vGM~~~A   74 (74)
T d1r4ia_          14 GAHYGALTCGSCKV----FFKRAAEGKQKYLCAS-RNDCTIDKFRRKNCPSCRLRKCYEAGMTLGA   74 (74)
T ss_dssp             EEETTEEEEHHHHH----HHHHHHTSCCCCCCSS-SSCCCCCTTTTTTCHHHHHHHHHHHTCCSCC
T ss_pred             ccCCCHHhhHHHHH----HHHHHHhcccceeeec-CCCcccCCCCcccchhhhHHHHHHcCCcCCC
Confidence            47999999999998    7788998888999986 6999999999999999999999999999764

>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=99.83  E-value=2.3e-22  Score=123.83  Aligned_cols=69  Identities=30%  Similarity=0.586  Sum_probs=62.1

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNS   75 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~   75 (120)
                      +-+||||.+|+||++    ||+|++.....+.|.. +++|.++...+..|++|||+|||++||.+++||.++..
T Consensus        11 ~g~hyGv~sC~aCk~----FFRR~~~~~~~~~c~~-~~~c~~~~~~r~~Cr~CR~~KCl~~GM~~~~v~~~~~~   79 (89)
T d1cita_          11 SCQHYGVRTCEGCKG----FFKRTVQKSAKYICLA-NKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTDSLK   79 (89)
T ss_dssp             CEEETTEEECHHHHH----HHHHHHHHTCCCCCSS-SSCCCCSTTTTTTCHHHHHHHHHHTTCCGGGSCCGGGT
T ss_pred             CccCCCcccchhhHH----HHHHHHHcCCceeecC-CCCccccCCccccCchhhHHHHHHcCCCHHHhcccccc
Confidence            347999999999998    7888988888899985 68999999999999999999999999999999987763

>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=99.82  E-value=4.3e-22  Score=117.78  Aligned_cols=61  Identities=34%  Similarity=0.712  Sum_probs=55.6

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCch
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKD   67 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~   67 (120)
                      +-+||||++|+||++    ||+|++.....+.|.. +++|.++...+..|++|||+|||++||+.+
T Consensus        11 ~g~hyGv~sC~aCk~----FFRR~v~~~~~~~c~~-~~~C~~~~~~r~~Cr~CR~~KCl~~GM~~e   71 (71)
T d1lata_          11 SGCHYGVLTCEGCKA----FFKRAVEGQHNYLCKY-EGKCIIDKIRRKNCPACRYRKCLQAGMNLE   71 (71)
T ss_dssp             CEEETTEEECHHHHH----HHHHHHHSCCCCCCSS-CSCCCCSTTTTTTCHHHHHHHHHHTTCCCC
T ss_pred             CceEcCHhhHHHHHH----HHHHHHhcCcceeeec-CcccccccCccccCCccchhHHhHccCCCC
Confidence            357999999999998    7889999889999985 799999999999999999999999999864

>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=99.80  E-value=1.5e-21  Score=116.27  Aligned_cols=60  Identities=37%  Similarity=0.689  Sum_probs=54.8

Q ss_pred             CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCc
Q psy13208          2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNK   66 (120)
Q Consensus         2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~   66 (120)
                      +-+||||.+|+||++    ||+|++.....+.|.. +++|.|+...+..|++|||+|||++||..
T Consensus        15 ~g~hyGv~sC~aC~~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~k   74 (74)
T d1hcqa_          15 SGYHYGVWSCEGCKA----FFKRSIQGHNDYMCPA-TNQCTIDKNRRKSCQACRLRKCYEVGMMK   74 (74)
T ss_dssp             CEEETTEEECHHHHH----HHHHHHSSCCCCCCSS-SSCCCCSTTTTTTCHHHHHHHHHHHTCCC
T ss_pred             CceEcCeeehHHHHH----HHHHHHHccccccccc-CCCCccCCCccccchHhhHHHHHHcCCcC
Confidence            358999999999998    7888998889999985 79999999999999999999999999973

>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=99.13  E-value=3.6e-12  Score=76.79  Aligned_cols=60  Identities=33%  Similarity=0.823  Sum_probs=51.0

Q ss_pred             CcccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         45 KAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        45 ~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      ..+-..|.+|.       ++++++++....     +.|..  .++|.++...+..|++|||+|||++||++++|
T Consensus        19 hyGv~sC~aCk-------~FFRR~v~~~~~-----~~c~~--~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~v   78 (84)
T d1dszb_          19 HYGVYSCEGCK-------GFFKRTVRKDLT-----YTCRD--NKDCLIDKRQRNRCQYCRYQKCLAMGMKREAV   78 (84)
T ss_dssp             ETTEECCHHHH-------HHHHHHHHHTCC-----CCCSS--CSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGS
T ss_pred             CCCHHHHHHhH-------HHHHHHHhcCCC-----eeccC--CCCcccCCCCCccCCCCccHHHHHcCCChHHc
Confidence            35567899999       888888887655     77754  57899999999999999999999999999876

>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=99.12  E-value=5.7e-12  Score=76.68  Aligned_cols=59  Identities=32%  Similarity=0.738  Sum_probs=50.3

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       +++++++.....     +.|..  .++|.|+...++.|++|||+|||++||++++|
T Consensus        15 yGv~sC~aC~-------~FFRR~v~~~~~-----~~c~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v   73 (89)
T d1kb2a_          15 FNAMTCEGCK-------GFFRRSMKRKAL-----FTCPF--NGDCRITKDNRRHCQACRLKRCVDIGMMKEFI   73 (89)
T ss_dssp             TTEECCHHHH-------HHHHHHHHTTCC-----CCCSS--CSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGS
T ss_pred             CCHHHHHHHH-------HHHHHHHhcCCC-----eecCC--CCccCCCCcCCccCchhhHHHHHHcCCCHhhc
Confidence            3456899999       888888877665     77754  57999999999999999999999999999876

>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=99.12  E-value=5e-12  Score=74.45  Aligned_cols=58  Identities=29%  Similarity=0.689  Sum_probs=48.1

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCC
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDG  117 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~  117 (120)
                      .+-..|.+|.       +++++.+..+..     +.|..  .++|.|+...+..|++|||+|||++||+.+|
T Consensus        17 yGv~sC~aCk-------~FFRR~~~~~~~-----~~c~~--~~~C~~~~~~r~~C~~CR~~KCl~vGM~~~A   74 (74)
T d1r4ia_          17 YGALTCGSCK-------VFFKRAAEGKQK-----YLCAS--RNDCTIDKFRRKNCPSCRLRKCYEAGMTLGA   74 (74)
T ss_dssp             TTEEEEHHHH-------HHHHHHHTSCCC-----CCCSS--SSCCCCCTTTTTTCHHHHHHHHHHHTCCSCC
T ss_pred             CCHHhhHHHH-------HHHHHHHhcccc-----eeeec--CCCcccCCCCcccchhhhHHHHHHcCCcCCC
Confidence            4457899998       788777766554     77765  4789999999999999999999999999875

>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=99.11  E-value=6.3e-12  Score=74.19  Aligned_cols=59  Identities=34%  Similarity=0.836  Sum_probs=49.5

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+-..|.+|.       +++++.+..+..     +.|..  .++|.++...+..|++|||+|||++||++++|
T Consensus        14 yGv~sC~aC~-------~FFRR~v~~~~~-----~~c~~--~~~c~~~~~~r~~Cr~CR~~KCl~~GM~~~~v   72 (75)
T d1dsza_          14 YGVSACEGCK-------GFFRRSIQKNMV-----YTCHR--DKNCIINKVTRNRCQYCRLQKCFEVGMSKESV   72 (75)
T ss_dssp             TTEECCHHHH-------HHHHHHHHTTCC-----CCCSS--CSCCCCSTTTGGGCHHHHHHHHHHTTCCGGGS
T ss_pred             cCHHHhhhhH-------HHHHHHHhcCCc-----eeccc--CCccccCCccccccchhHHHHHHHhCCCHHHc
Confidence            3456899998       888888876655     77764  57899999999999999999999999999876

>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=99.11  E-value=2.7e-12  Score=78.24  Aligned_cols=60  Identities=33%  Similarity=0.671  Sum_probs=51.4

Q ss_pred             CcccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         45 KAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        45 ~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      ..+-..|.+|.       +++++++..+..     +.|..  .++|.|+..++..|++|||+|||++||++++|
T Consensus        18 hyG~~sC~aC~-------~FFRR~v~~~~~-----~~c~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V   77 (90)
T d1lo1a_          18 HYGVASCEACK-------AFFKRTIQGNIE-----YSCPA--TNECEITKRRRKSCQACRFMKALKVGMLKEGV   77 (90)
T ss_dssp             SSSSEECHHHH-------HHHHHHHHTTCC-----CCCSS--CSCCCCCHHHHHHCHHHHHHHHHHHTCCGGGS
T ss_pred             EcCeeechhhH-------HHHHHHHhcCCc-----cchhc--CCCCccCCCCccccchhhHHHHHHcCCCHHHh
Confidence            44557899999       888888877766     77764  58899999999999999999999999999887

>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=99.09  E-value=8.4e-12  Score=74.99  Aligned_cols=60  Identities=30%  Similarity=0.671  Sum_probs=51.1

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCcc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGKS  119 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~~  119 (120)
                      .+-..|.+|.       +++++++..+..     |.|..  .++|.|+...+..|++|||+|||++||++++|.
T Consensus        15 yGv~sC~aCk-------~FFRR~v~~~~~-----~~c~~--~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq   74 (83)
T d2hanb1          15 YNALTCEGCK-------GFFRRSVTKSAV-----YCCKF--GRACEMDMYMRRKCQECRLKKCLAVGMRPECVV   74 (83)
T ss_dssp             TTEEECHHHH-------HHHHHHHHTTCC-----CCCSS--CSCCCCSTTGGGTCHHHHHHHHHHTTCCGGGSS
T ss_pred             cCHHhHhHhH-------HHHHHHHhcCCc-----eeecC--CCCcccCCcccccCccchHHHHHHcCCCHHHcc
Confidence            4557899999       888888877655     77764  578999999999999999999999999998874

>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=99.07  E-value=8e-12  Score=74.26  Aligned_cols=60  Identities=30%  Similarity=0.662  Sum_probs=48.3

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      .+...|.+|.       +++++++..+..     +.|.. ..++|.|+..++..|++|||+|||++||++++|
T Consensus        15 yGv~sC~aCk-------~FFRR~~~~~~~-----~~~~~-~~~~c~~~~~~r~~Cr~CR~~KCl~~GM~~~~v   74 (78)
T d1a6ya_          15 YGVLACEGCK-------GFFRRSIQQNIQ-----YKRCL-KNENCSIVRINRNRCQQCRFKKCLSVGMSRDAV   74 (78)
T ss_dssp             TTEEECHHHH-------HHHHHHHSSCCC-----CCCCS-STTCCCCCTTTTTSCHHHHHHHHTTTTCCSTTC
T ss_pred             Ccchhhhhch-------hhhhhhhccCCc-----eeeec-cCCCcccCCCCCccchhhHHHHHHHhCCCHHHh
Confidence            4456899998       888888776544     54322 246899999999999999999999999999887

>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=99.06  E-value=1.8e-11  Score=76.30  Aligned_cols=62  Identities=35%  Similarity=0.754  Sum_probs=49.8

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCcc
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGKS  119 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~~  119 (120)
                      .+-..|.+|.       +++++++.....   +.+.|.  ..+.|.|+...+..|++|||+|||++||++++|.
T Consensus        16 fGv~sC~aCk-------aFFRR~v~~~~~---~~~~c~--~~~~c~~~~~~r~~Cr~CR~~KCl~vGM~~~~v~   77 (103)
T d2nllb_          16 YRCITCEGCK-------GFFRRTIQKNLH---PSYSCK--YEGKCVIDKVTRNQCQECRFKKCIYVGMATDLVL   77 (103)
T ss_dssp             TTEECCHHHH-------HHHHHHHHTTCG---GGCCCS--SCTTCCCSTTTTTSCHHHHHHHHHHTTCCGGGSC
T ss_pred             CchhhhHHHH-------HHhHHHhhcccc---ceeecc--cCCCCcCCCCccCCCccccchhHHHhhccHHhhh
Confidence            4557999999       888888876544   123343  3578999999999999999999999999998874

>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=99.03  E-value=2.3e-11  Score=73.94  Aligned_cols=60  Identities=37%  Similarity=0.761  Sum_probs=50.6

Q ss_pred             CcccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208         45 KAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK  118 (120)
Q Consensus        45 ~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~  118 (120)
                      ..+...|.+|.       +++++++.....     +.|..  .++|.++...+..|++|||+|||++||++++|
T Consensus        14 hyGv~sC~aCk-------~FFRR~~~~~~~-----~~c~~--~~~c~~~~~~r~~Cr~CR~~KCl~~GM~~~~v   73 (89)
T d1cita_          14 HYGVRTCEGCK-------GFFKRTVQKSAK-----YICLA--NKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVV   73 (89)
T ss_dssp             ETTEEECHHHH-------HHHHHHHHHTCC-----CCCSS--SSCCCCSTTTTTTCHHHHHHHHHHTTCCGGGS
T ss_pred             CCCcccchhhH-------HHHHHHHHcCCc-----eeecC--CCCccccCCccccCchhhHHHHHHcCCCHHHh
Confidence            35567999999       888888877665     77754  47899999999999999999999999998876

>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=99.01  E-value=2.7e-11  Score=70.70  Aligned_cols=57  Identities=37%  Similarity=0.814  Sum_probs=47.2

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcC
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKD  116 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~  116 (120)
                      .+...|.+|.       +++++++.....     +.|..  .++|.++...+..|++|||+|||++||+++
T Consensus        15 yGv~sC~aCk-------~FFRR~v~~~~~-----~~c~~--~~~C~~~~~~r~~Cr~CR~~KCl~~GM~~e   71 (71)
T d1lata_          15 YGVLTCEGCK-------AFFKRAVEGQHN-----YLCKY--EGKCIIDKIRRKNCPACRYRKCLQAGMNLE   71 (71)
T ss_dssp             TTEEECHHHH-------HHHHHHHHSCCC-----CCCSS--CSCCCCSTTTTTTCHHHHHHHHHHTTCCCC
T ss_pred             cCHhhHHHHH-------HHHHHHHhcCcc-----eeeec--CcccccccCccccCCccchhHHhHccCCCC
Confidence            4456899998       888888776655     66653  578999999999999999999999999874

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

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

Probab=98.96  E-value=4.3e-11  Score=70.35  Aligned_cols=55  Identities=35%  Similarity=0.790  Sum_probs=46.4

Q ss_pred             cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCC
Q psy13208         46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMN  114 (120)
Q Consensus        46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~  114 (120)
                      .+...|.+|.       +++++.+.....     +.|..  +++|.|+..++..|++|||+|||++||+
T Consensus        19 yGv~sC~aC~-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~   73 (74)
T d1hcqa_          19 YGVWSCEGCK-------AFFKRSIQGHND-----YMCPA--TNQCTIDKNRRKSCQACRLRKCYEVGMM   73 (74)
T ss_dssp             TTEEECHHHH-------HHHHHHHSSCCC-----CCCSS--SSCCCCSTTTTTTCHHHHHHHHHHHTCC
T ss_pred             cCeeehHHHH-------HHHHHHHHcccc-----ccccc--CCCCccCCCccccchHhhHHHHHHcCCc
Confidence            4456899998       888877766555     77864  5899999999999999999999999997