Psyllid ID: psy11507

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110---
Protein Sequence
MLRWSSKRLVELSVYLQTYTVEQKFRGSTDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQKKSSQIPKEKYNLAYLMSDSLDTTNRFN
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccEEccccccccccEEEccccccccHHHHHHHHccccEEEEccccccccccccccccccccccccccHHHHccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccccccccHcccEccccccEccEEEccEEEcHHHHHHHHHHHcccccEEEccccccEEcccccccccEEEEEEcccccccccccc
Coil and Loop (DISEMBL)
MLRWSSKRLVELSVYLQTYTVeqkfrgstdgikeeelprrlclvcgdvasgfhyGVASCEACKAFFKRTIQARASLVSlrghepqkkssqipkekYNLAYLMSdsldttnrfn
Flexible Loop (DISEMBL)
mlrwsskrlVELSVYLqtytveqkfrgstdgikeeelpRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASlvslrghepqkkssqipkekynLAYLmsdsldttnrfn
Low Complexity Region (SEG)
MLRWSSKRLVELSVYLQTYTVEQKFRGSTDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQKKSSQIPKEKYNLAYLMSDSLDTTNRFN
Disordered region (IsUnstruct)
*******RLVELSVYLQTYTVEQKFRGSTDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLV************************************
Disordered Region (DISOPRED)
******************************************LVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQKKSSQIPKEKYNLAYLMSDSLD******
Disordered Region (DISEMBL)
MLRWSSKRLVELSVYLQTYTVEQKFRGSTDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVS*************PKEKYNLAYLMSDSLDTTNRFN
Disordered Region (DISPRO)
***********************************ELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQKKSSQIPKEKYNLAYLMS**********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLRWSSKRLVELSVYLQTYTVEQKFRGSTDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQKKSSQIPKEKYNLAYLMSDSLDTTNRFN
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	113	2.2.26 [Sep-21-2011]
Q5QJV7	422	Steroid hormone receptor	yes	N/A	0.318	0.085	0.916	8e-15
O08580	422	Steroid hormone receptor	yes	N/A	0.318	0.085	0.916	8e-15
P11474	423	Steroid hormone receptor	yes	N/A	0.318	0.085	0.916	8e-15
Q6QMY5	422	Steroid hormone receptor	yes	N/A	0.318	0.085	0.916	8e-15
Q5RAM2	435	Estrogen-related receptor	no	N/A	0.318	0.082	0.861	1e-14
P62510	458	Estrogen-related receptor	no	N/A	0.318	0.078	0.861	1e-14
P62509	458	Estrogen-related receptor	no	N/A	0.318	0.078	0.861	1e-14
P62508	458	Estrogen-related receptor	no	N/A	0.318	0.078	0.861	1e-14
O95718	508	Steroid hormone receptor	no	N/A	0.318	0.070	0.861	2e-14
Q61539	433	Steroid hormone receptor	no	N/A	0.318	0.083	0.861	2e-14

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

 Score = 79.0 bits (193), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 33/36 (91%), Positives = 35/36 (97%)

Query: 37  LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQA 72
           LP+RLCLVCGDVASG+HYGVASCEACKAFFKRTIQ 
Sbjct: 74  LPKRLCLVCGDVASGYHYGVASCEACKAFFKRTIQG 109

Binds to an ERR-alpha response element (ERRE) containing a single consensus half-site, 5'-TNAAGGTCA-3'. Can bind to the medium-chain acyl coenzyme A dehydrogenase (MCAD) response element NRRE-1 and may act as an important regulator of MCAD promoter. Binds to the C1 region of the lactoferrin gene promoter. Requires dimerization and the coactivator, PGC-1A, for full activity. The ERRalpha/PGC1alpha complex is a regulator of energy metabolism.
Rattus norvegicus (taxid: 10116)

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

 Score = 79.0 bits (193), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 33/36 (91%), Positives = 35/36 (97%)

Query: 37  LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQA 72
           LP+RLCLVCGDVASG+HYGVASCEACKAFFKRTIQ 
Sbjct: 74  LPKRLCLVCGDVASGYHYGVASCEACKAFFKRTIQG 109

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

Mus musculus (taxid: 10090)

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

 Score = 79.0 bits (193), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 33/36 (91%), Positives = 35/36 (97%)

Query: 37  LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQA 72
           LP+RLCLVCGDVASG+HYGVASCEACKAFFKRTIQ 
Sbjct: 74  LPKRLCLVCGDVASGYHYGVASCEACKAFFKRTIQG 109

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

Homo sapiens (taxid: 9606)

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

 Score = 79.0 bits (193), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 33/36 (91%), Positives = 35/36 (97%)

Query: 37  LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQA 72
           LP+RLCLVCGDVASG+HYGVASCEACKAFFKRTIQ 
Sbjct: 74  LPKRLCLVCGDVASGYHYGVASCEACKAFFKRTIQG 109

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

Canis familiaris (taxid: 9615)

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

 Score = 78.6 bits (192), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 31/36 (86%), Positives = 35/36 (97%)

Query: 37  LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQA 72
           +P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQ 
Sbjct: 100 MPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQG 135

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

Pongo abelii (taxid: 9601)

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

 Score = 78.2 bits (191), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 31/36 (86%), Positives = 35/36 (97%)

Query: 37  LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQA 72
           +P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQ 
Sbjct: 123 MPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQG 158

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

Rattus norvegicus (taxid: 10116)

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

 Score = 78.2 bits (191), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 31/36 (86%), Positives = 35/36 (97%)

Query: 37  LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQA 72
           +P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQ 
Sbjct: 123 MPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQG 158

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

Mus musculus (taxid: 10090)

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

 Score = 78.2 bits (191), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 31/36 (86%), Positives = 35/36 (97%)

Query: 37  LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQA 72
           +P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQ 
Sbjct: 123 MPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQG 158

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

Homo sapiens (taxid: 9606)

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

 Score = 77.8 bits (190), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 31/36 (86%), Positives = 35/36 (97%)

Query: 37  LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQA 72
           +P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQ 
Sbjct: 98  IPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQG 133

Nuclear receptor, may regulate ESR1 transcriptional activity.

Homo sapiens (taxid: 9606)

>sp|Q61539|ERR2_MOUSE Steroid hormone receptor ERR2 OS=Mus musculus GN=Esrrb PE=1 SV=2

 Score = 77.4 bits (189), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 31/36 (86%), Positives = 35/36 (97%)

Query: 37  LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQA 72
           +P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQ 
Sbjct: 98  IPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQG 133

Nuclear receptor, may regulate ESR1 transcriptional activity.

Mus musculus (taxid: 10090)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	113
307201567	426	Steroid hormone receptor ERR2 [Harpegnat	0.442	0.117	0.784	2e-16
151188219	434	estrogen-related receptor [Polyrhachis v	0.442	0.115	0.803	3e-16
332023527	440	Steroid hormone receptor ERR2 [Acromyrme	0.442	0.113	0.803	3e-16
307166258	558	Steroid hormone receptor ERR2 [Camponotu	0.380	0.077	0.886	4e-16
345496190	438	PREDICTED: steroid hormone receptor ERR2	0.442	0.114	0.784	5e-16
345496188	450	PREDICTED: steroid hormone receptor ERR2	0.442	0.111	0.784	5e-16
242117914	434	estrogen-related receptor [Apis mellifer	0.442	0.115	0.784	7e-16
242021609	448	retinoid X receptor, putative [Pediculus	0.362	0.091	0.902	8e-16
213513284	415	estrogen-related receptor [Tribolium cas	0.380	0.103	0.883	1e-15
158301679	507	AGAP001743-PA [Anopheles gambiae str. PE	0.389	0.086	0.911	1e-15

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

 Score = 90.1 bits (222), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 40/51 (78%), Positives = 44/51 (86%), Gaps = 1/51 (1%)

Query: 23  QKFRGSTDGIKEEEL-PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQA 72
           Q    + DG+KEE++ PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 
Sbjct: 82  QPLGATDDGVKEEDMMPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQG 132

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|151188219|gb|ABR88112.1| estrogen-related receptor [Polyrhachis vicina]

 Score = 89.4 bits (220), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 41/51 (80%), Positives = 43/51 (84%), Gaps = 1/51 (1%)

Query: 23  QKFRGSTDGIKEEEL-PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQA 72
           Q      DGIKEE++ PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 
Sbjct: 89  QPLGTPEDGIKEEDMIPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQG 139

Source: Polyrhachis vicina

Species: Polyrhachis vicina

Genus: Polyrhachis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332023527|gb|EGI63763.1| Steroid hormone receptor ERR2 [Acromyrmex echinatior]

 Score = 89.0 bits (219), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 41/51 (80%), Positives = 43/51 (84%), Gaps = 1/51 (1%)

Query: 23  QKFRGSTDGIKEEEL-PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQA 72
           Q      DG+KEE+L PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 
Sbjct: 83  QPLGTPEDGMKEEDLLPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQG 133

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307166258|gb|EFN60472.1| Steroid hormone receptor ERR2 [Camponotus floridanus]

 Score = 88.6 bits (218), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 39/44 (88%), Positives = 42/44 (95%), Gaps = 1/44 (2%)

Query: 30  DGIKEEEL-PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQA 72
           DG+KEE++ PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 
Sbjct: 204 DGVKEEDMIPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQG 247

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 88.6 bits (218), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 40/51 (78%), Positives = 43/51 (84%), Gaps = 1/51 (1%)

Query: 23  QKFRGSTDGIKEEEL-PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQA 72
           Q      DG+KEE++ PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 
Sbjct: 93  QPLGTPEDGVKEEDMMPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQG 143

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 88.6 bits (218), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 40/51 (78%), Positives = 43/51 (84%), Gaps = 1/51 (1%)

Query: 23  QKFRGSTDGIKEEEL-PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQA 72
           Q      DG+KEE++ PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 
Sbjct: 93  QPLGTPEDGVKEEDMMPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQG 143

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 87.8 bits (216), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 40/51 (78%), Positives = 44/51 (86%), Gaps = 1/51 (1%)

Query: 23  QKFRGSTDGIKEEEL-PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQA 72
           Q    S +G+KEE++ PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 
Sbjct: 89  QPLGTSEEGVKEEDMIPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQG 139

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 87.8 bits (216), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 37/41 (90%), Positives = 40/41 (97%)

Query: 32  IKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQA 72
           I+E++LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 
Sbjct: 106 IREDDLPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQG 146

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 87.0 bits (214), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 38/43 (88%), Positives = 40/43 (93%)

Query: 30  DGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQA 72
           D +KEE+ PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 
Sbjct: 87  DEMKEEDSPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQG 129

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 87.0 bits (214), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 41/45 (91%), Positives = 41/45 (91%), Gaps = 1/45 (2%)

Query: 28  STDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQA 72
           S D IKEE LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 
Sbjct: 104 SHDTIKEE-LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQG 147

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

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	113
FB|FBgn0035849	496	ERR "estrogen-related receptor	0.389	0.088	0.822	1.8e-15
UNIPROTKB|F1SA88	396	ESRRG "Uncharacterized protein	0.539	0.154	0.630	1.3e-14
UNIPROTKB|F5GWT5	109	ESRRA "Steroid hormone recepto	0.309	0.321	0.942	1.4e-14
UNIPROTKB|F1MBX3	422	ESRRA "Uncharacterized protein	0.309	0.082	0.942	7.3e-14
UNIPROTKB|Q6QMY5	422	ESRRA "Steroid hormone recepto	0.309	0.082	0.942	7.3e-14
UNIPROTKB|F1RQP2	422	ESRRA "Uncharacterized protein	0.309	0.082	0.942	7.3e-14
MGI|MGI:1346831	422	Esrra "estrogen related recept	0.309	0.082	0.942	7.3e-14
RGD|1583866	422	Esrra "estrogen related recept	0.309	0.082	0.942	7.3e-14
UNIPROTKB|P11474	423	ESRRA "Steroid hormone recepto	0.309	0.082	0.942	7.3e-14
ZFIN|ZDB-GENE-990415-68	436	esrra "estrogen-related recept	0.309	0.080	0.942	7.9e-14

FB|FBgn0035849 ERR "estrogen-related receptor" [Drosophila melanogaster (taxid:7227)]

 Score = 190 (71.9 bits), Expect = 1.8e-15, Sum P(2) = 1.8e-15
 Identities = 37/45 (82%), Positives = 39/45 (86%)

Query:    27 GSTDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
             G+  G   +EL RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ
Sbjct:   113 GAGSGSVRDEL-RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 156

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0005496 "steroid binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

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

GO:0005975 "carbohydrate metabolic process" evidence=IDA

UNIPROTKB|F1SA88 ESRRG "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 192 (72.6 bits), Expect = 1.3e-14, P = 1.3e-14
 Identities = 41/65 (63%), Positives = 47/65 (72%)

Query:    37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQKKSSQIPKEKY 96
             +P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQ    L  +RG   QK   +I  E  
Sbjct:   100 MPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQG-VRLDRVRGGR-QKYKRRIDAE-- 155

Query:    97 NLAYL 101
             N  YL
Sbjct:   156 NSPYL 160

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

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

GO:0005634 "nucleus" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

UNIPROTKB|F5GWT5 ESRRA "Steroid hormone receptor ERR1" [Homo sapiens (taxid:9606)]

 Score = 186 (70.5 bits), Expect = 1.4e-14, P = 1.4e-14
 Identities = 33/35 (94%), Positives = 35/35 (100%)

Query:    37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
             LP+RLCLVCGDVASG+HYGVASCEACKAFFKRTIQ
Sbjct:    74 LPKRLCLVCGDVASGYHYGVASCEACKAFFKRTIQ 108

GO:0008270 "zinc ion binding" evidence=IEA

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

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

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

GO:0005634 "nucleus" evidence=IEA

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

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

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

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

GO:0051216 "cartilage development" evidence=IEA

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

 Score = 186 (70.5 bits), Expect = 7.3e-14, P = 7.3e-14
 Identities = 33/35 (94%), Positives = 35/35 (100%)

Query:    37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
             LP+RLCLVCGDVASG+HYGVASCEACKAFFKRTIQ
Sbjct:    74 LPKRLCLVCGDVASGYHYGVASCEACKAFFKRTIQ 108

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

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

GO:0005634 "nucleus" evidence=IEA

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

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

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005496 "steroid binding" evidence=IEA

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

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

 Score = 186 (70.5 bits), Expect = 7.3e-14, P = 7.3e-14
 Identities = 33/35 (94%), Positives = 35/35 (100%)

Query:    37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
             LP+RLCLVCGDVASG+HYGVASCEACKAFFKRTIQ
Sbjct:    74 LPKRLCLVCGDVASGYHYGVASCEACKAFFKRTIQ 108

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005496 "steroid binding" evidence=IEA

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

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

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

 Score = 186 (70.5 bits), Expect = 7.3e-14, P = 7.3e-14
 Identities = 33/35 (94%), Positives = 35/35 (100%)

Query:    37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
             LP+RLCLVCGDVASG+HYGVASCEACKAFFKRTIQ
Sbjct:    74 LPKRLCLVCGDVASGYHYGVASCEACKAFFKRTIQ 108

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

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

GO:0005634 "nucleus" evidence=IEA

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

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

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005496 "steroid binding" evidence=IEA

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

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

 Score = 186 (70.5 bits), Expect = 7.3e-14, P = 7.3e-14
 Identities = 33/35 (94%), Positives = 35/35 (100%)

Query:    37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
             LP+RLCLVCGDVASG+HYGVASCEACKAFFKRTIQ
Sbjct:    74 LPKRLCLVCGDVASGYHYGVASCEACKAFFKRTIQ 108

GO:0003677 "DNA binding" evidence=IDA

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

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

GO:0005496 "steroid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0030278 "regulation of ossification" evidence=ISO

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

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

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

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

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

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

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

GO:0046872 "metal ion binding" evidence=IEA

GO:0051216 "cartilage development" evidence=ISO

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

 Score = 186 (70.5 bits), Expect = 7.3e-14, P = 7.3e-14
 Identities = 33/35 (94%), Positives = 35/35 (100%)

Query:    37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
             LP+RLCLVCGDVASG+HYGVASCEACKAFFKRTIQ
Sbjct:    74 LPKRLCLVCGDVASGYHYGVASCEACKAFFKRTIQ 108

GO:0003677 "DNA binding" evidence=ISO

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

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

GO:0005496 "steroid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;ISO

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0030278 "regulation of ossification" evidence=IMP

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

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

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

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

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

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

GO:0051216 "cartilage development" evidence=IMP

UNIPROTKB|P11474 ESRRA "Steroid hormone receptor ERR1" [Homo sapiens (taxid:9606)]

 Score = 186 (70.5 bits), Expect = 7.3e-14, P = 7.3e-14
 Identities = 33/35 (94%), Positives = 35/35 (100%)

Query:    37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
             LP+RLCLVCGDVASG+HYGVASCEACKAFFKRTIQ
Sbjct:    74 LPKRLCLVCGDVASGYHYGVASCEACKAFFKRTIQ 108

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

GO:0005496 "steroid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

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

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

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

GO:0051216 "cartilage development" evidence=IEA

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

GO:0005515 "protein binding" evidence=IPI

GO:0003677 "DNA binding" evidence=TAS

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

GO:0005634 "nucleus" 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:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=ISS

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

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

 Score = 186 (70.5 bits), Expect = 7.9e-14, P = 7.9e-14
 Identities = 33/35 (94%), Positives = 35/35 (100%)

Query:    37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
             LP+RLCLVCGDVASG+HYGVASCEACKAFFKRTIQ
Sbjct:    95 LPKRLCLVCGDVASGYHYGVASCEACKAFFKRTIQ 129

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

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IEA;IC

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0005496 "steroid binding" evidence=IEA

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

GO:0046872 "metal ion binding" evidence=IEA

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

---

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	113
cd07170	97	cd07170, NR_DBD_ERR, DNA-binding domain of estroge	4e-20
cd07155	75	cd07155, NR_DBD_ER_like, DNA-binding domain of est	2e-18
pfam00105	70	pfam00105, zf-C4, Zinc finger, C4 type (two domain	1e-17
cd06916	72	cd06916, NR_DBD_like, DNA-binding domain of nuclea	1e-17
smart00399	70	smart00399, ZnF_C4, c4 zinc finger in nuclear horm	1e-15
cd07171	82	cd07171, NR_DBD_ER, DNA-binding domain of estrogen	4e-15
cd06960	76	cd06960, NR_DBD_HNF4A, DNA-binding domain of hepto	7e-14
cd07166	89	cd07166, NR_DBD_REV_ERB, DNA-binding domain of REV	8e-14
cd07158	73	cd07158, NR_DBD_Ppar_like, The DNA-binding domain	9e-14
cd06961	85	cd06961, NR_DBD_TR, DNA-binding domain of thyroid	3e-13
cd06959	73	cd06959, NR_DBD_EcR_like, The DNA-binding domain o	6e-13
cd06965	84	cd06965, NR_DBD_Ppar, DNA-binding domain of peroxi	9e-13
cd07165	81	cd07165, NR_DBD_DmE78_like, DNA-binding domain of	1e-12
cd07168	90	cd07168, NR_DBD_DHR4_like, DNA-binding domain of e	1e-12
cd07167	93	cd07167, NR_DBD_Lrh-1_like, The DNA-binding domain	2e-12
cd06969	75	cd06969, NR_DBD_NGFI-B, DNA-binding domain of the	2e-12
cd06964	85	cd06964, NR_DBD_RAR, DNA-binding domain of retinoi	2e-12
cd06967	87	cd06967, NR_DBD_TR2_like, DNA-binding domain of th	2e-12
cd07169	90	cd07169, NR_DBD_GCNF_like, DNA-binding domain of G	1e-11
cd07160	101	cd07160, NR_DBD_LXR, DNA-binding domain of Liver X	1e-11
cd07172	78	cd07172, NR_DBD_GR_PR, DNA-binding domain of gluco	1e-11
cd06956	77	cd06956, NR_DBD_RXR, DNA-binding domain of retinoi	5e-11
cd07156	72	cd07156, NR_DBD_VDR_like, The DNA-binding domain o	8e-11
cd07164	78	cd07164, NR_DBD_PNR_like_1, DNA-binding domain of	2e-10
cd06962	84	cd06962, NR_DBD_FXR, DNA-binding domain of Farneso	3e-10
cd07179	74	cd07179, 2DBD_NR_DBD2, The second DNA-binding doma	3e-10
cd07161	91	cd07161, NR_DBD_EcR, DNA-binding domain of Ecdyson	3e-10
cd07173	82	cd07173, NR_DBD_AR, DNA-binding domain of androgen	4e-10
cd06958	73	cd06958, NR_DBD_COUP_TF, DNA-binding domain of chi	7e-10
cd06955	107	cd06955, NR_DBD_VDR, DNA-binding domain of vitamin	2e-09
cd06968	95	cd06968, NR_DBD_ROR, DNA-binding domain of Retinoi	2e-09
cd06963	73	cd06963, NR_DBD_GR_like, The DNA binding domain of	3e-09
cd06970	92	cd06970, NR_DBD_PNR, DNA-binding domain of the pho	4e-09
cd07157	86	cd07157, 2DBD_NR_DBD1, The first DNA-binding domai	5e-09
cd07154	73	cd07154, NR_DBD_PNR_like, The DNA-binding domain o	1e-08
cd07163	92	cd07163, NR_DBD_TLX, DNA-binding domain of Tailles	2e-08
cd06957	82	cd06957, NR_DBD_PNR_like_2, DNA-binding domain of	2e-08
cd06966	94	cd06966, NR_DBD_CAR, DNA-binding domain of constit	6e-08
cd07162	87	cd07162, NR_DBD_PXR, DNA-binding domain of pregnan	2e-07

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

 Score = 77.6 bits (191), Expect = 4e-20
 Identities = 31/34 (91%), Positives = 34/34 (100%)

Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQ
Sbjct: 3  PKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQ 36

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

>gnl|CDD|143530 cd07155, NR_DBD_ER_like, DNA-binding domain of estrogen receptor (ER) and estrogen related receptors (ERR) is composed of two C4-type zinc fingers

 Score = 72.5 bits (178), Expect = 2e-18
 Identities = 28/30 (93%), Positives = 30/30 (100%)

Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          CLVCGD+ASG+HYGVASCEACKAFFKRTIQ
Sbjct: 1  CLVCGDIASGYHYGVASCEACKAFFKRTIQ 30

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

 Score = 70.7 bits (174), Expect = 1e-17
 Identities = 22/32 (68%), Positives = 26/32 (81%)

Query: 40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
           LC VCGD ASG+HYGV +CE CK FF+R+IQ
Sbjct: 1  ELCKVCGDKASGYHYGVLTCEGCKGFFRRSIQ 32

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

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

 Score = 70.7 bits (174), Expect = 1e-17
 Identities = 19/36 (52%), Positives = 25/36 (69%)

Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLV 77
          C VCGD ASG+HYGV +CE CK FF+R+++      
Sbjct: 1  CAVCGDKASGYHYGVLTCEGCKGFFRRSVRRNLEYT 36

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

 Score = 65.2 bits (160), Expect = 1e-15
 Identities = 24/33 (72%), Positives = 27/33 (81%)

Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
          LC VCGD ASGFH+GV SC ACKAFF+RT+  R
Sbjct: 1  LCCVCGDHASGFHFGVCSCRACKAFFRRTVNLR 33

Length = 70

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

 Score = 64.5 bits (157), Expect = 4e-15
 Identities = 23/34 (67%), Positives = 25/34 (73%)

Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
              C VC D ASG+HYGV SCE CKAFFKR+IQ
Sbjct: 2  DTHFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQ 35

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

 Score = 61.1 bits (149), Expect = 7e-14
 Identities = 18/29 (62%), Positives = 22/29 (75%)

Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTI 70
          C VCGD A+G HYGV SC  CK FF+R++
Sbjct: 1  CAVCGDRATGKHYGVLSCNGCKGFFRRSV 29

DNA-binding domain of hepatocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. HNF4 interacts with a DNA site, composed of two direct repeats of AGTTCA with 1 bp spacer, which is upstream of target genes and modulates the rate of transcriptional initiation. HNF4 is a member of the nuclear receptor superfamily. HNF4 plays a key role in establishing and maintenance of hepatocyte differentiation in the liver. It is also expressed in gut, kidney, and pancreatic beta cells. HNF4 was originally classified as an orphan receptor, but later it is found that HNF4 binds with very high affinity to a variety of fatty acids. However, unlike other nuclear receptors, the ligands do not act as a molecular switch for HNF4. They seem to constantly bind to the receptor, which is constitutively active as a transcription activator. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, HNF4 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 76

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

 Score = 61.4 bits (149), Expect = 8e-14
 Identities = 23/31 (74%), Positives = 26/31 (83%)

Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          LC VCGD ASGFHYGV +CE CK FF+R+IQ
Sbjct: 5  LCKVCGDKASGFHYGVHACEGCKGFFRRSIQ 35

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

 Score = 60.7 bits (147), Expect = 9e-14
 Identities = 24/30 (80%), Positives = 25/30 (83%)

Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          C VCGD ASGFHYGV SCE CK FF+RTIQ
Sbjct: 1  CKVCGDKASGFHYGVHSCEGCKGFFRRTIQ 30

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

 Score = 59.7 bits (145), Expect = 3e-13
 Identities = 18/31 (58%), Positives = 24/31 (77%)

Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
           C+VCGD A+G+HY   +CE CK FF+RT+Q
Sbjct: 1  PCVVCGDKATGYHYRCITCEGCKGFFRRTVQ 31

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

>gnl|CDD|143517 cd06959, NR_DBD_EcR_like, The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers

 Score = 58.6 bits (142), Expect = 6e-13
 Identities = 21/31 (67%), Positives = 25/31 (80%)

Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
           C+VCGD ASGFHYGV SCE CK FF+R++ 
Sbjct: 1  NCVVCGDKASGFHYGVLSCEGCKGFFRRSVT 31

The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: Ecdysone receptor (EcR), Liver X receptor (LXR) and Farnesoid X receptor (FXR). The DNA binding activity is regulated by their corresponding ligands. The ligands for EcR are ecdysteroids; LXR is regulated by oxidized cholesterol derivatives or oxysterols; and bile acids control FXR's activities. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcR-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 73

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

 Score = 58.6 bits (142), Expect = 9e-13
 Identities = 22/31 (70%), Positives = 25/31 (80%)

Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
           C VCGD ASGFHYGV +CE CK FF+RTI+
Sbjct: 1  ECRVCGDKASGFHYGVHACEGCKGFFRRTIR 31

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

>gnl|CDD|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 = 58.3 bits (141), Expect = 1e-12
 Identities = 24/40 (60%), Positives = 28/40 (70%)

Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRG 81
          C VCGD ASG+HYGV SCE CK FF+R+IQ +     LR 
Sbjct: 1  CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYRCLRD 40

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|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 = 58.3 bits (141), Expect = 1e-12
 Identities = 20/40 (50%), Positives = 29/40 (72%)

Query: 34 EEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
          +E+   +LC +C D A+G HYG+ +CE CK FFKRT+Q +
Sbjct: 1  DEDESPKLCSICEDKATGLHYGIITCEGCKGFFKRTVQNK 40

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|143541 cd07167, NR_DBD_Lrh-1_like, The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers

 Score = 58.2 bits (141), Expect = 2e-12
 Identities = 20/30 (66%), Positives = 25/30 (83%)

Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          C VCGD  SG+HYG+ +CE+CK FFKRT+Q
Sbjct: 1  CPVCGDKVSGYHYGLLTCESCKGFFKRTVQ 30

The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This nuclear receptor family includes at least three subgroups of receptors that function in embryo development and differentiation, and other processes. FTZ-F1 interacts with the cis-acting DNA motif of ftz gene, which is required at several stages of development. Particularly, FTZ-F1 regulated genes are strongly linked to steroid biosynthesis and sex-determination; LRH-1 is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development; SF-1 is an essential regulator of endocrine development and function and is considered a master regulator of reproduction; SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). However, the ligand for FTZ-F1 has not yet been identified. Most nuclear receptors function as homodimer or heterodimers. However, LRH-1 and SF-1 bind to DNA as monomers. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, receptors in this family have a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 93

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

 Score = 57.5 bits (139), Expect = 2e-12
 Identities = 24/39 (61%), Positives = 27/39 (69%)

Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSL 79
          LC VCGD A+  HYGV +CE CK FFKRT+Q  A  V L
Sbjct: 2  LCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCL 40

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

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

 Score = 57.6 bits (139), Expect = 2e-12
 Identities = 19/32 (59%), Positives = 26/32 (81%)

Query: 40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          + C VC D +SG+HYGV++CE CK FF+R+IQ
Sbjct: 5  KPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQ 36

DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RARs mediate the biological effect of retinoids, including both natural dietary vitamin A (retinol) metabolites and active synthetic analogs. Retinoids play key roles in a wide variety of essential biological processes, such as vertebrate embryonic morphogenesis and organogenesis, differentiation and apoptosis, and homeostasis. RAR function as a heterodimer with retinoic X receptor by binding to specific RAR response elements (RAREs), which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair and found in the promoter regions of retinoid target genes. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, retinoic acid receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). Length = 85

>gnl|CDD|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 = 57.5 bits (139), Expect = 2e-12
 Identities = 23/37 (62%), Positives = 26/37 (70%)

Query: 37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
           P  LC+VCGD ASG HYG  SCE CK FFKR+I+  
Sbjct: 1  QPVELCVVCGDKASGRHYGAVSCEGCKGFFKRSIRKN 37

DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. TR2 and TR4 interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. TR4 and TR2 are orphan nuclear receptors; the physiological ligand is as yet unidentified. TR2 is abundantly expressed in the androgen-sensitive prostate. TR4 transcripts are expressed in many tissues, including central nervous system, adrenal gland, spleen, thyroid gland, and prostate. It has been shown that human TR2 binds to a wide spectrum of natural hormone response elements (HREs) with distinct affinities suggesting that TR2 may cross-talk with other gene expression regulation systems. The genes responding to TR2 or TR4 include genes that are regulated by retinoic acid receptor, vitamin D receptor, and peroxisome proliferator-activated receptor. TR4/2 binds to HREs as dimers. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TR2-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 87

>gnl|CDD|143543 cd07169, NR_DBD_GCNF_like, DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers

 Score = 56.0 bits (135), Expect = 1e-11
 Identities = 21/31 (67%), Positives = 25/31 (80%)

Query: 40 RLCLVCGDVASGFHYGVASCEACKAFFKRTI 70
          R CL+CGD A+G HYG+ SCE CK FFKR+I
Sbjct: 7  RTCLICGDRATGLHYGIISCEGCKGFFKRSI 37

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

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

 Score = 56.0 bits (135), Expect = 1e-11
 Identities = 20/30 (66%), Positives = 24/30 (80%)

Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTI 70
          +C VCGD ASGFHY V SCE CK FF+R++
Sbjct: 20 VCSVCGDKASGFHYNVLSCEGCKGFFRRSV 49

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

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

 Score = 55.6 bits (134), Expect = 1e-11
 Identities = 20/34 (58%), Positives = 27/34 (79%)

Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          P+++CLVC D ASG HYGV +C +CK FFKR ++
Sbjct: 1  PQKICLVCSDEASGCHYGVLTCGSCKVFFKRAVE 34

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

 Score = 53.7 bits (129), Expect = 5e-11
 Identities = 21/31 (67%), Positives = 25/31 (80%)

Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          +C +CGD ASG HYGV SCE CK FFKRT++
Sbjct: 2  ICAICGDRASGKHYGVYSCEGCKGFFKRTVR 32

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|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 = 53.2 bits (128), Expect = 8e-11
 Identities = 16/35 (45%), Positives = 25/35 (71%)

Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASL 76
          C VCGD A+G+H+   +CE CK FF+R+++ +A  
Sbjct: 1  CGVCGDRATGYHFNAMTCEGCKGFFRRSMKRKARF 35

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|143538 cd07164, NR_DBD_PNR_like_1, DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers

 Score = 52.5 bits (126), Expect = 2e-10
 Identities = 20/30 (66%), Positives = 24/30 (80%)

Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          C VCGD ASG HYGV SC+ C+ FFKR+I+
Sbjct: 1  CRVCGDRASGKHYGVPSCDGCRGFFKRSIR 30

DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of nuclear receptor superfamily of the ligand-activated transcription factors. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 78

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

 Score = 52.3 bits (125), Expect = 3e-10
 Identities = 20/34 (58%), Positives = 25/34 (73%)

Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQARA 74
          LC+VCGD ASG+HY   +CE CK FF+R+I   A
Sbjct: 3  LCVVCGDKASGYHYNALTCEGCKGFFRRSITKNA 36

DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. FXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. FXR is a member of the nuclear receptor family of ligand activated transcription factors. Bile acids are endogenous ligands for FXRs. Upon binding of a ligand, FXR binds to FXR response element (FXRE), which is an inverted repeat of TGACCT spaced by one nucleotide, either as a monomer or as a heterodimer with retinoid X receptor (RXR), to regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, FXR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 84

>gnl|CDD|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 = 51.7 bits (124), Expect = 3e-10
 Identities = 19/36 (52%), Positives = 24/36 (66%)

Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLV 77
          C VCG  +SGFH+G  +CE CK FF+RT  +  S V
Sbjct: 1  CRVCGGKSSGFHFGALTCEGCKGFFRRTELSSNSYV 36

The second DNA-binding domain (DBD) of the 2DBD nuclear receptor (NR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. The proteins contain two DBDs in tandem, probably resulting from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown. Length = 74

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

 Score = 52.2 bits (125), Expect = 3e-10
 Identities = 20/34 (58%), Positives = 25/34 (73%)

Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQARA 74
          LCLVCGD ASG+HY   +CE CK FF+R++   A
Sbjct: 3  LCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSA 36

DNA-binding domain of Ecdysone receptor (EcR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with highly degenerate pseudo-palindromic response elements, resembling inverted repeats of 5'-AGGTCA-3' separated by 1 bp, upstream of the target gene and modulates the rate of transcriptional initiation. EcR is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. EcR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of EcR are ecdysteroids, the endogenous steroidal hormones found in invertebrates. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcRs have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). Length = 91

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

 Score = 51.5 bits (123), Expect = 4e-10
 Identities = 19/36 (52%), Positives = 26/36 (72%)

Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
          P++ CL+CGD ASG HYG  +C +CK FFKR  + +
Sbjct: 2  PQKTCLICGDEASGCHYGALTCGSCKVFFKRAAEGK 37

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

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

 Score = 51.0 bits (122), Expect = 7e-10
 Identities = 18/30 (60%), Positives = 25/30 (83%)

Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          C+VCGD +SG HYG  +CE CK+FFKR+++
Sbjct: 1  CVVCGDKSSGKHYGQFTCEGCKSFFKRSVR 30

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

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

 Score = 50.7 bits (121), Expect = 2e-09
 Identities = 18/37 (48%), Positives = 27/37 (72%)

Query: 40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASL 76
          R+C VCGD A+GFH+   +CE CK FF+R+++ +A  
Sbjct: 7  RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALF 43

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

 Score = 50.2 bits (120), Expect = 2e-09
 Identities = 19/34 (55%), Positives = 24/34 (70%)

Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARAS 75
          C +CGD +SG HYGV +CE CK FF+R+ Q   S
Sbjct: 8  CKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVS 41

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

 Score = 49.2 bits (117), Expect = 3e-09
 Identities = 19/32 (59%), Positives = 24/32 (75%)

Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
          CL+CGD ASG HYGV +C +CK FFKR  + +
Sbjct: 1  CLICGDEASGCHYGVLTCGSCKVFFKRAAEGQ 32

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

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

 Score = 49.6 bits (118), Expect = 4e-09
 Identities = 18/36 (50%), Positives = 25/36 (69%)

Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
          P  LC VCGD +SG HYG+ +C  C  FFKR+++ +
Sbjct: 5  PGLLCRVCGDTSSGKHYGIYACNGCSGFFKRSVRRK 40

DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of the nuclear receptor superfamily of the ligand-activated transcription factors. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 92

>gnl|CDD|143532 cd07157, 2DBD_NR_DBD1, The first DNA-binding domain (DBD) of the 2DBD nuclear receptors is composed of two C4-type zinc fingers

 Score = 49.0 bits (117), Expect = 5e-09
 Identities = 18/32 (56%), Positives = 22/32 (68%)

Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
          C VCG+ A+GFH+G   CEACK FF R+  A 
Sbjct: 3  CQVCGEPAAGFHHGAYVCEACKKFFMRSSNAI 34

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

 Score = 47.9 bits (114), Expect = 1e-08
 Identities = 18/30 (60%), Positives = 23/30 (76%)

Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          C VCGD +SG HYGV +C+ C  FFKR+I+
Sbjct: 1  CKVCGDRSSGKHYGVYACDGCSGFFKRSIR 30

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

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

 Score = 47.9 bits (114), Expect = 2e-08
 Identities = 17/30 (56%), Positives = 23/30 (76%)

Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          C VCGD +SG HYG+ +C+ C  FFKR+I+
Sbjct: 9  CKVCGDRSSGKHYGIYACDGCSGFFKRSIR 38

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

>gnl|CDD|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 = 17/40 (42%), Positives = 23/40 (57%)

Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRG 81
          C VCGD + G HYGV  C+ C  FFKR+++       + G
Sbjct: 1  CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKGIIYTCIAG 40

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

 Score = 46.3 bits (110), Expect = 6e-08
 Identities = 15/29 (51%), Positives = 23/29 (79%)

Query: 40 RLCLVCGDVASGFHYGVASCEACKAFFKR 68
          ++C VCGD A G+++   +CE+CKAFF+R
Sbjct: 1  KICGVCGDKALGYNFNAITCESCKAFFRR 29

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

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

 Score = 44.9 bits (106), Expect = 2e-07
 Identities = 17/36 (47%), Positives = 25/36 (69%)

Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQARASL 76
          +C VCGD A+G+H+   +CE CK FF+R ++  A L
Sbjct: 1  ICRVCGDRATGYHFNAMTCEGCKGFFRRAMKRNARL 36

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	113
cd07170	97	NR_DBD_ERR DNA-binding domain of estrogen related	99.91
cd06956	77	NR_DBD_RXR DNA-binding domain of retinoid X recept	99.91
cd07160	101	NR_DBD_LXR DNA-binding domain of Liver X receptors	99.91
cd07168	90	NR_DBD_DHR4_like DNA-binding domain of ecdysone-in	99.91
cd07155	75	NR_DBD_ER_like DNA-binding domain of estrogen rece	99.91
cd06961	85	NR_DBD_TR DNA-binding domain of thyroid hormone re	99.9
cd06959	73	NR_DBD_EcR_like The DNA-binding domain of Ecdysone	99.9
cd07173	82	NR_DBD_AR DNA-binding domain of androgen receptor	99.9
cd07172	78	NR_DBD_GR_PR DNA-binding domain of glucocorticoid	99.9
cd07171	82	NR_DBD_ER DNA-binding domain of estrogen receptors	99.9
cd06964	85	NR_DBD_RAR DNA-binding domain of retinoic acid rec	99.9
cd07161	91	NR_DBD_EcR DNA-binding domain of Ecdysone receptor	99.9
cd06970	92	NR_DBD_PNR DNA-binding domain of the photoreceptor	99.9
cd06967	87	NR_DBD_TR2_like DNA-binding domain of the TR2 and	99.9
cd07164	78	NR_DBD_PNR_like_1 DNA-binding domain of the photor	99.89
cd06969	75	NR_DBD_NGFI-B DNA-binding domain of the orphan nuc	99.89
cd07179	74	2DBD_NR_DBD2 The second DNA-binding domain (DBD) o	99.89
cd07165	81	NR_DBD_DmE78_like DNA-binding domain of Drosophila	99.89
cd06963	73	NR_DBD_GR_like The DNA binding domain of GR_like n	99.89
cd07169	90	NR_DBD_GCNF_like DNA-binding domain of Germ cell n	99.89
cd06958	73	NR_DBD_COUP_TF DNA-binding domain of chicken ovalb	99.89
cd07156	72	NR_DBD_VDR_like The DNA-binding domain of vitamin	99.89
KOG4846|consensus	538		99.89
cd06960	76	NR_DBD_HNF4A DNA-binding domain of heptocyte nucle	99.89
cd07158	73	NR_DBD_Ppar_like The DNA-binding domain of peroxis	99.89
cd07167	93	NR_DBD_Lrh-1_like The DNA-binding domain of Lrh-1	99.89
cd06966	94	NR_DBD_CAR DNA-binding domain of constitutive andr	99.89
cd07163	92	NR_DBD_TLX DNA-binding domain of Tailless (TLX) is	99.88
cd06962	84	NR_DBD_FXR DNA-binding domain of Farnesoid X recep	99.88
cd06968	95	NR_DBD_ROR DNA-binding domain of Retinoid-related	99.88
cd07157	86	2DBD_NR_DBD1 The first DNA-binding domain (DBD) of	99.88
cd07162	87	NR_DBD_PXR DNA-binding domain of pregnane X recept	99.88
smart00399	70	ZnF_C4 c4 zinc finger in nuclear hormone receptors	99.88
cd06955	107	NR_DBD_VDR DNA-binding domain of vitamin D recepto	99.88
cd07154	73	NR_DBD_PNR_like The DNA-binding domain of the phot	99.88
cd06916	72	NR_DBD_like DNA-binding domain of nuclear receptor	99.88
PF00105	70	zf-C4: Zinc finger, C4 type (two domains); InterPr	99.88
cd07166	89	NR_DBD_REV_ERB DNA-binding domain of REV-ERB recep	99.88
cd06957	82	NR_DBD_PNR_like_2 DNA-binding domain of the photor	99.88
KOG4215|consensus	432		99.87
cd06965	84	NR_DBD_Ppar DNA-binding domain of peroxisome proli	99.87
KOG4217|consensus	605		99.85
KOG4216|consensus	479		99.84
KOG4218|consensus	475		99.78

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

Probab=99.91  E-value=2.8e-25  Score=150.36  Aligned_cols=75  Identities=51%  Similarity=0.746  Sum_probs=67.0

Q ss_pred             CCCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhccC
Q psy11507         38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNRF  112 (113)
Q Consensus        38 ~~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~~  112 (113)
                      +..+|.||++++.|+||||.+|++|++||||++.....|.|..++.|.+     ..|++|||+|||+|||..+..+..|.
T Consensus         3 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~vq~~r~   82 (97)
T cd07170           3 PKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRV   82 (97)
T ss_pred             CCCCCeecCCcCcceEECceeehhhhHHHHHHhccCCceeecCCCccccCcccCccCCccccchhhhcCCCHHHcccccC
Confidence            3456999999999999999999999999999999998999998888853     47999999999999999987777663

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

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

Probab=99.91  E-value=3.5e-25  Score=144.01  Aligned_cols=71  Identities=37%  Similarity=0.598  Sum_probs=64.9

Q ss_pred             cceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhcc
Q psy11507         41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNR  111 (113)
Q Consensus        41 ~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~  111 (113)
                      +|.||+++++++||||.+|++|++||||++..+..|.|..++.|.+     ..|++|||+|||++||..+..+..|
T Consensus         2 ~C~VC~~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r   77 (77)
T cd06956           2 ICAICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER   77 (77)
T ss_pred             CCcccCCcCcceEECceeehhHHHHHHHHhhCCCccccCCCCccccCCCccccCccchhHHHhHhCCCHHHhccCC
Confidence            5999999999999999999999999999999999999998888853     4799999999999999998777655

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

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

Probab=99.91  E-value=8e-25  Score=149.13  Aligned_cols=74  Identities=35%  Similarity=0.576  Sum_probs=66.1

Q ss_pred             CCCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhcc
Q psy11507         38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNR  111 (113)
Q Consensus        38 ~~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~  111 (113)
                      ...+|.||+++++++||||.+|++|++||||++.....|.|..++.|.+     ..|++|||+|||++||+.+..+..|
T Consensus        17 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~   95 (101)
T cd07160          17 GNEVCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAQYVCKNGGKCQMDMYMRRKCQECRLRKCREAGMREQCVLSEE   95 (101)
T ss_pred             CCCCCeecCCcCcceEECcceehhhhhhhhhcccccCccccCCCCccccCCcccccCccchhHHHHHhCCCHHHhcChh
Confidence            3567999999999999999999999999999999999999998888853     4799999999999999998765543

DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. LXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. LXR operates as cholesterol sensor which protects cells from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. LXR functions as a heterodimer with the retinoid X receptor (RXR) which may be activated by either LXR agonist or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. The ideal LXRE seq

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

Probab=99.91  E-value=6.4e-25  Score=146.73  Aligned_cols=76  Identities=29%  Similarity=0.534  Sum_probs=68.0

Q ss_pred             CCCCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhcc
Q psy11507         37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNR  111 (113)
Q Consensus        37 ~~~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~  111 (113)
                      ....+|.||+++++++||||.+|++|++||||++..+..|.|..++.|.+     ..|++|||+|||++||.....+..|
T Consensus         4 ~~~~~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R   83 (90)
T cd07168           4 ESPKLCSICEDKATGLHYGIITCEGCKGFFKRTVQNKRVYTCVGDGRCEITKAQRNRCQYCRFRKCIRKGMMLAAVREDR   83 (90)
T ss_pred             ccCCCCcccCCcCcceEECceehhhhhHhhhhhhcCCCCccCCCCCCccccccccccccccchhhhhhcCCCHHHhhccc
Confidence            34567999999999999999999999999999999988999998888853     4799999999999999998877776


Q ss_pred             C
Q psy11507        112 F  112 (113)
Q Consensus       112 ~  112 (113)
                      .
T Consensus        84 ~   84 (90)
T cd07168          84 M   84 (90)
T ss_pred             C
Confidence            4

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

>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=99.91  E-value=9e-25  Score=141.41  Aligned_cols=70  Identities=50%  Similarity=0.723  Sum_probs=63.8

Q ss_pred             ceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhcc
Q psy11507         42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNR  111 (113)
Q Consensus        42 C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~  111 (113)
                      |.||+++++++||||.+|++|++||||++..+..|.|..++.|.+     ..|++|||+|||++||+.+..+.+|
T Consensus         1 C~VC~~~~~g~hygv~sC~aCk~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r   75 (75)
T cd07155           1 CLVCGDIASGYHYGVASCEACKAFFKRTIQGNLGYSCPSTSECEVDKKRRKSCQACRLQKCLKVGMLKEGVRLDR   75 (75)
T ss_pred             CcccCccCcceEEChhhhhhhHHHHHHHhhCCCceeCCcCCCcccCCcccccCccchhhhhhHhCCCHHHcccCC
Confidence            789999999999999999999999999999999999998888853     4799999999999999998776655

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=99.90  E-value=1e-24  Score=144.34  Aligned_cols=72  Identities=35%  Similarity=0.581  Sum_probs=65.3

Q ss_pred             cceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhccC
Q psy11507         41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNRF  112 (113)
Q Consensus        41 ~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~~  112 (113)
                      +|.||++.++++||||.+|++|++||||++..+..|.|..++.|.+     ..|++|||+|||++||+++..+..|.
T Consensus         1 ~C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~   77 (85)
T cd06961           1 PCVVCGDKATGYHYRCITCEGCKGFFRRTVQKKLSYSCKGEGKCEIDKVTRNQCQECRFKKCIAVGMAKDLVLDDRK   77 (85)
T ss_pred             CCceeCCcCcceEEChhhhhhhhHhhHhhhccCCccccCCCCccccCccccccCccchhhhhhhccCCHHHcccccC
Confidence            4999999999999999999999999999999999999998888853     47999999999999999987776653

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

>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=99.90  E-value=1.5e-24  Score=139.70  Aligned_cols=67  Identities=39%  Similarity=0.629  Sum_probs=61.3

Q ss_pred             cceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccch
Q psy11507         41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLD  107 (113)
Q Consensus        41 ~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~  107 (113)
                      +|.||+++++++||||.+|++|++||||++..+..|.|..++.|.+     ..|++|||+|||++||.++..
T Consensus         1 ~C~vCg~~~~~~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v   72 (73)
T cd06959           1 NCVVCGDKASGFHYGVLSCEGCKGFFRRSVTKGAVYACKFGNKCEMDMYMRRKCQECRLRKCKAAGMRPDCL   72 (73)
T ss_pred             CCceeCCcCcceEECceeehhhHHHHHHhhcCCCCccCCCCCcCCcCCcccccCccchhHHHHHhCCChhhc
Confidence            5999999999999999999999999999999889999998888853     479999999999999998753

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

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

Probab=99.90  E-value=2.6e-24  Score=141.69  Aligned_cols=70  Identities=29%  Similarity=0.567  Sum_probs=63.1

Q ss_pred             CCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchh
Q psy11507         39 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDT  108 (113)
Q Consensus        39 ~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~  108 (113)
                      ..+|.||+++++++||||.+|++|++||||++..+..|.|..++.|.+     ..|++|||+|||++||......
T Consensus         3 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~~~   77 (82)
T cd07173           3 QKTCLICGDEASGCHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCFEAGMTLGARK   77 (82)
T ss_pred             CCCCeecCCcCcceEECcchhhhHHHHHHHHhcCCCceecCCCCccccCCCccCcCcchhhhhhhhcCCCcChHH
Confidence            456999999999999999999999999999999999999998888853     4799999999999999987544

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

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

Probab=99.90  E-value=2.1e-24  Score=140.82  Aligned_cols=67  Identities=33%  Similarity=0.618  Sum_probs=61.4

Q ss_pred             CCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCcc
Q psy11507         39 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDS  105 (113)
Q Consensus        39 ~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~  105 (113)
                      ..+|.||+++++++||||.+|++|++||||++..+..|.|..++.|.+     ..|++|||+|||++||...
T Consensus         2 ~~~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~   73 (78)
T cd07172           2 QKICLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCLQAGMNLG   73 (78)
T ss_pred             CCCCeecCCcCcceEECceeehhhHHhHHHHeeCCCceeCCCCCccccCCcccccCccchhHHHHHhCCCcc
Confidence            457999999999999999999999999999999999999998888853     4799999999999999875

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

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

Probab=99.90  E-value=1.8e-24  Score=142.35  Aligned_cols=71  Identities=38%  Similarity=0.583  Sum_probs=63.8

Q ss_pred             CCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhh
Q psy11507         39 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTT  109 (113)
Q Consensus        39 ~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~  109 (113)
                      ..+|.||+++++++||||.+|++|++||||++.....|.|..++.|.+     ..|++|||+|||++||.++....
T Consensus         3 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~   78 (82)
T cd07171           3 THFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRR   78 (82)
T ss_pred             CCCCeecCCcCcceEECceeehhhHHhHHHHeeCCCceeCCCCCccccCCcccccCccchhHHHhHhcCCHHHHHH
Confidence            356999999999999999999999999999999999999998888853     47999999999999999975544

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

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

Probab=99.90  E-value=4e-25  Score=146.34  Aligned_cols=74  Identities=32%  Similarity=0.568  Sum_probs=66.7

Q ss_pred             CCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhccC
Q psy11507         39 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNRF  112 (113)
Q Consensus        39 ~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~~  112 (113)
                      ..+|.||+++++++||||.+|++|++||||++.....|.|..++.|.+     ..|++|||+|||++||.++..+..|.
T Consensus         4 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~R~   82 (85)
T cd06964           4 YKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRN   82 (85)
T ss_pred             CCCCcccCCcCcccEECcceeeeeeeEEeeeecCCCCeECCCCCccccCCcccccCccchhhhhhhhCCCHHHhhcccc
Confidence            357999999999999999999999999999999888899998888853     47999999999999999988877764

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

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

Probab=99.90  E-value=2.5e-24  Score=144.17  Aligned_cols=71  Identities=35%  Similarity=0.611  Sum_probs=64.1

Q ss_pred             CcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhc
Q psy11507         40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTN  110 (113)
Q Consensus        40 ~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~  110 (113)
                      .+|.||+++++++||||.+|++|++||||++.....|.|..++.|.+     ..|++|||+|||++||++...+..
T Consensus         2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~   77 (91)
T cd07161           2 ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYHCKYGRACEMDMYMRRKCQECRLKKCLSVGMRPECVVPE   77 (91)
T ss_pred             CCCeeCCCcCcceEECceeehhhHHHHHHHhccCCceecCCCCccccCccccccCccchhhHHhHcCCCHHHcCch
Confidence            35999999999999999999999999999999999999998888853     479999999999999999866554

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

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

Probab=99.90  E-value=5.2e-25  Score=147.81  Aligned_cols=76  Identities=32%  Similarity=0.518  Sum_probs=66.9

Q ss_pred             CCCCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCC-CCCCC-----CCCcchHHhHhHHhcCCccchhhc
Q psy11507         37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRG-HEPQK-----KSSQIPKEKYNLAYLMSDSLDTTN  110 (113)
Q Consensus        37 ~~~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~-~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~  110 (113)
                      .+..+|.||+++++++|||+.+|++|++||||++..+..|.|..+ +.|.+     ..|++|||+|||++||..+..+..
T Consensus         4 ~p~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~   83 (92)
T cd06970           4 NPGLLCRVCGDTSSGKHYGIYACNGCSGFFKRSVRRKLIYRCQAGTGMCPVDKAHRNQCQACRLKKCLQAGMNKDAVQNE   83 (92)
T ss_pred             CCCCCCeecCCcCcccEECccEEeeeeeEeeeeeecCCCceeecCCCcCccCCCccccCccchhhHhhHhCCCHHHcccc
Confidence            345579999999999999999999999999999999999999885 67753     479999999999999999877766


Q ss_pred             cC
Q psy11507        111 RF  112 (113)
Q Consensus       111 ~~  112 (113)
                      |+
T Consensus        84 R~   85 (92)
T cd06970          84 RQ   85 (92)
T ss_pred             cC
Confidence            64

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

>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=99.90  E-value=5.7e-25  Score=146.14  Aligned_cols=75  Identities=37%  Similarity=0.584  Sum_probs=67.7

Q ss_pred             CCCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhccC
Q psy11507         38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNRF  112 (113)
Q Consensus        38 ~~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~~  112 (113)
                      |..+|.||++.+.++||||.+|++|++||||++..+..|.|..++.|.+     ..|++|||+|||++||+....+..|+
T Consensus         2 ~~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~R~   81 (87)
T cd06967           2 PVELCVVCGDKASGRHYGAVSCEGCKGFFKRSIRKNLGYSCRGSKDCVINKHHRNRCQYCRLQKCLAMGMKSDSVQCERK   81 (87)
T ss_pred             CCCCCeecCCcCCcCEeCcceEeeeeeEeeeeeeCCCCcccCCCCccccCccccccCccchhhhhhHcCCCHHHhccccC
Confidence            4567999999999999999999999999999999888999998888853     47999999999999999988877764

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

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

Probab=99.89  E-value=3.5e-24  Score=139.58  Aligned_cols=71  Identities=37%  Similarity=0.575  Sum_probs=64.9

Q ss_pred             ceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhccC
Q psy11507         42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNRF  112 (113)
Q Consensus        42 C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~~  112 (113)
                      |.||+++++++||||.+|++|++||||++..+..|.|..++.|.+     ..|++|||+|||+|||.....+..|.
T Consensus         1 C~VCg~~~~g~hyG~~~C~~C~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~   76 (78)
T cd07164           1 CRVCGDRASGKHYGVPSCDGCRGFFKRSIRRNLAYVCKENGSCVVDVARRNQCQACRFKKCLQVNMNRDAVQHERA   76 (78)
T ss_pred             CcccCccCcceEECcchhhhhhhhhhhhccCCCCccCCCCCcccccCcccccCccchhhhhhHhcCCHHHhccCCC
Confidence            789999999999999999999999999999889999998888853     47999999999999999988777664

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

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

Probab=99.89  E-value=1.3e-24  Score=140.79  Aligned_cols=69  Identities=39%  Similarity=0.605  Sum_probs=62.2

Q ss_pred             CcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchh
Q psy11507         40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDT  108 (113)
Q Consensus        40 ~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~  108 (113)
                      ++|.||++++.++||||.+|++|++||||++..+..|.|..++.|.+     ..|++|||+|||++||+++..+
T Consensus         1 ~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~   74 (75)
T cd06969           1 GLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLQVGMVKEVVR   74 (75)
T ss_pred             CCCeecCCcCcceEECcceeeeeeeeeeeeeecCCcccCCcCCccccCCcccccCcccHhHHHHHhCCCHHHcc
Confidence            36999999999999999999999999999999888999998877753     4799999999999999987543

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=99.89  E-value=6.2e-24  Score=137.23  Aligned_cols=66  Identities=36%  Similarity=0.621  Sum_probs=60.6

Q ss_pred             ceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccch
Q psy11507         42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLD  107 (113)
Q Consensus        42 C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~  107 (113)
                      |.||+++++++||||.+|++|++||||++..+..|.|..++.|.+     ..|++|||+|||++||+++..
T Consensus         1 C~VCg~~~~g~hygv~sC~aC~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v   71 (74)
T cd07179           1 CRVCGGKSSGFHFGALTCEGCKGFFRRTELSSNSYVCPGGQNCAITPATRNACKSCRFRRCLAVGMSKTGS   71 (74)
T ss_pred             CcccCccCcceEECceeehhHHHHHHHHhhCCCcccCCCCCccccCCcccccCccchhHHHHHhCCCHhHe
Confidence            789999999999999999999999999999999999998888853     479999999999999998754

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.

>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=99.89  E-value=4.9e-24  Score=139.82  Aligned_cols=71  Identities=44%  Similarity=0.680  Sum_probs=64.9

Q ss_pred             ceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhccC
Q psy11507         42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNRF  112 (113)
Q Consensus        42 C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~~  112 (113)
                      |.||+++++++||||.+|++|++||||++.....|.|..++.|.+     ..|++|||+|||++||.+...+..|.
T Consensus         1 C~VCg~~~~g~hyG~~sC~aC~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~V~~~r~   76 (81)
T cd07165           1 CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYRCLRDGKCEIIRLNRNRCQYCRFKKCLAAGMSKDSVRYGRI   76 (81)
T ss_pred             CCccCccCcceEECchhhhhHHHHHHhHhccCCceeCCCCCCccccccccccccchhhhhcccccCCHHHcccCCC
Confidence            789999999999999999999999999999899999998888853     47999999999999999988777764

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,

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

Probab=99.89  E-value=6.8e-24  Score=136.76  Aligned_cols=64  Identities=33%  Similarity=0.604  Sum_probs=59.5

Q ss_pred             ceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCcc
Q psy11507         42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDS  105 (113)
Q Consensus        42 C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~  105 (113)
                      |.||+++++++||||.+|++|++||||++..+..|.|..++.|.+     ..|++|||+|||++||..+
T Consensus         1 C~VCg~~a~~~hygv~sC~aCk~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~   69 (73)
T cd06963           1 CLICGDEASGCHYGVLTCGSCKVFFKRAAEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCYQAGMTLG   69 (73)
T ss_pred             CcccCccCcceEECceeehhhhHhHHHhhcCCCceeCCCCCccccCCcccccCccchhhHHHHcCCChh
Confidence            789999999999999999999999999999999999998888853     4799999999999999876

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

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

Probab=99.89  E-value=6.7e-24  Score=141.83  Aligned_cols=73  Identities=34%  Similarity=0.586  Sum_probs=65.2

Q ss_pred             CCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhcc
Q psy11507         39 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNR  111 (113)
Q Consensus        39 ~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~  111 (113)
                      ..+|.||+++++++||||.+|++|++||||++..+..|.|..++.|.+     ..|++|||+|||++||.++..+..|
T Consensus         6 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r   83 (90)
T cd07169           6 QRTCLICGDRATGLHYGIISCEGCKGFFKRSICNKRVYRCSRDKNCVMSRKQRNRCQYCRLLKCLQMGMNRKAIREDG   83 (90)
T ss_pred             CCCCeecCCcCcceEECcceehhhHHHHHHHhcCCCceecCCCCcccccccccccccccchhhhccccCCHHHhcccc
Confidence            456999999999999999999999999999999999999998888853     4799999999999999998665544

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

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

Probab=99.89  E-value=6e-24  Score=136.90  Aligned_cols=66  Identities=33%  Similarity=0.569  Sum_probs=60.5

Q ss_pred             ceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccch
Q psy11507         42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLD  107 (113)
Q Consensus        42 C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~  107 (113)
                      |.||++++.++||||.+|++|++||||++..+..|.|..++.|.+     ..|++|||+|||++||+++..
T Consensus         1 C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v   71 (73)
T cd06958           1 CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRGNRNCPIDQHHRNQCQYCRLKKCLKVGMRREAV   71 (73)
T ss_pred             CCccCccCcceEEChhhhhhhhhhhhhhhcCCCceeCCCCCcCccCCcccccCccchhhHhhHhCCCHHHc
Confidence            789999999999999999999999999999998999998888853     479999999999999998754

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

>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=99.89  E-value=4.1e-24  Score=137.33  Aligned_cols=65  Identities=31%  Similarity=0.632  Sum_probs=59.9

Q ss_pred             ceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccc
Q psy11507         42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSL  106 (113)
Q Consensus        42 C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~  106 (113)
                      |.||+++++++||||.+|++|++||||++..+..|.|..++.|.+     ..|++|||+|||++||+++.
T Consensus         1 C~VC~~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~   70 (72)
T cd07156           1 CGVCGDRATGYHFNAMTCEGCKGFFRRSMKRKARFTCPFNGDCEITKDNRRHCQACRLKKCLDIGMKKEM   70 (72)
T ss_pred             CCccCccCcccEECcceehhhhhhhchhccCcCccccCCCCccccCCcccccCccchhHHHHHhCCCHHH
Confidence            789999999999999999999999999999888899998888853     47999999999999999864

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

>KOG4846|consensus

Probab=99.89  E-value=2.6e-24  Score=175.20  Aligned_cols=69  Identities=43%  Similarity=0.693  Sum_probs=63.3

Q ss_pred             CcceEcCCCCcceeechhcchhhHHHHHHhHhhccce-ecCCCCCCCCC-----CCcchHHhHhHHhcCCccchh
Q psy11507         40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASL-VSLRGHEPQKK-----SSQIPKEKYNLAYLMSDSLDT  108 (113)
Q Consensus        40 ~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~-~C~~~~~c~~~-----~C~~CR~~kcl~~GM~~~~~~  108 (113)
                      .+|.||||.++||||||.+|+|||+||||+|+.+..| .|-+..+|.+.     .|+.|||+|||+|||+...++
T Consensus       133 ~lCkVCgDkASGfHYGV~aCEGCKGFFRRSIQqkI~YrrClk~e~C~I~R~nRNRCQ~CRfKKCL~vGMSrDaVR  207 (538)
T KOG4846|consen  133 SLCKVCGDKASGFHYGVTACEGCKGFFRRSIQQKIDYRRCLKQEVCEIKRENRNRCQYCRFKKCLDVGMSRDAVR  207 (538)
T ss_pred             EeehhhccccccceeceeecccchHHHHHHHHHhhhHHHHhhhhceehhhhccchhhhhhHHHHHhcccchhhhh
Confidence            5799999999999999999999999999999999999 59999888544     699999999999999998665

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

Probab=99.89  E-value=2.5e-24  Score=139.46  Aligned_cols=71  Identities=32%  Similarity=0.543  Sum_probs=64.6

Q ss_pred             ceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhccC
Q psy11507         42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNRF  112 (113)
Q Consensus        42 C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~~  112 (113)
                      |.||+++++++||||.+|++|++||||++..+..|.|..++.|.+     ..|++|||+|||++||.+...+..|+
T Consensus         1 C~vCg~~~~~~hygv~~C~aC~~FFrR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~   76 (76)
T cd06960           1 CAVCGDRATGKHYGVLSCNGCKGFFRRSVRKNRTYTCRFGGNCVVDKDKRNACRYCRFKKCLEVGMDPEAVQNERD   76 (76)
T ss_pred             CCccCccCcccEECcceeeeehheeCccccCCCceeCCCCCcccccCcccccCccchhhhhhhcCCCHHHcccCCC
Confidence            789999999999999999999999999999888999998888853     47999999999999999987776664

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

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

Probab=99.89  E-value=9.5e-24  Score=135.83  Aligned_cols=65  Identities=48%  Similarity=0.737  Sum_probs=59.8

Q ss_pred             ceEcCCCCcceeechhcchhhHHHHHHhHhhccce-ecCCCCCCCC-----CCCcchHHhHhHHhcCCccc
Q psy11507         42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASL-VSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSL  106 (113)
Q Consensus        42 C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~-~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~  106 (113)
                      |.||+++++++||||.+|++|++||||++..+..| .|..++.|.+     ..|++|||+|||++||++..
T Consensus         1 C~VCg~~~~g~hyGv~~C~aC~~FFRR~v~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~   71 (73)
T cd07158           1 CKVCGDKASGFHYGVHSCEGCKGFFRRTIQHNLTYRRCLNGGKCVIQRKNRNRCQYCRFKKCLSVGMSRNA   71 (73)
T ss_pred             CcccCccCcceEECcchhhHHHHHHhhhhcCCCCcccCCCCCCcCCCccccccCccchhhhhhHccCChHH
Confidence            78999999999999999999999999999999888 7998888853     47999999999999999864

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).

>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=99.89  E-value=6.9e-24  Score=142.62  Aligned_cols=70  Identities=36%  Similarity=0.647  Sum_probs=63.9

Q ss_pred             ceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhcc
Q psy11507         42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNR  111 (113)
Q Consensus        42 C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~  111 (113)
                      |.||+++++++||||.+|++|++||||++..+..|.|..++.|.+     ..|++|||+|||++||..+..+..|
T Consensus         1 C~VCg~~a~g~hyGv~sC~aCk~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~Vq~~r   75 (93)
T cd07167           1 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADR   75 (93)
T ss_pred             CcccCccCcceEECchhhhhHHHHHHHHeeCCCccccCCCCccccCccccCcCCCcccchhhhccCCHHHhhhcc
Confidence            789999999999999999999999999999999999999888853     4799999999999999998766655

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=99.89  E-value=2.7e-24  Score=144.76  Aligned_cols=71  Identities=25%  Similarity=0.446  Sum_probs=64.7

Q ss_pred             cceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhcc
Q psy11507         41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNR  111 (113)
Q Consensus        41 ~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~  111 (113)
                      +|.||+++++++||||.+|.+|++||||++.....|.|..++.|.+     ..|++|||+|||++||.++.....|
T Consensus         2 ~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~r   77 (94)
T cd06966           2 ICGVCGDKALGYNFNAITCESCKAFFRRNALKNKEFKCPFNESCEINVVTRRFCQKCRLDKCFAIGMKKEWIMSEE   77 (94)
T ss_pred             CCeeCCCcCcceEECcceeeeehheehhcccCCCccccCCCCccccCccccccCccchhhhCcccCCCHHHccchh
Confidence            6999999999999999999999999999999888999998888853     4799999999999999998776654

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

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

Probab=99.88  E-value=2.6e-24  Score=144.27  Aligned_cols=75  Identities=28%  Similarity=0.464  Sum_probs=66.0

Q ss_pred             CCCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCC--CCCC-----CCCCcchHHhHhHHhcCCccchhhc
Q psy11507         38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRG--HEPQ-----KKSSQIPKEKYNLAYLMSDSLDTTN  110 (113)
Q Consensus        38 ~~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~--~~c~-----~~~C~~CR~~kcl~~GM~~~~~~~~  110 (113)
                      ...+|.||+++++++||||.+|++|++||||++..+..|.|..+  +.|.     ...|++|||+|||++||++...+..
T Consensus         5 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~   84 (92)
T cd07163           5 LDIPCKVCGDRSSGKHYGIYACDGCSGFFKRSIRRNRQYVCKSKGQGGCPVDKTHRNQCRACRLKKCFEVGMNKDAVQHE   84 (92)
T ss_pred             cCCCCcccCCcCcccEECceeeeeeeeEEeeeecCCCCcCCCCCCCCCCccCCCccccCccchhhhhhhhcCCHHHhhcc
Confidence            35679999999999999999999999999999998999999873  5664     3479999999999999999887776


Q ss_pred             cC
Q psy11507        111 RF  112 (113)
Q Consensus       111 ~~  112 (113)
                      |.
T Consensus        85 r~   86 (92)
T cd07163          85 RG   86 (92)
T ss_pred             cC
Confidence            63

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

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

Probab=99.88  E-value=3.8e-24  Score=141.42  Aligned_cols=69  Identities=33%  Similarity=0.596  Sum_probs=62.6

Q ss_pred             CcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCC-----CCCCcchHHhHhHHhcCCccchh
Q psy11507         40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQ-----KKSSQIPKEKYNLAYLMSDSLDT  108 (113)
Q Consensus        40 ~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~-----~~~C~~CR~~kcl~~GM~~~~~~  108 (113)
                      .+|.||+++++++||||.+|++|++||||++..+..|.|..++.|.     ...|++|||+|||++||......
T Consensus         2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~   75 (84)
T cd06962           2 ELCVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCEMDMYMRRKCQECRLRKCKEMGMLAECLL   75 (84)
T ss_pred             CCCeecCCcCcceEECcceeecceeeeeeeeccCCceecCCCCcCccCccccccCccchhhHHHHhCCChHHcc
Confidence            4599999999999999999999999999999988999999888885     34799999999999999987544

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

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

Probab=99.88  E-value=1.1e-23  Score=142.16  Aligned_cols=74  Identities=35%  Similarity=0.537  Sum_probs=65.9

Q ss_pred             CCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhccC
Q psy11507         39 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNRF  112 (113)
Q Consensus        39 ~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~~  112 (113)
                      ..+|.|||+++.++|||+.+|++|++||||++..+..|.|..++.|..     ..|++|||+|||++||.....+..|.
T Consensus         5 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~V~~~r~   83 (95)
T cd06968           5 VIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVSYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRM   83 (95)
T ss_pred             ccCCcccCCcCcceEECceeehhhHHhhHHheeCCCceecCCCcccccccCCceeccccchhhcccccCChhhcccCcC
Confidence            457999999999999999999999999999999888999998888853     47999999999999999987665553

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

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

Probab=99.88  E-value=3.3e-24  Score=142.19  Aligned_cols=71  Identities=34%  Similarity=0.445  Sum_probs=63.1

Q ss_pred             cceEcCCCCcceeechhcchhhHHHHHHhHhhcc--ceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhcc
Q psy11507         41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQARA--SLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNR  111 (113)
Q Consensus        41 ~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~--~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~  111 (113)
                      +|.||+++++++||||.+|++|++||||++....  .|.|..++.|.+     ..|++|||+|||+|||.......+|
T Consensus         2 ~C~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~~~~   79 (86)
T cd07157           2 TCQVCGEPAAGFHHGAYVCEACKKFFMRSSNAISFTISECPNGGKCIIDKKNRTKCQACRYRKCLNVGMSLGGPRYGR   79 (86)
T ss_pred             CCcccCCcCcccEECcceeeEeeeEEecceecCCCccccCCCCCccccCccccccCccchhhHHhHcCCCcccccccc
Confidence            5999999999999999999999999999998664  788998888853     4799999999999999988766665

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.

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

Probab=99.88  E-value=1.7e-23  Score=138.96  Aligned_cols=68  Identities=31%  Similarity=0.607  Sum_probs=61.7

Q ss_pred             cceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCC-----CCCCcchHHhHhHHhcCCccchh
Q psy11507         41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQ-----KKSSQIPKEKYNLAYLMSDSLDT  108 (113)
Q Consensus        41 ~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~-----~~~C~~CR~~kcl~~GM~~~~~~  108 (113)
                      +|.||+++++++||||.+|++|++||||++.....|.|..++.|.     ...|++|||+|||++||.++...
T Consensus         1 ~C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~   73 (87)
T cd07162           1 ICRVCGDRATGYHFNAMTCEGCKGFFRRAMKRNARLCCPFQKGCVITKSNRRQCQACRLRKCLSIGMKKELIM   73 (87)
T ss_pred             CCcccCCcCcceEECcceehhhHHHHHhhhccCceeEcCCCCceecCCcccccCccchhhHHhHhCCCHHHcc
Confidence            499999999999999999999999999999998999999888885     34799999999999999997543

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

>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors

Probab=99.88  E-value=1.5e-23  Score=133.83  Aligned_cols=64  Identities=44%  Similarity=0.715  Sum_probs=59.2

Q ss_pred             cceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCC-----CCCCcchHHhHhHHhcCCc
Q psy11507         41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQ-----KKSSQIPKEKYNLAYLMSD  104 (113)
Q Consensus        41 ~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~-----~~~C~~CR~~kcl~~GM~~  104 (113)
                      +|.||+++++++||||.+|++|++||||++..+..|.|..++.|.     ...|++|||+|||++||..
T Consensus         1 ~C~vC~~~~~~~hygv~~C~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~   69 (70)
T smart00399        1 LCCVCGDHASGFHFGVCSCRACKAFFRRTVNLRYKYRCDRKNNCSINKRYRCRCRACRLKKCLGVGMDP   69 (70)
T ss_pred             CCeEeCCcCcccEeCCcEechhhhhhhhheeCCCCeecCCCcccccCCCccccCccCcChhHhhccCcC
Confidence            499999999999999999999999999999989889999888785     3479999999999999986

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

Probab=99.88  E-value=1e-23  Score=145.03  Aligned_cols=69  Identities=30%  Similarity=0.598  Sum_probs=62.6

Q ss_pred             CCCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccc
Q psy11507         38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSL  106 (113)
Q Consensus        38 ~~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~  106 (113)
                      .+.+|.||++.++++||||.+|++|++||||++..+..|.|..++.|.+     ..|++|||+|||++||..+.
T Consensus         5 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~   78 (107)
T cd06955           5 VPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEF   78 (107)
T ss_pred             CCCCCeecCCcCcccEECcceeeeecceecceeccCCccccCCCCccccccCCccccccchhHHHHHcCCCchh
Confidence            4567999999999999999999999999999999999999998888853     47999999999999998854

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

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

Probab=99.88  E-value=4.7e-24  Score=137.32  Aligned_cols=66  Identities=33%  Similarity=0.563  Sum_probs=59.4

Q ss_pred             ceEcCCCCcceeechhcchhhHHHHHHhHhhccceecC-CCCCCC-----CCCCcchHHhHhHHhcCCccch
Q psy11507         42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSL-RGHEPQ-----KKSSQIPKEKYNLAYLMSDSLD  107 (113)
Q Consensus        42 C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~-~~~~c~-----~~~C~~CR~~kcl~~GM~~~~~  107 (113)
                      |.||+++++++||||.+|++|++||||++..+..|.|. .++.|.     ...|++|||+|||++||+++..
T Consensus         1 C~vCg~~~~~~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v   72 (73)
T cd07154           1 CKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNLLYTCKAGNGSCVVDKARRNQCQACRLKKCLEVSMNKDAV   72 (73)
T ss_pred             CcccCccCcceEECcceeeeeeeEeeeeecCCCCcccCCCCCCCccCCcccccCccchhhHhhHhCCChHHC
Confidence            78999999999999999999999999999999999998 566674     3479999999999999998753

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

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

Probab=99.88  E-value=4.3e-24  Score=137.18  Aligned_cols=66  Identities=38%  Similarity=0.652  Sum_probs=60.4

Q ss_pred             ceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccch
Q psy11507         42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLD  107 (113)
Q Consensus        42 C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~  107 (113)
                      |.||+++++++||||.+|++|++||||++..+..|.|..++.|.+     ..|++|||+|||++||.++..
T Consensus         1 C~vC~~~~~~~hygv~sC~aC~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v   71 (72)
T cd06916           1 CAVCGDKASGYHYGVLTCEGCKGFFRRSVRRNLEYTCPAGGNCVIDKRNRNRCQACRLKKCLAVGMRKEAV   71 (72)
T ss_pred             CCccCccCcccEECcceeeeeeeeEeEeecCCCCccCCCCCccccCCcccccCccchhhHhhHhCCChHHc
Confidence            789999999999999999999999999999998999998888853     479999999999999998643

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

>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=99.88  E-value=2.4e-23  Score=132.46  Aligned_cols=65  Identities=34%  Similarity=0.660  Sum_probs=56.3

Q ss_pred             CcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCc
Q psy11507         40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSD  104 (113)
Q Consensus        40 ~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~  104 (113)
                      +.|.||++++.+.||||.+|++|++||||++.....+.|..++.|.+     ..|++|||+|||++||..
T Consensus         1 ~~C~VCg~~~~~~~ygv~sC~~C~~FFrR~~~~~~~~~C~~~~~C~i~~~~~~~C~~CRf~KCl~~GM~k   70 (70)
T PF00105_consen    1 KKCKVCGDPASGYHYGVLSCNACKMFFRRSVKKKKPYKCKKNGNCKIDKDNRRKCRSCRFQKCLEVGMKK   70 (70)
T ss_dssp             -BSTTTSSBESEEETTEEEEHHHHHHHHHHHHTTCG-STSSSST---STTTTTTSHHHHHHHHHHTTBSG
T ss_pred             CCCeECCCccCcccccccccccceeeeeecccccccccccccccccccccCCCEeCcchHHHHHHHCCcC
Confidence            36999999999999999999999999999999998899998877743     479999999999999973

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 ....

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

Probab=99.88  E-value=7.8e-24  Score=141.20  Aligned_cols=73  Identities=41%  Similarity=0.644  Sum_probs=65.3

Q ss_pred             CcceEcCCCCcceeechhcchhhHHHHHHhHhhccce-ecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhccC
Q psy11507         40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASL-VSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNRF  112 (113)
Q Consensus        40 ~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~-~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~~  112 (113)
                      .+|.||++++.++|||+.+|++|++||||++..+..| .|..++.|.+     ..|++|||+|||++||.++..+..|.
T Consensus         4 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~   82 (89)
T cd07166           4 VLCKVCGDKASGFHYGVHACEGCKGFFRRSIQQKIQYRKCTKNETCSIMRINRNRCQYCRFKKCLAVGMSRDAVRFGRI   82 (89)
T ss_pred             CCCcccCccCcceEEChhhhhhHhhEecceeEcCCcchhhccCCcccccccccccccchhhhhcccccCCHHHhcCCCC
Confidence            4699999999999999999999999999999988888 5988888853     47999999999999999988777663

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

>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=3.1e-24  Score=141.12  Aligned_cols=71  Identities=27%  Similarity=0.464  Sum_probs=63.3

Q ss_pred             ceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCC-CCCCCC-----CCCcchHHhHhHHhcCCccchhhccC
Q psy11507         42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLR-GHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNRF  112 (113)
Q Consensus        42 C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~-~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~~  112 (113)
                      |.||+++++++||||.+|++|++||||++.....|.|.. ++.|.+     ..|++|||+|||++||..+..+..|.
T Consensus         1 C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~   77 (82)
T cd06957           1 CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKGIIYTCIAGNGNCVVDKARRNWCPFCRLQKCFAVGMNRAAVQEERG   77 (82)
T ss_pred             CCccCccCcceEECcceEeeeeeEEEEeecCCCceEccCccCCCccCCCccCcccCcchhhcccccCCHHHhccccC
Confidence            789999999999999999999999999999999999984 566743     47999999999999999987776663

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

>KOG4215|consensus

Probab=99.87  E-value=4.6e-23  Score=165.75  Aligned_cols=75  Identities=24%  Similarity=0.459  Sum_probs=68.0

Q ss_pred             CCCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhccC
Q psy11507         38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNRF  112 (113)
Q Consensus        38 ~~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~~  112 (113)
                      ....|.||||++.|.|||+.+|+|||+||||+|.++..|+|+-+++|..     +.||+|||+||+++||..+..+.-|+
T Consensus        18 ~~~~CaICGDkaTGKHYGA~SCdGCKGFFRRSVrk~~~YtCRF~k~C~VDKdkRNaCRyCRfqKC~~aGMK~eAiQnERD   97 (432)
T KOG4215|consen   18 VAEFCAICGDKATGKHYGAISCDGCKGFFRRSVRKNHQYTCRFNKQCVVDKDKRNACRYCRFQKCVRAGMKREAIQNERD   97 (432)
T ss_pred             ccchhheeCCcccccccceeecCcchHHHHHHHHhcceeeeeccccccccchhhhhhhHhhHHHHHHhcccHHhhhcccc
Confidence            3567999999999999999999999999999999999999999988853     26999999999999999987777664

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

Probab=99.87  E-value=3.8e-23  Score=136.54  Aligned_cols=70  Identities=39%  Similarity=0.610  Sum_probs=61.3

Q ss_pred             cceEcCCCCcceeechhcchhhHHHHHHhHhhcccee-cCCCCCCC-----CCCCcchHHhHhHHhcCCccchhhccC
Q psy11507         41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLV-SLRGHEPQ-----KKSSQIPKEKYNLAYLMSDSLDTTNRF  112 (113)
Q Consensus        41 ~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~-C~~~~~c~-----~~~C~~CR~~kcl~~GM~~~~~~~~~~  112 (113)
                      +|.||++.++++||||.+|++|++||||++..+..|. |...  |.     ...|++|||+|||++||..+..+..|.
T Consensus         1 ~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~~C~~~--C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~   76 (84)
T cd06965           1 ECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLVYKPCDLS--CKIHKKSRNKCQYCRFQKCLNVGMSHNAIRFGRM   76 (84)
T ss_pred             CCcccCccCcceEEChhhhhhhhhheeeeeecCCCccccccC--CCcCccccccccchhhhhhhhccCCHHHcccCCC
Confidence            4999999999999999999999999999999888885 8754  53     347999999999999999987776663

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

>KOG4217|consensus

Probab=99.85  E-value=3.4e-22  Score=164.86  Aligned_cols=73  Identities=40%  Similarity=0.628  Sum_probs=66.5

Q ss_pred             CCCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCC-----CCCCcchHHhHhHHhcCCccchhhc
Q psy11507         38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQ-----KKSSQIPKEKYNLAYLMSDSLDTTN  110 (113)
Q Consensus        38 ~~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~-----~~~C~~CR~~kcl~~GM~~~~~~~~  110 (113)
                      ..+.|.||||.+..-||||.+|+|||+||+|+|+++.+|+|..+++|-     .+.|++|||+|||+|||..+++++.
T Consensus       268 ~e~~CAVCgDnAaCqHYGvRTCEGCKGFFKRTVQKnaKYvClanKnCPVDKRrRnRCQyCRfQKCL~VGMVKEVVRtd  345 (605)
T KOG4217|consen  268 AEGLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLAVGMVKEVVRTD  345 (605)
T ss_pred             ccceeeecCChHHhhhcCccccccchHHHHHHHhcCCeeEeecCCCCCcchhhhhhchhhhHhHHHHhhhhhhheecc
Confidence            367899999999999999999999999999999999999999999883     2369999999999999999877653

>KOG4216|consensus

Probab=99.84  E-value=8e-22  Score=159.67  Aligned_cols=70  Identities=36%  Similarity=0.579  Sum_probs=63.9

Q ss_pred             CCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCC-----CCCCcchHHhHhHHhcCCccchh
Q psy11507         39 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQ-----KKSSQIPKEKYNLAYLMSDSLDT  108 (113)
Q Consensus        39 ~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~-----~~~C~~CR~~kcl~~GM~~~~~~  108 (113)
                      -.+|.||||.++|.||||.+|+|||+||||+...+..|.|.+.++|.     .+.|++||++|||++||++..+-
T Consensus        46 vIPCKiCGDKSSGiHYGVITCEGCKGFFRRSQ~s~a~YsCpRqknC~iDRtnRNRCQ~CRLqKClaLGMSRDAVK  120 (479)
T KOG4216|consen   46 IIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQSNANYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVK  120 (479)
T ss_pred             EEeeeeccCCCCcceeeeEeeccchHhhhhhhhccccccCCcccCCcccccccchhhHHHHHHHHHhccchhhHH
Confidence            35799999999999999999999999999999999999999999994     34799999999999999997543

>KOG4218|consensus

Probab=99.78  E-value=5.1e-20  Score=147.82  Aligned_cols=74  Identities=34%  Similarity=0.588  Sum_probs=67.3

Q ss_pred             CCCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCC-----CCCCcchHHhHhHHhcCCccchhhcc
Q psy11507         38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQ-----KKSSQIPKEKYNLAYLMSDSLDTTNR  111 (113)
Q Consensus        38 ~~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~-----~~~C~~CR~~kcl~~GM~~~~~~~~~  111 (113)
                      ..+.|.||||+.+|+|||..+|+.|++||+|+|+.+..|+|....+|.     .+.|-+|||+|||.|||.-+.+++.|
T Consensus        14 l~ElCPVCGDkVSGYHYGLLTCESCKGFFKRTVQNnK~YtC~e~qnC~iDkTqRKRCP~CRFQKCLtvGMklEAVRADR   92 (475)
T KOG4218|consen   14 LGELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKQYTCSEEQNCHIDKTQRKRCPSCRFQKCLTVGMKLEAVRADR   92 (475)
T ss_pred             cccccccccCccccceeeeeehhhhhhHHHHHhhcCcceecccccccccchHhhccCCchhHHHHhhhhhhHHHHHHhh
Confidence            356899999999999999999999999999999999999999998884     44799999999999999988777655

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	113
1lo1_A	98	Estrogen Related Receptor 2 Dna Binding Domain In C		5e-15
1hlz_A	94	Crystal Structure Of The Orphan Nuclear Receptor Re		4e-10
3dzu_D	419	Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp		2e-09
1hcq_A	84	The Crystal Structure Of The Estrogen Receptor Dna-		3e-09
1hcp_A	76	Dna Recognition By The Oestrogen Receptor: From Sol		3e-09
4aa6_E	71	The Oestrogen Receptor Recognizes An Imperfectly Pa		3e-09
4aa6_A	71	The Oestrogen Receptor Recognizes An Imperfectly Pa		4e-09
2a66_A	113	Human Liver Receptor Homologue Dna-Binding Domain (		7e-09
2env_A	88	Solution Sturcture Of The C4-Type Zinc Finger Domai		9e-09
1lat_A	82	Glucocorticoid Receptor MutantDNA COMPLEX Length =		1e-08
2ff0_A	102	Solution Structure Of Steroidogenic Factor 1 Dna Bi		1e-08
3dzu_A	467	Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp		1e-08
2han_A	93	Structural Basis Of Heterodimeric Ecdysteroid Recep		3e-08
1r0o_A	86	Crystal Structure Of The Heterodimeric Ecdysone Rec		4e-08
1ynw_B	99	Crystal Structure Of Vitamin D Receptor And 9-Cis R		4e-08
4hn6_A	114	Gr Dna Binding Domain R460d/d462r - Tslp Ngre Compl		4e-08
2han_B	119	Structural Basis Of Heterodimeric Ecdysteroid Recep		5e-08
2c7a_A	78	Structure Of The Progesterone Receptor-Dna Complex		5e-08
4hn5_A	117	Gr Dna Binding Domain - Tslp Ngre Complex Length =		5e-08
1cit_A	89	Dna-Binding Mechanism Of The Monomeric Orphan Nucle		6e-08
1dsz_B	85	Structure Of The RxrRAR DNA-Binding Domain Heterodi		8e-08
1rxr_A	83	High Resolution Solution Structure Of The Retinoid		8e-08
1by4_A	82	Structure And Mechanism Of The Homodimeric Assembly		8e-08
1hra_A	80	The Solution Structure Of The Human Retinoic Acid R		9e-08
2nll_B	103	Retinoid X Receptor-Thyroid Hormone Receptor Dna-Bi		1e-07
3m9e_A	105	Thyroid Hormone Beta Dna Binding Domain Homodimer W		1e-07
1r0n_A	81	Crystal Structure Of Heterodimeric Ecdsyone Recepto		1e-07
1dsz_A	86	Structure Of The RxrRAR DNA-Binding Domain Heterodi		1e-07
1r0n_B	109	Crystal Structure Of Heterodimeric Ecdsyone Recepto		2e-07
1r4i_A	105	Crystal Structure Of Androgen Receptor Dna-Binding		2e-07
1r4o_A	92	Crystallographic Analysis Of The Interaction Of The		2e-07
1r4r_B	92	Crystallographic Analysis Of The Interaction Of The		2e-07
1kb2_A	110	Crystal Structure Of Vdr Dna-Binding Domain Bound T		3e-07
1glu_A	81	Crystallographic Analysis Of The Interaction Of The		3e-07
1ynw_A	110	Crystal Structure Of Vitamin D Receptor And 9-Cis R		3e-07
2nll_A	66	Retinoid X Receptor-Thyroid Hormone Receptor Dna-Bi		4e-07
3g6t_A	91	Gr Gamma Dna-Binding Domain:fkbp5 16bp Complex-34 L		4e-07
3cbb_A	78	Crystal Structure Of Hepatocyte Nuclear Factor 4alp		1e-06
2gda_A	72	Refined Solution Structure Of The Glucocorticoid Re		1e-06
1gdc_A	72	Refined Solution Structure Of The Glucocorticoid Re		1e-06
3g9p_B	90	Gr Dna Binding Domain:sgk 16bp Complex-7 Length = 9		1e-06
2ebl_A	89	Solution Structure Of The Zinc Finger, C4-type Doma		3e-06
1rgd_A	71	Structure Refinement Of The Glucocorticoid Receptor		4e-06

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

Iteration: 1
 Score = 75.9 bits (185), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 31/36 (86%), Positives = 35/36 (97%)
Query: 37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQA 72
          +P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQ 
Sbjct: 2  IPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQG 37

>pdb|1HLZ|A Chain A, Crystal Structure Of The Orphan Nuclear Receptor Rev- Erb(Alpha) Dna-Binding Domain Bound To Its Cognate Response Element Length = 94

Iteration: 1
 Score = 59.7 bits (143), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 24/31 (77%), Positives = 27/31 (87%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          LC VCGDVASGFHYGV +CE CK FF+R+IQ
Sbjct: 9  LCKVCGDVASGFHYGVLACEGCKGFFRRSIQ 39

>pdb|3DZU|D Chain D, Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex On Dna Bound With Bvt.13, 9-Cis Retinoic Acid And Ncoa2 Peptide Length = 419

Iteration: 1
 Score = 57.4 bits (137), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 22/32 (68%), Positives = 26/32 (81%)
Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
          C VCGD ASGFHYGV +CE CK FF+RTI+ +
Sbjct: 53 CRVCGDKASGFHYGVHACEGCKGFFRRTIRLK 84

>pdb|1HCQ|A Chain A, The Crystal Structure Of The Estrogen Receptor Dna-Binding Domain Bound To Dna: How Receptors Discriminate Between Their Response Elements Length = 84

Iteration: 1
 Score = 57.0 bits (136), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 24/33 (72%), Positives = 26/33 (78%)
Query: 40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQA 72
          R C VC D ASG+HYGV SCE CKAFFKR+IQ 
Sbjct: 5  RYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQG 37

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 24/33 (72%), Positives = 26/33 (78%)
Query: 40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQA 72
          R C VC D ASG+HYGV SCE CKAFFKR+IQ 
Sbjct: 5  RYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQG 37

>pdb|4AA6|E Chain E, The Oestrogen Receptor Recognizes An Imperfectly Palindromic Response Element Through An Alternative Side- Chain Conformation Length = 71

Iteration: 1
 Score = 56.6 bits (135), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 24/33 (72%), Positives = 26/33 (78%)
Query: 40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQA 72
          R C VC D ASG+HYGV SCE CKAFFKR+IQ 
Sbjct: 2  RYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQG 34

>pdb|4AA6|A Chain A, The Oestrogen Receptor Recognizes An Imperfectly Palindromic Response Element Through An Alternative Side- Chain Conformation Length = 71

Iteration: 1
 Score = 56.6 bits (135), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 24/33 (72%), Positives = 26/33 (78%)
Query: 40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQA 72
          R C VC D ASG+HYGV SCE CKAFFKR+IQ 
Sbjct: 2  RYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQG 34

>pdb|2A66|A Chain A, Human Liver Receptor Homologue Dna-Binding Domain (Hlrh-1 Dbd) In Complex With Dsdna From The Hcyp7a1 Promoter Length = 113

Iteration: 1
 Score = 55.5 bits (132), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 23/50 (46%), Positives = 30/50 (60%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQKKSSQ 90
          LC VCGD  SG+HYG+ +CE+CK FFKRT+Q       +     Q   +Q
Sbjct: 11 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQNCQIDKTQ 60

>pdb|2ENV|A Chain A, Solution Sturcture Of The C4-Type Zinc Finger Domain From Human Peroxisome Proliferator-Activated Receptor Delta Length = 88

Iteration: 1
 Score = 55.1 bits (131), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 27/56 (48%), Positives = 36/56 (64%), Gaps = 6/56 (10%)
Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQKKSSQIPKEKYN 97
          C VCGD ASGFHYGV +CE CK FF+RTI+ +        +E  ++S +I K+  N
Sbjct: 10 CRVCGDKASGFHYGVHACEGCKGFFRRTIRMKLE------YEKCERSCKIQKKNRN 59

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

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 23/36 (63%), Positives = 27/36 (75%)
Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
          P R CLVC D ASG HYGV +CE CKAFFKR ++ +
Sbjct: 3  PARPCLVCSDEASGCHYGVLTCEGCKAFFKRAVEGQ 38

>pdb|2FF0|A Chain A, Solution Structure Of Steroidogenic Factor 1 Dna Binding Domain Bound To Its Target Sequence In The Inhibin Alpha- Subunit Promoter Length = 102

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 21/31 (67%), Positives = 26/31 (83%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          LC VCGD  SG+HYG+ +CE+CK FFKRT+Q
Sbjct: 3  LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQ 33

>pdb|3DZU|A Chain A, Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex On Dna Bound With Bvt.13, 9-Cis Retinoic Acid And Ncoa2 Peptide Length = 467

Iteration: 1
 Score = 54.3 bits (129), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 20/33 (60%), Positives = 26/33 (78%)
Query: 39  RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
           + +C +CGD +SG HYGV SCE CK FFKRT++
Sbjct: 137 KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVR 169

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 22/33 (66%), Positives = 26/33 (78%)
Query: 39 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          + LC +CGD ASG HYGV SCE CK FFKRT++
Sbjct: 10 KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVR 42

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 22/33 (66%), Positives = 26/33 (78%)
Query: 39 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          + LC +CGD ASG HYGV SCE CK FFKRT++
Sbjct: 8  KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVR 40

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 20/35 (57%), Positives = 26/35 (74%)
Query: 37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
            + +C +CGD +SG HYGV SCE CK FFKRT++
Sbjct: 1  FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVR 35

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 21/40 (52%), Positives = 28/40 (70%)
Query: 34 EEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
          +   P +LCLVC D ASG HYGV +C +CK FFKR ++ +
Sbjct: 21 QSNAPPKLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQ 60

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 24/48 (50%), Positives = 31/48 (64%), Gaps = 5/48 (10%)
Query: 27 GSTDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARA 74
          GS   ++EE     LCLVCGD ASG+HY   +CE CK FF+R++   A
Sbjct: 1  GSAPRVQEE-----LCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSA 43

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 20/36 (55%), Positives = 29/36 (80%)
Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
          P+++CL+CGD ASG HYGV +C +CK FFKR ++ +
Sbjct: 1  PQKICLICGDEASGCHYGVLTCGSCKVFFKRAMEGQ 36

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 21/36 (58%), Positives = 27/36 (75%)
Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
          P +LCLVC D ASG HYGV +C +CK FFKR ++ +
Sbjct: 28 PPKLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQ 63

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 23/38 (60%), Positives = 26/38 (68%)
Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSL 79
          C VCGD AS  HYGV +CE CK FFKRT+Q  A  + L
Sbjct: 3  CAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICL 40

>pdb|1DSZ|B Chain B, Structure Of The RxrRAR DNA-Binding Domain Heterodimer In Complex With The Retinoic Acid Response Element Dr1 Length = 85

Iteration: 1
 Score = 52.0 bits (123), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 20/35 (57%), Positives = 26/35 (74%)
Query: 37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
            + +C +CGD +SG HYGV SCE CK FFKRT++
Sbjct: 3  FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVR 37

>pdb|1RXR|A Chain A, High Resolution Solution Structure Of The Retinoid X Receptor Dna Binding Domain, Nmr, 20 Structure Length = 83

Iteration: 1
 Score = 52.0 bits (123), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 20/31 (64%), Positives = 25/31 (80%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          +C +CGD +SG HYGV SCE CK FFKRT++
Sbjct: 5  ICAICGDRSSGKHYGVYSCEGCKGFFKRTVR 35

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 20/35 (57%), Positives = 26/35 (74%)
Query: 37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
            + +C +CGD +SG HYGV SCE CK FFKRT++
Sbjct: 3  FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVR 37

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 21/37 (56%), Positives = 29/37 (78%), Gaps = 2/37 (5%)
Query: 37 LPR--RLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          +PR  + C VC D +SG+HYGV++CE CK FF+R+IQ
Sbjct: 1  MPRVYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQ 37

>pdb|2NLL|B Chain B, Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding Domain Heterodimer Bound To Thyroid Response Element Dna Length = 103

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 20/31 (64%), Positives = 25/31 (80%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          LC+VCGD A+G+HY   +CE CK FF+RTIQ
Sbjct: 3  LCVVCGDKATGYHYRCITCEGCKGFFRRTIQ 33

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 20/31 (64%), Positives = 25/31 (80%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          LC+VCGD A+G+HY   +CE CK FF+RTIQ
Sbjct: 5  LCVVCGDKATGYHYRCITCEGCKGFFRRTIQ 35

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 20/35 (57%), Positives = 26/35 (74%)
Query: 37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
            + +C +CGD +SG HYGV SCE CK FFKRT++
Sbjct: 1  FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVR 35

>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 = 51.2 bits (121), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 19/30 (63%), Positives = 25/30 (83%)
Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          C VC D +SG+HYGV++CE CK FF+R+IQ
Sbjct: 7  CFVCQDKSSGYHYGVSACEGCKGFFRRSIQ 36

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

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 19/30 (63%), Positives = 24/30 (80%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTI 70
          LCLVCGD ASG+HY   +CE CK FF+R++
Sbjct: 8  LCLVCGDRASGYHYNALTCEGCKGFFRRSV 37

>pdb|1R4I|A Chain A, Crystal Structure Of Androgen Receptor Dna-Binding Domain Bound To A Direct Repeat Response Element Length = 105

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 19/36 (52%), Positives = 26/36 (72%)
Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
          P++ CL+CGD ASG HYG  +C +CK FFKR  + +
Sbjct: 6  PQKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGK 41

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

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 21/36 (58%), Positives = 26/36 (72%)
Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
          P R CLVC D ASG HYGV +C +CK FFKR ++ +
Sbjct: 3  PARPCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQ 38

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

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 21/36 (58%), Positives = 26/36 (72%)
Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
          P R CLVC D ASG HYGV +C +CK FFKR ++ +
Sbjct: 3  PARPCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQ 38

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

Iteration: 1
 Score = 50.4 bits (119), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 18/35 (51%), Positives = 27/35 (77%)
Query: 40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQARA 74
          R+C VCGD A+GFH+   +CE CK FF+R+++ +A
Sbjct: 7  RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKA 41

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

Iteration: 1
 Score = 50.4 bits (119), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 21/36 (58%), Positives = 26/36 (72%)
Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
          P R CLVC D ASG HYGV +C +CK FFKR ++ +
Sbjct: 3  PARPCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQ 38

>pdb|1YNW|A Chain A, Crystal Structure Of Vitamin D Receptor And 9-Cis Retinoic Acid Receptor Dna-Binding Domains Bound To A Dr3 Response Element Length = 110

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 18/35 (51%), Positives = 27/35 (77%)
Query: 40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQARA 74
          R+C VCGD A+GFH+   +CE CK FF+R+++ +A
Sbjct: 7  RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKA 41

>pdb|2NLL|A Chain A, Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding Domain Heterodimer Bound To Thyroid Response Element Dna Length = 66

Iteration: 1
 Score = 50.1 bits (118), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 20/30 (66%), Positives = 24/30 (80%)
Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          C +CGD +SG HYGV SCE CK FFKRT++
Sbjct: 1  CAICGDRSSGKHYGVYSCEGCKGFFKRTVR 30

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 20/33 (60%), Positives = 25/33 (75%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
          +CLVC D ASG HYGV +C +CK FFKR ++ R
Sbjct: 4  MCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGR 36

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 17/31 (54%), Positives = 25/31 (80%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          LC +CGD A+G HYG +SC+ CK FF+R+++
Sbjct: 2  LCAICGDRATGKHYGASSCDGCKGFFRRSVR 32

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 20/33 (60%), Positives = 25/33 (75%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
          LCLVC D ASG HYGV +C +CK FFKR ++ +
Sbjct: 1  LCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQ 33

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 20/33 (60%), Positives = 25/33 (75%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
          LCLVC D ASG HYGV +C +CK FFKR ++ +
Sbjct: 1  LCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQ 33

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 19/33 (57%), Positives = 25/33 (75%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
          +CLVC D ASG HYGV +C +CK FFKR ++ +
Sbjct: 4  MCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQ 36

>pdb|2EBL|A Chain A, Solution Structure Of The Zinc Finger, C4-type Domain Of Human Coup Transcription Factor 1 Length = 89

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 18/30 (60%), Positives = 25/30 (83%)
Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          C+VCGD +SG HYG  +CE CK+FFKR+++
Sbjct: 10 CVVCGDKSSGKHYGQFTCEGCKSFFKRSVR 39

>pdb|1RGD|A Chain A, Structure Refinement Of The Glucocorticoid Receptor-Dna Binding Domain From Nmr Data By Relaxation Matrix Calculations Length = 71

Iteration: 1
 Score = 46.2 bits (108), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 19/32 (59%), Positives = 24/32 (75%)
Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
          CLVC D ASG HYGV +C +CK FFKR ++ +
Sbjct: 1  CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQ 32

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	113
1lo1_A	98	Steroid hormone receptor ERR2; estrogen related re	2e-20
1r4i_A	105	Androgen receptor; AR, steroid receptor, protein-D	3e-19
1hcq_A	84	Protein (estrogen receptor); protein-DNA complex,	4e-19
1ynw_B	99	Retinoic acid receptor RXR-alpha, retinoid X recep	7e-19
1dsz_B	85	RXR-alpha, retinoic acid receptor RXR-alpha; RAR,	1e-18
1a6y_A	94	Orphan nuclear receptor NR1D1; orphan receptor, DN	2e-18
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	2e-18
2a66_A	113	Orphan nuclear receptor NR5A2; protein-DNA complex	2e-18
2han_A	93	Protein ultraspiracle; transcription regulation, t	5e-18
1dsz_A	86	RAR-alpha, retinoic acid receptor alpha; RAR, nucl	7e-18
1kb2_A	110	Vitamin D3 receptor; VDR, nuclear receptor, protei	9e-18
3g9m_A	90	Glucocorticoid receptor; glucocorticoid, DNA-bindi	1e-17
1cit_A	89	NGFI-B, protein (orphan nuclear receptor NGFI-B);	2e-17
2ebl_A	89	COUP transcription factor 1; DNA-binding, metal-bi	1e-16
2han_B	119	Ecdysone receptor; transcription regulation, trans	2e-16
3cbb_A	78	HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DN	3e-16
2nll_B	103	Protein (thyroid hormone receptor); complex (trans	3e-16
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	3e-14

>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 = 77.8 bits (192), Expect = 2e-20
 Identities = 31/35 (88%), Positives = 35/35 (100%)

Query: 37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          +P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQ
Sbjct: 2  IPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQ 36

>1r4i_A Androgen receptor; AR, steroid receptor, protein-DNA complex, transcription/DNA complex; 3.10A {Rattus norvegicus} SCOP: g.39.1.2 Length = 105

 Score = 74.8 bits (184), Expect = 3e-19
 Identities = 19/34 (55%), Positives = 25/34 (73%)

Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          P++ CL+CGD ASG HYG  +C +CK FFKR  +
Sbjct: 6  PQKTCLICGDEASGAHYGALTCGSCKVFFKRAAE 39

>1hcq_A Protein (estrogen receptor); protein-DNA complex, complexed with drug, transcription/DNA complex; HET: DNA; 2.40A {Homo sapiens} SCOP: g.39.1.2 PDB: 1hcp_A 4aa6_A Length = 84

 Score = 74.3 bits (183), Expect = 4e-19
 Identities = 24/34 (70%), Positives = 26/34 (76%)

Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
            R C VC D ASG+HYGV SCE CKAFFKR+IQ
Sbjct: 3  ETRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQ 36

>1ynw_B Retinoic acid receptor RXR-alpha, retinoid X receptor; VDR, nuclear receptor, protein-DNA complex, transcripti complex; 3.00A {Homo sapiens} SCOP: g.39.1.2 Length = 99

 Score = 74.0 bits (182), Expect = 7e-19
 Identities = 20/35 (57%), Positives = 26/35 (74%)

Query: 37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
            + +C +CGD +SG HYGV SCE CK FFKRT++
Sbjct: 1  FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVR 35

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

 Score = 72.7 bits (179), Expect = 1e-18
 Identities = 20/35 (57%), Positives = 26/35 (74%)

Query: 37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
            + +C +CGD +SG HYGV SCE CK FFKRT++
Sbjct: 3  FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVR 37

>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 = 72.8 bits (179), Expect = 2e-18
 Identities = 24/34 (70%), Positives = 27/34 (79%)

Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
             LC VCGDVASGFHYGV +CE CK FF+R+IQ
Sbjct: 6  MVLLCKVCGDVASGFHYGVLACEGCKGFFRRSIQ 39

>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 = 77.8 bits (191), Expect = 2e-18
 Identities = 20/34 (58%), Positives = 26/34 (76%)

Query: 38  PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
            + +C +CGD +SG HYGV SCE CK FFKRT++
Sbjct: 136 TKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVR 169

>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 = 72.9 bits (179), Expect = 2e-18
 Identities = 23/41 (56%), Positives = 29/41 (70%)

Query: 31 GIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          G   +E    LC VCGD  SG+HYG+ +CE+CK FFKRT+Q
Sbjct: 1  GEFGDEDLEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQ 41

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

 Score = 71.6 bits (176), Expect = 5e-18
 Identities = 22/34 (64%), Positives = 26/34 (76%)

Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
           + LC +CGD ASG HYGV SCE CK FFKRT++
Sbjct: 9  SKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVR 42

>1dsz_A RAR-alpha, retinoic acid receptor alpha; RAR, nuclear receptor, protein-DNA, transcription/DNA complex; HET: DNA; 1.70A {Homo sapiens} SCOP: g.39.1.2 PDB: 1hra_A Length = 86

 Score = 71.2 bits (175), Expect = 7e-18
 Identities = 19/34 (55%), Positives = 26/34 (76%)

Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
            + C VC D +SG+HYGV++CE CK FF+R+IQ
Sbjct: 3  IYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQ 36

>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 = 71.4 bits (175), Expect = 9e-18
 Identities = 17/37 (45%), Positives = 26/37 (70%)

Query: 35 EELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          +    R+C VCGD A+GFH+   +CE CK FF+R+++
Sbjct: 2  DRNVPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMK 38

>3g9m_A Glucocorticoid receptor; glucocorticoid, DNA-binding, allostery, lever ARM, transcription, hormone; HET: DNA; 1.61A {Rattus norvegicus} PDB: 3g6p_A* 3g6q_B* 3g6r_B* 3g6u_A* 3g8u_A* 3g8x_A* 3g97_B* 3g99_A* 3g9i_A* 3g9j_A* 3fyl_A* 3g9o_B* 3g9p_B* 3g6t_A* 1r4o_A 1r4r_A 1glu_A* 1gdc_A 2gda_A 1rgd_A ... Length = 90

 Score = 70.5 bits (173), Expect = 1e-17
 Identities = 19/32 (59%), Positives = 24/32 (75%)

Query: 40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
           +CLVC D ASG HYGV +C +CK FFKR ++
Sbjct: 3  HMCLVCSDEASGCHYGVLTCGSCKVFFKRAVE 34

>1cit_A NGFI-B, protein (orphan nuclear receptor NGFI-B); early immediate response gene product, transcription factor, monomeric protein-DNA complex; HET: DNA; 2.70A {Rattus norvegicus} SCOP: g.39.1.2 Length = 89

 Score = 70.1 bits (172), Expect = 2e-17
 Identities = 21/30 (70%), Positives = 23/30 (76%)

Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          C VCGD AS  HYGV +CE CK FFKRT+Q
Sbjct: 3  CAVCGDNASCQHYGVRTCEGCKGFFKRTVQ 32

>2ebl_A COUP transcription factor 1; DNA-binding, metal-binding, nuclear protein, receptor, transcription regulation, zinc, EAR3, erbal3 tfcoup1; NMR {Homo sapiens} Length = 89

 Score = 68.1 bits (167), Expect = 1e-16
 Identities = 18/34 (52%), Positives = 25/34 (73%)

Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
              C+VCGD +SG HYG  +CE CK+FFKR+++
Sbjct: 6  SGIECVVCGDKSSGKHYGQFTCEGCKSFFKRSVR 39

>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 = 68.4 bits (167), Expect = 2e-16
 Identities = 19/32 (59%), Positives = 24/32 (75%)

Query: 40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
           LCLVCGD ASG+HY   +CE CK FF+R++ 
Sbjct: 9  ELCLVCGDRASGYHYNALTCEGCKGFFRRSVT 40

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

 Score = 66.9 bits (164), Expect = 3e-16
 Identities = 17/31 (54%), Positives = 25/31 (80%)

Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          LC +CGD A+G HYG +SC+ CK FF+R+++
Sbjct: 2  LCAICGDRATGKHYGASSCDGCKGFFRRSVR 32

>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 = 67.5 bits (165), Expect = 3e-16
 Identities = 20/31 (64%), Positives = 25/31 (80%)

Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          LC+VCGD A+G+HY   +CE CK FF+RTIQ
Sbjct: 3  LCVVCGDKATGYHYRCITCEGCKGFFRRTIQ 33

>3dzy_D Peroxisome proliferator-activated receptor gamma; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_D* 3e00_D* 2env_A Length = 419

 Score = 66.2 bits (161), Expect = 3e-14
 Identities = 24/54 (44%), Positives = 30/54 (55%)

Query: 18 TYTVEQKFRGSTDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
           Y+ + +            L    C VCGD ASGFHYGV +CE CK FF+RTI+
Sbjct: 29 YYSEKTQLYNKPHEEPSNSLMAIECRVCGDKASGFHYGVHACEGCKGFFRRTIR 82

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	113
2ebl_A	89	COUP transcription factor 1; DNA-binding, metal-bi	99.94
2han_A	93	Protein ultraspiracle; transcription regulation, t	99.94
3cbb_A	78	HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DN	99.94
1dsz_B	85	RXR-alpha, retinoic acid receptor RXR-alpha; RAR,	99.94
1hcq_A	84	Protein (estrogen receptor); protein-DNA complex,	99.93
1dsz_A	86	RAR-alpha, retinoic acid receptor alpha; RAR, nucl	99.93
1ynw_B	99	Retinoic acid receptor RXR-alpha, retinoid X recep	99.93
1lo1_A	98	Steroid hormone receptor ERR2; estrogen related re	99.93
1cit_A	89	NGFI-B, protein (orphan nuclear receptor NGFI-B);	99.93
2a66_A	113	Orphan nuclear receptor NR5A2; protein-DNA complex	99.92
1a6y_A	94	Orphan nuclear receptor NR1D1; orphan receptor, DN	99.92
4hn5_A	117	Glucocorticoid receptor; glucocorticoid receptor,	99.92
3g9m_A	90	Glucocorticoid receptor; glucocorticoid, DNA-bindi	99.92
2han_B	119	Ecdysone receptor; transcription regulation, trans	99.92
1kb2_A	110	Vitamin D3 receptor; VDR, nuclear receptor, protei	99.92
2nll_B	103	Protein (thyroid hormone receptor); complex (trans	99.92
1r4i_A	105	Androgen receptor; AR, steroid receptor, protein-D	99.91
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	99.88
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	99.87
2lze_A	87	A primordial catalytic fold generated by in vitro	99.53

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

Probab=99.94  E-value=2.3e-27  Score=157.44  Aligned_cols=74  Identities=30%  Similarity=0.458  Sum_probs=67.7

Q ss_pred             CCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhccC
Q psy11507         39 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNRF  112 (113)
Q Consensus        39 ~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~~  112 (113)
                      ..+|.||+++++|+||||.+|++|++||||++..+..|.|..+++|.+     ..|++|||+|||+|||..+..+.+|.
T Consensus         7 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~   85 (89)
T 2ebl_A            7 GIECVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRANRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQRGSG   85 (89)
T ss_dssp             SCBCTTTCSBCCSEETTEECCHHHHHHHHHHHTTTCCCCCSSCSCCCCCSSSSSCCSHHHHHHHHHHTCCHHHHSCSCC
T ss_pred             CCCCcEeCCCCcceEeCchhhHHhhhhhheeeeeccceecccCccCCcCccCccccccchHHHhhhccCCHHHcccCCC
Confidence            457999999999999999999999999999999999999998888853     36999999999999999998888775

>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=99.94  E-value=1.9e-27  Score=158.96  Aligned_cols=75  Identities=35%  Similarity=0.556  Sum_probs=67.4

Q ss_pred             CCCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCCC-----CCcchHHhHhHHhcCCccchhhccC
Q psy11507         38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQKK-----SSQIPKEKYNLAYLMSDSLDTTNRF  112 (113)
Q Consensus        38 ~~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~~-----~C~~CR~~kcl~~GM~~~~~~~~~~  112 (113)
                      ...+|.||+++++|+||||.+|++|++||||++..+..|.|..+++|.+.     .|++|||+|||+|||..+..+..|.
T Consensus         9 ~~~~C~VCgd~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~   88 (93)
T 2han_A            9 SKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYACRENRNCIIDKRQRNRCQYCRYQKCLTCGMKREAVQEERQ   88 (93)
T ss_dssp             -CCBCTTTCSBCCEEETTEEECHHHHHHHHHHHHHTCCCCCSSCSCCCCSTTTGGGCHHHHHHHHHHHTCCGGGSCCCC-
T ss_pred             CCCCCcEeCCCCcCeecCcchhHHHHHHHHhhhccccCcCcCCCCcCCcCCCCCccCccccHHHHhHhCCCHHHhhhccC
Confidence            35689999999999999999999999999999999999999998888643     5999999999999999998887774

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

Probab=99.94  E-value=2.3e-27  Score=153.98  Aligned_cols=72  Identities=28%  Similarity=0.509  Sum_probs=65.4

Q ss_pred             cceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhccC
Q psy11507         41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNRF  112 (113)
Q Consensus        41 ~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~~  112 (113)
                      +|.||+++++|+||||.+|++|++||||++..+..|.|..+++|.+     ..|++|||+|||++||..+..+..|+
T Consensus         2 ~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~Rd   78 (78)
T 3cbb_A            2 LCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNERD   78 (78)
T ss_dssp             BCTTTSSBCCSEETTEECCHHHHHHHHHHHHTTCCCCCSSCSCCCCSTTTTTTCHHHHHHHHHHHTCCGGGCCCC--
T ss_pred             CCeEeCCCCCceEeCCcchhhhceeeeEEEecccCcccccccccCcCccccccChhhhhHHHhHcCCCHHHccccCC
Confidence            5999999999999999999999999999999999999998888853     36999999999999999998888874

>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=99.94  E-value=2.5e-27  Score=156.00  Aligned_cols=74  Identities=34%  Similarity=0.571  Sum_probs=68.0

Q ss_pred             CCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhccC
Q psy11507         39 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNRF  112 (113)
Q Consensus        39 ~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~~  112 (113)
                      ..+|.||+++++|+||||.+|++|++||||++..+..|.|..+++|.+     ..|++|||+|||+|||..+..+..|.
T Consensus         5 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~   83 (85)
T 1dsz_B            5 KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQ   83 (85)
T ss_dssp             CEECTTTCCEESSEETTEECCHHHHHHHHHHHHHTCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCCCC
T ss_pred             CCCCCEeCCCCCceeeCccchHHHHHHHHHhhccccceeecccccccccccccccCcchhHHHHhHcCCCHHHhhcccC
Confidence            467999999999999999999999999999999999999999888863     36999999999999999998888875

>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=99.93  E-value=7.1e-27  Score=153.58  Aligned_cols=73  Identities=40%  Similarity=0.602  Sum_probs=61.4

Q ss_pred             CCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhcc
Q psy11507         39 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNR  111 (113)
Q Consensus        39 ~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~  111 (113)
                      ..+|.||+++++|+||||.+|++|++||||++..+..|.|..+++|.+     ..|++|||+|||++||..+..+.+|
T Consensus         4 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R   81 (84)
T 1hcq_A            4 TRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRKDR   81 (84)
T ss_dssp             CCBCTTTCSBCCEEETTEEECHHHHHHHHHHHSSCCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHHTCCC-------
T ss_pred             CCcCcEECCCCCCeeeCccchHHhhhhhhhccccccccccccCccCCcCCcCcccChhhhhHHHhHcCCCHHHhcccC
Confidence            457999999999999999999999999999999999999998888853     3699999999999999999887776

>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=99.93  E-value=6.7e-27  Score=154.25  Aligned_cols=74  Identities=32%  Similarity=0.568  Sum_probs=65.2

Q ss_pred             CCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCCC-----CCcchHHhHhHHhcCCccchhhccC
Q psy11507         39 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQKK-----SSQIPKEKYNLAYLMSDSLDTTNRF  112 (113)
Q Consensus        39 ~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~~-----~C~~CR~~kcl~~GM~~~~~~~~~~  112 (113)
                      ..+|.||+++++|+||||.+|++|++||||++..+..|.|..+++|.+.     .|++|||+|||++||..+..+..|.
T Consensus         4 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~   82 (86)
T 1dsz_A            4 YKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRN   82 (86)
T ss_dssp             --CCTTTCSCCCSEETTEECCHHHHHHHHHHHHTTCCCCCSSCSCCCCSTTTGGGCHHHHHHHHHHTTCCGGGSCCC--
T ss_pred             CCCCcEECCCccceeeCchhHHHHHHHHHHHhhcccceeeccCCccccCccccccchhhhHHHHHHhCCCHHHhhhccc
Confidence            4579999999999999999999999999999999999999998888643     5999999999999999998887764

>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=99.93  E-value=7.8e-27  Score=157.55  Aligned_cols=74  Identities=34%  Similarity=0.571  Sum_probs=63.7

Q ss_pred             CCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhccC
Q psy11507         39 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNRF  112 (113)
Q Consensus        39 ~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~~  112 (113)
                      ..+|.||+++++|+||||.+|++|++||||++..+..|.|..+++|.+     ..|++|||+|||+|||..+..+..|.
T Consensus         3 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~   81 (99)
T 1ynw_B            3 KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQ   81 (99)
T ss_dssp             --CBTTTBSCCCBCCTTSCBCSHHHHHHHHHHHTTCCCCCSSSSCCCCCSTTSSSCHHHHHHHHHHTTCCSTTCC----
T ss_pred             CCCCceeCCCCcceeeCccchHHHHHHHHhhhccccccccCCCCcccccccCCccCccccHHHHhHcCCCHHHhhhccc
Confidence            457999999999999999999999999999999999999999888863     36999999999999999988777764

>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=99.93  E-value=1.1e-26  Score=156.64  Aligned_cols=75  Identities=49%  Similarity=0.739  Sum_probs=68.2

Q ss_pred             CCCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCCC-----CCcchHHhHhHHhcCCccchhhccC
Q psy11507         38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQKK-----SSQIPKEKYNLAYLMSDSLDTTNRF  112 (113)
Q Consensus        38 ~~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~~-----~C~~CR~~kcl~~GM~~~~~~~~~~  112 (113)
                      +..+|.||+++++|+||||.+|++|++||||++..+..|.|..+++|.+.     .|++|||+|||+|||..+..+.+|.
T Consensus         3 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~   82 (98)
T 1lo1_A            3 PKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKALKVGMLKEGVRLDRV   82 (98)
T ss_dssp             CCCEETTTTEECSEESSSSEECHHHHHHHHHHHHTTCCCCCSSCSCCCCCHHHHHHCHHHHHHHHHHHTCCGGGSCSSCC
T ss_pred             CCCCCcEeCCCCcCeeeCccchhhhhhhheeeecccCccccCccccccccccccccccchhHHHHhHcCCCHHHeecccc
Confidence            35679999999999999999999999999999999999999999888754     5999999999999999988777663

>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=99.93  E-value=2.1e-26  Score=152.75  Aligned_cols=72  Identities=39%  Similarity=0.601  Sum_probs=65.0

Q ss_pred             CcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhcc
Q psy11507         40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNR  111 (113)
Q Consensus        40 ~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~  111 (113)
                      ++|.||+++++|+||||.+|++|++||||++..+..|.|..+++|.+     ..|++|||+|||++||..+..+..|
T Consensus         1 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~~   77 (89)
T 1cit_A            1 GRCAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTDS   77 (89)
T ss_dssp             CCCSSSCCCCCEEETTEEECHHHHHHHHHHHHHTCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHTTCCGGGSCCGG
T ss_pred             CCCeEeCCCCcceEeCccchhhhhhhceeeEEecceeeeccCCccccCCCCcccChhhhhHHHhHcCCCHHHeeccc
Confidence            36999999999999999999999999999999999999999888863     3699999999999999998776543

>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=99.92  E-value=2.9e-26  Score=158.02  Aligned_cols=75  Identities=35%  Similarity=0.611  Sum_probs=66.9

Q ss_pred             CCCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhccC
Q psy11507         38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNRF  112 (113)
Q Consensus        38 ~~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~~  112 (113)
                      ...+|.||+++++|+||||.+|++|++||||++..+..|.|..+++|.+     ..|++|||+|||+|||..+..+..|.
T Consensus         8 ~~~~C~VCgd~a~G~HyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~R~~Cr~CR~~KCl~vGM~~~~vq~~R~   87 (113)
T 2a66_A            8 LEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRM   87 (113)
T ss_dssp             --CBCTTTCCBEEEEETTEEEEHHHHHHHHHHHHTTCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCTTCC
T ss_pred             CCCCCcEeCCCCcceeeCcccHHHHHHHHhhhhhccccccccccccCCcCCCccccccchhHHHHhHhCCCHHHhccccc
Confidence            3567999999999999999999999999999999999999999888853     36999999999999999988877763

>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=99.92  E-value=2.9e-26  Score=153.46  Aligned_cols=74  Identities=42%  Similarity=0.651  Sum_probs=65.9

Q ss_pred             CCcceEcCCCCcceeechhcchhhHHHHHHhHhhccce-ecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhccC
Q psy11507         39 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASL-VSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNRF  112 (113)
Q Consensus        39 ~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~-~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~~  112 (113)
                      ..+|.||+++++|+||||.+|++|++||||++..+..| .|..+++|.+     ..|++|||+|||++||..+..+.+|.
T Consensus         7 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~   86 (94)
T 1a6y_A            7 VLLCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGRI   86 (94)
T ss_dssp             -CBCTTTSSBCCEEETTEEECHHHHHHHHHHHSSCCCCCCCSSTTCCCCCTTTTTSCHHHHHHHHTTTTCCSTTCCCCC-
T ss_pred             CCcCcEeCCCCcceEeCccchhhhhhehheeeecccceEEccCCCCCccCccccccccchhHHHhhHccCCHHHhccCcC
Confidence            46799999999999999999999999999999998888 5998888863     36999999999999999998887774

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

Probab=99.92  E-value=3.9e-26  Score=158.18  Aligned_cols=75  Identities=33%  Similarity=0.596  Sum_probs=62.7

Q ss_pred             CCCCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhcc
Q psy11507         37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNR  111 (113)
Q Consensus        37 ~~~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~  111 (113)
                      .++.+|.||+++++|+||||.+|++|++||||++..+..|.|..+++|.+     ..|++|||+|||++||..+..+..|
T Consensus        27 ~~~~~C~VCgd~a~G~HyGv~sC~aCk~FFRRsv~~~~~y~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~avq~kR  106 (117)
T 4hn5_A           27 APPKLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEARKTKK  106 (117)
T ss_dssp             ---CBCTTTCSBCCEEETTEEECHHHHHHHHHHHSSCCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHHTCCTTC-----
T ss_pred             CCCCcCCcCCCcCcccccCCcccchhhhhhhcceecCCceecCCCCccccCcccccCCcccchHHHhHcCCCHHHhcccc
Confidence            34567999999999999999999999999999999999999998888853     3799999999999999998766554

>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=99.92  E-value=5.5e-26  Score=150.85  Aligned_cols=73  Identities=30%  Similarity=0.559  Sum_probs=66.3

Q ss_pred             CCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCCC-----CCcchHHhHhHHhcCCccchhhcc
Q psy11507         39 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQKK-----SSQIPKEKYNLAYLMSDSLDTTNR  111 (113)
Q Consensus        39 ~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~~-----~C~~CR~~kcl~~GM~~~~~~~~~  111 (113)
                      ..+|.||+++++|+||||.+|++|++||||++..+..|.|..+++|.+.     .|++|||+|||++||..+..+..|
T Consensus         2 ~~~C~VCg~~a~g~hyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~avq~~r   79 (90)
T 3g9m_A            2 SHMCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEARKTKK   79 (90)
T ss_dssp             CCBCTTTCSBCCEEETTEEECHHHHHHHHHHHHSCCCCCCSSSSCCCCCTTGGGTCHHHHHHHHHHHTCCTTHHHHHC
T ss_pred             CCcCccCCCcCcccccCCccchhHhHHhhhhhhcCCceeCCCCCccccCcccccCCcchhhHHHHHcCCCHHHhcccc
Confidence            3579999999999999999999999999999999999999988888643     699999999999999998776655

>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=99.92  E-value=8.6e-26  Score=156.82  Aligned_cols=74  Identities=35%  Similarity=0.587  Sum_probs=66.0

Q ss_pred             CCCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCCC-----CCcchHHhHhHHhcCCccchhhcc
Q psy11507         38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQKK-----SSQIPKEKYNLAYLMSDSLDTTNR  111 (113)
Q Consensus        38 ~~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~~-----~C~~CR~~kcl~~GM~~~~~~~~~  111 (113)
                      ...+|.||+++++|+||||.+|++|++||||++..+..|.|..+++|.+.     .|++|||+|||+|||..+..+..|
T Consensus         7 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r   85 (119)
T 2han_B            7 QEELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECRLKKCLAVGMRPECVVPEN   85 (119)
T ss_dssp             CSCBCTTTCSBCCEEETTEEECHHHHHHHHHHHHTTCCCCCSSCSCCCCSTTGGGTCHHHHHHHHHHTTCCGGGSSCSS
T ss_pred             CCCcCeEeCCcCCcceECchhHHhhHHhhhhheEeccccccccccccccCccccccchhhHHHHHHHhCCCHHHccchh
Confidence            35679999999999999999999999999999999999999998888643     699999999999999998665543

>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=99.92  E-value=7.1e-26  Score=155.39  Aligned_cols=70  Identities=30%  Similarity=0.571  Sum_probs=62.7

Q ss_pred             CCCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccch
Q psy11507         38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLD  107 (113)
Q Consensus        38 ~~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~  107 (113)
                      .+.+|.||+++++|+||||.+|++|++||||++..+..|.|..+++|.+     ..|++|||+|||++||..+..
T Consensus         5 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v   79 (110)
T 1kb2_A            5 VPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFI   79 (110)
T ss_dssp             --CBCTTTCSBCCSEETTEECCHHHHHHHHHHHHTTCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGS
T ss_pred             cCCCCcEeCCCCCceEeCchhHhhhhhhheeeeecccceeeCCCCCccCCcccceecccccHhhhhhcCCcHHhc
Confidence            3567999999999999999999999999999999999999999888863     369999999999999999744

>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=99.92  E-value=1.1e-25  Score=152.78  Aligned_cols=72  Identities=35%  Similarity=0.556  Sum_probs=63.8

Q ss_pred             CcceEcCCCCcceeechhcchhhHHHHHHhHhhcc--ceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhcc
Q psy11507         40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQARA--SLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNR  111 (113)
Q Consensus        40 ~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~--~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~  111 (113)
                      .+|.|||++++|+||||.+|+||++||||++..+.  .|.|..+++|.+     ..|++|||+|||+|||..+..+..|
T Consensus         2 ~~C~VCgd~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~~   80 (103)
T 2nll_B            2 ELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQECRFKKCIYVGMATDLVLDDS   80 (103)
T ss_dssp             CBCTTTCSBCCSEETTEECCHHHHHHHHHHHHTTCGGGCCCSSCTTCCCSTTTTTSCHHHHHHHHHHTTCCGGGSCCHH
T ss_pred             CCCeEeCCcCcCeecCcccHHHhhhhheecccccccchhhhhccCCcCcCccCccccchhhhHhhhHhCCCHHHhhhhh
Confidence            47999999999999999999999999999999875  789998888863     3699999999999999998765543

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

Probab=99.91  E-value=1.9e-25  Score=152.16  Aligned_cols=70  Identities=30%  Similarity=0.586  Sum_probs=63.0

Q ss_pred             CCCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccch
Q psy11507         38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLD  107 (113)
Q Consensus        38 ~~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~  107 (113)
                      +..+|.||+++++|+||||.+|++|++||||++..+..|.|..+++|.+     ..|++|||+|||+|||.....
T Consensus         6 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~~   80 (105)
T 1r4i_A            6 PQKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLGAR   80 (105)
T ss_dssp             CCCBCSSSCSBEEEEETTEEEEHHHHHHHHHHHTSCCCCCCSSSSCCCCCTTTTTTCHHHHHHHHHHHTCCSCC-
T ss_pred             CCCCCcEeCCCCCceEeCCcchhhhhhhhceeEEecCceeeccCCccccCccccccchhchHHHHHhhhcccchh
Confidence            3568999999999999999999999999999999999999999888863     369999999999999998643

>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=99.88  E-value=1.4e-23  Score=172.12  Aligned_cols=73  Identities=34%  Similarity=0.591  Sum_probs=66.0

Q ss_pred             CCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhcc
Q psy11507         39 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNR  111 (113)
Q Consensus        39 ~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~  111 (113)
                      ...|.|||++++|+||||.+|+||++||||++.++..|.|+.++.|..     ..|++|||+||+++||..+..+..|
T Consensus       137 ~~~C~VCg~~a~g~hygv~sC~~Ck~FFrR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r  214 (467)
T 3dzy_A          137 KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER  214 (467)
T ss_dssp             CEECTTTSSEECSEETTEECCHHHHHHHHHHHHTTCCCCCSSSSCCCCCSSSSSSCHHHHHHHHHHTTCCGGGCCCCS
T ss_pred             CCcceeCCCCCCCCcCCCcchhhhhHhccccccCCCceeCCCCCCCCCCcccccccccchhhhhhhccccchhhhccc
Confidence            456999999999999999999999999999999999999999888853     3799999999999999998776655

>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=99.87  E-value=8.2e-23  Score=165.38  Aligned_cols=74  Identities=39%  Similarity=0.556  Sum_probs=62.4

Q ss_pred             CCCCcceEcCCCCcceeechhcchhhHHHHHHhHhhcccee-cCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhc
Q psy11507         37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLV-SLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTN  110 (113)
Q Consensus        37 ~~~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~-C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~  110 (113)
                      .....|.|||++++|+||||.+|+||++||||++..+..|. |.  ++|..     ..|++|||+||+++||.....+..
T Consensus        48 ~~~~~C~vC~~~~~g~hygv~~C~~C~~FFrR~~~~~~~~~~c~--~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~vq~~  125 (419)
T 3dzy_D           48 LMAIECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLIYDRCD--LNCRIHKKSRNKCQYCRFQKCLAVGMSHNAIRFG  125 (419)
T ss_dssp             --CCCCSSSCSCCCSBCSSSBCCHHHHHHHHHHHTTTCCCCCCC--SCCCCCTTGGGTCHHHHHHHHHHTTCCGGGCCCS
T ss_pred             CCCCcCeECCCcCCCCccCcccchhhhHHHccchhccccccccc--CCCCcccccCccchhhhHHHHhhcccchhheecc
Confidence            34567999999999999999999999999999999988885 64  34542     379999999999999999887776


Q ss_pred             cC
Q psy11507        111 RF  112 (113)
Q Consensus       111 ~~  112 (113)
                      |.
T Consensus       126 R~  127 (419)
T 3dzy_D          126 RM  127 (419)
T ss_dssp             CC
T ss_pred             cc
Confidence            63

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

Probab=99.53  E-value=4.6e-16  Score=102.58  Aligned_cols=56  Identities=14%  Similarity=0.050  Sum_probs=43.7

Q ss_pred             CCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCCC-----CCcchHHhHhHHhcCCcc
Q psy11507         48 VASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQKK-----SSQIPKEKYNLAYLMSDS  105 (113)
Q Consensus        48 ~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~~-----~C~~CR~~kcl~~GM~~~  105 (113)
                      +..+.||++. |.+|++||||++ ++..|+|+.+++|.+.     .|++|||+|||+|||+..
T Consensus        13 p~~g~h~c~v-Cgd~asfFRRt~-~~~~y~C~~~~~C~i~~~~R~~C~~CR~qKCl~VgM~~~   73 (87)
T 2lze_A           13 PRGGKHICAI-CGNNAEDYKHTD-MDLTYTDRDYKNCESYHKCSDLCQYCRYQKDLAIHHQHH   73 (87)
T ss_dssp             CSCCSSSCSS-SSSSSSSCTTTT-TSCTTTSCCCCCCCCSSCCSSSCSGGGTSCCHHHHCSSC
T ss_pred             CCCCCEEccC-CCCccceECccc-CCCeeEcCCCCccccCCCccCcCCcccChhhccCcCEec
Confidence            3445566654 666788899985 5677899998888543     699999999999999875

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	113
d1dszb_	84	g.39.1.2 (B:) Retinoid X receptor (RXR-alpha) DNA-	2e-14
d1lo1a_	90	g.39.1.2 (A:) Steroid hormone receptor Err2 DNA-bi	3e-13
d1r4ia_	74	g.39.1.2 (A:) Androgen receptor {Rat (Rattus norve	6e-13
d1kb2a_	89	g.39.1.2 (A:) Vitamin D3 receptor, VDR, DNA-bindin	2e-12
d1a6ya_	78	g.39.1.2 (A:) Orphan nuclear receptor reverb DNA-b	2e-12
d1hcqa_	74	g.39.1.2 (A:) Estrogen receptor DNA-binding domain	3e-12
d1dsza_	75	g.39.1.2 (A:) Retinoic acid receptor DNA-binding d	5e-12
d1lata_	71	g.39.1.2 (A:) Glucocorticoid receptor DNA-binding	1e-11
d1cita_	89	g.39.1.2 (A:) Orphan nuclear receptor NGFI-B DNA-b	1e-11
d2hanb1	83	g.39.1.2 (B:5-87) Ecdysone receptor DNA-binding do	2e-11
d2nllb_	103	g.39.1.2 (B:) Thyroid hormone receptor (TR-beta) D	2e-09

>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 = 61.1 bits (148), Expect = 2e-14
 Identities = 20/35 (57%), Positives = 26/35 (74%)

Query: 37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
            + +C +CGD +SG HYGV SCE CK FFKRT++
Sbjct: 3  FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVR 37

>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 = 58.1 bits (140), Expect = 3e-13
 Identities = 31/35 (88%), Positives = 35/35 (100%)

Query: 37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          +P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQ
Sbjct: 2  IPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQ 36

>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 = 57.0 bits (137), Expect = 6e-13
 Identities = 19/34 (55%), Positives = 25/34 (73%)

Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          P++ CL+CGD ASG HYG  +C +CK FFKR  +
Sbjct: 1  PQKTCLICGDEASGAHYGALTCGSCKVFFKRAAE 34

>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 = 56.2 bits (135), Expect = 2e-12
 Identities = 17/32 (53%), Positives = 25/32 (78%)

Query: 40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          R+C VCGD A+GFH+   +CE CK FF+R+++
Sbjct: 1  RICGVCGDRATGFHFNAMTCEGCKGFFRRSMK 32

>d1a6ya_ g.39.1.2 (A:) Orphan nuclear receptor reverb DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Length = 78

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

 Score = 55.8 bits (134), Expect = 2e-12
 Identities = 24/31 (77%), Positives = 27/31 (87%)

Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          LC VCGDVASGFHYGV +CE CK FF+R+IQ
Sbjct: 2  LCKVCGDVASGFHYGVLACEGCKGFFRRSIQ 32

>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 = 55.5 bits (133), Expect = 3e-12
 Identities = 24/34 (70%), Positives = 26/34 (76%)

Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
            R C VC D ASG+HYGV SCE CKAFFKR+IQ
Sbjct: 3  ETRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQ 36

>d1dsza_ g.39.1.2 (A:) Retinoic acid receptor DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Length = 75

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

 Score = 54.7 bits (131), Expect = 5e-12
 Identities = 19/30 (63%), Positives = 25/30 (83%)

Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          C VC D +SG+HYGV++CE CK FF+R+IQ
Sbjct: 2  CFVCQDKSSGYHYGVSACEGCKGFFRRSIQ 31

>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 = 53.5 bits (128), Expect = 1e-11
 Identities = 22/32 (68%), Positives = 25/32 (78%)

Query: 40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          R CLVC D ASG HYGV +CE CKAFFKR ++
Sbjct: 1  RPCLVCSDEASGCHYGVLTCEGCKAFFKRAVE 32

>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 = 54.3 bits (130), Expect = 1e-11
 Identities = 21/30 (70%), Positives = 23/30 (76%)

Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          C VCGD AS  HYGV +CE CK FFKRT+Q
Sbjct: 3  CAVCGDNASCQHYGVRTCEGCKGFFKRTVQ 32

>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 = 53.4 bits (128), Expect = 2e-11
 Identities = 19/31 (61%), Positives = 24/31 (77%)

Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          LCLVCGD ASG+HY   +CE CK FF+R++ 
Sbjct: 2  LCLVCGDRASGYHYNALTCEGCKGFFRRSVT 32

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

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

 Score = 48.6 bits (115), Expect = 2e-09
 Identities = 20/31 (64%), Positives = 25/31 (80%)

Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
          LC+VCGD A+G+HY   +CE CK FF+RTIQ
Sbjct: 3  LCVVCGDKATGYHYRCITCEGCKGFFRRTIQ 33

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	113
d1dszb_	84	Retinoid X receptor (RXR-alpha) DNA-binding domain	99.94
d2hanb1	83	Ecdysone receptor DNA-binding domain {Fruit fly (D	99.92
d1lo1a_	90	Steroid hormone receptor Err2 DNA-binding domain {	99.92
d1dsza_	75	Retinoic acid receptor DNA-binding domain {Human (	99.92
d1r4ia_	74	Androgen receptor {Rat (Rattus norvegicus) [TaxId:	99.92
d1lata_	71	Glucocorticoid receptor DNA-binding domain {Rat (R	99.92
d1a6ya_	78	Orphan nuclear receptor reverb DNA-binding domain	99.92
d1kb2a_	89	Vitamin D3 receptor, VDR, DNA-binding domain {Huma	99.92
d1cita_	89	Orphan nuclear receptor NGFI-B DNA-binding domain	99.92
d1hcqa_	74	Estrogen receptor DNA-binding domain {Human and ch	99.91
d2nllb_	103	Thyroid hormone receptor (TR-beta) DNA-binding dom	99.91

>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=99.94  E-value=1.1e-27  Score=155.85  Aligned_cols=75  Identities=33%  Similarity=0.563  Sum_probs=67.8

Q ss_pred             CCCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCCC-----CCcchHHhHhHHhcCCccchhhccC
Q psy11507         38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQKK-----SSQIPKEKYNLAYLMSDSLDTTNRF  112 (113)
Q Consensus        38 ~~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~~-----~C~~CR~~kcl~~GM~~~~~~~~~~  112 (113)
                      +..+|.||+++++|+||||.+|++|++||||++.....|.|...+.|...     .|++|||+|||+|||.++..+.+|+
T Consensus         4 ~~~~C~VC~~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~c~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~Rd   83 (84)
T d1dszb_           4 TKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQ   83 (84)
T ss_dssp             CCEECTTTCCEESSEETTEECCHHHHHHHHHHHHHTCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCCCC
T ss_pred             CCCcCccCCCcCCccCCCHHHHHHhHHHHHHHHhcCCCeeccCCCCcccCCCCCccCCCCccHHHHHcCCChHHcccccC
Confidence            45679999999999999999999999999999999999999888777433     6999999999999999998888775

>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=99.92  E-value=1.2e-26  Score=150.58  Aligned_cols=72  Identities=36%  Similarity=0.602  Sum_probs=65.1

Q ss_pred             CcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCCC-----CCcchHHhHhHHhcCCccchhhcc
Q psy11507         40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQKK-----SSQIPKEKYNLAYLMSDSLDTTNR  111 (113)
Q Consensus        40 ~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~~-----~C~~CR~~kcl~~GM~~~~~~~~~  111 (113)
                      ++|.||+++++++||||.+|++|++||||++..+..|.|...+.|...     .|++|||+|||++||.++..+..|
T Consensus         1 e~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~c~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r   77 (83)
T d2hanb1           1 ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECRLKKCLAVGMRPECVVPEN   77 (83)
T ss_dssp             CBCTTTCSBCCEEETTEEECHHHHHHHHHHHHTTCCCCCSSCSCCCCSTTGGGTCHHHHHHHHHHTTCCGGGSSCSS
T ss_pred             CcCccCCCcCCccCcCHHhHhHhHHHHHHHHhcCCceeecCCCCcccCCcccccCccchHHHHHHcCCCHHHccccc
Confidence            479999999999999999999999999999999999999888888553     799999999999999998776554

>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=99.92  E-value=8.6e-27  Score=153.39  Aligned_cols=75  Identities=49%  Similarity=0.739  Sum_probs=68.3

Q ss_pred             CCCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCCC-----CCcchHHhHhHHhcCCccchhhccC
Q psy11507         38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQKK-----SSQIPKEKYNLAYLMSDSLDTTNRF  112 (113)
Q Consensus        38 ~~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~~-----~C~~CR~~kcl~~GM~~~~~~~~~~  112 (113)
                      |..+|+|||++++++||||.+|++|++||||++..+..+.|...++|...     .|++|||+|||+|||.++..+..|.
T Consensus         3 P~~~C~VCg~~~~~~hyG~~sC~aC~~FFRR~v~~~~~~~c~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~r~   82 (90)
T d1lo1a_           3 PKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKALKVGMLKEGVRLDRV   82 (90)
T ss_dssp             CCCEETTTTEECSEESSSSEECHHHHHHHHHHHHTTCCCCCSSCSCCCCCHHHHHHCHHHHHHHHHHHTCCGGGSCSSCC
T ss_pred             CCCcCCcCCCcCCceEcCeeechhhHHHHHHHHhcCCccchhcCCCCccCCCCccccchhhHHHHHHcCCCHHHhccccc
Confidence            45689999999999999999999999999999999999999998888765     7999999999999999988776653

>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=99.92  E-value=1.2e-26  Score=148.15  Aligned_cols=68  Identities=34%  Similarity=0.592  Sum_probs=61.8

Q ss_pred             cceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCCC-----CCcchHHhHhHHhcCCccchh
Q psy11507         41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQKK-----SSQIPKEKYNLAYLMSDSLDT  108 (113)
Q Consensus        41 ~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~~-----~C~~CR~~kcl~~GM~~~~~~  108 (113)
                      +|.||+++++|+||||.+|++|++||||++.....|.|...+.|...     .|++|||+|||++||.++..+
T Consensus         1 PC~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~c~~~~~c~~~~~~r~~Cr~CR~~KCl~~GM~~~~vq   73 (75)
T d1dsza_           1 PCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVR   73 (75)
T ss_dssp             CCTTTCSCCCSEETTEECCHHHHHHHHHHHHTTCCCCCSSCSCCCCSTTTGGGCHHHHHHHHHHTTCCGGGSC
T ss_pred             CCccCCCcCCccCcCHHHhhhhHHHHHHHHhcCCceecccCCccccCCccccccchhHHHHHHHhCCCHHHcc
Confidence            59999999999999999999999999999999999999887777433     599999999999999998654

>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=99.92  E-value=1.2e-26  Score=147.71  Aligned_cols=68  Identities=29%  Similarity=0.597  Sum_probs=61.6

Q ss_pred             CCCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCCC-----CCcchHHhHhHHhcCCcc
Q psy11507         38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQKK-----SSQIPKEKYNLAYLMSDS  105 (113)
Q Consensus        38 ~~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~~-----~C~~CR~~kcl~~GM~~~  105 (113)
                      |.++|.||+++++++||||.+|++|++||||++..+..|.|..+++|.+.     .|++|||+|||++||..+
T Consensus         1 P~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~c~~~~~C~~~~~~r~~C~~CR~~KCl~vGM~~~   73 (74)
T d1r4ia_           1 PQKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLG   73 (74)
T ss_dssp             CCCBCSSSCSBEEEEETTEEEEHHHHHHHHHHHTSCCCCCCSSSSCCCCCTTTTTTCHHHHHHHHHHHTCCSC
T ss_pred             CCCcCccCCCcCCccCCCHHhhHHHHHHHHHHHhcccceeeecCCCcccCCCCcccchhhhHHHHHHcCCcCC
Confidence            35679999999999999999999999999999999999999988887533     699999999999999865

>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=99.92  E-value=1.9e-26  Score=145.73  Aligned_cols=66  Identities=38%  Similarity=0.606  Sum_probs=59.9

Q ss_pred             CcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCcc
Q psy11507         40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDS  105 (113)
Q Consensus        40 ~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~  105 (113)
                      ++|.||+++++|+||||.+|++|++||||++..+..+.|...+.|..     ..|++|||+|||++||+.+
T Consensus         1 k~C~VC~~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~c~~~~~C~~~~~~r~~Cr~CR~~KCl~~GM~~e   71 (71)
T d1lata_           1 RPCLVCSDEASGCHYGVLTCEGCKAFFKRAVEGQHNYLCKYEGKCIIDKIRRKNCPACRYRKCLQAGMNLE   71 (71)
T ss_dssp             CBCTTTCSBCCEEETTEEECHHHHHHHHHHHHSCCCCCCSSCSCCCCSTTTTTTCHHHHHHHHHHTTCCCC
T ss_pred             CcCeeCCCcCCceEcCHhhHHHHHHHHHHHHhcCcceeeecCcccccccCccccCCccchhHHhHccCCCC
Confidence            46999999999999999999999999999999999999988777743     3799999999999999863

>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=99.92  E-value=1.4e-26  Score=148.76  Aligned_cols=71  Identities=44%  Similarity=0.716  Sum_probs=62.2

Q ss_pred             cceEcCCCCcceeechhcchhhHHHHHHhHhhccceec-CCCCCCC-----CCCCcchHHhHhHHhcCCccchhhcc
Q psy11507         41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVS-LRGHEPQ-----KKSSQIPKEKYNLAYLMSDSLDTTNR  111 (113)
Q Consensus        41 ~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C-~~~~~c~-----~~~C~~CR~~kcl~~GM~~~~~~~~~  111 (113)
                      +|.||+++++|+||||.+|++|++||||++..+..|.| ..++.|.     ...|++|||+|||++||.++..+.+|
T Consensus         2 iC~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~~~~~~~~c~~~~~~r~~Cr~CR~~KCl~~GM~~~~vq~~R   78 (78)
T d1a6ya_           2 LCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGR   78 (78)
T ss_dssp             BCTTTSSBCCEEETTEEECHHHHHHHHHHHSSCCCCCCCSSTTCCCCCTTTTTSCHHHHHHHHTTTTCCSTTCCCCC
T ss_pred             CCeeCCCcCCcccCcchhhhhchhhhhhhhccCCceeeeccCCCcccCCCCCccchhhHHHHHHHhCCCHHHhcCCC
Confidence            69999999999999999999999999999999888874 4455453     23699999999999999999888776

>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=99.92  E-value=3e-26  Score=150.48  Aligned_cols=72  Identities=31%  Similarity=0.573  Sum_probs=64.2

Q ss_pred             CcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCCC-----CCcchHHhHhHHhcCCccchhhcc
Q psy11507         40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQKK-----SSQIPKEKYNLAYLMSDSLDTTNR  111 (113)
Q Consensus        40 ~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~~-----~C~~CR~~kcl~~GM~~~~~~~~~  111 (113)
                      ++|.|||++++|+||||.+|++|++||||++.....|.|..+++|.+.     .|++|||+|||+|||.++..+..|
T Consensus         1 r~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~c~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r   77 (89)
T d1kb2a_           1 RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDE   77 (89)
T ss_dssp             CBCTTTCSBCCSEETTEECCHHHHHHHHHHHHTTCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCHH
T ss_pred             CCCeeCCCcCCccCCCHHHHHHHHHHHHHHHhcCCCeecCCCCccCCCCcCCccCchhhHHHHHHcCCCHhhccccc
Confidence            479999999999999999999999999999999999999888888543     699999999999999998665544

>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=99.92  E-value=5.2e-26  Score=149.30  Aligned_cols=72  Identities=39%  Similarity=0.600  Sum_probs=64.4

Q ss_pred             CcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCCC-----CCcchHHhHhHHhcCCccchhhcc
Q psy11507         40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQKK-----SSQIPKEKYNLAYLMSDSLDTTNR  111 (113)
Q Consensus        40 ~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~~-----~C~~CR~~kcl~~GM~~~~~~~~~  111 (113)
                      ++|+||+++++++||||.+|++|++||||++.....|.|...+.|.+.     .|++|||+|||++||.++..+..|
T Consensus         1 g~C~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~c~~~~~c~~~~~~r~~Cr~CR~~KCl~~GM~~~~v~~~~   77 (89)
T d1cita_           1 GRCAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTDS   77 (89)
T ss_dssp             CCCSSSCCCCCEEETTEEECHHHHHHHHHHHHHTCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHTTCCGGGSCCGG
T ss_pred             CCCeECCCcCCccCCCcccchhhHHHHHHHHHcCCceeecCCCCccccCCccccCchhhHHHHHHcCCCHHHhcccc
Confidence            469999999999999999999999999999999999998887777544     799999999999999998766544

>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=99.91  E-value=9.9e-26  Score=143.49  Aligned_cols=66  Identities=41%  Similarity=0.657  Sum_probs=60.5

Q ss_pred             CCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCCC-----CCcchHHhHhHHhcCCc
Q psy11507         39 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQKK-----SSQIPKEKYNLAYLMSD  104 (113)
Q Consensus        39 ~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~~-----~C~~CR~~kcl~~GM~~  104 (113)
                      ..+|.||+++++++||||.+|++|++||||++.....+.|..+++|.+.     .|++|||+|||+|||..
T Consensus         4 ~~~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~k   74 (74)
T d1hcqa_           4 TRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMK   74 (74)
T ss_dssp             CCBCTTTCSBCCEEETTEEECHHHHHHHHHHHSSCCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHHTCCC
T ss_pred             CCCCccCCCcCCceEcCeeehHHHHHHHHHHHHcccccccccCCCCccCCCccccchHhhHHHHHHcCCcC
Confidence            4679999999999999999999999999999999999999988888533     79999999999999973

>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=99.91  E-value=2e-25  Score=149.89  Aligned_cols=71  Identities=34%  Similarity=0.543  Sum_probs=59.7

Q ss_pred             CcceEcCCCCcceeechhcchhhHHHHHHhHhhcccee--cCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhc
Q psy11507         40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLV--SLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTN  110 (113)
Q Consensus        40 ~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~--C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~  110 (113)
                      ++|.|||++++|+||||.+|+||++||||++.....+.  |..++.|..     ..|++|||+|||+|||.++.....
T Consensus         2 ~~C~VCg~~a~g~HfGv~sC~aCkaFFRR~v~~~~~~~~~c~~~~~c~~~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~   79 (103)
T d2nllb_           2 ELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQECRFKKCIYVGMATDLVLDD   79 (103)
T ss_dssp             CBCTTTCSBCCSEETTEECCHHHHHHHHHHHHTTCGGGCCCSSCTTCCCSTTTTTSCHHHHHHHHHHTTCCGGGSCCH
T ss_pred             CcCccCCCcCCcccCchhhhHHHHHHhHHHhhccccceeecccCCCCcCCCCccCCCccccchhHHHhhccHHhhhcc
Confidence            47999999999999999999999999999999876655  455565532     369999999999999998765443