Psyllid ID: psy752

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120---
Protein Sequence
NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEDLERNTEISVSMMSCDGDTSDLGGLSYIKKECNLNNIQCSPSSQRLYSPS
Secondary Structure (PSIPRED)
ccEEEccccccccccccccccccHHHHHHHHHHccccHHccccccccccccccccccccccccccccccccccccccccHHHccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccHHHccHHHHHHHHHHcccccccccccccccccccEcccccHHHccccHHcccccccccccccccccccccccccHHHHHccHHccccccccEEEccccHHHccccc
Coil and Loop (DISEMBL)
nieytcpasndceiNKRRRKACQACRFQKCLRKGmlkegvrldrvrggrqkyrrnpdllsqqwppnksipsledlerNTEISVSmmscdgdtsdlgglsyikkecnlnniqcspssqrlysps
Flexible Loop (DISEMBL)
nieytcpasndceinkrRRKACQACRfqkclrkgmlkegvrldrvrggrqkyrrnpdllsqqwppnksipsleDLERNTEISVSMMSCDGDTSDLGGLSYIKKEcnlnniqcspssqrlysps
Low Complexity Region (SEG)
NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEDLERNTEISVSMMSCDGDTSDLGGLSYIKKECNLNNIQCSPSSQRLYSPS
Disordered region (IsUnstruct)
************EINKRRRKACQACRFQKCLRKGMLKEGVRLDR**************************************************LGGLSYIKKECNLNNI*************
Disordered Region (DISOPRED)
NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGML****************************************************************************SPS***L****
Disordered Region (DISEMBL)
NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEDLERNTEISVSMMSCDGDTSDLGGLSYIKKECNLNNIQCS**********
Disordered Region (DISPRO)
*IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE*V******************************SLEDLERNTEISVSMMSCDGDTSDLGGLSYIKKECNLNNIQCSPSSQRLYS**
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEDLERNTEISVSMMSCDGDTSDLGGLSYIKKECNLNNIQCSPSSQRLYSPS
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	123	2.2.26 [Sep-21-2011]
Q6QMY5	422	Steroid hormone receptor	yes	N/A	0.520	0.151	0.765	2e-24
P11474	423	Steroid hormone receptor	yes	N/A	0.471	0.137	0.827	2e-24
Q5QJV7	422	Steroid hormone receptor	yes	N/A	0.471	0.137	0.827	3e-24
O08580	422	Steroid hormone receptor	yes	N/A	0.471	0.137	0.827	3e-24
P11475	433	Steroid hormone receptor	no	N/A	0.544	0.154	0.698	4e-23
Q5RAM2	435	Estrogen-related receptor	no	N/A	0.463	0.131	0.807	7e-23
P62510	458	Estrogen-related receptor	no	N/A	0.463	0.124	0.807	7e-23
P62509	458	Estrogen-related receptor	no	N/A	0.463	0.124	0.807	7e-23
P62508	458	Estrogen-related receptor	no	N/A	0.463	0.124	0.807	7e-23
O95718	508	Steroid hormone receptor	no	N/A	0.544	0.131	0.698	7e-23

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

 Score =  111 bits (277), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 49/64 (76%), Positives = 56/64 (87%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
           +IEY+CPASN+CEI KRRRKACQACRF KCLR GMLKEGVRLDRVRGGRQKY+R P++  
Sbjct: 110 SIEYSCPASNECEITKRRRKACQACRFTKCLRVGMLKEGVRLDRVRGGRQKYKRRPEVDP 169

Query: 61  QQWP 64
             +P
Sbjct: 170 LPFP 173

Binds to an ERR-alpha response element (ERRE) containing a single consensus half-site, 5'-TNAAGGTCA-3'. Can bind to the medium-chain acyl coenzyme A dehydrogenase (MCAD) response element NRRE-1 and may act as an important regulator of MCAD promoter. May function as a modulator of the estrogen signaling pathway in the uterus.
Canis familiaris (taxid: 9615)

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

 Score =  110 bits (276), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 48/58 (82%), Positives = 54/58 (93%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL 58
           +IEY+CPASN+CEI KRRRKACQACRF KCLR GMLKEGVRLDRVRGGRQKY+R P++
Sbjct: 110 SIEYSCPASNECEITKRRRKACQACRFTKCLRVGMLKEGVRLDRVRGGRQKYKRRPEV 167

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

Homo sapiens (taxid: 9606)

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

 Score =  110 bits (275), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 48/58 (82%), Positives = 54/58 (93%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL 58
           +IEY+CPASN+CEI KRRRKACQACRF KCLR GMLKEGVRLDRVRGGRQKY+R P++
Sbjct: 110 SIEYSCPASNECEITKRRRKACQACRFTKCLRVGMLKEGVRLDRVRGGRQKYKRRPEV 167

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

Rattus norvegicus (taxid: 10116)

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

 Score =  110 bits (275), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 48/58 (82%), Positives = 54/58 (93%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL 58
           +IEY+CPASN+CEI KRRRKACQACRF KCLR GMLKEGVRLDRVRGGRQKY+R P++
Sbjct: 110 SIEYSCPASNECEITKRRRKACQACRFTKCLRVGMLKEGVRLDRVRGGRQKYKRRPEV 167

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

Mus musculus (taxid: 10090)

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

 Score =  106 bits (265), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 51/73 (69%), Positives = 58/73 (79%), Gaps = 6/73 (8%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRR------ 54
           NIEY+CPA+N+CEI KRRRK+CQACRF KCL+ GMLKEGVRLDRVRGGRQKY+R      
Sbjct: 134 NIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRLDSEN 193

Query: 55  NPDLLSQQWPPNK 67
           +P L  Q  PP K
Sbjct: 194 SPYLSLQISPPAK 206

Nuclear receptor, may regulate ESR1 transcriptional activity.

Rattus norvegicus (taxid: 10116)

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

 Score =  105 bits (263), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 46/57 (80%), Positives = 52/57 (91%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPD 57
           NIEY+CPA+N+CEI KRRRK+CQACRF KCL+ GMLKEGVRLDRVRGGRQKY+R  D
Sbjct: 136 NIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRID 192

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

Pongo abelii (taxid: 9601)

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

 Score =  105 bits (263), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 46/57 (80%), Positives = 52/57 (91%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPD 57
           NIEY+CPA+N+CEI KRRRK+CQACRF KCL+ GMLKEGVRLDRVRGGRQKY+R  D
Sbjct: 159 NIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRID 215

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

Rattus norvegicus (taxid: 10116)

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

 Score =  105 bits (263), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 46/57 (80%), Positives = 52/57 (91%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPD 57
           NIEY+CPA+N+CEI KRRRK+CQACRF KCL+ GMLKEGVRLDRVRGGRQKY+R  D
Sbjct: 159 NIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRID 215

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

Mus musculus (taxid: 10090)

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

 Score =  105 bits (263), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 46/57 (80%), Positives = 52/57 (91%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPD 57
           NIEY+CPA+N+CEI KRRRK+CQACRF KCL+ GMLKEGVRLDRVRGGRQKY+R  D
Sbjct: 159 NIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRID 215

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

Homo sapiens (taxid: 9606)

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

 Score =  105 bits (263), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 51/73 (69%), Positives = 58/73 (79%), Gaps = 6/73 (8%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRR------ 54
           NIEY+CPA+N+CEI KRRRK+CQACRF KCL+ GMLKEGVRLDRVRGGRQKY+R      
Sbjct: 134 NIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRLDSES 193

Query: 55  NPDLLSQQWPPNK 67
           +P L  Q  PP K
Sbjct: 194 SPYLSLQISPPAK 206

Nuclear receptor, may regulate ESR1 transcriptional activity.

Homo sapiens (taxid: 9606)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	123
242021609	448	retinoid X receptor, putative [Pediculus	0.764	0.209	0.656	4e-27
259906648	401	estrogen receptor-like protein [Teleogry	0.471	0.144	0.965	1e-26
345496190	438	PREDICTED: steroid hormone receptor ERR2	0.739	0.207	0.62	2e-25
308756033	470	estrogen-related receptor [Tachypleus tr	0.601	0.157	0.783	2e-25
391338687	452	PREDICTED: estrogen-related receptor gam	0.463	0.126	0.929	2e-25
241727058	406	estrogen receptor beta, putative [Ixodes	0.463	0.140	0.964	4e-25
283825466	500	estrogen-related receptor [Scylla parama	0.707	0.174	0.666	7e-25
213513284	415	estrogen-related receptor [Tribolium cas	0.463	0.137	0.929	1e-24
383863647	434	PREDICTED: steroid hormone receptor ERR2	0.739	0.209	0.61	1e-24
170053275	446	estrogen-related receptor [Culex quinque	0.455	0.125	0.946	2e-24

>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 =  125 bits (313), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 67/102 (65%), Positives = 75/102 (73%), Gaps = 8/102 (7%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL-- 58
           NIEYTCPA+NDCEINKRRRKACQACRFQKCLR GMLKEGVRLDRVRGGRQKYRRN D   
Sbjct: 147 NIEYTCPAANDCEINKRRRKACQACRFQKCLRMGMLKEGVRLDRVRGGRQKYRRNTDTPY 206

Query: 59  -LSQQWPPNKSIPSLED---LERNT--EISVSMMSCDGDTSD 94
            +    P    +PSLED   LE  +  E  +S+M+ D   +D
Sbjct: 207 QIHSMLPLKPYLPSLEDNKILEALSLNEPDISVMAQDISNAD 248

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  123 bits (308), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 56/58 (96%), Positives = 57/58 (98%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL 58
           NIEYTCPA+NDCEINKRRRKACQACRFQKCLR GMLKEGVRLDRVRGGRQKYRRNPDL
Sbjct: 102 NIEYTCPAANDCEINKRRRKACQACRFQKCLRMGMLKEGVRLDRVRGGRQKYRRNPDL 159

Source: Teleogryllus emma

Species: Teleogryllus emma

Genus: Teleogryllus

Family: Gryllidae

Order: Orthoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  119 bits (299), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 62/100 (62%), Positives = 77/100 (77%), Gaps = 9/100 (9%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
           NIEYTCPA+ +CEINKRRRKACQACRFQKCLR+GMLKEGVRLDRVRGGRQKYRR+ D   
Sbjct: 144 NIEYTCPANGECEINKRRRKACQACRFQKCLRQGMLKEGVRLDRVRGGRQKYRRSTD--- 200

Query: 61  QQWPPNKSIPSLEDLERNTEISVSMMSCDGDTSDLGGLSY 100
             + P K+I +LED     ++  +++SC+ D   +  LS+
Sbjct: 201 -PYVPGKTI-TLED----NKMVEALISCEPDMLQVSTLSH 234

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|308756033|gb|ADO51071.1| estrogen-related receptor [Tachypleus tridentatus]

 Score =  119 bits (299), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 58/74 (78%), Positives = 61/74 (82%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
           NIEYTCPASNDCEINKRRRKACQACRFQKCL+ GMLKEGVRLDRVRGGRQKYRR+ D L 
Sbjct: 167 NIEYTCPASNDCEINKRRRKACQACRFQKCLKMGMLKEGVRLDRVRGGRQKYRRSADHLC 226

Query: 61  QQWPPNKSIPSLED 74
                    PSLE+
Sbjct: 227 NVPSLTLKKPSLEE 240

Source: Tachypleus tridentatus

Species: Tachypleus tridentatus

Genus: Tachypleus

Family: Limulidae

Order: Xiphosura

Class: Merostomata

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|391338687|ref|XP_003743687.1| PREDICTED: estrogen-related receptor gamma-like [Metaseiulus occidentalis]

 Score =  119 bits (299), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 53/57 (92%), Positives = 56/57 (98%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPD 57
           NIEYTCPA+NDCEINKRRRKACQACRFQKCL+ GMLKEGVRLDRVRGGRQKYRRNP+
Sbjct: 144 NIEYTCPANNDCEINKRRRKACQACRFQKCLKTGMLKEGVRLDRVRGGRQKYRRNPE 200

Source: Metaseiulus occidentalis

Species: Metaseiulus occidentalis

Genus: Metaseiulus

Family: Phytoseiidae

Order: Mesostigmata

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|241727058|ref|XP_002404502.1| estrogen receptor beta, putative [Ixodes scapularis] gi|215505447|gb|EEC14941.1| estrogen receptor beta, putative [Ixodes scapularis]

 Score =  118 bits (296), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 55/57 (96%), Positives = 56/57 (98%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPD 57
           NIEYTCPAS+DCEINKRRRKACQACRFQKCLR GMLKEGVRLDRVRGGRQKYRRNPD
Sbjct: 66  NIEYTCPASSDCEINKRRRKACQACRFQKCLRMGMLKEGVRLDRVRGGRQKYRRNPD 122

Source: Ixodes scapularis

Species: Ixodes scapularis

Genus: Ixodes

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|283825466|gb|ADB43256.1| estrogen-related receptor [Scylla paramamosain]

 Score =  117 bits (294), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 62/93 (66%), Positives = 71/93 (76%), Gaps = 6/93 (6%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL-L 59
           NIEYTCPA+NDCEINKRRRKACQACRF KCL  GMLKEGVRLDRVRGGRQKYRR  +   
Sbjct: 201 NIEYTCPAANDCEINKRRRKACQACRFHKCLHVGMLKEGVRLDRVRGGRQKYRRTTESPF 260

Query: 60  SQQWPPNKSIPSLEDLERNTEISVSMMSCDGDT 92
           S Q  P K + SLED     ++  S++SC+ D+
Sbjct: 261 SLQQMPVKKV-SLED----NKLLKSLISCEPDS 288

Source: Scylla paramamosain

Species: Scylla paramamosain

Genus: Scylla

Family: Portunidae

Order: Decapoda

Class: Malacostraca

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 =  117 bits (292), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 53/57 (92%), Positives = 55/57 (96%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPD 57
           NIEYTCPAS +CEINKRRRKACQACRF+KCLR GMLKEGVRLDRVRGGRQKYRRNPD
Sbjct: 130 NIEYTCPASGECEINKRRRKACQACRFRKCLRSGMLKEGVRLDRVRGGRQKYRRNPD 186

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383863647|ref|XP_003707291.1| PREDICTED: steroid hormone receptor ERR2-like [Megachile rotundata]

 Score =  117 bits (292), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 61/100 (61%), Positives = 75/100 (75%), Gaps = 9/100 (9%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
           NIEYTCPA+ +CEINKRRRKACQACRFQKCLR+GMLKEGVRLDRVRGGRQKYRR+ D   
Sbjct: 140 NIEYTCPANGECEINKRRRKACQACRFQKCLRQGMLKEGVRLDRVRGGRQKYRRSTD--- 196

Query: 61  QQWPPNKSIPSLEDLERNTEISVSMMSCDGDTSDLGGLSY 100
             + P K+ P LED     ++  ++ +C+ D   +  LS+
Sbjct: 197 -PYTPVKTAP-LED----NKMLEALAACEPDMLQVSNLSH 230

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  116 bits (291), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 53/56 (94%), Positives = 54/56 (96%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNP 56
           NIEYTCPASNDCEINKRRRKACQACRF+KCL  GMLKEGVRLDRVRGGRQKYRRNP
Sbjct: 113 NIEYTCPASNDCEINKRRRKACQACRFRKCLLMGMLKEGVRLDRVRGGRQKYRRNP 168

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

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	123
FB|FBgn0035849	496	ERR "estrogen-related receptor	0.455	0.112	0.928	2.2e-28
UNIPROTKB|F1MBX3	422	ESRRA "Uncharacterized protein	0.471	0.137	0.827	6e-25
UNIPROTKB|Q6QMY5	422	ESRRA "Steroid hormone recepto	0.471	0.137	0.827	6e-25
UNIPROTKB|F1RQP2	422	ESRRA "Uncharacterized protein	0.471	0.137	0.827	6e-25
MGI|MGI:1346831	422	Esrra "estrogen related recept	0.471	0.137	0.827	6e-25
RGD|1583866	422	Esrra "estrogen related recept	0.471	0.137	0.827	6e-25
UNIPROTKB|P11474	423	ESRRA "Steroid hormone recepto	0.471	0.137	0.827	6.2e-25
ZFIN|ZDB-GENE-990415-68	436	esrra "estrogen-related recept	0.674	0.190	0.635	1e-23
UNIPROTKB|F1PFF7	613	ESRRA "Steroid hormone recepto	0.471	0.094	0.827	1.1e-23
UNIPROTKB|F1NBB9	438	ESRRB "Uncharacterized protein	0.569	0.159	0.693	1.4e-22

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

 Score = 288 (106.4 bits), Expect = 2.2e-28, Sum P(3) = 2.2e-28
 Identities = 52/56 (92%), Positives = 54/56 (96%)

Query:     1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNP 56
             NIEYTCPA+N+CEINKRRRKACQACRFQKCL  GMLKEGVRLDRVRGGRQKYRRNP
Sbjct:   158 NIEYTCPANNECEINKRRRKACQACRFQKCLLMGMLKEGVRLDRVRGGRQKYRRNP 213

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

 Score = 270 (100.1 bits), Expect = 6.0e-25, Sum P(2) = 6.0e-25
 Identities = 48/58 (82%), Positives = 54/58 (93%)

Query:     1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL 58
             +IEY+CPASN+CEI KRRRKACQACRF KCLR GMLKEGVRLDRVRGGRQKY+R P++
Sbjct:   110 SIEYSCPASNECEITKRRRKACQACRFTKCLRVGMLKEGVRLDRVRGGRQKYKRRPEV 167

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

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

GO:0005634 "nucleus" evidence=IEA

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

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

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005496 "steroid binding" evidence=IEA

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

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

 Score = 270 (100.1 bits), Expect = 6.0e-25, Sum P(2) = 6.0e-25
 Identities = 48/58 (82%), Positives = 54/58 (93%)

Query:     1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL 58
             +IEY+CPASN+CEI KRRRKACQACRF KCLR GMLKEGVRLDRVRGGRQKY+R P++
Sbjct:   110 SIEYSCPASNECEITKRRRKACQACRFTKCLRVGMLKEGVRLDRVRGGRQKYKRRPEV 167

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005496 "steroid binding" evidence=IEA

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

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

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

 Score = 270 (100.1 bits), Expect = 6.0e-25, Sum P(2) = 6.0e-25
 Identities = 48/58 (82%), Positives = 54/58 (93%)

Query:     1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL 58
             +IEY+CPASN+CEI KRRRKACQACRF KCLR GMLKEGVRLDRVRGGRQKY+R P++
Sbjct:   110 SIEYSCPASNECEITKRRRKACQACRFTKCLRVGMLKEGVRLDRVRGGRQKYKRRPEV 167

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

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

GO:0005634 "nucleus" evidence=IEA

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

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

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005496 "steroid binding" evidence=IEA

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

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

 Score = 270 (100.1 bits), Expect = 6.0e-25, Sum P(2) = 6.0e-25
 Identities = 48/58 (82%), Positives = 54/58 (93%)

Query:     1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL 58
             +IEY+CPASN+CEI KRRRKACQACRF KCLR GMLKEGVRLDRVRGGRQKY+R P++
Sbjct:   110 SIEYSCPASNECEITKRRRKACQACRFTKCLRVGMLKEGVRLDRVRGGRQKYKRRPEV 167

GO:0003677 "DNA binding" evidence=IDA

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

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

GO:0005496 "steroid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0030278 "regulation of ossification" evidence=ISO

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

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

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

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

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

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

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

GO:0046872 "metal ion binding" evidence=IEA

GO:0051216 "cartilage development" evidence=ISO

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

 Score = 270 (100.1 bits), Expect = 6.0e-25, Sum P(2) = 6.0e-25
 Identities = 48/58 (82%), Positives = 54/58 (93%)

Query:     1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL 58
             +IEY+CPASN+CEI KRRRKACQACRF KCLR GMLKEGVRLDRVRGGRQKY+R P++
Sbjct:   110 SIEYSCPASNECEITKRRRKACQACRFTKCLRVGMLKEGVRLDRVRGGRQKYKRRPEV 167

GO:0003677 "DNA binding" evidence=ISO

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

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

GO:0005496 "steroid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;ISO

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0030278 "regulation of ossification" evidence=IMP

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

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

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

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

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

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

GO:0051216 "cartilage development" evidence=IMP

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

 Score = 270 (100.1 bits), Expect = 6.2e-25, Sum P(2) = 6.2e-25
 Identities = 48/58 (82%), Positives = 54/58 (93%)

Query:     1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL 58
             +IEY+CPASN+CEI KRRRKACQACRF KCLR GMLKEGVRLDRVRGGRQKY+R P++
Sbjct:   110 SIEYSCPASNECEITKRRRKACQACRFTKCLRVGMLKEGVRLDRVRGGRQKYKRRPEV 167

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 = 275 (101.9 bits), Expect = 1.0e-23, P = 1.0e-23
 Identities = 54/85 (63%), Positives = 68/85 (80%)

Query:     1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
             NIEY+CPASN+CEI KRRRKACQACRF KCL+ GMLKEGVRLDRVRGGRQKY+R P++ +
Sbjct:   131 NIEYSCPASNECEITKRRRKACQACRFTKCLKVGMLKEGVRLDRVRGGRQKYKRRPEVEN 190

Query:    61 QQWPPNKSIPSLEDLER-NTEISVS 84
               +  +  IP  ++ E+ ++ I VS
Sbjct:   191 ATYQ-SAPIPLRKEGEKGSSSIIVS 214

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

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

 Score = 270 (100.1 bits), Expect = 1.1e-23, Sum P(2) = 1.1e-23
 Identities = 48/58 (82%), Positives = 54/58 (93%)

Query:     1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL 58
             +IEY+CPASN+CEI KRRRKACQACRF KCLR GMLKEGVRLDRVRGGRQKY+R P++
Sbjct:   301 SIEYSCPASNECEITKRRRKACQACRFTKCLRVGMLKEGVRLDRVRGGRQKYKRRPEV 358

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

GO:0005634 "nucleus" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005496 "steroid binding" evidence=IEA

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

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

UNIPROTKB|F1NBB9 ESRRB "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 265 (98.3 bits), Expect = 1.4e-22, P = 1.4e-22
 Identities = 52/75 (69%), Positives = 58/75 (77%)

Query:     1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPD--- 57
             NIEY+CPA+N+CEI KRRRK+CQACRF KCL+ GMLKEGVRLDRVRGGRQKY+R  D   
Sbjct:   139 NIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRLDSES 198

Query:    58 --LLSQQWPPNKSIP 70
                LS Q PP    P
Sbjct:   199 STYLSLQIPPPAKKP 213

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

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

GO:0005496 "steroid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0001831 "trophectodermal cellular morphogenesis" evidence=IEA

GO:0001834 "trophectodermal cell proliferation" evidence=IEA

GO:0001892 "embryonic placenta development" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IEA

GO:0019827 "stem cell maintenance" evidence=IEA

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P11474	ERR1_HUMAN	No assigned EC number	0.8275	0.4715	0.1371	yes	N/A
Q6QMY5	ERR1_CANFA	No assigned EC number	0.7656	0.5203	0.1516	yes	N/A
Q19345	NHR25_CAEEL	No assigned EC number	0.52	0.4065	0.0874	yes	N/A
O08580	ERR1_MOUSE	No assigned EC number	0.8275	0.4715	0.1374	yes	N/A
Q5QJV7	ERR1_RAT	No assigned EC number	0.8275	0.4715	0.1374	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	123
cd07170	97	cd07170, NR_DBD_ERR, DNA-binding domain of estroge	1e-33
cd07155	75	cd07155, NR_DBD_ER_like, DNA-binding domain of est	1e-18
cd07167	93	cd07167, NR_DBD_Lrh-1_like, The DNA-binding domain	4e-18
cd06916	72	cd06916, NR_DBD_like, DNA-binding domain of nuclea	2e-17
pfam00105	70	pfam00105, zf-C4, Zinc finger, C4 type (two domain	1e-14
cd07168	90	cd07168, NR_DBD_DHR4_like, DNA-binding domain of e	1e-14
cd06961	85	cd06961, NR_DBD_TR, DNA-binding domain of thyroid	2e-14
cd07171	82	cd07171, NR_DBD_ER, DNA-binding domain of estrogen	5e-13
cd06969	75	cd06969, NR_DBD_NGFI-B, DNA-binding domain of the	4e-12
smart00399	70	smart00399, ZnF_C4, c4 zinc finger in nuclear horm	8e-12
cd06960	76	cd06960, NR_DBD_HNF4A, DNA-binding domain of hepto	3e-11
cd07156	72	cd07156, NR_DBD_VDR_like, The DNA-binding domain o	8e-11
cd07169	90	cd07169, NR_DBD_GCNF_like, DNA-binding domain of G	2e-10
cd07179	74	cd07179, 2DBD_NR_DBD2, The second DNA-binding doma	3e-10
cd07157	86	cd07157, 2DBD_NR_DBD1, The first DNA-binding domai	2e-09
cd06964	85	cd06964, NR_DBD_RAR, DNA-binding domain of retinoi	2e-09
cd06956	77	cd06956, NR_DBD_RXR, DNA-binding domain of retinoi	2e-09
cd06967	87	cd06967, NR_DBD_TR2_like, DNA-binding domain of th	3e-09
cd07164	78	cd07164, NR_DBD_PNR_like_1, DNA-binding domain of	9e-09
cd06966	94	cd06966, NR_DBD_CAR, DNA-binding domain of constit	2e-08
cd07162	87	cd07162, NR_DBD_PXR, DNA-binding domain of pregnan	7e-08
cd07165	81	cd07165, NR_DBD_DmE78_like, DNA-binding domain of	1e-07
cd07172	78	cd07172, NR_DBD_GR_PR, DNA-binding domain of gluco	2e-07
cd06968	95	cd06968, NR_DBD_ROR, DNA-binding domain of Retinoi	2e-07
cd06955	107	cd06955, NR_DBD_VDR, DNA-binding domain of vitamin	4e-07
cd06958	73	cd06958, NR_DBD_COUP_TF, DNA-binding domain of chi	6e-07
cd06963	73	cd06963, NR_DBD_GR_like, The DNA binding domain of	8e-07
cd07154	73	cd07154, NR_DBD_PNR_like, The DNA-binding domain o	9e-07
cd06965	84	cd06965, NR_DBD_Ppar, DNA-binding domain of peroxi	2e-06
cd07158	73	cd07158, NR_DBD_Ppar_like, The DNA-binding domain	3e-06
cd07166	89	cd07166, NR_DBD_REV_ERB, DNA-binding domain of REV	8e-06
cd07173	82	cd07173, NR_DBD_AR, DNA-binding domain of androgen	1e-05
cd06957	82	cd06957, NR_DBD_PNR_like_2, DNA-binding domain of	2e-05
cd07163	92	cd07163, NR_DBD_TLX, DNA-binding domain of Tailles	4e-05
cd06970	92	cd06970, NR_DBD_PNR, DNA-binding domain of the pho	6e-05
cd07161	91	cd07161, NR_DBD_EcR, DNA-binding domain of Ecdyson	1e-04
cd06962	84	cd06962, NR_DBD_FXR, DNA-binding domain of Farneso	0.001
cd06959	73	cd06959, NR_DBD_EcR_like, The DNA-binding domain o	0.004

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

 Score =  112 bits (281), Expect = 1e-33
 Identities = 46/58 (79%), Positives = 52/58 (89%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL 58
          NIEY+CPA+N+CEI KRRRK+CQACRF KCL+ GMLKEGVRLDRVRGGRQKY+R  D 
Sbjct: 38 NIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRIDA 95

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

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

 Score = 73.3 bits (180), Expect = 1e-18
 Identities = 30/44 (68%), Positives = 41/44 (93%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
          N+ Y+CP++++CE++K+RRK+CQACR QKCL+ GMLKEGVRLDR
Sbjct: 32 NLGYSCPSTSECEVDKKRRKSCQACRLQKCLKVGMLKEGVRLDR 75

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

>gnl|CDD|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 = 72.9 bits (179), Expect = 4e-18
 Identities = 28/51 (54%), Positives = 35/51 (68%)

Query: 3  EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYR 53
           YTC  + +C+I+K +RK C  CRFQKCL  GM  E VR DR+RGGR K+ 
Sbjct: 34 RYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMRGGRNKFG 84

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

>gnl|CDD|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 = 2e-17
 Identities = 26/41 (63%), Positives = 30/41 (73%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR 41
          N+EYTCPA  +C I+KR R  CQACR +KCL  GM KE VR
Sbjct: 32 NLEYTCPAGGNCVIDKRNRNRCQACRLKKCLAVGMRKEAVR 72

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

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

 Score = 63.4 bits (155), Expect = 1e-14
 Identities = 22/37 (59%), Positives = 25/37 (67%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLK 37
          NI YTCP + DC I+KR R  CQ CR +KCL  GM K
Sbjct: 34 NIVYTCPFNKDCVIDKRNRNRCQYCRLKKCLEVGMSK 70

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

>gnl|CDD|143542 cd07168, NR_DBD_DHR4_like, DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers

 Score = 63.7 bits (155), Expect = 1e-14
 Identities = 26/48 (54%), Positives = 31/48 (64%)

Query: 4  YTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQK 51
          YTC     CEI K +R  CQ CRF+KC+RKGM+   VR DR+ GGR  
Sbjct: 43 YTCVGDGRCEITKAQRNRCQYCRFRKCIRKGMMLAAVREDRMPGGRNS 90

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

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

 Score = 63.2 bits (154), Expect = 2e-14
 Identities = 23/51 (45%), Positives = 31/51 (60%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQK 51
           + Y+C     CEI+K  R  CQ CRF+KC+  GM K+ V  DR RG ++K
Sbjct: 33 KLSYSCKGEGKCEIDKVTRNQCQECRFKKCIAVGMAKDLVLDDRKRGAKRK 83

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

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

 Score = 59.5 bits (144), Expect = 5e-13
 Identities = 24/44 (54%), Positives = 32/44 (72%)

Query: 3  EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR 46
          +Y CPA+N C I+K RRK+CQACR +KC   GM+K G+R +R  
Sbjct: 39 DYICPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRRERRG 82

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

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

 Score = 56.7 bits (137), Expect = 4e-12
 Identities = 24/41 (58%), Positives = 31/41 (75%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR 41
          N +Y C A+ +C ++KRRR  CQ CRFQKCL+ GM+KE VR
Sbjct: 34 NAKYVCLANKNCPVDKRRRNRCQYCRFQKCLQVGMVKEVVR 74

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

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

 Score = 56.0 bits (136), Expect = 8e-12
 Identities = 19/38 (50%), Positives = 23/38 (60%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE 38
            +Y C   N+C INKR R  C+ACR +KCL  GM  E
Sbjct: 33 RYKYRCDRKNNCSINKRYRCRCRACRLKKCLGVGMDPE 70

Length = 70

>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 = 54.5 bits (132), Expect = 3e-11
 Identities = 20/45 (44%), Positives = 28/45 (62%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV 45
          N  YTC    +C ++K +R AC+ CRF+KCL  GM  E V+ +R 
Sbjct: 32 NRTYTCRFGGNCVVDKDKRNACRYCRFKKCLEVGMDPEAVQNERD 76

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

>gnl|CDD|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 = 53.5 bits (129), Expect = 8e-11
 Identities = 21/38 (55%), Positives = 25/38 (65%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE 38
             +TCP + DCEI K  R+ CQACR +KCL  GM KE
Sbjct: 32 KARFTCPFNGDCEITKDNRRHCQACRLKKCLDIGMKKE 69

The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: vitamin D receptors (VDR), constitutive androstane receptor (CAR) and pregnane X receptor (PXR). VDR regulates calcium metabolism, cellular proliferation and differentiation. PXR and CAR function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The DNA binding activity is regulated by their corresponding ligands. VDR is activated by Vitamin D; CAR and PXR respond to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. Like other nuclear receptors, xenobiotic receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 72

>gnl|CDD|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 = 53.0 bits (127), Expect = 2e-10
 Identities = 19/48 (39%), Positives = 30/48 (62%)

Query: 4  YTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQK 51
          Y C    +C +++++R  CQ CR  KCL+ GM ++ +R D + GGR K
Sbjct: 43 YRCSRDKNCVMSRKQRNRCQYCRLLKCLQMGMNRKAIREDGMPGGRNK 90

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

>gnl|CDD|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 = 52.1 bits (125), Expect = 3e-10
 Identities = 18/42 (42%), Positives = 25/42 (59%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRL 42
          +  Y CP   +C I    R AC++CRF++CL  GM K G R+
Sbjct: 32 SNSYVCPGGQNCAITPATRNACKSCRFRRCLAVGMSKTGSRI 73

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

>gnl|CDD|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 = 50.6 bits (121), Expect = 2e-09
 Identities = 19/43 (44%), Positives = 23/43 (53%)

Query: 3  EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV 45
             CP    C I+K+ R  CQACR++KCL  GM   G R  R 
Sbjct: 38 ISECPNGGKCIIDKKNRTKCQACRYRKCLNVGMSLGGPRYGRR 80

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

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

 Score = 50.3 bits (120), Expect = 2e-09
 Identities = 24/44 (54%), Positives = 26/44 (59%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
          N+ YTC    +C INK  R  CQ CR QKC   GM KE VR DR
Sbjct: 38 NMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDR 81

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

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

 Score = 49.9 bits (119), Expect = 2e-09
 Identities = 22/41 (53%), Positives = 29/41 (70%)

Query: 4  YTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
          YTC  + DC I+KR+R  CQ CR+QKCL  GM +E V+ +R
Sbjct: 37 YTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER 77

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

>gnl|CDD|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 = 49.8 bits (119), Expect = 3e-09
 Identities = 22/44 (50%), Positives = 27/44 (61%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
          N+ Y+C  S DC INK  R  CQ CR QKCL  GM  + V+ +R
Sbjct: 37 NLGYSCRGSKDCVINKHHRNRCQYCRLQKCLAMGMKSDSVQCER 80

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

>gnl|CDD|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 = 48.2 bits (115), Expect = 9e-09
 Identities = 18/44 (40%), Positives = 28/44 (63%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
          N+ Y C  +  C ++  RR  CQACRF+KCL+  M ++ V+ +R
Sbjct: 32 NLAYVCKENGSCVVDVARRNQCQACRFKKCLQVNMNRDAVQHER 75

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

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

 Score = 47.8 bits (114), Expect = 2e-08
 Identities = 18/36 (50%), Positives = 21/36 (58%)

Query: 3  EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE 38
          E+ CP +  CEIN   R+ CQ CR  KC   GM KE
Sbjct: 36 EFKCPFNESCEINVVTRRFCQKCRLDKCFAIGMKKE 71

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

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

 Score = 46.5 bits (110), Expect = 7e-08
 Identities = 19/38 (50%), Positives = 21/38 (55%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE 38
          N    CP    C I K  R+ CQACR +KCL  GM KE
Sbjct: 33 NARLCCPFQKGCVITKSNRRQCQACRLRKCLSIGMKKE 70

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

>gnl|CDD|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 = 45.6 bits (108), Expect = 1e-07
 Identities = 22/45 (48%), Positives = 26/45 (57%)

Query: 2  IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR 46
          IEY C     CEI +  R  CQ CRF+KCL  GM K+ VR  R+ 
Sbjct: 33 IEYRCLRDGKCEIIRLNRNRCQYCRFKKCLAAGMSKDSVRYGRIP 77

DNA-binding domain of proteins similar to Drosophila ecdysone-induced protein 78 (E78) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. E78 interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Drosophila ecdysone-induced protein 78 (E78) is a transcription factor belonging to the nuclear receptor superfamily. E78 is a product of the ecdysone-inducible gene found in an early late puff locus at position 78C during the onset of Drosophila metamorphosis. An E78 orthologue from the Platyhelminth Schistosoma mansoni (SmE78) has also been identified. It is the first E78 orthologue known outside of the molting animals--the Ecdysozoa. The SmE78 may be involved in transduction of an ecdysone signal in S. mansoni, consistent with its function in Drosophila. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, E78-like receptors have a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). Length = 81

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

 Score = 44.8 bits (106), Expect = 2e-07
 Identities = 19/39 (48%), Positives = 23/39 (58%)

Query: 4  YTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRL 42
          Y C   NDC I+K RRK C ACR +KCL+ GM     + 
Sbjct: 39 YLCAGRNDCIIDKIRRKNCPACRLRKCLQAGMNLGARKT 77

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

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

 Score = 45.2 bits (107), Expect = 2e-07
 Identities = 19/47 (40%), Positives = 28/47 (59%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG 47
          N+ Y+CP   +C I++  R  CQ CR QKCL  GM ++ V+  R+  
Sbjct: 39 NVSYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSK 85

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

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

 Score = 44.9 bits (106), Expect = 4e-07
 Identities = 19/40 (47%), Positives = 27/40 (67%)

Query: 4  YTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLD 43
          +TCP + DC I K  R+ CQACR ++C+  GM+KE +  D
Sbjct: 43 FTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTD 82

DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. VDR interacts with a VDR response element, a direct repeat of GGTTCA DNA site with 3 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high-affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of corepressors. Upon ligand binding, VDR forms a heterodimer with the retinoid X receptor (RXR) that binds to vitamin D response elements (VDREs), recruits coactivators. This leads to the expression of a large number of genes. Approximately 200 human genes are considered to be primary targets of VDR and even more genes are regulated indirectly. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, VDR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 107

>gnl|CDD|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 = 43.3 bits (102), Expect = 6e-07
 Identities = 18/41 (43%), Positives = 27/41 (65%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR 41
          N+ YTC  + +C I++  R  CQ CR +KCL+ GM +E V+
Sbjct: 32 NLTYTCRGNRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQ 72

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

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

 Score = 43.0 bits (101), Expect = 8e-07
 Identities = 19/39 (48%), Positives = 23/39 (58%)

Query: 4  YTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRL 42
          Y C   NDC I+K RRK C ACR +KC + GM     +L
Sbjct: 35 YLCAGRNDCIIDKIRRKNCPACRLRKCYQAGMTLGARKL 73

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

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

 Score = 42.9 bits (101), Expect = 9e-07
 Identities = 21/42 (50%), Positives = 27/42 (64%), Gaps = 1/42 (2%)

Query: 1  NIEYTCPASN-DCEINKRRRKACQACRFQKCLRKGMLKEGVR 41
          N+ YTC A N  C ++K RR  CQACR +KCL   M K+ V+
Sbjct: 32 NLLYTCKAGNGSCVVDKARRNQCQACRLKKCLEVSMNKDAVQ 73

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

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

 Score = 42.8 bits (101), Expect = 2e-06
 Identities = 19/41 (46%), Positives = 24/41 (58%), Gaps = 2/41 (4%)

Query: 5  TCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV 45
           C  S  C+I+K+ R  CQ CRFQKCL  GM    +R  R+
Sbjct: 38 PCDLS--CKIHKKSRNKCQYCRFQKCLNVGMSHNAIRFGRM 76

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

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

 Score = 41.8 bits (98), Expect = 3e-06
 Identities = 18/42 (42%), Positives = 23/42 (54%), Gaps = 1/42 (2%)

Query: 1  NIEYT-CPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR 41
          N+ Y  C     C I ++ R  CQ CRF+KCL  GM +  VR
Sbjct: 32 NLTYRRCLNGGKCVIQRKNRNRCQYCRFKKCLSVGMSRNAVR 73

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

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

 Score = 41.0 bits (96), Expect = 8e-06
 Identities = 19/46 (41%), Positives = 26/46 (56%), Gaps = 1/46 (2%)

Query: 1  NIEY-TCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV 45
           I+Y  C  +  C I +  R  CQ CRF+KCL  GM ++ VR  R+
Sbjct: 37 KIQYRKCTKNETCSIMRINRNRCQYCRFKKCLAVGMSRDAVRFGRI 82

DNA-binding domain of REV-ERB receptor- like is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. REV-ERB receptors are transcriptional regulators belonging to the nuclear receptor superfamily. They regulate a number of physiological functions including the circadian rhythm, lipid metabolism, and cellular differentiation. REV-ERB receptors bind as a monomer to a (A/G)GGTCA half-site with a 5' AT-rich extension or as a homodimer to a direct repeat 2 element (AGGTCA sequence with a 2-bp spacer), indicating functional diversity. When bound to the DNA, they recruit corepressors (NcoR/histone deacetylase 3) to the promoter, resulting in repression of the target genes. The porphyrin heme has been demonstrated to function as a ligand for REV-ERB receptor. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, REV-ERB receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). Length = 89

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

 Score = 40.3 bits (94), Expect = 1e-05
 Identities = 18/44 (40%), Positives = 26/44 (59%)

Query: 3  EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR 46
          +Y C + NDC I+K RRK C +CR +KC   GM     +L ++ 
Sbjct: 39 KYLCASRNDCTIDKFRRKNCPSCRLRKCFEAGMTLGARKLKKLG 82

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

>gnl|CDD|143515 cd06957, NR_DBD_PNR_like_2, DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like is composed of two C4-type zinc fingers

 Score = 39.8 bits (93), Expect = 2e-05
 Identities = 20/45 (44%), Positives = 26/45 (57%), Gaps = 1/45 (2%)

Query: 1  NIEYTCPASN-DCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
           I YTC A N +C ++K RR  C  CR QKC   GM +  V+ +R
Sbjct: 32 GIIYTCIAGNGNCVVDKARRNWCPFCRLQKCFAVGMNRAAVQEER 76

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

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

 Score = 39.0 bits (91), Expect = 4e-05
 Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 2/46 (4%)

Query: 1  NIEYTCPASN--DCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
          N +Y C +     C ++K  R  C+ACR +KC   GM K+ V+ +R
Sbjct: 40 NRQYVCKSKGQGGCPVDKTHRNQCRACRLKKCFEVGMNKDAVQHER 85

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

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

 Score = 38.8 bits (90), Expect = 6e-05
 Identities = 19/42 (45%), Positives = 27/42 (64%), Gaps = 1/42 (2%)

Query: 4  YTCPA-SNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
          Y C A +  C ++K  R  CQACR +KCL+ GM K+ V+ +R
Sbjct: 43 YRCQAGTGMCPVDKAHRNQCQACRLKKCLQAGMNKDAVQNER 84

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

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

 Score = 37.5 bits (87), Expect = 1e-04
 Identities = 16/40 (40%), Positives = 21/40 (52%)

Query: 4  YTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLD 43
          Y C     CE++   R+ CQ CR +KCL  GM  E V  +
Sbjct: 38 YHCKYGRACEMDMYMRRKCQECRLKKCLSVGMRPECVVPE 77

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

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

 Score = 35.3 bits (81), Expect = 0.001
 Identities = 16/38 (42%), Positives = 21/38 (55%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE 38
          N  Y C    +CE++   R+ CQ CR +KC   GML E
Sbjct: 35 NAVYKCKNGGNCEMDMYMRRKCQECRLRKCKEMGMLAE 72

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

>gnl|CDD|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 = 33.6 bits (77), Expect = 0.004
 Identities = 14/38 (36%), Positives = 19/38 (50%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE 38
             Y C   N CE++   R+ CQ CR +KC   GM  +
Sbjct: 33 GAVYACKFGNKCEMDMYMRRKCQECRLRKCKAAGMRPD 70

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	123
KOG4215|consensus	432		99.6
KOG4217|consensus	605		99.6
cd07170	97	NR_DBD_ERR DNA-binding domain of estrogen related	99.48
cd06961	85	NR_DBD_TR DNA-binding domain of thyroid hormone re	99.48
cd07169	90	NR_DBD_GCNF_like DNA-binding domain of Germ cell n	99.45
cd07167	93	NR_DBD_Lrh-1_like The DNA-binding domain of Lrh-1	99.44
cd07168	90	NR_DBD_DHR4_like DNA-binding domain of ecdysone-in	99.42
cd06964	85	NR_DBD_RAR DNA-binding domain of retinoic acid rec	99.4
KOG4846|consensus	538		99.39
cd07165	81	NR_DBD_DmE78_like DNA-binding domain of Drosophila	99.38
cd07164	78	NR_DBD_PNR_like_1 DNA-binding domain of the photor	99.38
cd06967	87	NR_DBD_TR2_like DNA-binding domain of the TR2 and	99.38
cd07155	75	NR_DBD_ER_like DNA-binding domain of estrogen rece	99.38
cd06956	77	NR_DBD_RXR DNA-binding domain of retinoid X recept	99.38
cd06957	82	NR_DBD_PNR_like_2 DNA-binding domain of the photor	99.37
cd07166	89	NR_DBD_REV_ERB DNA-binding domain of REV-ERB recep	99.37
cd06960	76	NR_DBD_HNF4A DNA-binding domain of heptocyte nucle	99.36
cd07160	101	NR_DBD_LXR DNA-binding domain of Liver X receptors	99.35
cd06966	94	NR_DBD_CAR DNA-binding domain of constitutive andr	99.34
cd07161	91	NR_DBD_EcR DNA-binding domain of Ecdysone receptor	99.33
cd06962	84	NR_DBD_FXR DNA-binding domain of Farnesoid X recep	99.33
cd07171	82	NR_DBD_ER DNA-binding domain of estrogen receptors	99.33
cd07163	92	NR_DBD_TLX DNA-binding domain of Tailless (TLX) is	99.32
cd06968	95	NR_DBD_ROR DNA-binding domain of Retinoid-related	99.32
cd06970	92	NR_DBD_PNR DNA-binding domain of the photoreceptor	99.31
KOG4218|consensus	475		99.28
cd07162	87	NR_DBD_PXR DNA-binding domain of pregnane X recept	99.27
KOG4216|consensus	479		99.27
cd07157	86	2DBD_NR_DBD1 The first DNA-binding domain (DBD) of	99.26
cd06969	75	NR_DBD_NGFI-B DNA-binding domain of the orphan nuc	99.25
cd06955	107	NR_DBD_VDR DNA-binding domain of vitamin D recepto	99.25
cd07179	74	2DBD_NR_DBD2 The second DNA-binding domain (DBD) o	99.25
cd06958	73	NR_DBD_COUP_TF DNA-binding domain of chicken ovalb	99.23
cd06916	72	NR_DBD_like DNA-binding domain of nuclear receptor	99.23
cd07158	73	NR_DBD_Ppar_like The DNA-binding domain of peroxis	99.22
cd07156	72	NR_DBD_VDR_like The DNA-binding domain of vitamin	99.22
cd06965	84	NR_DBD_Ppar DNA-binding domain of peroxisome proli	99.21
cd06959	73	NR_DBD_EcR_like The DNA-binding domain of Ecdysone	99.21
cd07154	73	NR_DBD_PNR_like The DNA-binding domain of the phot	99.21
cd06963	73	NR_DBD_GR_like The DNA binding domain of GR_like n	99.2
cd07172	78	NR_DBD_GR_PR DNA-binding domain of glucocorticoid	99.14
cd07173	82	NR_DBD_AR DNA-binding domain of androgen receptor	99.12
smart00399	70	ZnF_C4 c4 zinc finger in nuclear hormone receptors	99.03
PF00105	70	zf-C4: Zinc finger, C4 type (two domains); InterPr	98.92

>KOG4215|consensus

Probab=99.60  E-value=2.5e-16  Score=125.64  Aligned_cols=52  Identities=42%  Similarity=0.896  Sum_probs=47.8

Q ss_pred             CCceecCCCCCcccccccccccccccchhhhhccccccccccccccCccccc
Q psy752            1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKY   52 (123)
Q Consensus         1 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~~~~~~   52 (123)
                      +..|+|+++.+|.|||..|+.||||||+||+.+||.++|||++|++.+..+.
T Consensus        53 ~~~YtCRF~k~C~VDKdkRNaCRyCRfqKC~~aGMK~eAiQnERDrIg~Rr~  104 (432)
T KOG4215|consen   53 NHQYTCRFNKQCVVDKDKRNACRYCRFQKCVRAGMKREAIQNERDRIGSRRP  104 (432)
T ss_pred             cceeeeeccccccccchhhhhhhHhhHHHHHHhcccHHhhhcccccccccCC
Confidence            3579999999999999999999999999999999999999999998877443

>KOG4217|consensus

Probab=99.60  E-value=5.4e-16  Score=126.95  Aligned_cols=83  Identities=39%  Similarity=0.757  Sum_probs=66.4

Q ss_pred             CCceecCCCCCcccccccccccccccchhhhhccccccccccccccCccccccCCCCCCCCCCCCCCCCCChhHHhhHHH
Q psy752            1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEDLERNTE   80 (123)
Q Consensus         1 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~~~~~~~~~~~~~~~~~p~~~~~~s~e~~~~~~~   80 (123)
                      |..|+|-++++|.|||..|+.||||||||||+|||-++.||.|.-+++|.+...+.... +.+|++++          -.
T Consensus       303 naKYvClanKnCPVDKRrRnRCQyCRfQKCL~VGMVKEVVRtdSLkGRRGRLpSKpKs~-q~sppSpP----------i~  371 (605)
T KOG4217|consen  303 NAKYVCLANKNCPVDKRRRNRCQYCRFQKCLAVGMVKEVVRTDSLKGRRGRLPSKPKSR-QPSPPSPP----------IS  371 (605)
T ss_pred             CCeeEeecCCCCCcchhhhhhchhhhHhHHHHhhhhhhheeccccccccCCCCCCCCCC-CCCCCCCc----------hH
Confidence            46899999999999999999999999999999999999999999999888887665543 33333322          16


Q ss_pred             HHHHHHhccCCCCC
Q psy752           81 ISVSMMSCDGDTSD   94 (123)
Q Consensus        81 li~~L~~ae~~~~~   94 (123)
                      +|..|..|+-+++.
T Consensus       372 LltalvrAh~Dstp  385 (605)
T KOG4217|consen  372 LLTALVRAHVDSTP  385 (605)
T ss_pred             HHHHHHHHhhcCCC
Confidence            67777777666543

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

Probab=99.48  E-value=1.9e-14  Score=96.58  Aligned_cols=56  Identities=80%  Similarity=1.458  Sum_probs=50.3

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccccccccccccCccccccCCCC
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPD   57 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~~~~~~~~~~~   57 (123)
                      ..|.|.++++|.|+...|..|++|||+|||++||++++||.+|+..++++..+..+
T Consensus        39 ~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~vq~~r~~~~~~~~~~~~~   94 (97)
T cd07170          39 IEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRID   94 (97)
T ss_pred             CceeecCCCccccCcccCccCCccccchhhhcCCCHHHcccccCCCCCCCccCccc
Confidence            46899999999999999999999999999999999999999998888877765543

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

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

Probab=99.48  E-value=1.2e-14  Score=95.35  Aligned_cols=51  Identities=45%  Similarity=0.926  Sum_probs=46.7

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccccccccccccCccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKY   52 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~~~~~~   52 (123)
                      ..|.|..+++|.|+...|..|++|||+||+++||++++||.+|++.++++.
T Consensus        34 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~~~~~~   84 (85)
T cd06961          34 LSYSCKGEGKCEIDKVTRNQCQECRFKKCIAVGMAKDLVLDDRKRGAKRKL   84 (85)
T ss_pred             CccccCCCCccccCccccccCccchhhhhhhccCCHHHcccccCccccccc
Confidence            478999999999999999999999999999999999999999998776553

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

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

Probab=99.45  E-value=3e-14  Score=94.41  Aligned_cols=50  Identities=38%  Similarity=0.891  Sum_probs=46.6

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccccccccccccCcccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQK   51 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~~~~~   51 (123)
                      ..|.|..+++|.|+...|..|++|||+||+++||++++||.+|.++++++
T Consensus        41 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~~~~~   90 (90)
T cd07169          41 RVYRCSRDKNCVMSRKQRNRCQYCRLLKCLQMGMNRKAIREDGMPGGRNK   90 (90)
T ss_pred             CceecCCCCcccccccccccccccchhhhccccCCHHHhccccCCCCCCC
Confidence            46899999999999999999999999999999999999999999888764

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

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

Probab=99.44  E-value=3.6e-14  Score=94.55  Aligned_cols=52  Identities=54%  Similarity=1.048  Sum_probs=48.0

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccccccccccccCcccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYR   53 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~~~~~~~   53 (123)
                      ..|.|..+++|.|+...|..|++|||+||+++||++++||.+|..++++++.
T Consensus        33 ~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~Vq~~r~~~~~~~~~   84 (93)
T cd07167          33 KRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMRGGRNKFG   84 (93)
T ss_pred             CccccCCCCccccCccccCcCCCcccchhhhccCCHHHhhhcccCCCccccC
Confidence            5789999999999999999999999999999999999999999888877763

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

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

Probab=99.42  E-value=5.3e-14  Score=93.18  Aligned_cols=49  Identities=53%  Similarity=1.044  Sum_probs=45.5

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccccccccccccCccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQ   50 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~~~~   50 (123)
                      ..|.|..+++|.|+...|..|++|||+||+++||++++||.+|++++++
T Consensus        41 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R~~~~~~   89 (90)
T cd07168          41 RVYTCVGDGRCEITKAQRNRCQYCRFRKCIRKGMMLAAVREDRMPGGRN   89 (90)
T ss_pred             CCccCCCCCCccccccccccccccchhhhhhcCCCHHHhhcccCCCCCC
Confidence            4689999999999999999999999999999999999999999987764

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

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

Probab=99.40  E-value=9.5e-14  Score=91.09  Aligned_cols=45  Identities=51%  Similarity=0.933  Sum_probs=42.5

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhcccccccccccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR   46 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~   46 (123)
                      ..|.|.++++|.|+...|..|++|||+|||++||++++||.+|++
T Consensus        39 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~R~~   83 (85)
T cd06964          39 MVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNK   83 (85)
T ss_pred             CCeECCCCCccccCCcccccCccchhhhhhhhCCCHHHhhccccC
Confidence            468999999999999999999999999999999999999999976

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

>KOG4846|consensus

Probab=99.39  E-value=1.5e-13  Score=111.42  Aligned_cols=91  Identities=29%  Similarity=0.494  Sum_probs=67.3

Q ss_pred             Cce-ecCCCCCcccccccccccccccchhhhhccccccccccccccCccccccCCCCCCCCCCCCCCCCCChhHH-hhHH
Q psy752            2 IEY-TCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEDL-ERNT   79 (123)
Q Consensus         2 ~~y-~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~~~~~~~~~~~~~~~~~p~~~~~~s~e~~-~~~~   79 (123)
                      ..| .|-+..+|.|.++.|+.||+|||+|||.+||++++||.++.+. +.+.+...+++....+.... ...+.+ +.++
T Consensus       167 I~YrrClk~e~C~I~R~nRNRCQ~CRfKKCL~vGMSrDaVRFG~m~~-rnka~M~~~~~p~~V~sp~~-sq~~~Q~env~  244 (538)
T KOG4846|consen  167 IDYRRCLKQEVCEIKRENRNRCQYCRFKKCLDVGMSRDAVRFGQMKF-RNKAAMRDDKSPDSVFSPEI-SQLERQEENVD  244 (538)
T ss_pred             hhHHHHhhhhceehhhhccchhhhhhHHHHHhcccchhhhhhccccc-ccccccCCCCCCCCCCChhh-hhhhhhhccHH
Confidence            456 5999999999999999999999999999999999999998764 44555555554444333322 122333 3368


Q ss_pred             HHHHHHHhccCCCCC
Q psy752           80 EISVSMMSCDGDTSD   94 (123)
Q Consensus        80 ~li~~L~~ae~~~~~   94 (123)
                      +++++++.||.....
T Consensus       245 ~V~~~V~rAh~t~~~  259 (538)
T KOG4846|consen  245 AVYEAVLRAHTTFSF  259 (538)
T ss_pred             HHHHHHHHhhcchhh
Confidence            899999998876644

>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=99.38  E-value=1.6e-13  Score=89.17  Aligned_cols=46  Identities=48%  Similarity=0.957  Sum_probs=43.1

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccccccccccccC
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG   47 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~   47 (123)
                      ..|.|..+++|.|+...+..|++|||+|||++||++++||.+|.+.
T Consensus        33 ~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~V~~~r~~~   78 (81)
T cd07165          33 IEYRCLRDGKCEIIRLNRNRCQYCRFKKCLAAGMSKDSVRYGRIPN   78 (81)
T ss_pred             CceeCCCCCCccccccccccccchhhhhcccccCCHHHcccCCCCc
Confidence            4689999999999999999999999999999999999999999763

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

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

Probab=99.38  E-value=1.4e-13  Score=88.94  Aligned_cols=45  Identities=38%  Similarity=0.910  Sum_probs=42.4

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhcccccccccccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR   46 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~   46 (123)
                      ..|.|..+++|.|+...|..|++|||+|||++||++++||.+|++
T Consensus        33 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~   77 (78)
T cd07164          33 LAYVCKENGSCVVDVARRNQCQACRFKKCLQVNMNRDAVQHERAP   77 (78)
T ss_pred             CCccCCCCCcccccCcccccCccchhhhhhHhcCCHHHhccCCCC
Confidence            468999999999999999999999999999999999999999975

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

>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=99.38  E-value=1.4e-13  Score=90.68  Aligned_cols=46  Identities=46%  Similarity=0.884  Sum_probs=43.0

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccccccccccccC
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG   47 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~   47 (123)
                      ..|.|.++++|.|+...|..|++|||+||+++||++++||.+|++.
T Consensus        38 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~R~~~   83 (87)
T cd06967          38 LGYSCRGSKDCVINKHHRNRCQYCRLQKCLAMGMKSDSVQCERKPI   83 (87)
T ss_pred             CCcccCCCCccccCccccccCccchhhhhhHcCCCHHHhccccCCC
Confidence            4688999999999999999999999999999999999999999863

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

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

Probab=99.38  E-value=1.5e-13  Score=88.14  Aligned_cols=43  Identities=67%  Similarity=1.421  Sum_probs=40.7

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhcccccccccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR   44 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r   44 (123)
                      ..|.|..+++|.|+...|..|++|||+||+++||++++||.+|
T Consensus        33 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r   75 (75)
T cd07155          33 LGYSCPSTSECEVDKKRRKSCQACRLQKCLKVGMLKEGVRLDR   75 (75)
T ss_pred             CceeCCcCCCcccCCcccccCccchhhhhhHhCCCHHHcccCC
Confidence            4789999999999999999999999999999999999999886

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

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

Probab=99.38  E-value=1.2e-13  Score=88.93  Aligned_cols=43  Identities=51%  Similarity=1.059  Sum_probs=40.7

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhcccccccccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR   44 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r   44 (123)
                      ..|.|..+++|.|+...|..|++|||+||+++||++++||.+|
T Consensus        35 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r   77 (77)
T cd06956          35 LTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER   77 (77)
T ss_pred             CccccCCCCccccCCCccccCccchhHHHhHhCCCHHHhccCC
Confidence            4789999999999999999999999999999999999999886

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

>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=99.37  E-value=2.2e-13  Score=88.77  Aligned_cols=47  Identities=38%  Similarity=0.760  Sum_probs=42.4

Q ss_pred             CceecC-CCCCcccccccccccccccchhhhhccccccccccccccCc
Q psy752            2 IEYTCP-ASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG   48 (123)
Q Consensus         2 ~~y~C~-~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~~   48 (123)
                      ..|.|. .+++|.|+...|..|++|||+||+++||++++||.+|++..
T Consensus        33 ~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~p~~   80 (82)
T cd06957          33 IIYTCIAGNGNCVVDKARRNWCPFCRLQKCFAVGMNRAAVQEERGPRK   80 (82)
T ss_pred             CceEccCccCCCccCCCccCcccCcchhhcccccCCHHHhccccCcCC
Confidence            478999 56899999999999999999999999999999999987643

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

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

Probab=99.37  E-value=1.6e-13  Score=90.69  Aligned_cols=46  Identities=41%  Similarity=0.937  Sum_probs=42.3

Q ss_pred             Cce-ecCCCCCcccccccccccccccchhhhhccccccccccccccC
Q psy752            2 IEY-TCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG   47 (123)
Q Consensus         2 ~~y-~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~   47 (123)
                      ..| .|..+++|.|+...|..|++|||+|||++||++++||.+|++.
T Consensus        38 ~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~~~   84 (89)
T cd07166          38 IQYRKCTKNETCSIMRINRNRCQYCRFKKCLAVGMSRDAVRFGRIPK   84 (89)
T ss_pred             CcchhhccCCcccccccccccccchhhhhcccccCCHHHhcCCCCCC
Confidence            457 5999999999999999999999999999999999999999763

DNA-binding domain of REV-ERB receptor- like is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. REV-ERB receptors are transcriptional regulators belonging to the nuclear receptor superfamily. They regulate a number of physiological functions including the circadian rhythm, lipid metabolism, and cellular differentiation. REV-ERB receptors bind as a monomer to a (A/G)GGTCA half-site with a 5' AT-rich extension or as a homodimer to a direct repeat 2 element (AGGTCA sequence with a 2-bp spacer), indicating functional diversity. When bound to the DNA, they recruit corepressors (NcoR/histone deacetylase 3) to the promoter, resulting in repression of the target genes. The porphyr

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

Probab=99.36  E-value=2.2e-13  Score=87.51  Aligned_cols=44  Identities=43%  Similarity=0.887  Sum_probs=41.3

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccccccccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV   45 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~   45 (123)
                      ..|.|..+++|.|+...|..|++|||+|||++||++++||.+|+
T Consensus        33 ~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~   76 (76)
T cd06960          33 RTYTCRFGGNCVVDKDKRNACRYCRFKKCLEVGMDPEAVQNERD   76 (76)
T ss_pred             CceeCCCCCcccccCcccccCccchhhhhhhcCCCHHHcccCCC
Confidence            46899999999999999999999999999999999999999875

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

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

Probab=99.35  E-value=2.1e-13  Score=92.14  Aligned_cols=45  Identities=29%  Similarity=0.703  Sum_probs=42.3

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhcccccccccccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR   46 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~   46 (123)
                      ..|.|.++++|.|+...|..|++|||+|||++||++++||.+|+.
T Consensus        53 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~~~   97 (101)
T cd07160          53 AQYVCKNGGKCQMDMYMRRKCQECRLRKCREAGMREQCVLSEEQI   97 (101)
T ss_pred             CccccCCCCccccCCcccccCccchhHHHHHhCCCHHHhcChhhh
Confidence            468999999999999999999999999999999999999999865

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

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

Probab=99.34  E-value=1.5e-13  Score=91.75  Aligned_cols=50  Identities=36%  Similarity=0.773  Sum_probs=45.1

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccccccccccccCcccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQK   51 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~~~~~   51 (123)
                      ..|.|..+++|.|+...+..|++|||+|||++||++++||.+|+..++..
T Consensus        35 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~r~~~~~r~   84 (94)
T cd06966          35 KEFKCPFNESCEINVVTRRFCQKCRLDKCFAIGMKKEWIMSEEDKSEKRQ   84 (94)
T ss_pred             CccccCCCCccccCccccccCccchhhhCcccCCCHHHccchhhhhHHHH
Confidence            46899999999999999999999999999999999999999987655443

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

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

Probab=99.33  E-value=2.1e-13  Score=90.51  Aligned_cols=47  Identities=34%  Similarity=0.639  Sum_probs=43.0

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccccccccccccCc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG   48 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~~   48 (123)
                      ..|.|..+++|.|+...|..|++|||+|||++||++++||.+++...
T Consensus        36 ~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~~~~   82 (91)
T cd07161          36 AVYHCKYGRACEMDMYMRRKCQECRLKKCLSVGMRPECVVPESQCAI   82 (91)
T ss_pred             CceecCCCCccccCccccccCccchhhHHhHcCCCHHHcCchhhhhH
Confidence            47899999999999999999999999999999999999999985443

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

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

Probab=99.33  E-value=3.2e-13  Score=88.41  Aligned_cols=46  Identities=33%  Similarity=0.697  Sum_probs=42.4

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccccccccccccC
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG   47 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~   47 (123)
                      ..|.|.++++|.|+...|..|++|||+||+++||++++|+.++...
T Consensus        36 ~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~~~   81 (84)
T cd06962          36 AVYKCKNGGNCEMDMYMRRKCQECRLRKCKEMGMLAECLLTEIQCK   81 (84)
T ss_pred             CceecCCCCcCccCccccccCccchhhHHHHhCCChHHccCHHHHh
Confidence            5789999999999999999999999999999999999999998643

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

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

Probab=99.33  E-value=3.7e-13  Score=87.74  Aligned_cols=43  Identities=56%  Similarity=1.200  Sum_probs=40.8

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhcccccccccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR   44 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r   44 (123)
                      ..|.|..+++|.|+...|..|++|||+|||++||++++|+.+|
T Consensus        38 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~~   80 (82)
T cd07171          38 NDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRRER   80 (82)
T ss_pred             CceeCCCCCccccCCcccccCccchhHHHhHhcCCHHHHHHhh
Confidence            4789999999999999999999999999999999999999886

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

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

Probab=99.32  E-value=5.3e-13  Score=88.74  Aligned_cols=46  Identities=35%  Similarity=0.833  Sum_probs=41.7

Q ss_pred             CceecCC--CCCcccccccccccccccchhhhhccccccccccccccC
Q psy752            2 IEYTCPA--SNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG   47 (123)
Q Consensus         2 ~~y~C~~--~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~   47 (123)
                      ..|.|..  +++|.|+...|..|++|||+||+++||++++||.+|++.
T Consensus        41 ~~~~C~~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~r~p~   88 (92)
T cd07163          41 RQYVCKSKGQGGCPVDKTHRNQCRACRLKKCFEVGMNKDAVQHERGPR   88 (92)
T ss_pred             CCcCCCCCCCCCCccCCCccccCccchhhhhhhhcCCHHHhhcccCcC
Confidence            4688997  479999999999999999999999999999999999863

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).

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

Probab=99.32  E-value=6e-13  Score=88.96  Aligned_cols=46  Identities=39%  Similarity=0.978  Sum_probs=42.6

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccccccccccccC
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG   47 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~   47 (123)
                      ..|.|.++++|.|+...|..|++|||+||+++||++++|+.+|..+
T Consensus        40 ~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~V~~~r~~~   85 (95)
T cd06968          40 VSYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSK   85 (95)
T ss_pred             CceecCCCcccccccCCceeccccchhhcccccCChhhcccCcCCh
Confidence            4789999999999999999999999999999999999999998653

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

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

Probab=99.31  E-value=5.5e-13  Score=88.67  Aligned_cols=45  Identities=42%  Similarity=0.898  Sum_probs=41.8

Q ss_pred             CceecCCC-CCcccccccccccccccchhhhhcccccccccccccc
Q psy752            2 IEYTCPAS-NDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR   46 (123)
Q Consensus         2 ~~y~C~~~-~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~   46 (123)
                      ..|.|..+ ++|.++...|..|++|||+||+++||++++||.+|++
T Consensus        41 ~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R~~   86 (92)
T cd06970          41 LIYRCQAGTGMCPVDKAHRNQCQACRLKKCLQAGMNKDAVQNERQP   86 (92)
T ss_pred             CCceeecCCCcCccCCCccccCccchhhHhhHhCCCHHHcccccCc
Confidence            46899986 8999999999999999999999999999999999975

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

>KOG4218|consensus

Probab=99.28  E-value=6.8e-13  Score=105.69  Aligned_cols=52  Identities=56%  Similarity=1.114  Sum_probs=49.9

Q ss_pred             CCceecCCCCCcccccccccccccccchhhhhccccccccccccccCccccc
Q psy752            1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKY   52 (123)
Q Consensus         1 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~~~~~~   52 (123)
                      |+.|+|....+|.||+..|..|.+|||+|||.+||..++||.||.+++|.|.
T Consensus        49 nK~YtC~e~qnC~iDkTqRKRCP~CRFQKCLtvGMklEAVRADRMRGGRNKF  100 (475)
T KOG4218|consen   49 NKQYTCSEEQNCHIDKTQRKRCPSCRFQKCLTVGMKLEAVRADRMRGGRNKF  100 (475)
T ss_pred             CcceecccccccccchHhhccCCchhHHHHhhhhhhHHHHHHhhhccccccc
Confidence            5689999999999999999999999999999999999999999999999985

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

Probab=99.27  E-value=6.7e-13  Score=87.37  Aligned_cols=44  Identities=43%  Similarity=0.833  Sum_probs=41.0

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccccccccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV   45 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~   45 (123)
                      ..|.|..+++|.++...+..|++|||+|||++||++++|+.++.
T Consensus        34 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~~   77 (87)
T cd07162          34 ARLCCPFQKGCVITKSNRRQCQACRLRKCLSIGMKKELIMSDEA   77 (87)
T ss_pred             ceeEcCCCCceecCCcccccCccchhhHHhHhCCCHHHccCHHH
Confidence            46899999999999999999999999999999999999999853

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

>KOG4216|consensus

Probab=99.27  E-value=7.9e-13  Score=106.46  Aligned_cols=47  Identities=40%  Similarity=0.962  Sum_probs=43.7

Q ss_pred             CCceecCCCCCcccccccccccccccchhhhhccccccccccccccC
Q psy752            1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG   47 (123)
Q Consensus         1 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~   47 (123)
                      |..|.|++..+|.||+..|+.|++||++|||++||+++||..+|.-+
T Consensus        80 ~a~YsCpRqknC~iDRtnRNRCQ~CRLqKClaLGMSRDAVKFGRMSK  126 (479)
T KOG4216|consen   80 NANYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSK  126 (479)
T ss_pred             cccccCCcccCCcccccccchhhHHHHHHHHHhccchhhHHhccccH
Confidence            35799999999999999999999999999999999999999999653

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

Probab=99.26  E-value=2.4e-12  Score=84.57  Aligned_cols=45  Identities=42%  Similarity=0.852  Sum_probs=41.5

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhcccccccccccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR   46 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~   46 (123)
                      ..|.|.++++|.++...|..|++|||+|||++||+++.++.+|+.
T Consensus        37 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~~~~~~   81 (86)
T cd07157          37 TISECPNGGKCIIDKKNRTKCQACRYRKCLNVGMSLGGPRYGRRS   81 (86)
T ss_pred             ccccCCCCCccccCccccccCccchhhHHhHcCCCcccccccccc
Confidence            378899999999999999999999999999999999999988753

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.

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

Probab=99.25  E-value=1.7e-12  Score=83.17  Aligned_cols=41  Identities=56%  Similarity=1.112  Sum_probs=38.2

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhcccccccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRL   42 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~   42 (123)
                      ..|.|..+++|.|++..|..|++|||+||+++||++++||.
T Consensus        35 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~   75 (75)
T cd06969          35 AKYVCLANKNCPVDKRRRNRCQYCRFQKCLQVGMVKEVVRT   75 (75)
T ss_pred             CcccCCcCCccccCCcccccCcccHhHHHHHhCCCHHHccC
Confidence            46899999999999999999999999999999999999973

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

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

Probab=99.25  E-value=9.7e-13  Score=89.72  Aligned_cols=43  Identities=44%  Similarity=0.952  Sum_probs=39.9

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhcccccccccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR   44 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r   44 (123)
                      ..|.|..+++|.|+...+..|++|||+|||++||++++|+.+.
T Consensus        41 ~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~   83 (107)
T cd06955          41 ALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDE   83 (107)
T ss_pred             CccccCCCCccccccCCccccccchhHHHHHcCCCchhccCHH
Confidence            4689999999999999999999999999999999999888874

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

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

Probab=99.25  E-value=2.2e-12  Score=82.50  Aligned_cols=41  Identities=44%  Similarity=1.058  Sum_probs=38.5

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhcccccccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRL   42 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~   42 (123)
                      ..|.|..+++|.++...|..|++|||+||+++||++++|+.
T Consensus        33 ~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~   73 (74)
T cd07179          33 NSYVCPGGQNCAITPATRNACKSCRFRRCLAVGMSKTGSRI   73 (74)
T ss_pred             CcccCCCCCccccCCcccccCccchhHHHHHhCCCHhHeeC
Confidence            47899999999999999999999999999999999999985

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.

>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=99.23  E-value=3e-12  Score=81.63  Aligned_cols=40  Identities=43%  Similarity=1.036  Sum_probs=37.8

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR   41 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~   41 (123)
                      ..|.|..+++|.++...|..|++|||+|||++||++++||
T Consensus        33 ~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   72 (73)
T cd06958          33 LTYTCRGNRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQ   72 (73)
T ss_pred             CceeCCCCCcCccCCcccccCccchhhHhhHhCCCHHHcc
Confidence            4689999999999999999999999999999999999987

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

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

Probab=99.23  E-value=2.9e-12  Score=81.47  Aligned_cols=40  Identities=63%  Similarity=1.222  Sum_probs=37.5

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR   41 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~   41 (123)
                      ..|.|.++++|.|+...|..|++|||+||+++||++++||
T Consensus        33 ~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   72 (72)
T cd06916          33 LEYTCPAGGNCVIDKRNRNRCQACRLKKCLAVGMRKEAVR   72 (72)
T ss_pred             CCccCCCCCccccCCcccccCccchhhHhhHhCCChHHcC
Confidence            4688999999999999999999999999999999999886

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

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

Probab=99.22  E-value=3.5e-12  Score=81.30  Aligned_cols=40  Identities=43%  Similarity=0.998  Sum_probs=37.2

Q ss_pred             Cce-ecCCCCCcccccccccccccccchhhhhccccccccc
Q psy752            2 IEY-TCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR   41 (123)
Q Consensus         2 ~~y-~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~   41 (123)
                      ..| .|.++++|.|+...|..|++|||+|||++||++++|+
T Consensus        33 ~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   73 (73)
T cd07158          33 LTYRRCLNGGKCVIQRKNRNRCQYCRFKKCLSVGMSRNAVR   73 (73)
T ss_pred             CCcccCCCCCCcCCCccccccCccchhhhhhHccCChHHcC
Confidence            467 7999999999999999999999999999999999885

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).

>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=99.22  E-value=3.5e-12  Score=81.18  Aligned_cols=40  Identities=53%  Similarity=1.041  Sum_probs=37.2

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR   41 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~   41 (123)
                      ..|.|..+++|.++...|..|++|||+||+++||++++|.
T Consensus        33 ~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   72 (72)
T cd07156          33 ARFTCPFNGDCEITKDNRRHCQACRLKKCLDIGMKKEMIL   72 (72)
T ss_pred             CccccCCCCccccCCcccccCccchhHHHHHhCCCHHHcC
Confidence            4689999999999999999999999999999999999874

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

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

Probab=99.21  E-value=4e-12  Score=83.20  Aligned_cols=44  Identities=45%  Similarity=0.981  Sum_probs=38.8

Q ss_pred             Ccee-cCCCCCcccccccccccccccchhhhhccccccccccccccC
Q psy752            2 IEYT-CPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG   47 (123)
Q Consensus         2 ~~y~-C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~   47 (123)
                      ..|. |...  |.|+...|..|++|||+||+++||++++||.+|++.
T Consensus        34 ~~~~~C~~~--C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~~~   78 (84)
T cd06965          34 LVYKPCDLS--CKIHKKSRNKCQYCRFQKCLNVGMSHNAIRFGRMPR   78 (84)
T ss_pred             CCccccccC--CCcCccccccccchhhhhhhhccCCHHHcccCCCCc
Confidence            3564 8754  999999999999999999999999999999999763

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

>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=99.21  E-value=4.8e-12  Score=80.73  Aligned_cols=40  Identities=35%  Similarity=0.790  Sum_probs=37.2

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR   41 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~   41 (123)
                      ..|.|..+++|.|+...|..|++|||+||+++||+++.|+
T Consensus        34 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~   73 (73)
T cd06959          34 AVYACKFGNKCEMDMYMRRKCQECRLRKCKAAGMRPDCLL   73 (73)
T ss_pred             CCccCCCCCcCCcCCcccccCccchhHHHHHhCCChhhcC
Confidence            4689999999999999999999999999999999998874

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

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

Probab=99.21  E-value=4.5e-12  Score=80.83  Aligned_cols=40  Identities=45%  Similarity=0.980  Sum_probs=36.9

Q ss_pred             CceecC-CCCCcccccccccccccccchhhhhccccccccc
Q psy752            2 IEYTCP-ASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR   41 (123)
Q Consensus         2 ~~y~C~-~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~   41 (123)
                      ..|.|. .+++|.|+...|..|++|||+||+++||++++||
T Consensus        33 ~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~vq   73 (73)
T cd07154          33 LLYTCKAGNGSCVVDKARRNQCQACRLKKCLEVSMNKDAVQ   73 (73)
T ss_pred             CCcccCCCCCCCccCCcccccCccchhhHhhHhCCChHHCC
Confidence            468899 6789999999999999999999999999999886

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

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

Probab=99.20  E-value=6.3e-12  Score=80.23  Aligned_cols=40  Identities=45%  Similarity=0.924  Sum_probs=37.2

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR   41 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~   41 (123)
                      ..|.|.++++|.|+...|..|++|||+||+++||++++|.
T Consensus        33 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~a~~   72 (73)
T cd06963          33 HNYLCAGRNDCIIDKIRRKNCPACRLRKCYQAGMTLGARK   72 (73)
T ss_pred             CceeCCCCCccccCCcccccCccchhhHHHHcCCChhhcc
Confidence            4689999999999999999999999999999999998874

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

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

Probab=99.14  E-value=2.2e-11  Score=78.69  Aligned_cols=40  Identities=48%  Similarity=0.943  Sum_probs=37.1

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR   41 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~   41 (123)
                      ..|.|.++++|.|+...|..|++|||+||+++||+..+++
T Consensus        37 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~   76 (78)
T cd07172          37 HNYLCAGRNDCIIDKIRRKNCPACRLRKCLQAGMNLGARK   76 (78)
T ss_pred             CceeCCCCCccccCCcccccCccchhHHHHHhCCCccccc
Confidence            4688999999999999999999999999999999988775

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

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

Probab=99.12  E-value=2.5e-11  Score=79.14  Aligned_cols=43  Identities=42%  Similarity=0.936  Sum_probs=38.1

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhcccccccccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR   44 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r   44 (123)
                      ..|.|..+++|.|+...|..|++|||+||+++||++.....++
T Consensus        38 ~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~~~~~~   80 (82)
T cd07173          38 QKYLCASRNDCTIDKFRRKNCPSCRLRKCFEAGMTLGARKLKK   80 (82)
T ss_pred             CceecCCCCccccCCCccCcCcchhhhhhhhcCCCcChHHhhc
Confidence            4689999999999999999999999999999999987665443

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

>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors

Probab=99.03  E-value=1.2e-10  Score=73.48  Aligned_cols=37  Identities=51%  Similarity=1.011  Sum_probs=34.2

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhcccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE   38 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~   38 (123)
                      ..|.|..+++|.+++..+..|++|||+||+++||+++
T Consensus        34 ~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~   70 (70)
T smart00399       34 YKYRCDRKNNCSINKRYRCRCRACRLKKCLGVGMDPE   70 (70)
T ss_pred             CCeecCCCcccccCCCccccCccCcChhHhhccCcCC
Confidence            4688999999999999999999999999999999864

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

Probab=98.92  E-value=3.1e-10  Score=71.44  Aligned_cols=36  Identities=47%  Similarity=1.089  Sum_probs=29.3

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLK   37 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~   37 (123)
                      ..|.|..+++|.+++..+..|++|||+||+++||+.
T Consensus        35 ~~~~C~~~~~C~i~~~~~~~C~~CRf~KCl~~GM~k   70 (70)
T PF00105_consen   35 KPYKCKKNGNCKIDKDNRRKCRSCRFQKCLEVGMKK   70 (70)
T ss_dssp             CG-STSSSST---STTTTTTSHHHHHHHHHHTTBSG
T ss_pred             ccccccccccccccccCCCEeCcchHHHHHHHCCcC
Confidence            358899999999999999999999999999999974

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

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Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	123
1lo1_A	98	Estrogen Related Receptor 2 Dna Binding Domain In C		1e-21
2ff0_A	102	Solution Structure Of Steroidogenic Factor 1 Dna Bi		1e-10
2a66_A	113	Human Liver Receptor Homologue Dna-Binding Domain (		4e-10
1hcq_A	84	The Crystal Structure Of The Estrogen Receptor Dna-		4e-10
1cit_A	89	Dna-Binding Mechanism Of The Monomeric Orphan Nucle		3e-09
3dzu_A	467	Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp		3e-08
1hcp_A	76	Dna Recognition By The Oestrogen Receptor: From Sol		9e-08
1ynw_B	99	Crystal Structure Of Vitamin D Receptor And 9-Cis R		1e-07
1dsz_B	85	Structure Of The RxrRAR DNA-Binding Domain Heterodi		2e-07
4aa6_A	71	The Oestrogen Receptor Recognizes An Imperfectly Pa		3e-07
4aa6_E	71	The Oestrogen Receptor Recognizes An Imperfectly Pa		3e-07
1by4_A	82	Structure And Mechanism Of The Homodimeric Assembly		2e-06
1ynw_A	110	Crystal Structure Of Vitamin D Receptor And 9-Cis R		2e-06
1rxr_A	83	High Resolution Solution Structure Of The Retinoid		2e-06
1dsz_A	86	Structure Of The RxrRAR DNA-Binding Domain Heterodi		2e-06
1r0n_A	81	Crystal Structure Of Heterodimeric Ecdsyone Recepto		4e-06
1kb2_A	110	Crystal Structure Of Vdr Dna-Binding Domain Bound T		5e-06
2ebl_A	89	Solution Structure Of The Zinc Finger, C4-type Doma		2e-05
1hra_A	80	The Solution Structure Of The Human Retinoic Acid R		2e-05
3dzu_D	419	Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp		3e-05
2han_A	93	Structural Basis Of Heterodimeric Ecdysteroid Recep		3e-05
1r0o_A	86	Crystal Structure Of The Heterodimeric Ecdysone Rec		3e-05
4hn5_A	117	Gr Dna Binding Domain - Tslp Ngre Complex Length =		4e-05
2nll_A	66	Retinoid X Receptor-Thyroid Hormone Receptor Dna-Bi		6e-05
3g9p_B	90	Gr Dna Binding Domain:sgk 16bp Complex-7 Length = 9		6e-05
3g6t_A	91	Gr Gamma Dna-Binding Domain:fkbp5 16bp Complex-34 L		7e-05
1gdc_A	72	Refined Solution Structure Of The Glucocorticoid Re		7e-05
2gda_A	72	Refined Solution Structure Of The Glucocorticoid Re		7e-05
1r4o_A	92	Crystallographic Analysis Of The Interaction Of The		7e-05
1r4r_B	92	Crystallographic Analysis Of The Interaction Of The		8e-05
1rgd_A	71	Structure Refinement Of The Glucocorticoid Receptor		8e-05
1glu_A	81	Crystallographic Analysis Of The Interaction Of The		9e-05
4hn6_A	114	Gr Dna Binding Domain R460d/d462r - Tslp Ngre Compl		3e-04
1hlz_A	94	Crystal Structure Of The Orphan Nuclear Receptor Re		3e-04
3cbb_A	78	Crystal Structure Of Hepatocyte Nuclear Factor 4alp		4e-04
2c7a_A	78	Structure Of The Progesterone Receptor-Dna Complex		4e-04
1r4i_A	105	Crystal Structure Of Androgen Receptor Dna-Binding		6e-04

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

Iteration: 1
 Score = 98.2 bits (243), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 45/57 (78%), Positives = 51/57 (89%)
Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPD 57
          NIEY+CPA+N+CEI KRRRK+CQACRF K L+ GMLKEGVRLDRVRGGRQKY+R  D
Sbjct: 38 NIEYSCPATNECEITKRRRKSCQACRFMKALKVGMLKEGVRLDRVRGGRQKYKRRLD 94

>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 = 61.6 bits (148), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 30/52 (57%), Positives = 35/52 (67%)
Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKY 52
          N  YTC  S  C+I+K +RK C  CRFQKCL  GM  E VR DR+RGGR K+
Sbjct: 35 NKHYTCTESQSCKIDKTQRKRCPFCRFQKCLTVGMRLEAVRADRMRGGRNKF 86

>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 = 59.7 bits (143), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 29/52 (55%), Positives = 36/52 (69%)
Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKY 52
          N  YTC  + +C+I+K +RK C  CRFQKCL  GM  E VR DR+RGGR K+
Sbjct: 43 NKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMRGGRNKF 94

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

Iteration: 1
 Score = 59.7 bits (143), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 28/46 (60%), Positives = 35/46 (76%), Gaps = 1/46 (2%)
Query: 3  EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG 48
          +Y CPA+N C I+K RRK+CQACR +KC   GM+K G+R DR RGG
Sbjct: 40 DYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRKDR-RGG 84

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 28/54 (51%), Positives = 36/54 (66%)
Query: 3  EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNP 56
          +Y C A+ DC ++KRRR  CQ CRFQKCL  GM+KE VR D ++G R +    P
Sbjct: 36 KYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTDSLKGRRGRLPSKP 89

>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 = 53.5 bits (127), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 24/47 (51%), Positives = 33/47 (70%)
Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG 47
           ++ YTC  + DC I+KR+R  CQ CR+QKCL  GM +E V+ +R RG
Sbjct: 171 DLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRG 217

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 22/37 (59%), Positives = 28/37 (75%)
Query: 3  EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEG 39
          +Y CPA+N C I+K RRK+CQACR +KC   GM+K G
Sbjct: 40 DYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGG 76

>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 = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 24/47 (51%), Positives = 33/47 (70%)
Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG 47
          ++ YTC  + DC I+KR+R  CQ CR+QKCL  GM +E V+ +R RG
Sbjct: 37 DLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRG 83

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 24/47 (51%), Positives = 33/47 (70%)
Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG 47
          ++ YTC  + DC I+KR+R  CQ CR+QKCL  GM +E V+ +R RG
Sbjct: 39 DLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRG 85

>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 = 50.1 bits (118), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 21/35 (60%), Positives = 27/35 (77%)
Query: 3  EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLK 37
          +Y CPA+N C I+K RRK+CQACR +KC   GM+K
Sbjct: 37 DYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMK 71

>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 = 50.1 bits (118), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 21/35 (60%), Positives = 27/35 (77%)
Query: 3  EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLK 37
          +Y CPA+N C I+K RRK+CQACR +KC   GM+K
Sbjct: 37 DYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMK 71

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/44 (50%), Positives = 31/44 (70%)
Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
          ++ YTC  + DC I+KR+R  CQ CR+QKCL  GM +E V+ +R
Sbjct: 39 DLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER 82

>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 = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 20/40 (50%), Positives = 28/40 (70%)
Query: 4  YTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLD 43
          +TC A+ DC I K  R+ACQACR ++C+  GM+KE +  D
Sbjct: 43 FTCAANGDCRITKDNRRACQACRLKRCVDIGMMKEFILTD 82

>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 = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 32/47 (68%)
Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG 47
          ++ YTC  + DC I+KR+R  CQ CR+QK L  GM +E V+ +R RG
Sbjct: 37 DLTYTCRDNKDCLIDKRQRNRCQYCRYQKALAMGMKREAVQEERQRG 83

>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 = 47.0 bits (110), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/44 (54%), Positives = 26/44 (59%)
Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
          N+ YTC    +C INK  R  CQ CR QKC   GM KE VR DR
Sbjct: 38 NMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDR 81

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 21/40 (52%), Positives = 28/40 (70%)
Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGV 40
          ++ YTC  + DC I+KR+R  CQ CR+QKCL  GM +E V
Sbjct: 37 DLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAV 76

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 19/40 (47%), Positives = 27/40 (67%)
Query: 4  YTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLD 43
          +TCP + DC I K  R+ CQACR ++C+  GM+KE +  D
Sbjct: 43 FTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTD 82

>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 = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 19/41 (46%), Positives = 28/41 (68%)
Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR 41
          N+ YTC A+ +C I++  R  CQ CR +KCL+ GM +E V+
Sbjct: 41 NLTYTCRANRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQ 81

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/41 (53%), Positives = 24/41 (58%)
Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR 41
          N+ YTC    +C INK  R  CQ CR QKC   GM KE VR
Sbjct: 39 NMIYTCHRDKNCVINKVTRNRCQYCRLQKCFEVGMSKESVR 79

>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 = 43.5 bits (101), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 17/35 (48%), Positives = 22/35 (62%)
Query: 11  DCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV 45
           +C I+K+ R  CQ CRFQKCL  GM    +R  R+
Sbjct: 93  NCRIHKKSRNKCQYCRFQKCLAVGMSHNAIRFGRM 127

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 20/44 (45%), Positives = 30/44 (68%)
Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
          ++ Y C  + +C I+KR+R  CQ CR+QKCL  GM +E V+ +R
Sbjct: 44 DLTYACRENRNCIIDKRQRNRCQYCRYQKCLTCGMKREAVQEER 87

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 20/44 (45%), Positives = 30/44 (68%)
Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
          ++ Y C  + +C I+KR+R  CQ CR+QKCL  GM +E V+ +R
Sbjct: 42 DLTYACRENRNCIIDKRQRNRCQYCRYQKCLTCGMKREAVQEER 85

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 19/32 (59%), Positives = 23/32 (71%)
Query: 4  YTCPASNDCEINKRRRKACQACRFQKCLRKGM 35
          Y C   NDC I+K RRK C ACR++KCL+ GM
Sbjct: 66 YLCAGRNDCIIDKIRRKNCPACRYRKCLQAGM 97

>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 = 42.7 bits (99), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 19/35 (54%), Positives = 25/35 (71%)
Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGM 35
          ++ YTC  + DC I+KR+R  CQ CR+QKCL  GM
Sbjct: 32 DLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGM 66

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 19/32 (59%), Positives = 23/32 (71%)
Query: 4  YTCPASNDCEINKRRRKACQACRFQKCLRKGM 35
          Y C   NDC I+K RRK C ACR++KCL+ GM
Sbjct: 39 YLCAGRNDCIIDKIRRKNCPACRYRKCLQAGM 70

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 19/32 (59%), Positives = 23/32 (71%)
Query: 4  YTCPASNDCEINKRRRKACQACRFQKCLRKGM 35
          Y C   NDC I+K RRK C ACR++KCL+ GM
Sbjct: 40 YLCAGRNDCIIDKIRRKNCPACRYRKCLQAGM 71

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 19/32 (59%), Positives = 23/32 (71%)
Query: 4  YTCPASNDCEINKRRRKACQACRFQKCLRKGM 35
          Y C   NDC I+K RRK C ACR++KCL+ GM
Sbjct: 36 YLCAGRNDCIIDKIRRKNCPACRYRKCLQAGM 67

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 19/32 (59%), Positives = 23/32 (71%)
Query: 4  YTCPASNDCEINKRRRKACQACRFQKCLRKGM 35
          Y C   NDC I+K RRK C ACR++KCL+ GM
Sbjct: 36 YLCAGRNDCIIDKIRRKNCPACRYRKCLQAGM 67

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 19/32 (59%), Positives = 23/32 (71%)
Query: 4  YTCPASNDCEINKRRRKACQACRFQKCLRKGM 35
          Y C   NDC I+K RRK C ACR++KCL+ GM
Sbjct: 41 YLCAGRNDCIIDKIRRKNCPACRYRKCLQAGM 72

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 19/32 (59%), Positives = 23/32 (71%)
Query: 4  YTCPASNDCEINKRRRKACQACRFQKCLRKGM 35
          Y C   NDC I+K RRK C ACR++KCL+ GM
Sbjct: 41 YLCAGRNDCIIDKIRRKNCPACRYRKCLQAGM 72

>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 = 42.0 bits (97), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 19/32 (59%), Positives = 23/32 (71%)
Query: 4  YTCPASNDCEINKRRRKACQACRFQKCLRKGM 35
          Y C   NDC I+K RRK C ACR++KCL+ GM
Sbjct: 35 YLCAGRNDCIIDKIRRKNCPACRYRKCLQAGM 66

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 19/32 (59%), Positives = 23/32 (71%)
Query: 4  YTCPASNDCEINKRRRKACQACRFQKCLRKGM 35
          Y C   NDC I+K RRK C ACR++KCL+ GM
Sbjct: 41 YLCAGRNDCIIDKIRRKNCPACRYRKCLQAGM 72

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

Iteration: 1
 Score = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 18/32 (56%), Positives = 22/32 (68%)
Query: 4  YTCPASNDCEINKRRRKACQACRFQKCLRKGM 35
          Y C   N C I+K RRK C ACR++KCL+ GM
Sbjct: 63 YLCAGDNRCIIDKIRRKNCPACRYRKCLQAGM 94

>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 = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/46 (43%), Positives = 28/46 (60%), Gaps = 1/46 (2%)
Query: 1  NIEYT-CPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV 45
          NI+Y  C  + +C I +  R  CQ CRF+KCL  GM ++ VR  R+
Sbjct: 41 NIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGRI 86

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

Iteration: 1
 Score = 40.0 bits (92), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 19/44 (43%), Positives = 27/44 (61%)
Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
          N  Y+C  S  C ++K +R  C+ CR +KC R GM KE V+ +R
Sbjct: 34 NHMYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNER 77

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

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 18/36 (50%), Positives = 23/36 (63%)
Query: 4  YTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEG 39
          Y C   NDC ++K RRK C ACR +KC + GM+  G
Sbjct: 39 YLCAGRNDCIVDKIRRKNCPACRLRKCCQAGMVLGG 74

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

Iteration: 1
 Score = 39.3 bits (90), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 17/33 (51%), Positives = 22/33 (66%)
Query: 3  EYTCPASNDCEINKRRRKACQACRFQKCLRKGM 35
          +Y C + NDC I+K RRK C +CR +KC   GM
Sbjct: 43 KYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGM 75

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	123
1lo1_A	98	Steroid hormone receptor ERR2; estrogen related re	1e-24
1cit_A	89	NGFI-B, protein (orphan nuclear receptor NGFI-B);	2e-23
2a66_A	113	Orphan nuclear receptor NR5A2; protein-DNA complex	3e-23
3g9m_A	90	Glucocorticoid receptor; glucocorticoid, DNA-bindi	2e-21
1r4i_A	105	Androgen receptor; AR, steroid receptor, protein-D	7e-21
1hcq_A	84	Protein (estrogen receptor); protein-DNA complex,	4e-20
1kb2_A	110	Vitamin D3 receptor; VDR, nuclear receptor, protei	1e-19
1ynw_B	99	Retinoic acid receptor RXR-alpha, retinoid X recep	1e-19
1dsz_B	85	RXR-alpha, retinoic acid receptor RXR-alpha; RAR,	1e-19
2han_A	93	Protein ultraspiracle; transcription regulation, t	2e-19
1dsz_A	86	RAR-alpha, retinoic acid receptor alpha; RAR, nucl	4e-19
2han_B	119	Ecdysone receptor; transcription regulation, trans	2e-17
1a6y_A	94	Orphan nuclear receptor NR1D1; orphan receptor, DN	1e-16
2nll_B	103	Protein (thyroid hormone receptor); complex (trans	2e-16
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	2e-16
2ebl_A	89	COUP transcription factor 1; DNA-binding, metal-bi	4e-16
3cbb_A	78	HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DN	9e-16
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	3e-15
1z5x_E	310	Ecdysone receptor ligand binding domain; ponastero	3e-07
1ovl_A	271	Orphan nuclear receptor NURR1 (MSe 414, 496, 511);	4e-07
1lbd_A	282	RXR_LBD, retinoid X receptor; transcription factor	5e-06
2hc4_A	302	Vitamin D receptor; alpha helical sandwich, gene r	5e-05

>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 = 89.0 bits (221), Expect = 1e-24
 Identities = 45/57 (78%), Positives = 51/57 (89%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPD 57
          NIEY+CPA+N+CEI KRRRK+CQACRF K L+ GMLKEGVRLDRVRGGRQKY+R  D
Sbjct: 38 NIEYSCPATNECEITKRRRKSCQACRFMKALKVGMLKEGVRLDRVRGGRQKYKRRLD 94

>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 = 85.9 bits (213), Expect = 2e-23
 Identities = 28/56 (50%), Positives = 37/56 (66%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNP 56
          + +Y C A+ DC ++KRRR  CQ CRFQKCL  GM+KE VR D ++G R +    P
Sbjct: 34 SAKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTDSLKGRRGRLPSKP 89

>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 = 86.0 bits (213), Expect = 3e-23
 Identities = 30/69 (43%), Positives = 39/69 (56%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
           N  YTC  + +C+I+K +RK C  CRFQKCL  GM  E VR DR+RGGR K+        
Sbjct: 43  NKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMRGGRNKFGPMYKRDR 102

Query: 61  QQWPPNKSI 69
                 K++
Sbjct: 103 ALKQQKKAL 111

>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 = 80.5 bits (199), Expect = 2e-21
 Identities = 22/53 (41%), Positives = 29/53 (54%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYR 53
             Y C   NDC I+K RRK C ACR++KCL+ GM  E  +  +   G Q+  
Sbjct: 36 QHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEARKTKKKIKGIQQAT 88

>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 = 79.4 bits (196), Expect = 7e-21
 Identities = 18/57 (31%), Positives = 28/57 (49%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPD 57
            +Y C + NDC I+K RRK C +CR +KC   GM     +L ++   + +      
Sbjct: 41 KQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLGARKLKKLGNLKLQEEGENS 97

>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 = 77.0 bits (190), Expect = 4e-20
 Identities = 26/47 (55%), Positives = 34/47 (72%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG 47
          + +Y CPA+N C I+K RRK+CQACR +KC   GM+K G+R DR  G
Sbjct: 38 HNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRKDRRGG 84

>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 = 76.8 bits (189), Expect = 1e-19
 Identities = 19/56 (33%), Positives = 30/56 (53%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNP 56
             +TCP + DC I K  R+ CQACR ++C+  GM+KE +  D     +++     
Sbjct: 40 KALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDEEVQRKREMILKR 95

>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 = 76.3 bits (188), Expect = 1e-19
 Identities = 25/62 (40%), Positives = 35/62 (56%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
          ++ YTC  + DC I+KR+R  CQ CR+QKCL  GM +E V+ +R RG  +         S
Sbjct: 37 DLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRGKDRNENEVESTSS 96

Query: 61 QQ 62
            
Sbjct: 97 AN 98

>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 = 75.8 bits (187), Expect = 1e-19
 Identities = 24/47 (51%), Positives = 33/47 (70%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG 47
          ++ YTC  + DC I+KR+R  CQ CR+QKCL  GM +E V+ +R RG
Sbjct: 39 DLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRG 85

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

 Score = 75.5 bits (186), Expect = 2e-19
 Identities = 21/49 (42%), Positives = 31/49 (63%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGR 49
          ++ Y C  + +C I+KR+R  CQ CR+QKCL  GM +E V+ +R    R
Sbjct: 44 DLTYACRENRNCIIDKRQRNRCQYCRYQKCLTCGMKREAVQEERQGIHR 92

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

 Score = 74.7 bits (184), Expect = 4e-19
 Identities = 24/49 (48%), Positives = 28/49 (57%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGR 49
          N+ YTC    +C INK  R  CQ CR QKC   GM KE VR DR +  +
Sbjct: 38 NMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNKKKK 86

>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 = 71.5 bits (175), Expect = 2e-17
 Identities = 16/55 (29%), Positives = 27/55 (49%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRN 55
          +  Y C     CE++   R+ CQ CR +KCL  GM  E V  +     +++ ++ 
Sbjct: 42 SAVYCCKFGRACEMDMYMRRKCQECRLKKCLAVGMRPECVVPENQCAMKRREKKA 96

>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 = 68.5 bits (168), Expect = 1e-16
 Identities = 23/54 (42%), Positives = 32/54 (59%), Gaps = 2/54 (3%)

Query: 1  NIEYT-CPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYR 53
          NI+Y  C  + +C I +  R  CQ CRF+KCL  GM ++ VR  R+   R+K R
Sbjct: 41 NIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGRIP-KREKQR 93

>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 = 68.2 bits (167), Expect = 2e-16
 Identities = 19/49 (38%), Positives = 26/49 (53%)

Query: 3  EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQK 51
           Y+C     C I+K  R  CQ CRF+KC+  GM  + V  D  R  ++K
Sbjct: 39 SYSCKYEGKCVIDKVTRNQCQECRFKKCIYVGMATDLVLDDSKRLAKRK 87

>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 = 72.4 bits (177), Expect = 2e-16
 Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 2/80 (2%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS 60
           ++ YTC  + DC I+KR+R  CQ CR+QKCL  GM +E V+ +R RG  +         +
Sbjct: 171 DLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRGKDRNENEVES--T 228

Query: 61  QQWPPNKSIPSLEDLERNTE 80
                +  +  + + E   E
Sbjct: 229 SSANEDMPVERILEAELAVE 248

>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 = 66.9 bits (164), Expect = 4e-16
 Identities = 19/45 (42%), Positives = 28/45 (62%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV 45
          N+ YTC A+ +C I++  R  CQ CR +KCL+ GM +E V+    
Sbjct: 41 NLTYTCRANRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQRGSG 85

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

 Score = 65.8 bits (161), Expect = 9e-16
 Identities = 19/44 (43%), Positives = 27/44 (61%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
          N  Y+C  S  C ++K +R  C+ CR +KC R GM KE V+ +R
Sbjct: 34 NHMYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNER 77

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

 Score = 69.7 bits (170), Expect = 3e-15
 Identities = 25/101 (24%), Positives = 42/101 (41%), Gaps = 3/101 (2%)

Query: 1   NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDL-- 58
            + Y     N C I+K+ R  CQ CRFQKCL  GM    +R  R+    ++         
Sbjct: 84  KLIYDRCDLN-CRIHKKSRNKCQYCRFQKCLAVGMSHNAIRFGRMPQAEKEKLLAEISSD 142

Query: 59  LSQQWPPNKSIPSLEDLERNTEISVSMMSCDGDTSDLGGLS 99
           + Q  P +  + +L     ++ I    ++     + L G +
Sbjct: 143 IDQLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKT 183

>1z5x_E Ecdysone receptor ligand binding domain; ponasterone A, nuclear receptor, ECR, USP, hormone/growth factor receptor complex; HET: P1A; 3.07A {Bemisia tabaci} Length = 310

 Score = 46.7 bits (111), Expect = 3e-07
 Identities = 6/48 (12%), Positives = 15/48 (31%), Gaps = 1/48 (2%)

Query: 10 NDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPD 57
            C + KR+ K  Q  + +         +G++ +          +   
Sbjct: 21 FQCAV-KRKEKKAQKDKDKPNSTTSCSPDGIKQEIDPQRLDTDSQLLS 67

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

 Score = 45.9 bits (109), Expect = 4e-07
 Identities = 12/41 (29%), Positives = 20/41 (48%)

Query: 35 MLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEDL 75
          M+KE VR D ++G R +    P    +  PP+  +  +  L
Sbjct: 1  MVKEVVRTDSLKGRRGRLPSKPKSPQEPSPPSPPVSLISAL 41

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

 Score = 42.9 bits (101), Expect = 5e-06
 Identities = 13/85 (15%), Positives = 27/85 (31%), Gaps = 5/85 (5%)

Query: 19  RKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLS--QQWPPNKSIPSLEDLE 76
                +    +       +E V+ +R RG  +         S  +  P  + + +   +E
Sbjct: 7   HHHHSSGLVPRG---SHKREAVQEERQRGKDRNENEVESTSSANEDMPVERILEAELAVE 63

Query: 77  RNTEISVSMMSCDGDTSDLGGLSYI 101
             TE  V        +S    ++ I
Sbjct: 64  PKTETYVEANMGLNPSSPNDPVTNI 88

>2hc4_A Vitamin D receptor; alpha helical sandwich, gene regulation; HET: VDX; 2.20A {Danio rerio} PDB: 2hbh_A* 2hcd_A* 3dr1_A* 3o1d_A* 3o1e_A* Length = 302

 Score = 40.2 bits (94), Expect = 5e-05
 Identities = 12/80 (15%), Positives = 22/80 (27%), Gaps = 1/80 (1%)

Query: 22  CQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEDLERNTEI 81
               RF+  +R+G +                  +    S +    K   S   L    + 
Sbjct: 29  SDFVRFRPPVREGPVTRSASRAASLHSLSDASSDSFNHSPESVDTKLNFSNL-LMMYQDS 87

Query: 82  SVSMMSCDGDTSDLGGLSYI 101
                S +   S L  L ++
Sbjct: 88  GSPDSSEEDQQSRLSMLPHL 107

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	123
1lo1_A	98	Steroid hormone receptor ERR2; estrogen related re	99.57
1cit_A	89	NGFI-B, protein (orphan nuclear receptor NGFI-B);	99.53
1dsz_A	86	RAR-alpha, retinoic acid receptor alpha; RAR, nucl	99.52
2han_A	93	Protein ultraspiracle; transcription regulation, t	99.52
1dsz_B	85	RXR-alpha, retinoic acid receptor RXR-alpha; RAR,	99.51
3cbb_A	78	HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DN	99.51
2a66_A	113	Orphan nuclear receptor NR5A2; protein-DNA complex	99.49
1ynw_B	99	Retinoic acid receptor RXR-alpha, retinoid X recep	99.49
2ebl_A	89	COUP transcription factor 1; DNA-binding, metal-bi	99.48
1kb2_A	110	Vitamin D3 receptor; VDR, nuclear receptor, protei	99.46
1a6y_A	94	Orphan nuclear receptor NR1D1; orphan receptor, DN	99.44
1hcq_A	84	Protein (estrogen receptor); protein-DNA complex,	99.44
3g9m_A	90	Glucocorticoid receptor; glucocorticoid, DNA-bindi	99.43
4hn5_A	117	Glucocorticoid receptor; glucocorticoid receptor,	99.41
2han_B	119	Ecdysone receptor; transcription regulation, trans	99.39
2nll_B	103	Protein (thyroid hormone receptor); complex (trans	99.36
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	99.33
2lze_A	87	A primordial catalytic fold generated by in vitro	99.31
1r4i_A	105	Androgen receptor; AR, steroid receptor, protein-D	99.3
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	99.13
1lbd_A	282	RXR_LBD, retinoid X receptor; transcription factor	97.61
1ovl_A	271	Orphan nuclear receptor NURR1 (MSe 414, 496, 511);	94.63
1xdk_B	303	RAR-beta, retinoic acid receptor, beta; nuclear re	89.87

>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=99.57  E-value=3.3e-16  Score=104.28  Aligned_cols=56  Identities=79%  Similarity=1.389  Sum_probs=49.6

Q ss_pred             CCceecCCCCCcccccccccccccccchhhhhccccccccccccccCccccccCCC
Q psy752            1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNP   56 (123)
Q Consensus         1 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~~~~~~~~~~   56 (123)
                      +..|.|..+++|.|++..|..|++|||+|||++||++++||.+|+++++++.++..
T Consensus        38 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~~~r~k~~~~~   93 (98)
T 1lo1_A           38 NIEYSCPATNECEITKRRRKSCQACRFMKALKVGMLKEGVRLDRVRGGRQKYKRRL   93 (98)
T ss_dssp             TCCCCCSSCSCCCCCHHHHHHCHHHHHHHHHHHTCCGGGSCSSCCTTCCCCCC---
T ss_pred             cCccccCccccccccccccccccchhHHHHhHcCCCHHHeecccccCcccccCCCC
Confidence            35789999999999999999999999999999999999999999999988876653

>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=99.53  E-value=2.7e-15  Score=98.30  Aligned_cols=53  Identities=51%  Similarity=0.990  Sum_probs=47.3

Q ss_pred             CCceecCCCCCcccccccccccccccchhhhhccccccccccccccCcccccc
Q psy752            1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYR   53 (123)
Q Consensus         1 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~~~~~~~   53 (123)
                      +..|.|..+++|.|++..|+.|++|||+|||++||++++||.|+...++.+.+
T Consensus        34 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~~~~~~r~r~p   86 (89)
T 1cit_A           34 SAKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTDSLKGRRGRLP   86 (89)
T ss_dssp             TCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHTTCCGGGSCCGGGTTCCSCCC
T ss_pred             cceeeeccCCccccCCCCcccChhhhhHHHhHcCCCHHHeecccccCccccCC
Confidence            35789999999999999999999999999999999999999998776666553

>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=99.52  E-value=2.3e-15  Score=98.06  Aligned_cols=47  Identities=49%  Similarity=0.878  Sum_probs=40.5

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccccccccccccCc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG   48 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~~   48 (123)
                      ..|.|..+++|.|++..|+.|++|||+|||++||++++||.+|++++
T Consensus        39 ~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~~k   85 (86)
T 1dsz_A           39 MVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNKKK   85 (86)
T ss_dssp             CCCCCSSCSCCCCSTTTGGGCHHHHHHHHHHTTCCGGGSCCC-----
T ss_pred             cceeeccCCccccCccccccchhhhHHHHHHhCCCHHHhhhcccccc
Confidence            57899999999999999999999999999999999999999998654

>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=99.52  E-value=2.1e-15  Score=99.49  Aligned_cols=49  Identities=43%  Similarity=0.882  Sum_probs=41.9

Q ss_pred             CCceecCCCCCcccccccccccccccchhhhhccccccccccccccCcc
Q psy752            1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGR   49 (123)
Q Consensus         1 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~~~   49 (123)
                      +..|.|..+++|.|++..|..|++|||+|||++||++++||.+|++.++
T Consensus        44 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~~~~   92 (93)
T 2han_A           44 DLTYACRENRNCIIDKRQRNRCQYCRYQKCLTCGMKREAVQEERQGIHR   92 (93)
T ss_dssp             TCCCCCSSCSCCCCSTTTGGGCHHHHHHHHHHHTCCGGGSCCCC-----
T ss_pred             ccCcCcCCCCcCCcCCCCCccCccccHHHHhHhCCCHHHhhhccCcccC
Confidence            3578999999999999999999999999999999999999999987554

>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=99.51  E-value=3.3e-15  Score=97.11  Aligned_cols=46  Identities=50%  Similarity=1.029  Sum_probs=43.2

Q ss_pred             CCceecCCCCCcccccccccccccccchhhhhcccccccccccccc
Q psy752            1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR   46 (123)
Q Consensus         1 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~   46 (123)
                      +..|.|..+++|.|++..|..|++|||+|||++||++++||.+|++
T Consensus        39 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~   84 (85)
T 1dsz_B           39 DLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQR   84 (85)
T ss_dssp             TCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCCCCC
T ss_pred             ccceeecccccccccccccccCcchhHHHHhHcCCCHHHhhcccCC
Confidence            3578999999999999999999999999999999999999999975

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

Probab=99.51  E-value=3e-15  Score=95.82  Aligned_cols=45  Identities=42%  Similarity=0.891  Sum_probs=40.8

Q ss_pred             CCceecCCCCCcccccccccccccccchhhhhccccccccccccc
Q psy752            1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV   45 (123)
Q Consensus         1 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~   45 (123)
                      +..|.|+.+++|.|++..|+.|++|||+|||++||++++||.+|+
T Consensus        34 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~Rd   78 (78)
T 3cbb_A           34 NHMYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNERD   78 (78)
T ss_dssp             TCCCCCSSCSCCCCSTTTTTTCHHHHHHHHHHHTCCGGGCCCC--
T ss_pred             ccCcccccccccCcCccccccChhhhhHHHhHcCCCHHHccccCC
Confidence            357899999999999999999999999999999999999999985

>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=99.49  E-value=6.6e-15  Score=100.25  Aligned_cols=52  Identities=56%  Similarity=1.078  Sum_probs=47.9

Q ss_pred             CCceecCCCCCcccccccccccccccchhhhhccccccccccccccCccccc
Q psy752            1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKY   52 (123)
Q Consensus         1 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~~~~~~   52 (123)
                      +..|.|..+++|.|++..|..|++|||+|||++||++++||.+|++.++.+.
T Consensus        43 ~~~y~C~~~~~C~i~~~~R~~Cr~CR~~KCl~vGM~~~~vq~~R~~~~r~~~   94 (113)
T 2a66_A           43 NKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMRGGRNKF   94 (113)
T ss_dssp             TCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCTTCCCSSCCTT
T ss_pred             cccccccccccCCcCCCccccccchhHHHHhHhCCCHHHhccccccCCCCCc
Confidence            3578999999999999999999999999999999999999999998887764

>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=99.49  E-value=4.5e-15  Score=98.96  Aligned_cols=49  Identities=49%  Similarity=1.001  Sum_probs=39.0

Q ss_pred             CCceecCCCCCcccccccccccccccchhhhhccccccccccccccCcc
Q psy752            1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGR   49 (123)
Q Consensus         1 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~~~   49 (123)
                      +..|.|..+++|.|++..|..|++|||+|||++||++++||.+|++.+.
T Consensus        37 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~~~~   85 (99)
T 1ynw_B           37 DLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRGKD   85 (99)
T ss_dssp             TCCCCCSSSSCCCCCSTTSSSCHHHHHHHHHHTTCCSTTCC--------
T ss_pred             ccccccCCCCcccccccCCccCccccHHHHhHcCCCHHHhhhccccccc
Confidence            3578999999999999999999999999999999999999999987554

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

Probab=99.48  E-value=5.6e-15  Score=96.77  Aligned_cols=47  Identities=40%  Similarity=0.880  Sum_probs=43.5

Q ss_pred             CCceecCCCCCcccccccccccccccchhhhhccccccccccccccC
Q psy752            1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG   47 (123)
Q Consensus         1 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~   47 (123)
                      +..|.|+.+++|.|++..|+.|++|||+|||++||++++||.+|++.
T Consensus        41 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~~   87 (89)
T 2ebl_A           41 NLTYTCRANRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQRGSGPS   87 (89)
T ss_dssp             TCCCCCSSCSCCCCCSSSSSCCSHHHHHHHHHHTCCHHHHSCSCCCC
T ss_pred             ccceecccCccCCcCccCccccccchHHHhhhccCCHHHcccCCCCC
Confidence            35789999999999999999999999999999999999999999753

>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=99.46  E-value=4.3e-15  Score=100.77  Aligned_cols=46  Identities=41%  Similarity=0.868  Sum_probs=42.7

Q ss_pred             CCceecCCCCCcccccccccccccccchhhhhcccccccccccccc
Q psy752            1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR   46 (123)
Q Consensus         1 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~   46 (123)
                      +..|.|..+++|.|++..|..|++|||+|||++||++++|+.+|..
T Consensus        40 ~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~   85 (110)
T 1kb2_A           40 KALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDEEV   85 (110)
T ss_dssp             TCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCHHHH
T ss_pred             ccceeeCCCCCccCCcccceecccccHhhhhhcCCcHHhcccHHHH
Confidence            3578999999999999999999999999999999999999999865

>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=99.44  E-value=2e-14  Score=95.02  Aligned_cols=47  Identities=40%  Similarity=0.923  Sum_probs=40.6

Q ss_pred             Cce-ecCCCCCcccccccccccccccchhhhhccccccccccccccCc
Q psy752            2 IEY-TCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG   48 (123)
Q Consensus         2 ~~y-~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~~   48 (123)
                      ..| .|..+++|.|++..|..|++|||+|||++||++++||.+|++..
T Consensus        42 ~~y~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~~~   89 (94)
T 1a6y_A           42 IQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGRIPKR   89 (94)
T ss_dssp             CCCCCCSSTTCCCCCTTTTTSCHHHHHHHHTTTTCCSTTCCCCC----
T ss_pred             cceEEccCCCCCccCccccccccchhHHHhhHccCCHHHhccCcCcCc
Confidence            457 59999999999999999999999999999999999999997543

>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=99.44  E-value=1.7e-14  Score=93.47  Aligned_cols=44  Identities=57%  Similarity=1.174  Sum_probs=34.6

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccccccccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV   45 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~   45 (123)
                      ..|.|..+++|.|++..|..|++|||+|||++||++++||.+|.
T Consensus        39 ~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~   82 (84)
T 1hcq_A           39 NDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRKDRR   82 (84)
T ss_dssp             CCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHHTCCC--------
T ss_pred             cccccccCccCCcCCcCcccChhhhhHHHhHcCCCHHHhcccCC
Confidence            57899999999999999999999999999999999999999985

>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=99.43  E-value=1.5e-14  Score=94.82  Aligned_cols=49  Identities=45%  Similarity=0.846  Sum_probs=41.2

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccccccccccccCccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQ   50 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~~~~   50 (123)
                      ..|.|..+++|.|++..|..|++|||+|||++||++++||.+|+..+.+
T Consensus        37 ~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~avq~~r~~~~~~   85 (90)
T 3g9m_A           37 HNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEARKTKKKIKGIQ   85 (90)
T ss_dssp             CCCCCSSSSCCCCCTTGGGTCHHHHHHHHHHHTCCTTHHHHHC------
T ss_pred             CceeCCCCCccccCcccccCCcchhhHHHHHcCCCHHHhcccccccccc
Confidence            5689999999999999999999999999999999999999998654443

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

Probab=99.41  E-value=3.1e-14  Score=97.47  Aligned_cols=48  Identities=44%  Similarity=0.845  Sum_probs=36.5

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccccccccccccCcc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGR   49 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~~~   49 (123)
                      ..|.|.++++|.|++..|..|++|||+|||++||++++||.+|+.++.
T Consensus        64 ~~y~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~avq~kR~~k~~  111 (117)
T 4hn5_A           64 HNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEARKTKKKIKGI  111 (117)
T ss_dssp             CCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHHTCCTTC----------
T ss_pred             CceecCCCCccccCcccccCCcccchHHHhHcCCCHHHhccccccccc
Confidence            568999999999999999999999999999999999999999865443

>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=99.39  E-value=4.1e-14  Score=97.17  Aligned_cols=46  Identities=35%  Similarity=0.687  Sum_probs=42.6

Q ss_pred             CCceecCCCCCcccccccccccccccchhhhhcccccccccccccc
Q psy752            1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR   46 (123)
Q Consensus         1 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~   46 (123)
                      +..|.|..+++|.|++..|+.|++|||+|||++||++++|+.+|+.
T Consensus        42 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~   87 (119)
T 2han_B           42 SAVYCCKFGRACEMDMYMRRKCQECRLKKCLAVGMRPECVVPENQC   87 (119)
T ss_dssp             TCCCCCSSCSCCCCSTTGGGTCHHHHHHHHHHTTCCGGGSSCSSHH
T ss_pred             ccccccccccccccCccccccchhhHHHHHHHhCCCHHHccchhhh
Confidence            3578999999999999999999999999999999999999998864

>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=99.36  E-value=5.3e-14  Score=94.37  Aligned_cols=49  Identities=39%  Similarity=0.752  Sum_probs=44.5

Q ss_pred             ceecCCCCCcccccccccccccccchhhhhccccccccccccccCcccc
Q psy752            3 EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQK   51 (123)
Q Consensus         3 ~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~~~~~   51 (123)
                      .|.|..+++|.|++..|..|++|||+||+++||++++||.++.+..+.+
T Consensus        39 ~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~~~~~~k~~   87 (103)
T 2nll_B           39 SYSCKYEGKCVIDKVTRNQCQECRFKKCIYVGMATDLVLDDSKRLAKRK   87 (103)
T ss_dssp             GCCCSSCTTCCCSTTTTTSCHHHHHHHHHHTTCCGGGSCCHHHHHHHHH
T ss_pred             hhhhhccCCcCcCccCccccchhhhHhhhHhCCCHHHhhhhhhhHHhhh
Confidence            6999999999999999999999999999999999999999987655444

>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=99.33  E-value=9.2e-13  Score=107.90  Aligned_cols=49  Identities=49%  Similarity=1.001  Sum_probs=44.7

Q ss_pred             CCceecCCCCCcccccccccccccccchhhhhccccccccccccccCcc
Q psy752            1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGR   49 (123)
Q Consensus         1 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~~~   49 (123)
                      +..|.|+++++|.+++..|+.|++|||+||+++||++++||.+|++.++
T Consensus       171 ~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~~k~  219 (467)
T 3dzy_A          171 DLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRGKD  219 (467)
T ss_dssp             TCCCCCSSSSCCCCCSSSSSSCHHHHHHHHHHTTCCGGGCCCCSCCCCC
T ss_pred             CCceeCCCCCCCCCCcccccccccchhhhhhhccccchhhhcccccccc
Confidence            3578999999999999999999999999999999999999999976543

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

Probab=99.31  E-value=5.2e-13  Score=87.00  Aligned_cols=42  Identities=26%  Similarity=0.400  Sum_probs=37.6

Q ss_pred             CCceecCCCCCcccccccccccccccchhhhhcccccccccc
Q psy752            1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRL   42 (123)
Q Consensus         1 ~~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~   42 (123)
                      +..|.|+.+++|.|++..|+.|++|||+|||+|||....+..
T Consensus        36 ~~~y~C~~~~~C~i~~~~R~~C~~CR~qKCl~VgM~~~~~~~   77 (87)
T 2lze_A           36 DLTYTDRDYKNCESYHKCSDLCQYCRYQKDLAIHHQHHHGGS   77 (87)
T ss_dssp             SCTTTSCCCCCCCCSSCCSSSCSGGGTSCCHHHHCSSCCCCC
T ss_pred             CCeeEcCCCCccccCCCccCcCCcccChhhccCcCEeccCcc
Confidence            457999999999999999999999999999999998875543

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

Probab=99.30  E-value=3.9e-13  Score=90.40  Aligned_cols=44  Identities=41%  Similarity=0.913  Sum_probs=36.4

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccccccccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV   45 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~   45 (123)
                      ..|.|..+++|.|++..|..|++|||+|||++||++++++..+.
T Consensus        42 ~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~~k~~k~   85 (105)
T 1r4i_A           42 QKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLGARKLKKL   85 (105)
T ss_dssp             CCCCCSSSSCCCCCTTTTTTCHHHHHHHHHHHTCCSCC------
T ss_pred             CceeeccCCccccCccccccchhchHHHHHhhhcccchhhhccc
Confidence            57899999999999999999999999999999999999887764

>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=99.13  E-value=5.5e-11  Score=96.05  Aligned_cols=45  Identities=42%  Similarity=0.922  Sum_probs=39.4

Q ss_pred             cee-cCCCCCcccccccccccccccchhhhhccccccccccccccCcc
Q psy752            3 EYT-CPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGR   49 (123)
Q Consensus         3 ~y~-C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~~~   49 (123)
                      .|. |  .++|.|++..|+.|++|||+||+++||++++||.+|++.++
T Consensus        86 ~~~~c--~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~vq~~R~~~~~  131 (419)
T 3dzy_D           86 IYDRC--DLNCRIHKKSRNKCQYCRFQKCLAVGMSHNAIRFGRMPQAE  131 (419)
T ss_dssp             CCCCC--CSCCCCCTTGGGTCHHHHHHHHHHTTCCGGGCCCSCCTTTT
T ss_pred             ccccc--cCCCCcccccCccchhhhHHHHhhcccchhheecccccccc
Confidence            454 5  46899999999999999999999999999999999976543

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

Probab=97.61  E-value=2.6e-05  Score=59.19  Aligned_cols=57  Identities=16%  Similarity=0.116  Sum_probs=13.3

Q ss_pred             cchhhhhccccccccccccccCccccccCCCCCCCCCCCCCCCCCChhHHhhHHHHHHHHHhccCCCC
Q psy752           26 RFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEDLERNTEISVSMMSCDGDTS   93 (123)
Q Consensus        26 R~~kCl~~GM~~~~V~~~r~~~~~~~~~~~~~~~~~~~p~~~~~~s~e~~~~~~~li~~L~~ae~~~~   93 (123)
                      .--||+++||+++|||.+|++.+++....   ....  .+......      .+.+++++..+|++..
T Consensus        11 ~~~kCl~vGMkkeaVq~~R~~~~~~~~~~---~~~~--~~~~~~~~------~~~i~~~~~~~e~~~~   67 (282)
T 1lbd_A           11 SSGLVPRGSHKREAVQEERQRGKDRNENE---VEST--SSANEDMP------VERILEAELAVEPKTE   67 (282)
T ss_dssp             ---------------------------------------CCTTTSC------HHHHHHHHHTTCCCHH
T ss_pred             CCCCcCccCCcHHhhcCCCCCCCCCCCCC---CCCC--CCCCCCCC------HHHHHHHHHhcCCccc
Confidence            34699999999999999998765543111   0010  11111111      2589999999988653

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

Probab=94.63  E-value=0.0048  Score=46.25  Aligned_cols=51  Identities=24%  Similarity=0.410  Sum_probs=10.9

Q ss_pred             ccccccccccccCccccccCCCCCCCCCCCCCCCCCChhHHhhHHHHHHHHHhccCCCCCC
Q psy752           35 MLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEDLERNTEISVSMMSCDGDTSDL   95 (123)
Q Consensus        35 M~~~~V~~~r~~~~~~~~~~~~~~~~~~~p~~~~~~s~e~~~~~~~li~~L~~ae~~~~~~   95 (123)
                      |.+++||.||.++++++..++.......+++.+     +     ..+|..|+.||.++++.
T Consensus         1 M~kE~Vr~dr~~~~r~~~~~~~~~~~~~~~~~~-----~-----~~li~~l~~a~~~~~~~   51 (271)
T 1ovl_A            1 MVKEVVRTDSLKGRRGRLPSKPKSPQEPSPPSP-----P-----VSLISALVRAHVDSNPA   51 (271)
T ss_dssp             ---------------------------------------------CHHHHHHHHHHHTSCC
T ss_pred             CCccccccCccccCCCCCCCCCCCcccCCCCCC-----H-----HHHHHHHHHHHHHhCCC
Confidence            889999999999888876655443222222111     1     26777777777766553

>1xdk_B RAR-beta, retinoic acid receptor, beta; nuclear receptor, coactivator, ligand, hormone/growth factor receptor complex; HET: REA; 2.90A {Mus musculus} SCOP: a.123.1.1

Probab=89.87  E-value=0.065  Score=40.87  Aligned_cols=47  Identities=19%  Similarity=0.203  Sum_probs=12.3

Q ss_pred             ccccccccccccCccccccCCCCCCCCCCCCCCCCCChhHHhhHHHHHHHHHhccCCCC
Q psy752           35 MLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEDLERNTEISVSMMSCDGDTS   93 (123)
Q Consensus        35 M~~~~V~~~r~~~~~~~~~~~~~~~~~~~p~~~~~~s~e~~~~~~~li~~L~~ae~~~~   93 (123)
                      |++++||.+|.++++++......        ....++.+.    +.+|+.|+.||.+++
T Consensus         1 M~rEaVr~~R~~~~~~~~~~~~~--------~~~~~~~~~----~~li~~l~~a~~~~~   47 (303)
T 1xdk_B            1 MSKESVRNDRNKKKKEPSKQECT--------ESYEMTAEL----DDLTEKIRKAHQETF   47 (303)
T ss_dssp             -------------------------------------CCT----HHHHHHHHHHHHHHS
T ss_pred             CCHHHHhhccccccccccccCCC--------CCCCCCHHH----HHHHHHHHHHHHHhC
Confidence            88999999998766544322110        011122222    478888888887654

---

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	123
d1lo1a_	90	g.39.1.2 (A:) Steroid hormone receptor Err2 DNA-bi	4e-14
d1cita_	89	g.39.1.2 (A:) Orphan nuclear receptor NGFI-B DNA-b	9e-13
d1dszb_	84	g.39.1.2 (B:) Retinoid X receptor (RXR-alpha) DNA-	4e-11
d1kb2a_	89	g.39.1.2 (A:) Vitamin D3 receptor, VDR, DNA-bindin	2e-10
d2hanb1	83	g.39.1.2 (B:5-87) Ecdysone receptor DNA-binding do	2e-10
d1a6ya_	78	g.39.1.2 (A:) Orphan nuclear receptor reverb DNA-b	5e-10
d1dsza_	75	g.39.1.2 (A:) Retinoic acid receptor DNA-binding d	1e-08
d1r4ia_	74	g.39.1.2 (A:) Androgen receptor {Rat (Rattus norve	4e-08
d1lata_	71	g.39.1.2 (A:) Glucocorticoid receptor DNA-binding	4e-07
d2nllb_	103	g.39.1.2 (B:) Thyroid hormone receptor (TR-beta) D	5e-07
d1hcqa_	74	g.39.1.2 (A:) Estrogen receptor DNA-binding domain	6e-07

>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 = 60.8 bits (147), Expect = 4e-14
 Identities = 43/53 (81%), Positives = 49/53 (92%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYR 53
          NIEY+CPA+N+CEI KRRRK+CQACRF K L+ GMLKEGVRLDRVRGGRQKY+
Sbjct: 38 NIEYSCPATNECEITKRRRKSCQACRFMKALKVGMLKEGVRLDRVRGGRQKYK 90

>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 = 57.4 bits (138), Expect = 9e-13
 Identities = 28/56 (50%), Positives = 37/56 (66%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNP 56
          + +Y C A+ DC ++KRRR  CQ CRFQKCL  GM+KE VR D ++G R +    P
Sbjct: 34 SAKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTDSLKGRRGRLPSKP 89

>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 = 53.0 bits (127), Expect = 4e-11
 Identities = 23/46 (50%), Positives = 32/46 (69%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR 46
          ++ YTC  + DC I+KR+R  CQ CR+QKCL  GM +E V+ +R R
Sbjct: 39 DLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQR 84

>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 = 51.6 bits (123), Expect = 2e-10
 Identities = 19/51 (37%), Positives = 30/51 (58%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQK 51
             +TCP + DC I K  R+ CQACR ++C+  GM+KE +  D     +++
Sbjct: 34 KALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDEEVQRKRE 84

>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 = 51.1 bits (122), Expect = 2e-10
 Identities = 16/49 (32%), Positives = 23/49 (46%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGR 49
          +  Y C     CE++   R+ CQ CR +KCL  GM  E V  +     +
Sbjct: 34 SAVYCCKFGRACEMDMYMRRKCQECRLKKCLAVGMRPECVVPENQCAMK 82

>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 = 50.0 bits (119), Expect = 5e-10
 Identities = 17/41 (41%), Positives = 23/41 (56%)

Query: 4  YTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44
            C  + +C I +  R  CQ CRF+KCL  GM ++ VR  R
Sbjct: 38 KRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGR 78

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

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

 Score = 46.2 bits (109), Expect = 1e-08
 Identities = 23/43 (53%), Positives = 25/43 (58%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLD 43
          N+ YTC    +C INK  R  CQ CR QKC   GM KE VR D
Sbjct: 33 NMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRND 75

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

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

 Score = 45.1 bits (106), Expect = 4e-08
 Identities = 17/38 (44%), Positives = 22/38 (57%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE 38
            +Y C + NDC I+K RRK C +CR +KC   GM   
Sbjct: 36 KQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLG 73

>d1lata_ g.39.1.2 (A:) Glucocorticoid receptor DNA-binding domain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 71

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

 Score = 42.4 bits (99), Expect = 4e-07
 Identities = 18/38 (47%), Positives = 22/38 (57%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE 38
             Y C     C I+K RRK C ACR++KCL+ GM  E
Sbjct: 34 QHNYLCKYEGKCIIDKIRRKNCPACRYRKCLQAGMNLE 71

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

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

 Score = 42.9 bits (100), Expect = 5e-07
 Identities = 19/54 (35%), Positives = 27/54 (50%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRR 54
          +  Y+C     C I+K  R  CQ CRF+KC+  GM  + V  D  R  ++K   
Sbjct: 37 HPSYSCKYEGKCVIDKVTRNQCQECRFKKCIYVGMATDLVLDDSKRLAKRKLIE 90

>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 = 42.0 bits (98), Expect = 6e-07
 Identities = 21/37 (56%), Positives = 28/37 (75%)

Query: 1  NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLK 37
          + +Y CPA+N C I+K RRK+CQACR +KC   GM+K
Sbjct: 38 HNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMK 74

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	123
d1lo1a_	90	Steroid hormone receptor Err2 DNA-binding domain {	99.51
d2hanb1	83	Ecdysone receptor DNA-binding domain {Fruit fly (D	99.42
d1cita_	89	Orphan nuclear receptor NGFI-B DNA-binding domain	99.42
d1dszb_	84	Retinoid X receptor (RXR-alpha) DNA-binding domain	99.41
d1kb2a_	89	Vitamin D3 receptor, VDR, DNA-binding domain {Huma	99.38
d1dsza_	75	Retinoic acid receptor DNA-binding domain {Human (	99.36
d1a6ya_	78	Orphan nuclear receptor reverb DNA-binding domain	99.34
d2nllb_	103	Thyroid hormone receptor (TR-beta) DNA-binding dom	99.27
d1r4ia_	74	Androgen receptor {Rat (Rattus norvegicus) [TaxId:	99.19
d1lata_	71	Glucocorticoid receptor DNA-binding domain {Rat (R	99.11
d1hcqa_	74	Estrogen receptor DNA-binding domain {Human and ch	99.07

>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=99.51  E-value=8.8e-16  Score=99.22  Aligned_cols=51  Identities=82%  Similarity=1.465  Sum_probs=47.1

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccccccccccccCccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKY   52 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~~~~~~   52 (123)
                      ..|.|..+++|.++...|..|++|||+|||++||++++||.+|++.+++++
T Consensus        39 ~~~~c~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~r~~~~r~k~   89 (90)
T d1lo1a_          39 IEYSCPATNECEITKRRRKSCQACRFMKALKVGMLKEGVRLDRVRGGRQKY   89 (90)
T ss_dssp             CCCCCSSCSCCCCCHHHHHHCHHHHHHHHHHHTCCGGGSCSSCCTTCCCCC
T ss_pred             CccchhcCCCCccCCCCccccchhhHHHHHHcCCCHHHhccccccccccCC
Confidence            468899999999999999999999999999999999999999998777765

>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=99.42  E-value=8.2e-15  Score=93.28  Aligned_cols=47  Identities=34%  Similarity=0.645  Sum_probs=43.3

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccccccccccccCc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG   48 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~~   48 (123)
                      ..|.|...++|.+++..+..|++|||+|||++||++++||.+|+..+
T Consensus        35 ~~~~c~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~~   81 (83)
T d2hanb1          35 AVYCCKFGRACEMDMYMRRKCQECRLKKCLAVGMRPECVVPENQCAM   81 (83)
T ss_dssp             CCCCCSSCSCCCCSTTGGGTCHHHHHHHHHHTTCCGGGSSCSSHHHH
T ss_pred             CceeecCCCCcccCCcccccCccchHHHHHHcCCCHHHccccchhcc
Confidence            46889999999999999999999999999999999999999987544

>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=99.42  E-value=2.5e-14  Score=92.13  Aligned_cols=52  Identities=52%  Similarity=1.004  Sum_probs=46.3

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccccccccccccCcccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYR   53 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~~~~~~~   53 (123)
                      ..|.|..+++|.++...|..|++|||+|||++||++++||.+++..++.+++
T Consensus        35 ~~~~c~~~~~c~~~~~~r~~Cr~CR~~KCl~~GM~~~~v~~~~~~~~r~~~p   86 (89)
T d1cita_          35 AKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTDSLKGRRGRLP   86 (89)
T ss_dssp             CCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHTTCCGGGSCCGGGTTCCSCCC
T ss_pred             CceeecCCCCccccCCccccCchhhHHHHHHcCCCHHHhcccccccccCCCC
Confidence            4678999999999999999999999999999999999999998876665553

>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=99.41  E-value=2.1e-14  Score=91.51  Aligned_cols=45  Identities=51%  Similarity=1.035  Sum_probs=42.1

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhcccccccccccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR   46 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~   46 (123)
                      ..|.|..+++|.+++..|..|++|||+|||++||++++||.+|++
T Consensus        40 ~~~~c~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~Rdr   84 (84)
T d1dszb_          40 LTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQR   84 (84)
T ss_dssp             CCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCCCCC
T ss_pred             CCeeccCCCCcccCCCCCccCCCCccHHHHHcCCChHHcccccCC
Confidence            468899999999999999999999999999999999999999874

>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=99.38  E-value=1.6e-14  Score=93.08  Aligned_cols=47  Identities=40%  Similarity=0.829  Sum_probs=42.9

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccccccccccccCc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG   48 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~~   48 (123)
                      ..|.|..+++|.|+...|..|++|||+|||++||++++||.+|+...
T Consensus        35 ~~~~c~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~~   81 (89)
T d1kb2a_          35 ALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDEEVQR   81 (89)
T ss_dssp             CCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCHHHHHH
T ss_pred             CCeecCCCCccCCCCcCCccCchhhHHHHHHcCCCHhhccccchhch
Confidence            46889999999999999999999999999999999999999986543

>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=99.36  E-value=6.7e-14  Score=87.42  Aligned_cols=42  Identities=52%  Similarity=0.958  Sum_probs=39.5

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccccccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLD   43 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~   43 (123)
                      ..|.|...++|.++...+..|++|||+|||++||++++||.|
T Consensus        34 ~~~~c~~~~~c~~~~~~r~~Cr~CR~~KCl~~GM~~~~vq~d   75 (75)
T d1dsza_          34 MVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRND   75 (75)
T ss_dssp             CCCCCSSCSCCCCSTTTGGGCHHHHHHHHHHTTCCGGGSCCC
T ss_pred             CceecccCCccccCCccccccchhHHHHHHHhCCCHHHccCC
Confidence            468899999999999999999999999999999999999976

>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=99.34  E-value=1.2e-13  Score=86.88  Aligned_cols=43  Identities=44%  Similarity=1.011  Sum_probs=38.6

Q ss_pred             Ccee-cCCCCCcccccccccccccccchhhhhcccccccccccc
Q psy752            2 IEYT-CPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR   44 (123)
Q Consensus         2 ~~y~-C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r   44 (123)
                      ..|. |..+++|.+++..+..|++|||+|||++||++++||.+|
T Consensus        35 ~~~~~~~~~~~c~~~~~~r~~Cr~CR~~KCl~~GM~~~~vq~~R   78 (78)
T d1a6ya_          35 IQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGR   78 (78)
T ss_dssp             CCCCCCSSTTCCCCCTTTTTSCHHHHHHHHTTTTCCSTTCCCCC
T ss_pred             CceeeeccCCCcccCCCCCccchhhHHHHHHHhCCCHHHhcCCC
Confidence            3565 566889999999999999999999999999999999886

>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=99.27  E-value=1.2e-13  Score=90.95  Aligned_cols=49  Identities=39%  Similarity=0.752  Sum_probs=43.0

Q ss_pred             ceecCCCCCcccccccccccccccchhhhhccccccccccccccCcccc
Q psy752            3 EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQK   51 (123)
Q Consensus         3 ~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~V~~~r~~~~~~~   51 (123)
                      .|.|...++|.++...|..|++|||+|||++||++++|+.+|++..+.+
T Consensus        39 ~~~c~~~~~c~~~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~~~~~   87 (103)
T d2nllb_          39 SYSCKYEGKCVIDKVTRNQCQECRFKKCIYVGMATDLVLDDSKRLAKRK   87 (103)
T ss_dssp             GCCCSSCTTCCCSTTTTTSCHHHHHHHHHHTTCCGGGSCCHHHHHHHHH
T ss_pred             eeecccCCCCcCCCCccCCCccccchhHHHhhccHHhhhccccchhhhh
Confidence            3567889999999999999999999999999999999999987655444

>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=99.19  E-value=1.5e-12  Score=80.88  Aligned_cols=38  Identities=45%  Similarity=0.972  Sum_probs=35.4

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEG   39 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~~   39 (123)
                      ..|.|..+++|.++...|..|++|||+|||++||+.+|
T Consensus        37 ~~~~c~~~~~C~~~~~~r~~C~~CR~~KCl~vGM~~~A   74 (74)
T d1r4ia_          37 QKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLGA   74 (74)
T ss_dssp             CCCCCSSSSCCCCCTTTTTTCHHHHHHHHHHHTCCSCC
T ss_pred             cceeeecCCCcccCCCCcccchhhhHHHHHHcCCcCCC
Confidence            46889999999999999999999999999999999875

>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=99.11  E-value=7e-12  Score=77.26  Aligned_cols=37  Identities=49%  Similarity=0.979  Sum_probs=34.4

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhcccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE   38 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~~   38 (123)
                      ..|.|...++|.++...+..|++|||+|||++||++|
T Consensus        35 ~~~~c~~~~~C~~~~~~r~~Cr~CR~~KCl~~GM~~e   71 (71)
T d1lata_          35 HNYLCKYEGKCIIDKIRRKNCPACRYRKCLQAGMNLE   71 (71)
T ss_dssp             CCCCCSSCSCCCCSTTTTTTCHHHHHHHHHHTTCCCC
T ss_pred             cceeeecCcccccccCccccCCccchhHHhHccCCCC
Confidence            4678999999999999999999999999999999975

>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=99.07  E-value=1.1e-11  Score=76.99  Aligned_cols=36  Identities=58%  Similarity=1.259  Sum_probs=33.6

Q ss_pred             CceecCCCCCcccccccccccccccchhhhhccccc
Q psy752            2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLK   37 (123)
Q Consensus         2 ~~y~C~~~~~C~i~~~~r~~C~~CR~~kCl~~GM~~   37 (123)
                      ..|.|..+++|.|+...|..|++|||+|||++||+.
T Consensus        39 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~k   74 (74)
T d1hcqa_          39 NDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMK   74 (74)
T ss_dssp             CCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHHTCCC
T ss_pred             cccccccCCCCccCCCccccchHhhHHHHHHcCCcC
Confidence            468899999999999999999999999999999974