Psyllid ID: psy16683

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------14
MNQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRRSNWFKIHCLLQEQQQQAEQQTERTKLGHPDLLLKLDKFTNNNTIVTNNNLILQLLQNP
cccccccccccccccccccccccccccccHHccccccccccccccccEEEcccccccccHHcccHHHHHcccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHccccccccccccHHHHHHHHHccc
ccccccccccEccccEccEcccHHHHHHHHHHHcccccccccccccccccccccccccHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHccccccEEEccccccccccccHHHHHHHHHccc
mnqtckvcgepaagfhfgaftcegcksffgrsynnlpsisecknnneciinkknrtsckscrlrkclmvgmsksgsrygrrsnWFKIHCLLQEQQQQAEQQTErtklghpdlllkldkftnnntivtnNNLILQLLQNP
MNQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSisecknnneciinkknrtsckscrlrkCLMVGMSKSGSRYGRRSNWFKIHCLLQEQQQQAEQQTERTKLGHPDLLLKLDKftnnntivtnnnlilqllqnp
MNQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISecknnneciinkknRTSCKSCRLRKCLMVGMSKSGSRYGRRSNWFKIHCLLqeqqqqaeqqteRTKLGHPDLLLKLDKFtnnntivtnnnlilqllqnP
****CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRRSNWFKIHCLLQ*****************PDLLLKLDKFTNNNTIVTNNNLILQLL***
*NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMS************************************************************LQLLQ**
MNQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRRSNWFKIHCLLQE************KLGHPDLLLKLDKFTNNNTIVTNNNLILQLLQNP
MNQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSK*************************************DLLLKL*******TIVTNNNLILQL****
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MNQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRRSNWFKIHCLLQEQQQQAEQQTERTKLGHPDLLLKLDKFTNNNTIVTNNNLILQLLQNP
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query139 2.2.26 [Sep-21-2011]
P13054 647 Knirps-related protein OS yes N/A 0.654 0.140 0.934 8e-50
P10734 429 Zygotic gap protein knirp no N/A 0.690 0.223 0.854 4e-48
Q24753 481 Zygotic gap protein knirp N/A N/A 0.690 0.199 0.854 5e-48
P15370 373 Protein embryonic gonad O no N/A 0.683 0.254 0.852 7e-48
O01639 690 Ecdysone-inducible protei N/A N/A 0.769 0.155 0.401 4e-20
P50239 711 Ecdysone-inducible protei N/A N/A 0.805 0.157 0.391 7e-20
Q08893 699 Ecdysone-inducible protei N/A N/A 0.769 0.153 0.401 8e-20
P13055 1412 Ecdysone-induced protein no N/A 0.784 0.077 0.407 1e-19
P17671 1199 Ecdysone-induced protein no N/A 0.784 0.090 0.407 2e-19
P49868 557 Probable nuclear hormone N/A N/A 0.553 0.138 0.461 8e-19
>sp|P13054|KNRL_DROME Knirps-related protein OS=Drosophila melanogaster GN=knrl PE=2 SV=1 Back     alignment and function desciption
 Score =  195 bits (495), Expect = 8e-50,   Method: Composition-based stats.
 Identities = 85/91 (93%), Positives = 89/91 (97%)

Query: 1   MNQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKS 60
           MNQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNL SIS+CKNN ECIINKKNRT+CK+
Sbjct: 10  MNQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLSSISDCKNNGECIINKKNRTACKA 69

Query: 61  CRLRKCLMVGMSKSGSRYGRRSNWFKIHCLL 91
           CRL+KCLMVGMSKSGSRYGRRSNWFKIHCLL
Sbjct: 70  CRLKKCLMVGMSKSGSRYGRRSNWFKIHCLL 100

Drosophila melanogaster (taxid: 7227)
>sp|P10734|KNIR_DROME Zygotic gap protein knirps OS=Drosophila melanogaster GN=kni PE=1 SV=1 Back     alignment and function description
>sp|Q24753|KNIR_DROVI Zygotic gap protein knirps OS=Drosophila virilis GN=kni PE=3 SV=1 Back     alignment and function description
>sp|P15370|EGON_DROME Protein embryonic gonad OS=Drosophila melanogaster GN=eg PE=2 SV=2 Back     alignment and function description
>sp|O01639|E75_CHOFU Ecdysone-inducible protein E75 OS=Choristoneura fumiferana GN=E75 PE=2 SV=1 Back     alignment and function description
>sp|P50239|E75_GALME Ecdysone-inducible protein E75 OS=Galleria mellonella GN=E75 PE=2 SV=1 Back     alignment and function description
>sp|Q08893|E75_MANSE Ecdysone-inducible protein E75 OS=Manduca sexta GN=E75 PE=2 SV=2 Back     alignment and function description
>sp|P13055|E75BB_DROME Ecdysone-induced protein 75B, isoform B OS=Drosophila melanogaster GN=Eip75B PE=2 SV=2 Back     alignment and function description
>sp|P17671|E75BC_DROME Ecdysone-induced protein 75B, isoforms C/D OS=Drosophila melanogaster GN=Eip75B PE=2 SV=2 Back     alignment and function description
>sp|P49868|HR3_GALME Probable nuclear hormone receptor HR3 OS=Galleria mellonella GN=HR3 PE=2 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query139
332031559 434 Protein embryonic gonad [Acromyrmex echi 0.726 0.232 0.861 2e-49
194749753 674 GF24122 [Drosophila ananassae] gi|190624 0.654 0.135 0.934 8e-49
383848131 422 PREDICTED: uncharacterized protein LOC10 0.726 0.239 0.851 1e-48
307213125 435 Protein embryonic gonad [Harpegnathos sa 0.726 0.232 0.851 1e-48
307171692 438 Protein embryonic gonad [Camponotus flor 0.726 0.230 0.851 3e-48
328710681 489 PREDICTED: hypothetical protein LOC10057 0.676 0.192 0.914 4e-48
242019625 480 knirps related protein, putative [Pedicu 0.690 0.2 0.895 4e-48
28574803 647 knirps-like [Drosophila melanogaster] gi 0.654 0.140 0.934 6e-48
195591922 599 GD12173 [Drosophila simulans] gi|1941976 0.654 0.151 0.934 7e-48
195348321 643 GM22199 [Drosophila sechellia] gi|194122 0.654 0.141 0.934 7e-48
>gi|332031559|gb|EGI71031.1| Protein embryonic gonad [Acromyrmex echinatior] Back     alignment and taxonomy information
 Score =  199 bits (507), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 87/101 (86%), Positives = 94/101 (93%)

Query: 1   MNQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKS 60
           MNQ C+VCGEPAAGFHFGAFTCEGCKSFFGR+YNNL SISECKN   C+INKKNRT+CK+
Sbjct: 54  MNQLCRVCGEPAAGFHFGAFTCEGCKSFFGRTYNNLGSISECKNGGVCVINKKNRTACKA 113

Query: 61  CRLRKCLMVGMSKSGSRYGRRSNWFKIHCLLQEQQQQAEQQ 101
           CRLRKCLMVGMSKSGSRYGRRSNWFKIHCLLQEQ QQA+ +
Sbjct: 114 CRLRKCLMVGMSKSGSRYGRRSNWFKIHCLLQEQSQQAQNR 154

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|194749753|ref|XP_001957301.1| GF24122 [Drosophila ananassae] gi|190624583|gb|EDV40107.1| GF24122 [Drosophila ananassae] Back     alignment and taxonomy information
>gi|383848131|ref|XP_003699705.1| PREDICTED: uncharacterized protein LOC100878095 [Megachile rotundata] Back     alignment and taxonomy information
>gi|307213125|gb|EFN88647.1| Protein embryonic gonad [Harpegnathos saltator] Back     alignment and taxonomy information
>gi|307171692|gb|EFN63427.1| Protein embryonic gonad [Camponotus floridanus] Back     alignment and taxonomy information
>gi|328710681|ref|XP_003244332.1| PREDICTED: hypothetical protein LOC100575402 [Acyrthosiphon pisum] Back     alignment and taxonomy information
>gi|242019625|ref|XP_002430260.1| knirps related protein, putative [Pediculus humanus corporis] gi|212515367|gb|EEB17522.1| knirps related protein, putative [Pediculus humanus corporis] Back     alignment and taxonomy information
>gi|28574803|ref|NP_788552.1| knirps-like [Drosophila melanogaster] gi|125519|sp|P13054.1|KNRL_DROME RecName: Full=Knirps-related protein; AltName: Full=Nuclear receptor subfamily 0 group A member 2 gi|8156|emb|CAA32365.1| unnamed protein product [Drosophila melanogaster] gi|18447289|gb|AAL68221.1| LD23140p [Drosophila melanogaster] gi|23094177|gb|AAF51627.2| knirps-like [Drosophila melanogaster] gi|220942344|gb|ACL83715.1| knrl-PA [synthetic construct] gi|220960286|gb|ACL92679.1| knrl-PA [synthetic construct] gi|226215|prf||1501350A knirps related gene Back     alignment and taxonomy information
>gi|195591922|ref|XP_002085685.1| GD12173 [Drosophila simulans] gi|194197694|gb|EDX11270.1| GD12173 [Drosophila simulans] Back     alignment and taxonomy information
>gi|195348321|ref|XP_002040697.1| GM22199 [Drosophila sechellia] gi|194122207|gb|EDW44250.1| GM22199 [Drosophila sechellia] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query139
FB|FBgn0001323 647 knrl "knirps-like" [Drosophila 0.654 0.140 0.802 9.4e-37
FB|FBgn0000560 373 eg "eagle" [Drosophila melanog 0.654 0.243 0.747 1.9e-35
FB|FBgn0001320 429 kni "knirps" [Drosophila melan 0.654 0.212 0.758 2.4e-35
UNIPROTKB|F1P101 302 F1P101 "Uncharacterized protei 0.553 0.254 0.435 2.1e-14
UNIPROTKB|H0YLS5153 RORA "Nuclear receptor ROR-alp 0.553 0.503 0.423 6.2e-14
UNIPROTKB|F1SJB4 452 RORB "Uncharacterized protein" 0.553 0.170 0.435 1.4e-13
WB|WBGene00003675 514 nhr-85 [Caenorhabditis elegans 0.546 0.147 0.434 1.4e-13
UNIPROTKB|Q98934 459 RORB "Uncharacterized protein" 0.553 0.167 0.435 1.5e-13
UNIPROTKB|F1MWS0 459 RORB "Uncharacterized protein" 0.553 0.167 0.435 1.5e-13
ZFIN|ZDB-GENE-061204-2 466 rorb "RAR-related orphan recep 0.553 0.165 0.435 1.5e-13
FB|FBgn0001323 knrl "knirps-like" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
 Score = 400 (145.9 bits), Expect = 9.4e-37, P = 9.4e-37
 Identities = 73/91 (80%), Positives = 76/91 (83%)

Query:     1 MNQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKS 60
             MNQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNL SIS              RT+CK+
Sbjct:    10 MNQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLSSISDCKNNGECIINKKNRTACKA 69

Query:    61 CRLRKCLMVGMSKSGSRYGRRSNWFKIHCLL 91
             CRL+KCLMVGMSKSGSRYGRRSNWFKIHCLL
Sbjct:    70 CRLKKCLMVGMSKSGSRYGRRSNWFKIHCLL 100
GO:0004879 "ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity" evidence=ISS;NAS
GO:0005634 "nucleus" evidence=ISS;NAS
GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS
GO:0007427 "epithelial cell migration, open tracheal system" evidence=TAS
GO:0035151 "regulation of tube size, open tracheal system" evidence=TAS
GO:0046845 "branched duct epithelial cell fate determination, open tracheal system" evidence=TAS
GO:0007088 "regulation of mitosis" evidence=IMP
GO:0007424 "open tracheal system development" evidence=TAS
GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA
GO:0043565 "sequence-specific DNA binding" evidence=IEA
GO:0008270 "zinc ion binding" evidence=IEA
GO:0003707 "steroid hormone receptor activity" evidence=IEA
FB|FBgn0000560 eg "eagle" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
FB|FBgn0001320 kni "knirps" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
UNIPROTKB|F1P101 F1P101 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|H0YLS5 RORA "Nuclear receptor ROR-alpha" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|F1SJB4 RORB "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
WB|WBGene00003675 nhr-85 [Caenorhabditis elegans (taxid:6239)] Back     alignment and assigned GO terms
UNIPROTKB|Q98934 RORB "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|F1MWS0 RORB "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-061204-2 rorb "RAR-related orphan receptor B" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms

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) ?
P13054KNRL_DROMENo assigned EC number0.93400.65460.1406yesN/A

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query139
cd0715786 cd07157, 2DBD_NR_DBD1, The first DNA-binding domai 4e-40
pfam0010570 pfam00105, zf-C4, Zinc finger, C4 type (two domain 2e-30
cd0691672 cd06916, NR_DBD_like, DNA-binding domain of nuclea 2e-28
cd0717974 cd07179, 2DBD_NR_DBD2, The second DNA-binding doma 5e-27
cd0717182 cd07171, NR_DBD_ER, DNA-binding domain of estrogen 7e-24
smart0039970 smart00399, ZnF_C4, c4 zinc finger in nuclear horm 1e-23
cd0716689 cd07166, NR_DBD_REV_ERB, DNA-binding domain of REV 1e-23
cd0715672 cd07156, NR_DBD_VDR_like, The DNA-binding domain o 2e-23
cd0696076 cd06960, NR_DBD_HNF4A, DNA-binding domain of hepto 2e-22
cd0696895 cd06968, NR_DBD_ROR, DNA-binding domain of Retinoi 1e-21
cd0715873 cd07158, NR_DBD_Ppar_like, The DNA-binding domain 2e-21
cd0696584 cd06965, NR_DBD_Ppar, DNA-binding domain of peroxi 2e-20
cd0696185 cd06961, NR_DBD_TR, DNA-binding domain of thyroid 1e-19
cd0715575 cd07155, NR_DBD_ER_like, DNA-binding domain of est 1e-19
cd0716581 cd07165, NR_DBD_DmE78_like, DNA-binding domain of 2e-19
cd0717097 cd07170, NR_DBD_ERR, DNA-binding domain of estroge 3e-19
cd0716287 cd07162, NR_DBD_PXR, DNA-binding domain of pregnan 7e-19
cd0695973 cd06959, NR_DBD_EcR_like, The DNA-binding domain o 7e-19
cd06955107 cd06955, NR_DBD_VDR, DNA-binding domain of vitamin 8e-19
cd0696787 cd06967, NR_DBD_TR2_like, DNA-binding domain of th 9e-19
cd0716478 cd07164, NR_DBD_PNR_like_1, DNA-binding domain of 1e-18
cd0696975 cd06969, NR_DBD_NGFI-B, DNA-binding domain of the 3e-18
cd0696485 cd06964, NR_DBD_RAR, DNA-binding domain of retinoi 1e-17
cd0716890 cd07168, NR_DBD_DHR4_like, DNA-binding domain of e 2e-17
cd0716392 cd07163, NR_DBD_TLX, DNA-binding domain of Tailles 6e-17
cd0716793 cd07167, NR_DBD_Lrh-1_like, The DNA-binding domain 1e-16
cd07160101 cd07160, NR_DBD_LXR, DNA-binding domain of Liver X 2e-16
cd0695873 cd06958, NR_DBD_COUP_TF, DNA-binding domain of chi 2e-16
cd0695677 cd06956, NR_DBD_RXR, DNA-binding domain of retinoi 2e-16
cd0696694 cd06966, NR_DBD_CAR, DNA-binding domain of constit 3e-16
cd0716990 cd07169, NR_DBD_GCNF_like, DNA-binding domain of G 4e-16
cd0716191 cd07161, NR_DBD_EcR, DNA-binding domain of Ecdyson 8e-16
cd0717382 cd07173, NR_DBD_AR, DNA-binding domain of androgen 4e-15
cd0696284 cd06962, NR_DBD_FXR, DNA-binding domain of Farneso 6e-15
cd0715473 cd07154, NR_DBD_PNR_like, The DNA-binding domain o 6e-15
cd0696373 cd06963, NR_DBD_GR_like, The DNA binding domain of 6e-14
cd0717278 cd07172, NR_DBD_GR_PR, DNA-binding domain of gluco 7e-14
cd0695782 cd06957, NR_DBD_PNR_like_2, DNA-binding domain of 2e-13
cd0697092 cd06970, NR_DBD_PNR, DNA-binding domain of the pho 8e-13
>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 Back     alignment and domain information 
 Score =  129 bits (325), Expect = 4e-40
 Identities = 57/86 (66%), Positives = 65/86 (75%), Gaps = 1/86 (1%)

Query: 3  QTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNN-LPSISECKNNNECIINKKNRTSCKSC 61
          QTC+VCGEPAAGFH GA+ CE CK FF RS N    +ISEC N  +CII+KKNRT C++C
Sbjct: 1  QTCQVCGEPAAGFHHGAYVCEACKKFFMRSSNAISFTISECPNGGKCIIDKKNRTKCQAC 60

Query: 62 RLRKCLMVGMSKSGSRYGRRSNWFKI 87
          R RKCL VGMS  G RYGRRS+  KI
Sbjct: 61 RYRKCLNVGMSLGGPRYGRRSDISKI 86

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|201004 pfam00105, zf-C4, Zinc finger, C4 type (two domains) Back     alignment and domain information
>gnl|CDD|143512 cd06916, NR_DBD_like, DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers Back     alignment and domain information
>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 Back     alignment and domain information
>gnl|CDD|143545 cd07171, NR_DBD_ER, DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers Back     alignment and domain information
>gnl|CDD|197701 smart00399, ZnF_C4, c4 zinc finger in nuclear hormone receptors Back     alignment and domain information
>gnl|CDD|143540 cd07166, NR_DBD_REV_ERB, DNA-binding domain of REV-ERB receptor-like is composed of two C4-type zinc fingers Back     alignment and domain information
>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 Back     alignment and domain information
>gnl|CDD|143518 cd06960, NR_DBD_HNF4A, DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers Back     alignment and domain information
>gnl|CDD|143526 cd06968, NR_DBD_ROR, DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers Back     alignment and domain information
>gnl|CDD|143533 cd07158, NR_DBD_Ppar_like, The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family Back     alignment and domain information
>gnl|CDD|143523 cd06965, NR_DBD_Ppar, DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers Back     alignment and domain information
>gnl|CDD|143519 cd06961, NR_DBD_TR, DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers Back     alignment and domain information
>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 Back     alignment and domain information
>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 Back     alignment and domain information
>gnl|CDD|143544 cd07170, NR_DBD_ERR, DNA-binding domain of estrogen related receptors (ERR) is composed of two C4-type zinc fingers Back     alignment and domain information
>gnl|CDD|143536 cd07162, NR_DBD_PXR, DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers Back     alignment and domain information
>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 Back     alignment and domain information
>gnl|CDD|143513 cd06955, NR_DBD_VDR, DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers Back     alignment and domain information
>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 Back     alignment and domain information
>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 Back     alignment and domain information
>gnl|CDD|143527 cd06969, NR_DBD_NGFI-B, DNA-binding domain of the orphan nuclear receptor, nerve growth factor-induced-B Back     alignment and domain information
>gnl|CDD|143522 cd06964, NR_DBD_RAR, DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers Back     alignment and domain information
>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 Back     alignment and domain information
>gnl|CDD|143537 cd07163, NR_DBD_TLX, DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers Back     alignment and domain information
>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 Back     alignment and domain information
>gnl|CDD|143534 cd07160, NR_DBD_LXR, DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers Back     alignment and domain information
>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 Back     alignment and domain information
>gnl|CDD|143514 cd06956, NR_DBD_RXR, DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers Back     alignment and domain information
>gnl|CDD|143524 cd06966, NR_DBD_CAR, DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers Back     alignment and domain information
>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 Back     alignment and domain information
>gnl|CDD|143535 cd07161, NR_DBD_EcR, DNA-binding domain of Ecdysone receptor (ECR) family is composed of two C4-type zinc fingers Back     alignment and domain information
>gnl|CDD|143547 cd07173, NR_DBD_AR, DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers Back     alignment and domain information
>gnl|CDD|143520 cd06962, NR_DBD_FXR, DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers Back     alignment and domain information
>gnl|CDD|143529 cd07154, NR_DBD_PNR_like, The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family Back     alignment and domain information
>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 Back     alignment and domain information
>gnl|CDD|143546 cd07172, NR_DBD_GR_PR, DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers Back     alignment and domain information
>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 Back     alignment and domain information
>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 Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 139
cd0716689 NR_DBD_REV_ERB DNA-binding domain of REV-ERB recep 99.97
cd0696485 NR_DBD_RAR DNA-binding domain of retinoic acid rec 99.96
cd0716392 NR_DBD_TLX DNA-binding domain of Tailless (TLX) is 99.96
cd0696787 NR_DBD_TR2_like DNA-binding domain of the TR2 and 99.96
cd0695782 NR_DBD_PNR_like_2 DNA-binding domain of the photor 99.96
cd0696584 NR_DBD_Ppar DNA-binding domain of peroxisome proli 99.96
cd0696185 NR_DBD_TR DNA-binding domain of thyroid hormone re 99.96
cd0697092 NR_DBD_PNR DNA-binding domain of the photoreceptor 99.96
cd0716890 NR_DBD_DHR4_like DNA-binding domain of ecdysone-in 99.96
cd0717097 NR_DBD_ERR DNA-binding domain of estrogen related 99.96
cd0695677 NR_DBD_RXR DNA-binding domain of retinoid X recept 99.96
cd0696076 NR_DBD_HNF4A DNA-binding domain of heptocyte nucle 99.96
cd0715786 2DBD_NR_DBD1 The first DNA-binding domain (DBD) of 99.96
cd0716478 NR_DBD_PNR_like_1 DNA-binding domain of the photor 99.96
cd0717182 NR_DBD_ER DNA-binding domain of estrogen receptors 99.96
cd0715575 NR_DBD_ER_like DNA-binding domain of estrogen rece 99.96
cd0716581 NR_DBD_DmE78_like DNA-binding domain of Drosophila 99.95
cd0696895 NR_DBD_ROR DNA-binding domain of Retinoid-related 99.95
cd07160101 NR_DBD_LXR DNA-binding domain of Liver X receptors 99.95
cd0716990 NR_DBD_GCNF_like DNA-binding domain of Germ cell n 99.95
cd0716191 NR_DBD_EcR DNA-binding domain of Ecdysone receptor 99.95
cd0696694 NR_DBD_CAR DNA-binding domain of constitutive andr 99.95
KOG4215|consensus 432 99.95
cd0696975 NR_DBD_NGFI-B DNA-binding domain of the orphan nuc 99.95
cd0696284 NR_DBD_FXR DNA-binding domain of Farnesoid X recep 99.95
KOG4216|consensus 479 99.95
cd0717974 2DBD_NR_DBD2 The second DNA-binding domain (DBD) o 99.95
cd0716793 NR_DBD_Lrh-1_like The DNA-binding domain of Lrh-1 99.95
cd0715473 NR_DBD_PNR_like The DNA-binding domain of the phot 99.95
cd0691672 NR_DBD_like DNA-binding domain of nuclear receptor 99.95
cd0715873 NR_DBD_Ppar_like The DNA-binding domain of peroxis 99.95
cd06955107 NR_DBD_VDR DNA-binding domain of vitamin D recepto 99.95
cd0695873 NR_DBD_COUP_TF DNA-binding domain of chicken ovalb 99.94
cd0715672 NR_DBD_VDR_like The DNA-binding domain of vitamin 99.94
KOG4846|consensus 538 99.94
cd0695973 NR_DBD_EcR_like The DNA-binding domain of Ecdysone 99.94
cd0717278 NR_DBD_GR_PR DNA-binding domain of glucocorticoid 99.94
cd0716287 NR_DBD_PXR DNA-binding domain of pregnane X recept 99.94
cd0717382 NR_DBD_AR DNA-binding domain of androgen receptor 99.94
cd0696373 NR_DBD_GR_like The DNA binding domain of GR_like n 99.94
smart0039970 ZnF_C4 c4 zinc finger in nuclear hormone receptors 99.93
PF0010570 zf-C4: Zinc finger, C4 type (two domains); InterPr 99.91
KOG4217|consensus 605 99.87
KOG4218|consensus 475 99.87
>cd07166 NR_DBD_REV_ERB DNA-binding domain of REV-ERB receptor-like is composed of two C4-type zinc fingers Back     alignment and domain information 
Probab=99.97  E-value=8.4e-32  Score=181.32  Aligned_cols=86  Identities=47%  Similarity=0.972  Sum_probs=78.5

Q ss_pred             CCCcCcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcccCC
Q psy16683          1 MNQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGR   80 (139)
Q Consensus         1 ~~~~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R   80 (139)
                      |..+|.|||++++|+||||++|+||++||||++..+..+..|..+++|.++...+..|++|||+||+++||++++||++|
T Consensus         2 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r   81 (89)
T cd07166           2 MVVLCKVCGDKASGFHYGVHACEGCKGFFRRSIQQKIQYRKCTKNETCSIMRINRNRCQYCRFKKCLAVGMSRDAVRFGR   81 (89)
T ss_pred             CCCCCcccCccCcceEEChhhhhhHhhEecceeEcCCcchhhccCCcccccccccccccchhhhhcccccCCHHHhcCCC
Confidence            57789999999999999999999999999999987655436998999999999999999999999999999999999999


Q ss_pred             CCchhh
Q psy16683         81 RSNWFK   86 (139)
Q Consensus        81 ~~~~~k   86 (139)
                      ++..+|
T Consensus        82 ~~~~~~   87 (89)
T cd07166          82 IPKREK   87 (89)
T ss_pred             CCCccc
Confidence            997543

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
>cd06964 NR_DBD_RAR DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers Back     alignment and domain information
>cd07163 NR_DBD_TLX DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers Back     alignment and domain information
>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 Back     alignment and domain information
>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 Back     alignment and domain information
>cd06965 NR_DBD_Ppar DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers Back     alignment and domain information
>cd06961 NR_DBD_TR DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers Back     alignment and domain information
>cd06970 NR_DBD_PNR DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers Back     alignment and domain information
>cd07168 NR_DBD_DHR4_like DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers Back     alignment and domain information
>cd07170 NR_DBD_ERR DNA-binding domain of estrogen related receptors (ERR) is composed of two C4-type zinc fingers Back     alignment and domain information
>cd06956 NR_DBD_RXR DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers Back     alignment and domain information
>cd06960 NR_DBD_HNF4A DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers Back     alignment and domain information
>cd07157 2DBD_NR_DBD1 The first DNA-binding domain (DBD) of the 2DBD nuclear receptors is composed of two C4-type zinc fingers Back     alignment and domain information
>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 Back     alignment and domain information
>cd07171 NR_DBD_ER DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers Back     alignment and domain information
>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 Back     alignment and domain information
>cd07165 NR_DBD_DmE78_like DNA-binding domain of Drosophila ecdysone-induced protein 78 (E78) like is composed of two C4-type zinc fingers Back     alignment and domain information
>cd06968 NR_DBD_ROR DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers Back     alignment and domain information
>cd07160 NR_DBD_LXR DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers Back     alignment and domain information
>cd07169 NR_DBD_GCNF_like DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers Back     alignment and domain information
>cd07161 NR_DBD_EcR DNA-binding domain of Ecdysone receptor (ECR) family is composed of two C4-type zinc fingers Back     alignment and domain information
>cd06966 NR_DBD_CAR DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers Back     alignment and domain information
>KOG4215|consensus Back     alignment and domain information
>cd06969 NR_DBD_NGFI-B DNA-binding domain of the orphan nuclear receptor, nerve growth factor-induced-B Back     alignment and domain information
>cd06962 NR_DBD_FXR DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers Back     alignment and domain information
>KOG4216|consensus Back     alignment and domain information
>cd07179 2DBD_NR_DBD2 The second DNA-binding domain (DBD) of the 2DBD nuclear receptor is composed of two C4-type zinc fingers Back     alignment and domain information
>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 Back     alignment and domain information
>cd07154 NR_DBD_PNR_like The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family Back     alignment and domain information
>cd06916 NR_DBD_like DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers Back     alignment and domain information
>cd07158 NR_DBD_Ppar_like The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family Back     alignment and domain information
>cd06955 NR_DBD_VDR DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers Back     alignment and domain information
>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 Back     alignment and domain information
>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 Back     alignment and domain information
>KOG4846|consensus Back     alignment and domain information
>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 Back     alignment and domain information
>cd07172 NR_DBD_GR_PR DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers Back     alignment and domain information
>cd07162 NR_DBD_PXR DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers Back     alignment and domain information
>cd07173 NR_DBD_AR DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers Back     alignment and domain information
>cd06963 NR_DBD_GR_like The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers Back     alignment and domain information
>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors Back     alignment and domain information
>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 Back     alignment and domain information
>KOG4217|consensus Back     alignment and domain information
>KOG4218|consensus Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query139
3dzu_D 419 Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp 3e-13
1hlz_A94 Crystal Structure Of The Orphan Nuclear Receptor Re 5e-13
1hcq_A84 The Crystal Structure Of The Estrogen Receptor Dna- 2e-10
1ynw_A110 Crystal Structure Of Vitamin D Receptor And 9-Cis R 1e-09
1hcp_A76 Dna Recognition By The Oestrogen Receptor: From Sol 2e-09
2env_A88 Solution Sturcture Of The C4-Type Zinc Finger Domai 4e-09
1r0n_B109 Crystal Structure Of Heterodimeric Ecdsyone Recepto 4e-09
2han_B119 Structural Basis Of Heterodimeric Ecdysteroid Recep 5e-09
4aa6_E71 The Oestrogen Receptor Recognizes An Imperfectly Pa 6e-09
1kb2_A110 Crystal Structure Of Vdr Dna-Binding Domain Bound T 6e-09
4aa6_A71 The Oestrogen Receptor Recognizes An Imperfectly Pa 6e-09
2ebl_A89 Solution Structure Of The Zinc Finger, C4-type Doma 7e-09
2nll_B103 Retinoid X Receptor-Thyroid Hormone Receptor Dna-Bi 8e-09
1lo1_A98 Estrogen Related Receptor 2 Dna Binding Domain In C 2e-08
2a66_A113 Human Liver Receptor Homologue Dna-Binding Domain ( 2e-08
3m9e_A105 Thyroid Hormone Beta Dna Binding Domain Homodimer W 2e-08
2ff0_A102 Solution Structure Of Steroidogenic Factor 1 Dna Bi 3e-08
1dsz_A86 Structure Of The RxrRAR DNA-Binding Domain Heterodi 5e-08
1hra_A80 The Solution Structure Of The Human Retinoic Acid R 7e-08
1r0o_A86 Crystal Structure Of The Heterodimeric Ecdysone Rec 4e-07
1ynw_B99 Crystal Structure Of Vitamin D Receptor And 9-Cis R 5e-07
2han_A93 Structural Basis Of Heterodimeric Ecdysteroid Recep 5e-07
3cbb_A78 Crystal Structure Of Hepatocyte Nuclear Factor 4alp 5e-07
1dsz_B85 Structure Of The RxrRAR DNA-Binding Domain Heterodi 6e-07
1by4_A82 Structure And Mechanism Of The Homodimeric Assembly 6e-07
1lat_A82 Glucocorticoid Receptor MutantDNA COMPLEX Length = 7e-07
1r4i_A105 Crystal Structure Of Androgen Receptor Dna-Binding 8e-07
1r0n_A81 Crystal Structure Of Heterodimeric Ecdsyone Recepto 9e-07
3dzu_A 467 Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp 2e-06
2nll_A66 Retinoid X Receptor-Thyroid Hormone Receptor Dna-Bi 2e-06
1cit_A89 Dna-Binding Mechanism Of The Monomeric Orphan Nucle 3e-06
1rxr_A83 High Resolution Solution Structure Of The Retinoid 4e-06
2c7a_A78 Structure Of The Progesterone Receptor-Dna Complex 5e-06
3g6t_A91 Gr Gamma Dna-Binding Domain:fkbp5 16bp Complex-34 L 6e-06
4hn6_A114 Gr Dna Binding Domain R460d/d462r - Tslp Ngre Compl 5e-05
4hn5_A117 Gr Dna Binding Domain - Tslp Ngre Complex Length = 5e-05
3g9p_B90 Gr Dna Binding Domain:sgk 16bp Complex-7 Length = 9 5e-05
1r4o_A92 Crystallographic Analysis Of The Interaction Of The 5e-05
1r4r_B92 Crystallographic Analysis Of The Interaction Of The 5e-05
1glu_A81 Crystallographic Analysis Of The Interaction Of The 5e-05
1gdc_A72 Refined Solution Structure Of The Glucocorticoid Re 6e-05
2gda_A72 Refined Solution Structure Of The Glucocorticoid Re 6e-05
1rgd_A71 Structure Refinement Of The Glucocorticoid Receptor 6e-05
>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 Back     alignment and structure 
Iteration: 1

 Score = 70.5 bits (171), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 32/80 (40%), Positives = 42/80 (52%), Gaps = 2/80 (2%)
Query: 1   MNQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKS 60
           M   C+VCG+ A+GFH+G   CEGCK FF R+      +               R  C+ 
Sbjct: 49  MAIECRVCGDKASGFHYGVHACEGCKGFFRRTIR--LKLIYDRCDLNCRIHKKSRNKCQY 106
Query: 61  CRLRKCLMVGMSKSGSRYGR 80
           CR +KCL VGMS +  R+GR
Sbjct: 107 CRFQKCLAVGMSHNAIRFGR 126
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>pdb|1HCP|A Chain A, Dna Recognition By The Oestrogen Receptor: From Solution To The Crystal Length = 76 Back     alignment and structure
>pdb|2ENV|A Chain A, Solution Sturcture Of The C4-Type Zinc Finger Domain From Human Peroxisome Proliferator-Activated Receptor Delta Length = 88 Back     alignment and structure
>pdb|1R0N|B Chain B, Crystal Structure Of Heterodimeric Ecdsyone Receptor Dna Binding Complex Length = 109 Back     alignment and structure
>pdb|2HAN|B Chain B, Structural Basis Of Heterodimeric Ecdysteroid Receptor Interaction With Natural Response Element Hsp27 Gene Promoter Length = 119 Back     alignment and structure
>pdb|4AA6|E Chain E, The Oestrogen Receptor Recognizes An Imperfectly Palindromic Response Element Through An Alternative Side- Chain Conformation Length = 71 Back     alignment and structure
>pdb|1KB2|A Chain A, Crystal Structure Of Vdr Dna-Binding Domain Bound To Mouse Osteopontin (Spp) Response Element Length = 110 Back     alignment and structure
>pdb|4AA6|A Chain A, The Oestrogen Receptor Recognizes An Imperfectly Palindromic Response Element Through An Alternative Side- Chain Conformation Length = 71 Back     alignment and structure
>pdb|2EBL|A Chain A, Solution Structure Of The Zinc Finger, C4-type Domain Of Human Coup Transcription Factor 1 Length = 89 Back     alignment and structure
>pdb|2NLL|B Chain B, Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding Domain Heterodimer Bound To Thyroid Response Element Dna Length = 103 Back     alignment and structure
>pdb|1LO1|A Chain A, Estrogen Related Receptor 2 Dna Binding Domain In Complex With Dna Length = 98 Back     alignment and structure
>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 Back     alignment and structure
>pdb|3M9E|A Chain A, Thyroid Hormone Beta Dna Binding Domain Homodimer With Inverted Palindrome Tre Length = 105 Back     alignment and structure
>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 Back     alignment and structure
>pdb|1DSZ|A Chain A, Structure Of The RxrRAR DNA-Binding Domain Heterodimer In Complex With The Retinoic Acid Response Element Dr1 Length = 86 Back     alignment and structure
>pdb|1HRA|A Chain A, The Solution Structure Of The Human Retinoic Acid Receptor- Beta Dna-Binding Domain Length = 80 Back     alignment and structure
>pdb|1R0O|A Chain A, Crystal Structure Of The Heterodimeric Ecdysone Receptor Dna-Binding Complex Length = 86 Back     alignment and structure
>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 Back     alignment and structure
>pdb|2HAN|A Chain A, Structural Basis Of Heterodimeric Ecdysteroid Receptor Interaction With Natural Response Element Hsp27 Gene Promoter Length = 93 Back     alignment and structure
>pdb|3CBB|A Chain A, Crystal Structure Of Hepatocyte Nuclear Factor 4alpha In Complex With Dna: Diabetes Gene Product Length = 78 Back     alignment and structure
>pdb|1DSZ|B Chain B, Structure Of The RxrRAR DNA-Binding Domain Heterodimer In Complex With The Retinoic Acid Response Element Dr1 Length = 85 Back     alignment and structure
>pdb|1BY4|A Chain A, Structure And Mechanism Of The Homodimeric Assembly Of The Rxr On Dna Length = 82 Back     alignment and structure
>pdb|1LAT|A Chain A, Glucocorticoid Receptor MutantDNA COMPLEX Length = 82 Back     alignment and structure
>pdb|1R4I|A Chain A, Crystal Structure Of Androgen Receptor Dna-Binding Domain Bound To A Direct Repeat Response Element Length = 105 Back     alignment and structure
>pdb|1R0N|A Chain A, Crystal Structure Of Heterodimeric Ecdsyone Receptor Dna Binding Complex Length = 81 Back     alignment and structure
>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 Back     alignment and structure
>pdb|2NLL|A Chain A, Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding Domain Heterodimer Bound To Thyroid Response Element Dna Length = 66 Back     alignment and structure
>pdb|1CIT|A Chain A, Dna-Binding Mechanism Of The Monomeric Orphan Nuclear Receptor Ngfi-B Length = 89 Back     alignment and structure
>pdb|1RXR|A Chain A, High Resolution Solution Structure Of The Retinoid X Receptor Dna Binding Domain, Nmr, 20 Structure Length = 83 Back     alignment and structure
>pdb|2C7A|A Chain A, Structure Of The Progesterone Receptor-Dna Complex Length = 78 Back     alignment and structure
>pdb|3G6T|A Chain A, Gr Gamma Dna-Binding Domain:fkbp5 16bp Complex-34 Length = 91 Back     alignment and structure
>pdb|4HN6|A Chain A, Gr Dna Binding Domain R460d/d462r - Tslp Ngre Complex Length = 114 Back     alignment and structure
>pdb|4HN5|A Chain A, Gr Dna Binding Domain - Tslp Ngre Complex Length = 117 Back     alignment and structure
>pdb|3G9P|B Chain B, Gr Dna Binding Domain:sgk 16bp Complex-7 Length = 90 Back     alignment and structure
>pdb|1R4O|A Chain A, Crystallographic Analysis Of The Interaction Of The Glucocorticoid Receptor With Dna Length = 92 Back     alignment and structure
>pdb|1R4R|B Chain B, Crystallographic Analysis Of The Interaction Of The Glucocorticoid Receptor With Dna Length = 92 Back     alignment and structure
>pdb|1GLU|A Chain A, Crystallographic Analysis Of The Interaction Of The Glucocorticoid Receptor With Dna Length = 81 Back     alignment and structure
>pdb|1GDC|A Chain A, Refined Solution Structure Of The Glucocorticoid Receptor Dna-Binding Domain Length = 72 Back     alignment and structure
>pdb|2GDA|A Chain A, Refined Solution Structure Of The Glucocorticoid Receptor Dna-Binding Domain Length = 72 Back     alignment and structure
>pdb|1RGD|A Chain A, Structure Refinement Of The Glucocorticoid Receptor-Dna Binding Domain From Nmr Data By Relaxation Matrix Calculations Length = 71 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query139
1a6y_A94 Orphan nuclear receptor NR1D1; orphan receptor, DN 3e-28
2nll_B103 Protein (thyroid hormone receptor); complex (trans 8e-27
1hcq_A84 Protein (estrogen receptor); protein-DNA complex, 2e-26
2a66_A113 Orphan nuclear receptor NR5A2; protein-DNA complex 2e-26
1kb2_A110 Vitamin D3 receptor; VDR, nuclear receptor, protei 2e-26
1lo1_A98 Steroid hormone receptor ERR2; estrogen related re 5e-26
1dsz_A86 RAR-alpha, retinoic acid receptor alpha; RAR, nucl 7e-26
1r4i_A105 Androgen receptor; AR, steroid receptor, protein-D 7e-26
1cit_A89 NGFI-B, protein (orphan nuclear receptor NGFI-B); 9e-26
2ebl_A89 COUP transcription factor 1; DNA-binding, metal-bi 1e-25
2han_B119 Ecdysone receptor; transcription regulation, trans 1e-25
1dsz_B85 RXR-alpha, retinoic acid receptor RXR-alpha; RAR, 3e-25
2han_A93 Protein ultraspiracle; transcription regulation, t 3e-25
3g9m_A90 Glucocorticoid receptor; glucocorticoid, DNA-bindi 4e-25
1ynw_B99 Retinoic acid receptor RXR-alpha, retinoid X recep 1e-24
3dzy_A 467 Retinoic acid receptor RXR-alpha; DNA-binding, HOS 2e-24
3cbb_A78 HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DN 2e-24
3dzy_D 419 Peroxisome proliferator-activated receptor gamma; 1e-22
>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 Back     alignment and structure
 Score = 98.6 bits (246), Expect = 3e-28
 Identities = 39/80 (48%), Positives = 47/80 (58%)

Query: 1  MNQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKS 60
          M   CKVCG+ A+GFH+G   CEGCK FF RS         C  N  C I + NR  C+ 
Sbjct: 6  MVLLCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQ 65

Query: 61 CRLRKCLMVGMSKSGSRYGR 80
          CR +KCL VGMS+   R+GR
Sbjct: 66 CRFKKCLSVGMSRDAVRFGR 85
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>1r4i_A Androgen receptor; AR, steroid receptor, protein-DNA complex, transcription/DNA complex; 3.10A {Rattus norvegicus} SCOP: g.39.1.2 Length = 105 Back     alignment and structure
>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 Back     alignment and structure
>2ebl_A COUP transcription factor 1; DNA-binding, metal-binding, nuclear protein, receptor, transcription regulation, zinc, EAR3, erbal3 tfcoup1; NMR {Homo sapiens} Length = 89 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>3cbb_A HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DNA binding domain, nuclear; zinc finger; 2.00A {Homo sapiens} Length = 78 Back     alignment and structure
>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 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query139
1a6y_A94 Orphan nuclear receptor NR1D1; orphan receptor, DN 99.98
2ebl_A89 COUP transcription factor 1; DNA-binding, metal-bi 99.97
3cbb_A78 HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DN 99.97
1dsz_A86 RAR-alpha, retinoic acid receptor alpha; RAR, nucl 99.97
1dsz_B85 RXR-alpha, retinoic acid receptor RXR-alpha; RAR, 99.97
1ynw_B99 Retinoic acid receptor RXR-alpha, retinoid X recep 99.97
1hcq_A84 Protein (estrogen receptor); protein-DNA complex, 99.97
2han_A93 Protein ultraspiracle; transcription regulation, t 99.97
1lo1_A98 Steroid hormone receptor ERR2; estrogen related re 99.97
1cit_A89 NGFI-B, protein (orphan nuclear receptor NGFI-B); 99.97
2a66_A113 Orphan nuclear receptor NR5A2; protein-DNA complex 99.96
2han_B119 Ecdysone receptor; transcription regulation, trans 99.96
3g9m_A90 Glucocorticoid receptor; glucocorticoid, DNA-bindi 99.96
2nll_B103 Protein (thyroid hormone receptor); complex (trans 99.96
4hn5_A117 Glucocorticoid receptor; glucocorticoid receptor, 99.96
1kb2_A110 Vitamin D3 receptor; VDR, nuclear receptor, protei 99.96
1r4i_A105 Androgen receptor; AR, steroid receptor, protein-D 99.96
3dzy_D 419 Peroxisome proliferator-activated receptor gamma; 99.93
3dzy_A 467 Retinoic acid receptor RXR-alpha; DNA-binding, HOS 99.93
2lze_A87 A primordial catalytic fold generated by in vitro 99.78
1lbd_A 282 RXR_LBD, retinoid X receptor; transcription factor 93.76
>1a6y_A Orphan nuclear receptor NR1D1; orphan receptor, DNA-binding, reverb, REV- ERB, transcription regulation, transcription/DNA complex; HET: DNA 5IU; 2.30A {Homo sapiens} SCOP: g.39.1.2 PDB: 1ga5_A* 1hlz_A Back     alignment and structure
Probab=99.98  E-value=1.9e-34  Score=194.87  Aligned_cols=85  Identities=46%  Similarity=0.965  Sum_probs=73.0

Q ss_pred             CCcCcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcccCCC
Q psy16683          2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRR   81 (139)
Q Consensus         2 ~~~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R~   81 (139)
                      ..+|.|||++|+|+||||+||+||++||||++..+..+..|..+++|.+++..++.|++|||+||+++||++++||++|+
T Consensus         7 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~y~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~   86 (94)
T 1a6y_A            7 VLLCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGRI   86 (94)
T ss_dssp             -CBCTTTSSBCCEEETTEEECHHHHHHHHHHHSSCCCCCCCSSTTCCCCCTTTTTSCHHHHHHHHTTTTCCSTTCCCCC-
T ss_pred             CCcCcEeCCCCcceEeCccchhhhhhehheeeecccceEEccCCCCCccCccccccccchhHHHhhHccCCHHHhccCcC
Confidence            46899999999999999999999999999999875444369999999999999999999999999999999999999999


Q ss_pred             Cchhh
Q psy16683         82 SNWFK   86 (139)
Q Consensus        82 ~~~~k   86 (139)
                      ++..|
T Consensus        87 ~~~~k   91 (94)
T 1a6y_A           87 PKREK   91 (94)
T ss_dssp             -----
T ss_pred             cCchh
Confidence            97544
>2ebl_A COUP transcription factor 1; DNA-binding, metal-binding, nuclear protein, receptor, transcription regulation, zinc, EAR3, erbal3 tfcoup1; NMR {Homo sapiens} Back     alignment and structure
>3cbb_A HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DNA binding domain, nuclear; zinc finger; 2.00A {Homo sapiens} Back     alignment and structure
>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 Back     alignment and structure
>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* Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 ... Back     alignment and structure
>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* Back     alignment and structure
>4hn5_A Glucocorticoid receptor; glucocorticoid receptor, steroid receptors, NGRE, repre transcription; HET: DNA; 1.90A {Homo sapiens} PDB: 4hn6_A* Back     alignment and structure
>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 Back     alignment and structure
>1r4i_A Androgen receptor; AR, steroid receptor, protein-DNA complex, transcription/DNA complex; 3.10A {Rattus norvegicus} SCOP: g.39.1.2 Back     alignment and structure
>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 Back     alignment and structure
>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* Back     alignment and structure
>2lze_A A primordial catalytic fold generated by in vitro evolution; ligase, de novo protein; NMR {Synthetic construct} Back     alignment and structure
>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 Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

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

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 139
d1dszb_84 g.39.1.2 (B:) Retinoid X receptor (RXR-alpha) DNA- 2e-23
d1a6ya_78 g.39.1.2 (A:) Orphan nuclear receptor reverb DNA-b 6e-23
d1lo1a_90 g.39.1.2 (A:) Steroid hormone receptor Err2 DNA-bi 3e-21
d1kb2a_89 g.39.1.2 (A:) Vitamin D3 receptor, VDR, DNA-bindin 4e-20
d1r4ia_74 g.39.1.2 (A:) Androgen receptor {Rat (Rattus norve 5e-20
d2hanb183 g.39.1.2 (B:5-87) Ecdysone receptor DNA-binding do 1e-19
d1hcqa_74 g.39.1.2 (A:) Estrogen receptor DNA-binding domain 3e-19
d1cita_89 g.39.1.2 (A:) Orphan nuclear receptor NGFI-B DNA-b 3e-19
d1dsza_75 g.39.1.2 (A:) Retinoic acid receptor DNA-binding d 8e-19
d2nllb_103 g.39.1.2 (B:) Thyroid hormone receptor (TR-beta) D 3e-18
d1lata_71 g.39.1.2 (A:) Glucocorticoid receptor DNA-binding 1e-17
>d1dszb_ g.39.1.2 (B:) Retinoid X receptor (RXR-alpha) DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Length = 84 Back     information, alignment and structure

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 = 85.0 bits (210), Expect = 2e-23
 Identities = 29/80 (36%), Positives = 51/80 (63%), Gaps = 1/80 (1%)

Query: 2  NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSC 61
             C +CG+ ++G H+G ++CEGCK FF R+     + + C++N +C+I+K+ R  C+ C
Sbjct: 5  KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYT-CRDNKDCLIDKRQRNRCQYC 63

Query: 62 RLRKCLMVGMSKSGSRYGRR 81
          R +KCL +GM +   +  R+
Sbjct: 64 RYQKCLAMGMKREAVQEERQ 83
>d1a6ya_ g.39.1.2 (A:) Orphan nuclear receptor reverb DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Length = 78 Back     information, alignment and structure
>d1lo1a_ g.39.1.2 (A:) Steroid hormone receptor Err2 DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Length = 90 Back     information, alignment and structure
>d1kb2a_ g.39.1.2 (A:) Vitamin D3 receptor, VDR, DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89 Back     information, alignment and structure
>d1r4ia_ g.39.1.2 (A:) Androgen receptor {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 74 Back     information, alignment and structure
>d2hanb1 g.39.1.2 (B:5-87) Ecdysone receptor DNA-binding domain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 83 Back     information, alignment and structure
>d1hcqa_ g.39.1.2 (A:) Estrogen receptor DNA-binding domain {Human and chicken (Homo sapiens) and (Gallus gallus) [TaxId: 9606]} Length = 74 Back     information, alignment and structure
>d1cita_ g.39.1.2 (A:) Orphan nuclear receptor NGFI-B DNA-binding domain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 89 Back     information, alignment and structure
>d1dsza_ g.39.1.2 (A:) Retinoic acid receptor DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Length = 75 Back     information, alignment and structure
>d2nllb_ g.39.1.2 (B:) Thyroid hormone receptor (TR-beta) DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Length = 103 Back     information, alignment and structure
>d1lata_ g.39.1.2 (A:) Glucocorticoid receptor DNA-binding domain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 71 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query139
d1a6ya_78 Orphan nuclear receptor reverb DNA-binding domain 99.97
d1dszb_84 Retinoid X receptor (RXR-alpha) DNA-binding domain 99.97
d1dsza_75 Retinoic acid receptor DNA-binding domain {Human ( 99.96
d2hanb183 Ecdysone receptor DNA-binding domain {Fruit fly (D 99.96
d1kb2a_89 Vitamin D3 receptor, VDR, DNA-binding domain {Huma 99.96
d2nllb_103 Thyroid hormone receptor (TR-beta) DNA-binding dom 99.96
d1lo1a_90 Steroid hormone receptor Err2 DNA-binding domain { 99.96
d1cita_89 Orphan nuclear receptor NGFI-B DNA-binding domain 99.95
d1r4ia_74 Androgen receptor {Rat (Rattus norvegicus) [TaxId: 99.95
d1lata_71 Glucocorticoid receptor DNA-binding domain {Rat (R 99.95
d1hcqa_74 Estrogen receptor DNA-binding domain {Human and ch 99.94
>d1a6ya_ g.39.1.2 (A:) Orphan nuclear receptor reverb DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
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=99.97  E-value=7e-33  Score=179.74  Aligned_cols=77  Identities=49%  Similarity=1.096  Sum_probs=71.0

Q ss_pred             cCcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcccCC
Q psy16683          4 TCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGR   80 (139)
Q Consensus         4 ~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R   80 (139)
                      .|.|||++|+|+||||++|+||++||||++..+..+..|..+++|.+++..+..|++|||+||+++||++++||++|
T Consensus         2 iC~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~~~~~~~~c~~~~~~r~~Cr~CR~~KCl~~GM~~~~vq~~R   78 (78)
T d1a6ya_           2 LCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGR   78 (78)
T ss_dssp             BCTTTSSBCCEEETTEEECHHHHHHHHHHHSSCCCCCCCSSTTCCCCCTTTTTSCHHHHHHHHTTTTCCSTTCCCCC
T ss_pred             CCeeCCCcCCcccCcchhhhhchhhhhhhhccCCceeeeccCCCcccCCCCCccchhhHHHHHHHhCCCHHHhcCCC
Confidence            69999999999999999999999999999986555545777889999999999999999999999999999999987
>d1dszb_ g.39.1.2 (B:) Retinoid X receptor (RXR-alpha) DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1dsza_ g.39.1.2 (A:) Retinoic acid receptor DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2hanb1 g.39.1.2 (B:5-87) Ecdysone receptor DNA-binding domain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1kb2a_ g.39.1.2 (A:) Vitamin D3 receptor, VDR, DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2nllb_ g.39.1.2 (B:) Thyroid hormone receptor (TR-beta) DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1lo1a_ g.39.1.2 (A:) Steroid hormone receptor Err2 DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1cita_ g.39.1.2 (A:) Orphan nuclear receptor NGFI-B DNA-binding domain {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1r4ia_ g.39.1.2 (A:) Androgen receptor {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1lata_ g.39.1.2 (A:) Glucocorticoid receptor DNA-binding domain {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1hcqa_ g.39.1.2 (A:) Estrogen receptor DNA-binding domain {Human and chicken (Homo sapiens) and (Gallus gallus) [TaxId: 9606]} Back     information, alignment and structure