Psyllid ID: psy1782

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
MYSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRISCRRPSYEETTANNGLSVNSLLNAEMLSRQVGAVREEVSLFGSLLVT
ccccccccccccccccccccHHHHHHHHHcccHHHHHHccccccccccccccccccccccHHHHHHHHHHHccccccccccccccccccc
ccccccccccccccccccHHHHHHHHHHccccHHHcccccccccccccccccccccccccHHHHHHHHHHHHccccccHHHHHcccEEEc
MYSKLHKQLVdkdkrnqcryCRLKKCFKAGMKKEAVQNerdriscrrpsyeettannglsVNSLLNAEMLSRQVGAVREEVSLFGSLLVT
mysklhkqlvdkdkrnqcryCRLKKcfkagmkkeavqnerdriscrrpsyeettannglsvnSLLNAEMLSRQVGAVREEVSLFGSLLVT
MYSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRISCRRPSYEETTANNGLSVNSLLNAEMLSRQVGAVREEVSLFGSLLVT
****************QCRYCRLKKCFKAG*******************************************VGAVR**VSLF******
MYSK*HKQLVDKDKRNQCRYCRLKKCFKAGMK*****************************************************S****
********LVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRISCRRPSYEETTANNGLSVNSLLNAEMLSRQVGAVREEVSLFGSLLVT
*****HKQLVDKDKRNQCRYCRLKKCFKAGMKK*************************LSVNSLLNAEMLSRQVGAVREEVSLFGSLLVT
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MYSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRISCRRPSYEETTANNGLSVNSLLNAEMLSRQVGAVREEVSLFGSLLVT
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 ?
Query90 2.2.26 [Sep-21-2011]
P49866 666 Transcription factor HNF- yes N/A 0.8 0.108 0.716 1e-22
P41235 474 Hepatocyte nuclear factor yes N/A 0.788 0.149 0.697 2e-22
P49698 474 Hepatocyte nuclear factor yes N/A 0.788 0.149 0.684 9e-22
P22449 474 Hepatocyte nuclear factor yes N/A 0.788 0.149 0.684 9e-22
Q91766 464 Hepatocyte nuclear factor N/A N/A 0.788 0.153 0.671 3e-21
P79926 446 Hepatocyte nuclear factor N/A N/A 0.733 0.147 0.681 3e-20
Q14541 408 Hepatocyte nuclear factor no N/A 0.7 0.154 0.666 6e-19
Q9WUU6 408 Hepatocyte nuclear factor no N/A 0.7 0.154 0.681 1e-18
Q5I7G2 436 Retinoic acid receptor RX N/A N/A 0.677 0.139 0.460 5e-10
P28700 467 Retinoic acid receptor RX no N/A 0.677 0.130 0.476 5e-10
>sp|P49866|HNF4_DROME Transcription factor HNF-4 homolog OS=Drosophila melanogaster GN=Hnf4 PE=2 SV=2 Back     alignment and function desciption
 Score =  104 bits (260), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 53/74 (71%), Positives = 58/74 (78%), Gaps = 2/74 (2%)

Query: 9   LVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRISCRRPSYEETTANNGLSVNSLLNAE 68
           +VDKDKRNQCRYCRL+KCFKAGMKKEAVQNERDRISCRR S ++    NGLSV SL+ AE
Sbjct: 147 VVDKDKRNQCRYCRLRKCFKAGMKKEAVQNERDRISCRRTSNDDPDPGNGLSVISLVKAE 206

Query: 69  MLSRQ--VGAVREE 80
             SRQ   GA  E 
Sbjct: 207 NESRQSKAGAAMEP 220
Transcriptionally controlled transcription factor. Important for the differentiation of various specialized cell types that arise from both endoderm and mesoderm. May have a role in early gut formation.
Drosophila melanogaster (taxid: 7227)
>sp|P41235|HNF4A_HUMAN Hepatocyte nuclear factor 4-alpha OS=Homo sapiens GN=HNF4A PE=1 SV=3 Back     alignment and function description
>sp|P49698|HNF4A_MOUSE Hepatocyte nuclear factor 4-alpha OS=Mus musculus GN=Hnf4a PE=1 SV=2 Back     alignment and function description
>sp|P22449|HNF4A_RAT Hepatocyte nuclear factor 4-alpha OS=Rattus norvegicus GN=Hnf4a PE=1 SV=3 Back     alignment and function description
>sp|Q91766|HNF4A_XENLA Hepatocyte nuclear factor 4-alpha OS=Xenopus laevis GN=hnf4a PE=2 SV=2 Back     alignment and function description
>sp|P79926|HNF4B_XENLA Hepatocyte nuclear factor 4-beta OS=Xenopus laevis GN=hnf4b PE=2 SV=1 Back     alignment and function description
>sp|Q14541|HNF4G_HUMAN Hepatocyte nuclear factor 4-gamma OS=Homo sapiens GN=HNF4G PE=1 SV=3 Back     alignment and function description
>sp|Q9WUU6|HNF4G_MOUSE Hepatocyte nuclear factor 4-gamma OS=Mus musculus GN=Hnf4g PE=2 SV=2 Back     alignment and function description
>sp|Q5I7G2|RXR_LYMST Retinoic acid receptor RXR OS=Lymnaea stagnalis GN=RXR PE=1 SV=1 Back     alignment and function description
>sp|P28700|RXRA_MOUSE Retinoic acid receptor RXR-alpha OS=Mus musculus GN=Rxra PE=1 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 ?
Query90
270010979 502 hepatocyte nuclear factor 4 [Tribolium c 0.811 0.145 0.863 2e-30
189164166 507 putative hepatocyte nuclear factor 4 nuc 0.822 0.145 0.851 2e-30
189239605 405 PREDICTED: similar to hepatocyte nuclear 0.811 0.180 0.863 4e-30
242019940 362 retinoid X receptor, putative [Pediculus 0.722 0.179 0.907 1e-27
383864113 539 PREDICTED: transcription factor HNF-4 ho 0.788 0.131 0.861 2e-27
340726819 485 PREDICTED: transcription factor HNF-4 ho 0.788 0.146 0.847 7e-27
340726817 453 PREDICTED: transcription factor HNF-4 ho 0.788 0.156 0.847 7e-27
350421758 444 PREDICTED: transcription factor HNF-4 ho 0.788 0.159 0.847 8e-27
112984316 436 hepatocyte nuclear factor 4 isoform a [B 0.733 0.151 0.863 4e-26
290555896 410 hepatocyte nuclear factor 4 isoform b [B 0.733 0.160 0.863 5e-26
>gi|270010979|gb|EFA07427.1| hepatocyte nuclear factor 4 [Tribolium castaneum] Back     alignment and taxonomy information
 Score =  136 bits (342), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 63/73 (86%), Positives = 67/73 (91%)

Query: 9   LVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRISCRRPSYEETTANNGLSVNSLLNAE 68
           +VDKDKRNQCRYCRL+KCFKAGMKKEAVQNERDRISCRRPSYEE   NNGLSV SLLNAE
Sbjct: 116 IVDKDKRNQCRYCRLRKCFKAGMKKEAVQNERDRISCRRPSYEENNQNNGLSVGSLLNAE 175

Query: 69  MLSRQVGAVREEV 81
           MLSRQVGA  E++
Sbjct: 176 MLSRQVGAALEQM 188

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|189164166|gb|ACD77184.1| putative hepatocyte nuclear factor 4 nuclear hormone receptor [Callosobruchus maculatus] Back     alignment and taxonomy information
>gi|189239605|ref|XP_968613.2| PREDICTED: similar to hepatocyte nuclear factor 4 [Tribolium castaneum] Back     alignment and taxonomy information
>gi|242019940|ref|XP_002430416.1| retinoid X receptor, putative [Pediculus humanus corporis] gi|212515546|gb|EEB17678.1| retinoid X receptor, putative [Pediculus humanus corporis] Back     alignment and taxonomy information
>gi|383864113|ref|XP_003707524.1| PREDICTED: transcription factor HNF-4 homolog [Megachile rotundata] Back     alignment and taxonomy information
>gi|340726819|ref|XP_003401750.1| PREDICTED: transcription factor HNF-4 homolog isoform 2 [Bombus terrestris] Back     alignment and taxonomy information
>gi|340726817|ref|XP_003401749.1| PREDICTED: transcription factor HNF-4 homolog isoform 1 [Bombus terrestris] Back     alignment and taxonomy information
>gi|350421758|ref|XP_003492948.1| PREDICTED: transcription factor HNF-4 homolog [Bombus impatiens] Back     alignment and taxonomy information
>gi|112984316|ref|NP_001037474.1| hepatocyte nuclear factor 4 isoform a [Bombyx mori] gi|2734850|gb|AAB93762.1| hepatocyte nuclear factor 4 isoform a [Bombyx mori] Back     alignment and taxonomy information
>gi|290555896|ref|NP_001166834.1| hepatocyte nuclear factor 4 isoform b [Bombyx mori] gi|2734852|gb|AAB93763.1| hepatocyte nuclear factor 4 isoform b [Bombyx mori] 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 ?
Query90
UNIPROTKB|E9PSV4 351 Hnf4a "Hepatocyte nuclear fact 0.788 0.202 0.684 9e-22
UNIPROTKB|F1M5T7190 Hnf4a "Hepatocyte nuclear fact 0.788 0.373 0.684 9e-22
UNIPROTKB|P41235 474 HNF4A "Hepatocyte nuclear fact 0.788 0.149 0.697 1.3e-21
ZFIN|ZDB-GENE-030131-1077 463 hnf4a "hepatocyte nuclear fact 0.811 0.157 0.653 1.5e-21
FB|FBgn0004914 666 Hnf4 "Hepatocyte nuclear facto 0.788 0.106 0.726 2.5e-21
UNIPROTKB|Q7YRQ5 455 HNF4A "Uncharacterized protein 0.788 0.156 0.684 3e-21
UNIPROTKB|E2R9S0 474 HNF4A "Uncharacterized protein 0.788 0.149 0.684 3.5e-21
UNIPROTKB|Q1I181 474 HNF4A "Uncharacterized protein 0.788 0.149 0.684 3.5e-21
MGI|MGI:109128 474 Hnf4a "hepatic nuclear factor 0.788 0.149 0.684 3.5e-21
RGD|2810 474 Hnf4a "hepatocyte nuclear fact 0.788 0.149 0.684 3.5e-21
UNIPROTKB|E9PSV4 Hnf4a "Hepatocyte nuclear factor 4-alpha" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
 Score = 254 (94.5 bits), Expect = 9.0e-22, P = 9.0e-22
 Identities = 52/76 (68%), Positives = 64/76 (84%)

Query:     1 MYS-KLHKQ-LVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRISCRRPSYEETTANNG 58
             MYS +  +Q +VDKDKRNQCRYCRLKKCF+AGMKKEAVQNERDRIS RR SYE+++    
Sbjct:    68 MYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNERDRISTRRSSYEDSSLP-- 125

Query:    59 LSVNSLLNAEMLSRQV 74
              S+N+LL AE+LS+Q+
Sbjct:   126 -SINALLQAEVLSQQI 140
GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA
GO:0003707 "steroid hormone receptor activity" evidence=IEA
GO:0005634 "nucleus" evidence=IEA
GO:0006351 "transcription, DNA-dependent" evidence=IEA
GO:0008270 "zinc ion binding" evidence=IEA
GO:0043565 "sequence-specific DNA binding" evidence=IEA
UNIPROTKB|F1M5T7 Hnf4a "Hepatocyte nuclear factor 4-alpha" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|P41235 HNF4A "Hepatocyte nuclear factor 4-alpha" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-030131-1077 hnf4a "hepatocyte nuclear factor 4, alpha" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
FB|FBgn0004914 Hnf4 "Hepatocyte nuclear factor 4" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
UNIPROTKB|Q7YRQ5 HNF4A "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|E2R9S0 HNF4A "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|Q1I181 HNF4A "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
MGI|MGI:109128 Hnf4a "hepatic nuclear factor 4, alpha" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|2810 Hnf4a "hepatocyte nuclear factor 4, alpha" [Rattus norvegicus (taxid:10116)] 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) ?
P22449HNF4A_RATNo assigned EC number0.68420.78880.1497yesN/A
O02151NHR14_CAEELNo assigned EC number0.52630.60.1241yesN/A
P41235HNF4A_HUMANNo assigned EC number0.69730.78880.1497yesN/A
P49698HNF4A_MOUSENo assigned EC number0.68420.78880.1497yesN/A
P49866HNF4_DROMENo assigned EC number0.71620.80.1081yesN/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 ?
Query90
cd0696076 cd06960, NR_DBD_HNF4A, DNA-binding domain of hepto 3e-16
cd0716392 cd07163, NR_DBD_TLX, DNA-binding domain of Tailles 2e-11
cd0691672 cd06916, NR_DBD_like, DNA-binding domain of nuclea 9e-11
cd0697092 cd06970, NR_DBD_PNR, DNA-binding domain of the pho 1e-10
cd0696185 cd06961, NR_DBD_TR, DNA-binding domain of thyroid 3e-10
cd0695782 cd06957, NR_DBD_PNR_like_2, DNA-binding domain of 2e-09
cd0695677 cd06956, NR_DBD_RXR, DNA-binding domain of retinoi 4e-09
cd0716478 cd07164, NR_DBD_PNR_like_1, DNA-binding domain of 9e-09
pfam0010570 pfam00105, zf-C4, Zinc finger, C4 type (two domain 2e-08
cd0695873 cd06958, NR_DBD_COUP_TF, DNA-binding domain of chi 4e-08
cd0715473 cd07154, NR_DBD_PNR_like, The DNA-binding domain o 4e-08
cd0696787 cd06967, NR_DBD_TR2_like, DNA-binding domain of th 5e-08
cd0696485 cd06964, NR_DBD_RAR, DNA-binding domain of retinoi 1e-07
smart0039970 smart00399, ZnF_C4, c4 zinc finger in nuclear horm 1e-07
cd0696975 cd06969, NR_DBD_NGFI-B, DNA-binding domain of the 3e-07
cd0716793 cd07167, NR_DBD_Lrh-1_like, The DNA-binding domain 8e-07
cd0696895 cd06968, NR_DBD_ROR, DNA-binding domain of Retinoi 2e-06
cd0716890 cd07168, NR_DBD_DHR4_like, DNA-binding domain of e 5e-06
cd0715672 cd07156, NR_DBD_VDR_like, The DNA-binding domain o 3e-05
cd0715873 cd07158, NR_DBD_Ppar_like, The DNA-binding domain 5e-05
cd0696694 cd06966, NR_DBD_CAR, DNA-binding domain of constit 7e-05
cd0715575 cd07155, NR_DBD_ER_like, DNA-binding domain of est 7e-05
cd0716990 cd07169, NR_DBD_GCNF_like, DNA-binding domain of G 7e-05
cd0716581 cd07165, NR_DBD_DmE78_like, DNA-binding domain of 1e-04
cd0717974 cd07179, 2DBD_NR_DBD2, The second DNA-binding doma 1e-04
cd0696584 cd06965, NR_DBD_Ppar, DNA-binding domain of peroxi 1e-04
cd0716689 cd07166, NR_DBD_REV_ERB, DNA-binding domain of REV 2e-04
cd0717182 cd07171, NR_DBD_ER, DNA-binding domain of estrogen 2e-04
cd0715786 cd07157, 2DBD_NR_DBD1, The first DNA-binding domai 0.001
cd0717278 cd07172, NR_DBD_GR_PR, DNA-binding domain of gluco 0.002
cd0716287 cd07162, NR_DBD_PXR, DNA-binding domain of pregnan 0.002
cd0717382 cd07173, NR_DBD_AR, DNA-binding domain of androgen 0.004
cd0717097 cd07170, NR_DBD_ERR, DNA-binding domain of estroge 0.004
>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 
 Score = 66.4 bits (163), Expect = 3e-16
 Identities = 25/33 (75%), Positives = 27/33 (81%)

Query: 9  LVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERD 41
          +VDKDKRN CRYCR KKC + GM  EAVQNERD
Sbjct: 44 VVDKDKRNACRYCRFKKCLEVGMDPEAVQNERD 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|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|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|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
>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|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|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|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|201004 pfam00105, zf-C4, Zinc finger, C4 type (two domains) 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|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|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|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|197701 smart00399, ZnF_C4, c4 zinc finger in nuclear hormone receptors 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|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|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|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|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|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|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|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|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|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|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|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|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|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|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
>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|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|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|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

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 90
KOG4215|consensus 432 99.72
cd0696185 NR_DBD_TR DNA-binding domain of thyroid hormone re 99.56
cd0696787 NR_DBD_TR2_like DNA-binding domain of the TR2 and 99.52
cd0717097 NR_DBD_ERR DNA-binding domain of estrogen related 99.51
cd0716689 NR_DBD_REV_ERB DNA-binding domain of REV-ERB recep 99.51
cd0696485 NR_DBD_RAR DNA-binding domain of retinoic acid rec 99.5
cd0716478 NR_DBD_PNR_like_1 DNA-binding domain of the photor 99.5
cd0716581 NR_DBD_DmE78_like DNA-binding domain of Drosophila 99.5
cd0695782 NR_DBD_PNR_like_2 DNA-binding domain of the photor 99.49
cd07160101 NR_DBD_LXR DNA-binding domain of Liver X receptors 99.49
cd0695677 NR_DBD_RXR DNA-binding domain of retinoid X recept 99.49
cd0715575 NR_DBD_ER_like DNA-binding domain of estrogen rece 99.49
cd0716890 NR_DBD_DHR4_like DNA-binding domain of ecdysone-in 99.48
KOG4217|consensus 605 99.48
cd0696076 NR_DBD_HNF4A DNA-binding domain of heptocyte nucle 99.48
cd0716392 NR_DBD_TLX DNA-binding domain of Tailless (TLX) is 99.46
cd0696694 NR_DBD_CAR DNA-binding domain of constitutive andr 99.46
cd0716793 NR_DBD_Lrh-1_like The DNA-binding domain of Lrh-1 99.46
cd0697092 NR_DBD_PNR DNA-binding domain of the photoreceptor 99.45
cd0717182 NR_DBD_ER DNA-binding domain of estrogen receptors 99.44
cd0716191 NR_DBD_EcR DNA-binding domain of Ecdysone receptor 99.44
cd0716990 NR_DBD_GCNF_like DNA-binding domain of Germ cell n 99.43
cd0696284 NR_DBD_FXR DNA-binding domain of Farnesoid X recep 99.43
cd0696895 NR_DBD_ROR DNA-binding domain of Retinoid-related 99.43
KOG4216|consensus 479 99.42
cd0715786 2DBD_NR_DBD1 The first DNA-binding domain (DBD) of 99.41
cd0696584 NR_DBD_Ppar DNA-binding domain of peroxisome proli 99.4
KOG4846|consensus 538 99.39
cd0696975 NR_DBD_NGFI-B DNA-binding domain of the orphan nuc 99.39
cd06955107 NR_DBD_VDR DNA-binding domain of vitamin D recepto 99.39
cd0716287 NR_DBD_PXR DNA-binding domain of pregnane X recept 99.38
cd0695873 NR_DBD_COUP_TF DNA-binding domain of chicken ovalb 99.37
cd0691672 NR_DBD_like DNA-binding domain of nuclear receptor 99.37
cd0717974 2DBD_NR_DBD2 The second DNA-binding domain (DBD) o 99.37
cd0715873 NR_DBD_Ppar_like The DNA-binding domain of peroxis 99.36
cd0715672 NR_DBD_VDR_like The DNA-binding domain of vitamin 99.34
cd0715473 NR_DBD_PNR_like The DNA-binding domain of the phot 99.34
cd0695973 NR_DBD_EcR_like The DNA-binding domain of Ecdysone 99.34
cd0696373 NR_DBD_GR_like The DNA binding domain of GR_like n 99.32
cd0717278 NR_DBD_GR_PR DNA-binding domain of glucocorticoid 99.27
cd0717382 NR_DBD_AR DNA-binding domain of androgen receptor 99.24
smart0039970 ZnF_C4 c4 zinc finger in nuclear hormone receptors 99.17
PF0010570 zf-C4: Zinc finger, C4 type (two domains); InterPr 99.14
KOG4218|consensus 475 99.11
>KOG4215|consensus Back     alignment and domain information 
Probab=99.72  E-value=2.4e-18  Score=124.44  Aligned_cols=75  Identities=55%  Similarity=0.911  Sum_probs=62.8

Q ss_pred             CCCCCCCceecCCCCCCCchhhhhHHHHhcCCcccccccccccccCCCCCcccccCCCCCccchhhHHHhhhhhhc
Q psy1782           1 MYSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRISCRRPSYEETTANNGLSVNSLLNAEMLSRQVGA   76 (90)
Q Consensus         1 ~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~   76 (90)
                      .|..+.+|.|||..||.||+|||+||+++||+++|||+|||+.+.+.+..+... .+..++..+..+|....++..
T Consensus        57 tCRF~k~C~VDKdkRNaCRyCRfqKC~~aGMK~eAiQnERDrIg~Rr~~~~~~n-~~~~~id~L~~aE~~~~q~~~  131 (432)
T KOG4215|consen   57 TCRFNKQCVVDKDKRNACRYCRFQKCVRAGMKREAIQNERDRIGSRRPSYEAGN-ENSPSIDALVQAEALVRQLRS  131 (432)
T ss_pred             eeeccccccccchhhhhhhHhhHHHHHHhcccHHhhhcccccccccCCCCCCCC-CCchhHHHHHhHHHHHhhhhc
Confidence            389999999999999999999999999999999999999999998777665443 345567788888876665544

>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>KOG4217|consensus 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
>cd07163 NR_DBD_TLX DNA-binding domain of Tailless (TLX) 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
>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
>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
>cd07171 NR_DBD_ER DNA-binding domain of estrogen receptors (ER) 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
>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
>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
>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
>KOG4216|consensus 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
>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
>KOG4846|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
>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
>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
>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
>cd06916 NR_DBD_like DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers 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
>cd07158 NR_DBD_Ppar_like The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family 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
>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
>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
>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
>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
>cd07173 NR_DBD_AR DNA-binding domain of androgen receptor (AR) 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
>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 ?
Query90
3cbb_A78 Crystal Structure Of Hepatocyte Nuclear Factor 4alp 5e-13
3dzu_A 467 Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp 7e-11
1ynw_B99 Crystal Structure Of Vitamin D Receptor And 9-Cis R 1e-06
1dsz_B85 Structure Of The RxrRAR DNA-Binding Domain Heterodi 1e-06
2ebl_A89 Solution Structure Of The Zinc Finger, C4-type Doma 2e-06
2han_A93 Structural Basis Of Heterodimeric Ecdysteroid Recep 2e-06
1r0o_A86 Crystal Structure Of The Heterodimeric Ecdysone Rec 4e-06
1by4_A82 Structure And Mechanism Of The Homodimeric Assembly 4e-06
1dsz_A86 Structure Of The RxrRAR DNA-Binding Domain Heterodi 5e-06
1rxr_A83 High Resolution Solution Structure Of The Retinoid 2e-05
1r0n_A81 Crystal Structure Of Heterodimeric Ecdsyone Recepto 5e-05
1hra_A80 The Solution Structure Of The Human Retinoic Acid R 5e-05
>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 
Iteration: 1

 Score = 69.3 bits (168), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 39/43 (90%), Gaps = 2/43 (4%)
Query: 1  MYS-KLHKQ-LVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERD 41
          MYS +  +Q +VDKDKRNQCRYCRLKKCF+AGMKKEAVQNERD
Sbjct: 36 MYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNERD 78
>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|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|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|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|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|1R0O|A Chain A, Crystal Structure Of The Heterodimeric Ecdysone Receptor Dna-Binding Complex Length = 86 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|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|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|1R0N|A Chain A, Crystal Structure Of Heterodimeric Ecdsyone Receptor Dna Binding Complex Length = 81 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

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query90
1ynw_B99 Retinoic acid receptor RXR-alpha, retinoid X recep 2e-18
3g9m_A90 Glucocorticoid receptor; glucocorticoid, DNA-bindi 1e-16
2han_A93 Protein ultraspiracle; transcription regulation, t 2e-16
3cbb_A78 HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DN 2e-16
1lbd_A 282 RXR_LBD, retinoid X receptor; transcription factor 3e-16
2han_B119 Ecdysone receptor; transcription regulation, trans 4e-16
2ebl_A89 COUP transcription factor 1; DNA-binding, metal-bi 7e-16
1dsz_B85 RXR-alpha, retinoic acid receptor RXR-alpha; RAR, 7e-16
1cit_A89 NGFI-B, protein (orphan nuclear receptor NGFI-B); 8e-16
2nll_B103 Protein (thyroid hormone receptor); complex (trans 1e-15
1dsz_A86 RAR-alpha, retinoic acid receptor alpha; RAR, nucl 2e-15
3dzy_A 467 Retinoic acid receptor RXR-alpha; DNA-binding, HOS 2e-15
1lo1_A98 Steroid hormone receptor ERR2; estrogen related re 6e-15
2a66_A113 Orphan nuclear receptor NR5A2; protein-DNA complex 7e-15
1a6y_A94 Orphan nuclear receptor NR1D1; orphan receptor, DN 7e-15
1hcq_A84 Protein (estrogen receptor); protein-DNA complex, 6e-14
1kb2_A110 Vitamin D3 receptor; VDR, nuclear receptor, protei 7e-14
1r4i_A105 Androgen receptor; AR, steroid receptor, protein-D 9e-14
3dzy_D 419 Peroxisome proliferator-activated receptor gamma; 3e-12
2hc4_A 302 Vitamin D receptor; alpha helical sandwich, gene r 1e-07
1ovl_A 271 Orphan nuclear receptor NURR1 (MSe 414, 496, 511); 2e-07
1xdk_B 303 RAR-beta, retinoic acid receptor, beta; nuclear re 1e-05
1z5x_E 310 Ecdysone receptor ligand binding domain; ponastero 2e-05
1z5x_E 310 Ecdysone receptor ligand binding domain; ponastero 6e-05
>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
 Score = 71.7 bits (176), Expect = 2e-18
 Identities = 24/49 (48%), Positives = 34/49 (69%)

Query: 9  LVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRISCRRPSYEETTANN 57
          L+DK +RN+C+YCR +KC   GMK+EAVQ ER R   R  +  E+T++ 
Sbjct: 49 LIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRGKDRNENEVESTSSA 97
>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
>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
>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
>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 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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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 Back     alignment and structure
>1ovl_A Orphan nuclear receptor NURR1 (MSe 414, 496, 511); NUUR1, LBD, transcription; 2.20A {Homo sapiens} SCOP: a.123.1.1 Length = 271 Back     alignment and structure
>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 Length = 303 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query90
1ynw_B99 Retinoic acid receptor RXR-alpha, retinoid X recep 99.63
3cbb_A78 HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DN 99.63
1dsz_A86 RAR-alpha, retinoic acid receptor alpha; RAR, nucl 99.61
1dsz_B85 RXR-alpha, retinoic acid receptor RXR-alpha; RAR, 99.61
2ebl_A89 COUP transcription factor 1; DNA-binding, metal-bi 99.6
2han_A93 Protein ultraspiracle; transcription regulation, t 99.6
1a6y_A94 Orphan nuclear receptor NR1D1; orphan receptor, DN 99.6
1hcq_A84 Protein (estrogen receptor); protein-DNA complex, 99.56
1lo1_A98 Steroid hormone receptor ERR2; estrogen related re 99.56
2a66_A113 Orphan nuclear receptor NR5A2; protein-DNA complex 99.55
1cit_A89 NGFI-B, protein (orphan nuclear receptor NGFI-B); 99.54
3g9m_A90 Glucocorticoid receptor; glucocorticoid, DNA-bindi 99.53
4hn5_A117 Glucocorticoid receptor; glucocorticoid receptor, 99.52
2han_B119 Ecdysone receptor; transcription regulation, trans 99.5
2nll_B103 Protein (thyroid hormone receptor); complex (trans 99.5
1kb2_A110 Vitamin D3 receptor; VDR, nuclear receptor, protei 99.49
1r4i_A105 Androgen receptor; AR, steroid receptor, protein-D 99.44
3dzy_A 467 Retinoic acid receptor RXR-alpha; DNA-binding, HOS 99.4
2lze_A87 A primordial catalytic fold generated by in vitro 99.37
3dzy_D 419 Peroxisome proliferator-activated receptor gamma; 99.3
1lbd_A 282 RXR_LBD, retinoid X receptor; transcription factor 97.86
>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
Probab=99.63  E-value=1.1e-16  Score=97.17  Aligned_cols=47  Identities=47%  Similarity=0.825  Sum_probs=35.8

Q ss_pred             CCCCCCCceecCCCCCCCchhhhhHHHHhcCCcccccccccccccCC
Q psy1782           1 MYSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRISCRR   47 (90)
Q Consensus         1 ~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~~~~~~   47 (90)
                      .|..+++|.|++..|+.|++|||+|||++||++++||.+|++...+.
T Consensus        41 ~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~~~~~~   87 (99)
T 1ynw_B           41 TCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRGKDRN   87 (99)
T ss_dssp             CCSSSSCCCCCSTTSSSCHHHHHHHHHHTTCCSTTCC----------
T ss_pred             ccCCCCcccccccCCccCccccHHHHhHcCCCHHHhhhccccccccC
Confidence            48899999999999999999999999999999999999999876543
>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
>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
>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
>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
>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
>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
>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
>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
>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
>4hn5_A Glucocorticoid receptor; glucocorticoid receptor, steroid receptors, NGRE, repre transcription; HET: DNA; 1.90A {Homo sapiens} PDB: 4hn6_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
>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
>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_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
>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
>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 90
d1dszb_84 g.39.1.2 (B:) Retinoid X receptor (RXR-alpha) DNA- 4e-11
d2hanb183 g.39.1.2 (B:5-87) Ecdysone receptor DNA-binding do 2e-10
d1lo1a_90 g.39.1.2 (A:) Steroid hormone receptor Err2 DNA-bi 2e-10
d1cita_89 g.39.1.2 (A:) Orphan nuclear receptor NGFI-B DNA-b 5e-10
d1dsza_75 g.39.1.2 (A:) Retinoic acid receptor DNA-binding d 2e-09
d1kb2a_89 g.39.1.2 (A:) Vitamin D3 receptor, VDR, DNA-bindin 3e-09
d1a6ya_78 g.39.1.2 (A:) Orphan nuclear receptor reverb DNA-b 6e-09
d1r4ia_74 g.39.1.2 (A:) Androgen receptor {Rat (Rattus norve 2e-08
d2nllb_103 g.39.1.2 (B:) Thyroid hormone receptor (TR-beta) D 7e-07
d1lata_71 g.39.1.2 (A:) Glucocorticoid receptor DNA-binding 6e-06
d1hcqa_74 g.39.1.2 (A:) Estrogen receptor DNA-binding domain 6e-06
>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 = 51.9 bits (124), Expect = 4e-11
 Identities = 20/33 (60%), Positives = 26/33 (78%)

Query: 10 VDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDR 42
          +DK +RN+C+YCR +KC   GMK+EAVQ ER R
Sbjct: 52 IDKRQRNRCQYCRYQKCLAMGMKREAVQEERQR 84
>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
>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
>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
>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
>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
>d1r4ia_ g.39.1.2 (A:) Androgen receptor {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 74 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
>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

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query90
d1lo1a_90 Steroid hormone receptor Err2 DNA-binding domain { 99.57
d1dszb_84 Retinoid X receptor (RXR-alpha) DNA-binding domain 99.55
d2hanb183 Ecdysone receptor DNA-binding domain {Fruit fly (D 99.54
d1a6ya_78 Orphan nuclear receptor reverb DNA-binding domain 99.52
d1kb2a_89 Vitamin D3 receptor, VDR, DNA-binding domain {Huma 99.51
d1cita_89 Orphan nuclear receptor NGFI-B DNA-binding domain 99.5
d1dsza_75 Retinoic acid receptor DNA-binding domain {Human ( 99.49
d2nllb_103 Thyroid hormone receptor (TR-beta) DNA-binding dom 99.45
d1r4ia_74 Androgen receptor {Rat (Rattus norvegicus) [TaxId: 99.37
d1lata_71 Glucocorticoid receptor DNA-binding domain {Rat (R 99.3
d1hcqa_74 Estrogen receptor DNA-binding domain {Human and ch 99.29
>d1lo1a_ g.39.1.2 (A:) Steroid hormone receptor Err2 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: Steroid hormone receptor Err2 DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=1.6e-16  Score=93.58  Aligned_cols=46  Identities=30%  Similarity=0.519  Sum_probs=42.0

Q ss_pred             CCCCCCceecCCCCCCCchhhhhHHHHhcCCcccccccccccccCC
Q psy1782           2 YSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRISCRR   47 (90)
Q Consensus         2 C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~~~~~~   47 (90)
                      |..+++|.|+...|+.|++|||+|||++||++++||.+|+..+++.
T Consensus        43 c~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~r~~~~r~k   88 (90)
T d1lo1a_          43 CPATNECEITKRRRKSCQACRFMKALKVGMLKEGVRLDRVRGGRQK   88 (90)
T ss_dssp             CSSCSCCCCCHHHHHHCHHHHHHHHHHHTCCGGGSCSSCCTTCCCC
T ss_pred             hhcCCCCccCCCCccccchhhHHHHHHcCCCHHHhccccccccccC
Confidence            7889999999999999999999999999999999999998766543
>d1dszb_ g.39.1.2 (B:) Retinoid X receptor (RXR-alpha) 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
>d1a6ya_ g.39.1.2 (A:) Orphan nuclear receptor reverb DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} 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
>d1cita_ g.39.1.2 (A:) Orphan nuclear receptor NGFI-B DNA-binding domain {Rat (Rattus norvegicus) [TaxId: 10116]} 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
>d2nllb_ g.39.1.2 (B:) Thyroid hormone receptor (TR-beta) DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} 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