Citrus Sinensis ID: 008908

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-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------55
MVTVCQQCGDKGFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEPKVAKPSTIVNPSSVLGGRCDSDSENLEIVQATQSNLRLKKNAVDRLSKNERKRNDSGSLAKAEVQKSGNSSSYLLQVHHSNNHEKDKKCGRRGELDGRSIYAEAESVKTKTSLATGGDSNSNPQYSRELLCNESDKNYEKLGRQIGLDGSSFNDEAESFRTRTSQVVTNDPPYTRECSSNAHKVVVIEVHSMGNDKKGYQFRRQRELVKNSSDTGTKSLKNSLVTTSHSFSIPKHSSNVSEKSIFEVQFKEDAVKDLSPIRWSGLNGGSSTEESESSKKETSLIASSRPSNIPEHCFVPAQPIIEPIWKGNLRLSSDKYGSIEGLVAHLSTSACSKVFQEAKLLPQLLCPELLPRSNSWPKSFHKWGPSDDNIALYLFPNNERSEKVYDSLVHDMISHDVALRAVVKNAALLLFTSNLLPFQFWRFQSKFYLWGVFRAKQASQSQTLAVDSVNAISISKPNGLVKALTQYPQSPGSPLSNSGSHGSGSVHSCQSML
ccccccccccccccccEEEccccccccEEccccccccccccccccEEEccccccccccccccccccccccccccccHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccHHccccccccccccccccccccccccccHHHccccccccccccccccccccccccccccccccHHHHccccccccccccccHHHHHcccccccccccccccccccccccccEEEEEcccccccccccccHHHHccccccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEccccccccccccccccccHHHHHHHHHHHcccccccEEccccccccccccccccccccEEEEEcccccccHHHHHHHHHHHHHcccEEEEEEccEEEEEccccccccHHHHccccEEEEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
ccEEEccccccccHHEEEEEcccccccEEEEHHccccccccccEEEEEcccccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccHHccccccccccEEccccccccccccccccccccccccccccccccccccHHcccccccccccccccEEcccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEccccccccccHHHcccccccccccccccccccccccccccccccccccccccccHcccccccccccccccccEccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEccccccccccEEEcccccccHHHHHHHHHcccEEEEEEcccHHccHHHHHHcccccccEEEEEEccccccHHHHHHHHHHHHHccEEEEEEEccEEEEEEEcccccHHcccEcccEEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHc
mvtvcqqcgdkgfYEALIGCEKCQTTAvhiyclpvlpasfeddvlwycedcepkvakpstivnpssvlggrcdsdsenLEIVQATQSNLRLKKNAVDRLSKnerkrndsgslAKAEvqksgnsssYLLQVHhsnnhekdkkcgrrgeldgrsiYAEAesvktktslatggdsnsnpqysRELLCNESDKNYEKLGRqigldgssfndeaesfrtrtsqvvtndppytrecssnaHKVVVIEVHSmgndkkgyqFRRQRelvknssdtgtkslknslvttshsfsipkhssnvseksiFEVQFKedavkdlspirwsglnggssteesesskkETSLIassrpsnipehcfvpaqpiiepiwkgnlrlssdkygsIEGLVAHLSTSACSKVFQEakllpqllcpellprsnswpksfhkwgpsddnialylfpnnerseKVYDSLVHDMISHDVALRAVVKNAALLLFTSNLLPFQFWRFQSKFYLwgvfrakqasqsqtlavdsvnaisiskpnglvkaltqypqspgsplsnsgshgsgsvhscqsml
MVTVCQQCGDKGFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEPkvakpstivnpssvlggrcdsdSENLEIVQatqsnlrlkknavdrlsknerkrndsgslakaevqksgnSSSYLLQVhhsnnhekdkkcgrrgeLDGRSIYAeaesvktktslatggdsnsnpqYSRELLCNESDKNYEKLGRQIgldgssfndEAESfrtrtsqvvtndppytrecssnaHKVVVIEVHsmgndkkgyqfrrqrelvknssdtgtkslknslvttshsfsipkhssnvseKSIFEVQFKedavkdlspirwsglnggssteesesskKETSLiassrpsnipEHCFVPAQPIIEPIWKGNLRLSSDKYGSIEGLVAHLSTSACSKVFQEAKLLPQLLCPELLPRSNSWPKSFHKWGPSDDNIALYLFPNNERSEKVYDSLVHDMISHDVALRAVVKNAALLLFTSNLLPFQFWRFQSKFYLWGVFRAKQASQSQTLAVDSVNAISISKPNGLVKALTQYPQSPGsplsnsgshgsgsvhscqsml
MVTVCQQCGDKGFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEPKVAKPSTIVNPSSVLGGRCDSDSENLEIVQATQSNLRLKKNAVDRLSKNERKRNDSGSLAKAEVQKSGNSSSYLLQVHHSNNHEKDKKCGRRGELDGRSIYAEAESVKTKTSLATGGDSNSNPQYSRELLCNESDKNYEKLGRQIGLDGSSFNDEAESFRTRTSQVVTNDPPYTRECSSNAHKVVVIEVHSMGNDKKGYQFRRQRELVKNSSDTGTKSLKNSLVTTSHSFSIPKHSSNVSEKSIFEVQFKEDAVKDLSPIRWSGLNGGssteesesskketsLIASSRPSNIPEHCFVPAQPIIEPIWKGNLRLSSDKYGSIEGLVAHLSTSACSKVFQEAKllpqllcpellpRSNSWPKSFHKWGPSDDNIALYLFPNNERSEKVYDSLVHDMISHDVALRAVVKNAALLLFTSNLLPFQFWRFQSKFYLWGVFRAKQASQSQTLAVDSVNAISISKPNGLVKALTQYPqspgsplsnsgshgsgsvhscqsML
**TVCQQCGDKGFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEPKVAK**TI****************************************************************************************************************************************************************************AHKVVVIEVH*******************************************************************************************************EHCFVPAQPIIEPIWKGNLRLSSDKYGSIEGLVAHLSTSACSKVFQEAKLLPQLLCPELLPRSNSWPKSFHKWGPSDDNIALYLFPNNERSEKVYDSLVHDMISHDVALRAVVKNAALLLFTSNLLPFQFWRFQSKFYLWGVFRAKQA****TLAVDSVNAISI***************************************
MVTVCQQCGDKGFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEP*********************************************************************************************************************************************************************************************************************************************************************************************************VPAQPIIEPIWKGNLRLSSDKYGSIEGLVAHLSTSACSKVFQEAKLLPQLLCPELLPRSNSWPKSFHKWGPSDDNIALYLFPNNERSEKVYDSLVHDMISHDVALRAVVKNAALLLFTSNLLPFQFWRFQSKFYLWGVFR********************************************************SML
MVTVCQQCGDKGFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEPKVAKPSTIVNPSSVLGGRCDSDSENLEIVQATQSNLRLKKNAVDRLSK**********************SSYLLQVHH*************GELDGRSIYAEAESVKTKTSLATGGDSNSNPQYSRELLCNESDKNYEKLGRQIGLDGSSFNDEAESFRTRTSQVVTNDPPYTRECSSNAHKVVVIEVHSMGNDKKGYQFRRQRELVKNSSDTGTKSLKNSLVTTSHSFSIPKHSSNVSEKSIFEVQFKEDAVKDLSPIRWSG************************PSNIPEHCFVPAQPIIEPIWKGNLRLSSDKYGSIEGLVAHLSTSACSKVFQEAKLLPQLLCPELLPRSNSWPKSFHKWGPSDDNIALYLFPNNERSEKVYDSLVHDMISHDVALRAVVKNAALLLFTSNLLPFQFWRFQSKFYLWGVFRAK********AVDSVNAISISKPNGLVKALTQY**************************
MVTVCQQCGDKGFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEPK************************************************************************************************************************************************************************************HKV***EVH*****************************************************************************************************IPEHCFVPAQPIIEPIWKGNLRLSSDKYGSIEGLVAHLSTSACSKVFQEAKLLPQLLCPELLPRSNSWPKSFHKWGPSDDNIALYLFPNNERSEKVYDSLVHDMISHDVALRAVVKNAALLLFTSNLLPFQFWRFQSKFYLWGVFRAKQ********************************************************
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MVTVCQQCGDKGFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEPKVAKPSTIVNPSSVLGGRCDSDSENLEIxxxxxxxxxxxxxxxxxxxxxERKRNDSGSLAKAEVQKSGNSSSYLLQVHHSNNHEKDKKCGRRGELDGRSIYAEAESVKTKTSLATGGDSNSNPQYSRELLCNESDKNYEKLGRQIGLDGSSFNDEAESFRTRTSQVVTNDPPYTRECSSNAHKVVVIEVHSMGNDKKGYQFRRQRELVKNSSDTGTKSLKNSLVTTSHSFSIPKHSSNVSEKSIFEVQFKEDAVKDLSPIRWSGLNGGSSTEESESSKKETSLIASSRPSNIPEHCFVPAQPIIEPIWKGNLRLSSDKYGSIEGLVAHLSTSACSKVFQEAKLLPQLLCPELLPRSNSWPKSFHKWGPSDDNIALYLFPNNERSEKVYDSLVHDMISHDVALRAVVKNAALLLFTSNLLPFQFWRFQSKFYLWGVFRAKQASQSQTLAVDSVNAISISKPNGLVKALTQYPQSPGSPLSNSGSHGSGSVHSCQSML
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

No hits with e-value below 0.001 by BLAST

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 ?
Query549
224085087456 predicted protein [Populus trichocarpa] 0.805 0.969 0.350 3e-74
186488901431 RING/FYVE/PHD zinc finger-containing pro 0.744 0.948 0.300 3e-44
356574534349 PREDICTED: uncharacterized protein LOC10 0.276 0.435 0.477 8e-38
297846780482 predicted protein [Arabidopsis lyrata su 0.792 0.902 0.287 3e-36
357443745369 hypothetical protein MTR_1g099270 [Medic 0.265 0.395 0.510 5e-36
357497831 984 PHD-finger family protein expressed [Med 0.256 0.143 0.5 8e-35
449443824145 PREDICTED: uncharacterized protein LOC10 0.214 0.813 0.554 1e-33
224093350388 predicted protein [Populus trichocarpa] 0.258 0.365 0.485 8e-33
356535812338 PREDICTED: uncharacterized protein LOC10 0.408 0.662 0.356 2e-32
357495505227 hypothetical protein MTR_5g098320 [Medic 0.267 0.647 0.503 4e-32
>gi|224085087|ref|XP_002307485.1| predicted protein [Populus trichocarpa] gi|222856934|gb|EEE94481.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  286 bits (731), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 189/539 (35%), Positives = 265/539 (49%), Gaps = 97/539 (17%)

Query: 2   VTVCQQCGDKGFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEPKVAKPSTI 61
           VT+CQ+CGD+GF  ALI C++CQ  AVH YCL VLPA+F++ V+W C  CE K  K S++
Sbjct: 7   VTICQKCGDRGFDAALIFCDECQAYAVHCYCLDVLPATFDEYVVWLCYHCESKAVKLSSL 66

Query: 62  VNPSSVLGGRCDSDSENLEIVQATQSNLRLKKNAVDRLSKNERKRNDSGSLAKAEVQKSG 121
             P+S +    DSDS  L+I+Q        KKN + RL    ++     SL  +++ +  
Sbjct: 67  DRPNSPISTESDSDS--LKIIQLK------KKNPLKRLEGKPKEMVFDCSLTNSDLLRPQ 118

Query: 122 NSSSYLLQVHHSNNHEKDKKCGRRGELDGRSIYAEAESVKTKTSLATGGDSNSNPQYSRE 181
            SS + L                                                    E
Sbjct: 119 ISSDFQL---------------------------------------------------VE 127

Query: 182 LLCNESDKNYEKLGRQIGLDGSSFNDEAESFRTRTSQVVTNDPPYTRECSSNAHKVVVIE 241
           + C E D   +KLG Q GL   S  + AE   ++                S    + +++
Sbjct: 128 VDCCEDDGKDQKLGSQNGLHEDSVPEVAEYLESKNP-------------VSPLPDLQLVD 174

Query: 242 VHSMGNDKKGYQFRRQRELVKNSSDTGTKSLKNSLVTTSHSFSIPKHSSNVSEKSIFEVQ 301
           V    ND+K  +              G  SL+ S    +           V +    ++ 
Sbjct: 175 VDCSQNDEKDQKL------------GGKNSLEESGFQETEPLRNKNSQLVVCDVQPLQIH 222

Query: 302 FKEDAVKDLSPIRWSGLNGGSSTEESESSKKETSLIASSRPSNIPEHCFVPAQPIIEPIW 361
            +ED        R + LN G+  EE E  K +   + +       E   +   PI +PIW
Sbjct: 223 CREDGGGSQKVGRQNDLNEGNFVEEDELDKTKICHVDAPY---FAEQSSIRVLPIRDPIW 279

Query: 362 KGNLRLSSDKYGSIEGLVAHLSTSACSKVFQEAKLLPQLLCPELLPRSNSWPKSFHKWGP 421
           +G++ +  + YG+  G+VAHLS+ ACS+  +EAK L  LL PELLPRS  WPKSF K GP
Sbjct: 280 RGSMSIFQNNYGAPGGIVAHLSSIACSRASEEAKGLSGLLSPELLPRSGVWPKSFRKLGP 339

Query: 422 SDDNIALYLFPNNERSEKVYDSLVHDMISHDVALRAVVKNAALLLFTSNLLPFQFWRFQS 481
           + D+I LY FP+NER+E V+DSLV+DMIS D+A+R V++NA LL++TS +LP   WRFQS
Sbjct: 340 AADHIGLYFFPDNERNEIVFDSLVNDMISQDLAMRVVIENAELLIYTSRILPMDCWRFQS 399

Query: 482 KFYLWGVFRAKQASQSQTLAVDSVNAISISKPNGLVKALTQYPQSPGSPLSNSGSHGSG 540
           KFYLWGVFR K+ S    +           +  GL KA+T   +SP SPLSN GS+GSG
Sbjct: 400 KFYLWGVFRPKKPSAPDVVP---------GEQQGLTKAITWERRSPVSPLSN-GSYGSG 448

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|186488901|ref|NP_001117432.1| RING/FYVE/PHD zinc finger-containing protein [Arabidopsis thaliana] gi|225898006|dbj|BAH30335.1| hypothetical protein [Arabidopsis thaliana] gi|332193874|gb|AEE31995.1| RING/FYVE/PHD zinc finger-containing protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|356574534|ref|XP_003555401.1| PREDICTED: uncharacterized protein LOC100796913 [Glycine max] Back     alignment and taxonomy information
>gi|297846780|ref|XP_002891271.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297337113|gb|EFH67530.1| predicted protein [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|357443745|ref|XP_003592150.1| hypothetical protein MTR_1g099270 [Medicago truncatula] gi|355481198|gb|AES62401.1| hypothetical protein MTR_1g099270 [Medicago truncatula] Back     alignment and taxonomy information
>gi|357497831|ref|XP_003619204.1| PHD-finger family protein expressed [Medicago truncatula] gi|355494219|gb|AES75422.1| PHD-finger family protein expressed [Medicago truncatula] Back     alignment and taxonomy information
>gi|449443824|ref|XP_004139676.1| PREDICTED: uncharacterized protein LOC101213907 [Cucumis sativus] gi|449533701|ref|XP_004173810.1| PREDICTED: uncharacterized LOC101213907 [Cucumis sativus] Back     alignment and taxonomy information
>gi|224093350|ref|XP_002309893.1| predicted protein [Populus trichocarpa] gi|222852796|gb|EEE90343.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|356535812|ref|XP_003536437.1| PREDICTED: uncharacterized protein LOC100817132 [Glycine max] Back     alignment and taxonomy information
>gi|357495505|ref|XP_003618041.1| hypothetical protein MTR_5g098320 [Medicago truncatula] gi|355519376|gb|AET01000.1| hypothetical protein MTR_5g098320 [Medicago truncatula] 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 ?
Query549
TAIR|locus:2029147431 AT1G43770 "AT1G43770" [Arabido 0.262 0.334 0.445 1.9e-48
TAIR|locus:2159421426 AT5G61120 [Arabidopsis thalian 0.085 0.110 0.346 3.3e-08
TAIR|locus:2029147 AT1G43770 "AT1G43770" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 325 (119.5 bits), Expect = 1.9e-48, Sum P(3) = 1.9e-48
 Identities = 65/146 (44%), Positives = 93/146 (63%)

Query:   353 AQPIIEPIWKGNLRLSSDKYGSIEGLVAHLSTSACSKVFQEAKXXXXXXXXXXXXRSNSW 412
             AQPI  PIW+G + +      +++G+VAH+S+ AC KV + A             R   W
Sbjct:   285 AQPIKIPIWRGLMSVKGGNSCTMDGIVAHVSSLACPKVHETASSLKGRLSAEILPRLEVW 344

Query:   413 PKSFHK-WGPSDDNIALYLFPNNERS-EKVYDSLVHDMISHDVALRAVVKNAALLLFTSN 470
             PK+F K  GP D+++AL+ FP++E + EKV+DSLV  M  +D A+R V+ +A LLLFTS 
Sbjct:   345 PKTFLKNGGPKDESVALFFFPSSESNDEKVFDSLVDKMKKNDSAMRCVLNDAELLLFTSY 404

Query:   471 LLPFQFWRFQSKFYLWGVFRAKQASQ 496
             +LP   W F SK+YLWGVF+ +Q S+
Sbjct:   405 MLPKDSWTFNSKYYLWGVFKPRQTSR 430
GO:0003677 "DNA binding" evidence=ISS
GO:0005634 "nucleus" evidence=ISM
GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS
GO:0008270 "zinc ion binding" evidence=IEA
TAIR|locus:2159421 AT5G61120 [Arabidopsis thaliana (taxid:3702)] 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

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

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
fgenesh4_pg.C_LG_V001073
hypothetical protein (456 aa)
(Populus trichocarpa)
Predicted Functional Partners:
 
Sorry, there are no predicted associations at the current settings.
 

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query549
smart0024947 smart00249, PHD, PHD zinc finger 1e-07
pfam0062851 pfam00628, PHD, PHD-finger 3e-06
>gnl|CDD|214584 smart00249, PHD, PHD zinc finger Back     alignment and domain information 
 Score = 48.0 bits (114), Expect = 1e-07
 Identities = 15/48 (31%), Positives = 17/48 (35%), Gaps = 1/48 (2%)

Query: 4  VCQQCGDKGFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDC 51
           C  CG       L+ C+ C     H  CL       E D  WYC  C
Sbjct: 1  YCSVCGKPDDGGELLQCDGCDR-WYHQTCLGPPLLEEEPDGKWYCPKC 47

The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers. Length = 47
>gnl|CDD|201356 pfam00628, PHD, PHD-finger Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 549
KOG0825 1134 consensus PHD Zn-finger protein [General function 98.85
PF0062851 PHD: PHD-finger; InterPro: IPR019787 Zinc finger ( 98.37
KOG4443694 consensus Putative transcription factor HALR/MLL3, 98.35
smart0024947 PHD PHD zinc finger. The plant homeodomain (PHD) f 98.23
KOG4299613 consensus PHD Zn-finger protein [General function 97.76
cd04718148 BAH_plant_2 BAH, or Bromo Adjacent Homology domain 97.72
KOG12451404 consensus Chromatin remodeling complex WSTF-ISWI, 97.67
KOG1512381 consensus PHD Zn-finger protein [General function 97.6
KOG0955 1051 consensus PHD finger protein BR140/LIN-49 [General 97.3
KOG0957707 consensus PHD finger protein [General function pre 96.94
PF1383136 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A. 96.72
KOG0383 696 consensus Predicted helicase [General function pre 96.59
KOG0956 900 consensus PHD finger protein AF10 [General functio 96.21
KOG4323464 consensus Polycomb-like PHD Zn-finger protein [Gen 95.31
KOG0954893 consensus PHD finger protein [General function pre 94.48
COG5141669 PHD zinc finger-containing protein [General functi 93.03
KOG1246 904 consensus DNA-binding protein jumonji/RBP2/SMCY, c 91.56
KOG4299613 consensus PHD Zn-finger protein [General function 83.66
>KOG0825 consensus PHD Zn-finger protein [General function prediction only] Back     alignment and domain information 
Probab=98.85  E-value=8.3e-10  Score=122.62  Aligned_cols=50  Identities=26%  Similarity=0.654  Sum_probs=46.6

Q ss_pred             CcccccccCcCCccceeeccCCCCCCcccccCCCCCCCCCCCCcccccCCC
Q 008908            2 VTVCQQCGDKGFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCE   52 (549)
Q Consensus         2 vtvC~iCGd~GfeDkLLlCD~Cd~~A~HtYCL~~~l~~VPe~~~WyCp~C~   52 (549)
                      ++-|.||+.-+-+|+||+||.|+++.||+|||++++.++|. ++|||+-|.
T Consensus       215 ~~~C~IC~~~DpEdVLLLCDsCN~~~YH~YCLDPdl~eiP~-~eWYC~NC~  264 (1134)
T KOG0825|consen  215 EVKCDICTVHDPEDVLLLCDSCNKVYYHVYCLDPDLSESPV-NEWYCTNCS  264 (1134)
T ss_pred             cccceeeccCChHHhheeecccccceeeccccCcccccccc-cceecCcch
Confidence            56799999999999999999999877999999999999997 599999994

>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule Back     alignment and domain information
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only] Back     alignment and domain information
>smart00249 PHD PHD zinc finger Back     alignment and domain information
>KOG4299 consensus PHD Zn-finger protein [General function prediction only] Back     alignment and domain information
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function Back     alignment and domain information
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics] Back     alignment and domain information
>KOG1512 consensus PHD Zn-finger protein [General function prediction only] Back     alignment and domain information
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only] Back     alignment and domain information
>KOG0957 consensus PHD finger protein [General function prediction only] Back     alignment and domain information
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A Back     alignment and domain information
>KOG0383 consensus Predicted helicase [General function prediction only] Back     alignment and domain information
>KOG0956 consensus PHD finger protein AF10 [General function prediction only] Back     alignment and domain information
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only] Back     alignment and domain information
>KOG0954 consensus PHD finger protein [General function prediction only] Back     alignment and domain information
>COG5141 PHD zinc finger-containing protein [General function prediction only] Back     alignment and domain information
>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only] Back     alignment and domain information
>KOG4299 consensus PHD Zn-finger protein [General function prediction only] Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query549
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 3e-11
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 5e-08
1f62_A51 Transcription factor WSTF; Zn-finger; NMR {Homo sa 1e-06
2k16_A75 Transcription initiation factor TFIID subunit 3; p 3e-06
2ku3_A71 Bromodomain-containing protein 1; PHD finger, chro 5e-06
2e6s_A77 E3 ubiquitin-protein ligase UHRF2; PHD domain, str 8e-06
2puy_A60 PHD finger protein 21A; PHD finger, histone CODE, 3e-05
3asl_A70 E3 ubiquitin-protein ligase UHRF1; histone reader 4e-05
2e6r_A92 Jumonji/ARID domain-containing protein 1D; PHD dom 4e-05
2yql_A56 PHD finger protein 21A; PHD domain, structural gen 6e-05
2l43_A88 N-teminal domain from histone H3.3, linker, PHD1 f 6e-05
3v43_A112 Histone acetyltransferase KAT6A; MOZ, PHD finger, 7e-05
1mm2_A61 MI2-beta; PHD, zinc finger, protein scaffold, DNA 7e-05
2l5u_A61 Chromodomain-helicase-DNA-binding protein 4; CHD4, 8e-05
1xwh_A66 Autoimmune regulator; PHD domain, Zn binding domai 1e-04
2yt5_A66 Metal-response element-binding transcription facto 1e-04
2kwj_A114 Zinc finger protein DPF3; acetyl-lysine, transcrip 1e-04
3shb_A77 E3 ubiquitin-protein ligase UHRF1; unmodified hist 2e-04
1we9_A64 PHD finger family protein; structural genomics, PH 2e-04
1wev_A88 Riken cDNA 1110020M19; structural genomics, PHD do 3e-04
2lbm_A142 Transcriptional regulator ATRX; metal binding prot 3e-04
2ysm_A111 Myeloid/lymphoid or mixed-lineage leukemia protein 4e-04
3ask_A226 E3 ubiquitin-protein ligase UHRF1; histone reader 4e-04
3ql9_A129 Transcriptional regulator ATRX; zinc finger, trans 7e-04
1fp0_A88 KAP-1 corepressor; PHD domain, C3HC4 type zinc bin 9e-04
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
 Score = 65.3 bits (158), Expect = 3e-11
 Identities = 96/618 (15%), Positives = 173/618 (27%), Gaps = 175/618 (28%)

Query: 26  TAVHIYC----LPVLPASFEDDVLWYCEDCEPKVAKPSTIVNPSSVLGGRCDSDSENLEI 81
           T  H Y     L V   +F D+    C+D +           P S+L     S  E   I
Sbjct: 11  TGEHQYQYKDILSVFEDAFVDNF--DCKDVQDM---------PKSIL-----SKEEIDHI 54

Query: 82  VQATQSNLRL----------KKNAVDRLSKNERKRNDS---GSLAKAEVQKSGNSSSYLL 128
           + +  +              ++  V +  +   + N       +   + Q S  +  Y+ 
Sbjct: 55  IMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIE 114

Query: 129 QVH--HSNNHEKDKKCGRRGE--LDGRSIYAEAESVKT----------KTSLATGGDSNS 174
           Q    +++N    K    R +  L  R    E    K           KT +A     + 
Sbjct: 115 QRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSY 174

Query: 175 NPQYSREL--------LCNESD---KNYEKLGRQIGLDGSSFNDEAESFRTRTSQVVTN- 222
             Q   +          CN  +   +  +KL  QI  + +S +D + + + R   +    
Sbjct: 175 KVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAEL 234

Query: 223 -----DPPY----------------------------TRECS-SNAHKVVVIEVHSMGND 248
                  PY                            TR    ++          S+ + 
Sbjct: 235 RRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHH 294

Query: 249 KKGYQFRRQRELVKNSSDTGTKSLKNSLVTTSHSFSIPKHSSNVSEKSIFEVQFKEDAVK 308
                    + L+    D   + L   ++TT+     P+  S ++E        ++    
Sbjct: 295 SMTLTPDEVKSLLLKYLDCRPQDLPREVLTTN-----PRRLSIIAES------IRDG--- 340

Query: 309 DLSPIRWSGLNGGSSTEESESSKKETSLIASS----RPSNI----------PEHCFVPAQ 354
                 W          +  +  K T++I SS     P+            P    +P  
Sbjct: 341 ---LATWDNW-------KHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTI 390

Query: 355 PIIEPIWKGNLRLSSDKYGSIEGLVAHL-STSACSKVFQEAKL-LPQLLCPELLPRSN-- 410
            ++  IW             +  +V  L   S   K  +E+ + +P +     +   N  
Sbjct: 391 -LLSLIW------FDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEY 443

Query: 411 ----------SWPKSFHKWGPSDDNIALYLFPNNERSEKVYDSLVHDMISHDVALRAVVK 460
                     + PK+F         +  Y           Y  + H    H   L+ +  
Sbjct: 444 ALHRSIVDHYNIPKTFDSDDLIPPYLDQY----------FYSHIGH----H---LKNIEH 486

Query: 461 NAALLLFTSNLLPFQFWRFQSKFYLWGVFRAKQASQSQTLAVDSV--NAISISKP--NGL 516
              + LF    L F+F   + K            S   TL         I  + P    L
Sbjct: 487 PERMTLFRMVFLDFRF--LEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERL 544

Query: 517 VKALTQYPQSPGSPLSNS 534
           V A+  +       L  S
Sbjct: 545 VNAILDFLPKIEENLICS 562
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2 Length = 51 Back     alignment and structure
>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A* Length = 75 Back     alignment and structure
>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens} Length = 71 Back     alignment and structure
>2e6s_A E3 ubiquitin-protein ligase UHRF2; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 77 Back     alignment and structure
>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens} Length = 60 Back     alignment and structure
>3asl_A E3 ubiquitin-protein ligase UHRF1; histone reader module, epigenetic regulation, LI binding protein complex; 1.41A {Homo sapiens} PDB: 3sou_A 3sow_A* 3sox_A 3zvy_A 2lgg_A 2lgk_A* 2lgl_A 3t6r_A 3zvz_B Length = 70 Back     alignment and structure
>2e6r_A Jumonji/ARID domain-containing protein 1D; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92 Back     alignment and structure
>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 56 Back     alignment and structure
>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens} Length = 88 Back     alignment and structure
>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A Length = 112 Back     alignment and structure
>1mm2_A MI2-beta; PHD, zinc finger, protein scaffold, DNA binding protein; NMR {Homo sapiens} SCOP: g.50.1.2 PDB: 2l75_A* 1mm3_A Length = 61 Back     alignment and structure
>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens} Length = 61 Back     alignment and structure
>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A Length = 66 Back     alignment and structure
>2yt5_A Metal-response element-binding transcription factor 2; zinc-regulated factor 1, ZIRF1, metal-response element DNA-binding protein M96; NMR {Mus musculus} Length = 66 Back     alignment and structure
>2kwj_A Zinc finger protein DPF3; acetyl-lysine, transcription regulation, nucleus, metal BIND protein; HET: ALY; NMR {Homo sapiens} PDB: 2kwk_A 2kwn_A* 2kwo_A* Length = 114 Back     alignment and structure
>3shb_A E3 ubiquitin-protein ligase UHRF1; unmodified histone, methylation, UHRF1, PHD, ligase-NUCL protein complex; 1.80A {Homo sapiens} Length = 77 Back     alignment and structure
>1we9_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2 Length = 64 Back     alignment and structure
>1wev_A Riken cDNA 1110020M19; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: g.50.1.2 Length = 88 Back     alignment and structure
>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A Length = 142 Back     alignment and structure
>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens} Length = 111 Back     alignment and structure
>3ask_A E3 ubiquitin-protein ligase UHRF1; histone reader modules, epigenetic regulation, trimethylaion of lysine residue, ligase-DNA binding protein; HET: M3L; 2.90A {Homo sapiens} Length = 226 Back     alignment and structure
>3ql9_A Transcriptional regulator ATRX; zinc finger, transcription, lysine trimethylation, protein, histone-binding protein, transcription-structural complex; HET: M3L; 0.93A {Homo sapiens} PDB: 3qla_A* 3qlc_A 3qln_A 2jm1_A Length = 129 Back     alignment and structure
>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2 Length = 88 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query549
1f62_A51 Transcription factor WSTF; Zn-finger; NMR {Homo sa 99.25
3shb_A77 E3 ubiquitin-protein ligase UHRF1; unmodified hist 99.18
2e6s_A77 E3 ubiquitin-protein ligase UHRF2; PHD domain, str 99.17
3asl_A70 E3 ubiquitin-protein ligase UHRF1; histone reader 99.15
2e6r_A92 Jumonji/ARID domain-containing protein 1D; PHD dom 99.11
2lri_C66 Autoimmune regulator; Zn binding protein domain, a 99.11
1mm2_A61 MI2-beta; PHD, zinc finger, protein scaffold, DNA 99.1
1wev_A88 Riken cDNA 1110020M19; structural genomics, PHD do 99.06
1xwh_A66 Autoimmune regulator; PHD domain, Zn binding domai 99.0
1fp0_A88 KAP-1 corepressor; PHD domain, C3HC4 type zinc bin 99.0
2ku3_A71 Bromodomain-containing protein 1; PHD finger, chro 99.0
2yt5_A66 Metal-response element-binding transcription facto 99.0
2yql_A56 PHD finger protein 21A; PHD domain, structural gen 98.99
2ysm_A111 Myeloid/lymphoid or mixed-lineage leukemia protein 98.99
2l43_A88 N-teminal domain from histone H3.3, linker, PHD1 f 98.94
3v43_A112 Histone acetyltransferase KAT6A; MOZ, PHD finger, 98.93
2l5u_A61 Chromodomain-helicase-DNA-binding protein 4; CHD4, 98.91
2puy_A60 PHD finger protein 21A; PHD finger, histone CODE, 98.91
2kwj_A114 Zinc finger protein DPF3; acetyl-lysine, transcrip 98.9
3o36_A184 Transcription intermediary factor 1-alpha; TRIM24, 98.87
3u5n_A207 E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b 98.85
2ro1_A189 Transcription intermediary factor 1-beta; KAP, TIF 98.81
2k16_A75 Transcription initiation factor TFIID subunit 3; p 98.73
2lv9_A98 Histone-lysine N-methyltransferase MLL5; zinc fing 98.69
2ysm_A111 Myeloid/lymphoid or mixed-lineage leukemia protein 98.39
4gne_A107 Histone-lysine N-methyltransferase NSD3; zinc fing 98.27
1wen_A71 Inhibitor of growth family, member 4; ING1-like pr 98.09
2vnf_A60 ING 4, P29ING4, inhibitor of growth protein 4; ace 98.06
1weu_A91 Inhibitor of growth family, member 4; structural g 98.0
3c6w_A59 P28ING5, inhibitor of growth protein 5; chromatin, 97.86
2jmi_A90 Protein YNG1, ING1 homolog 1; PHD, histone, recogn 97.78
1we9_A64 PHD finger family protein; structural genomics, PH 97.69
2g6q_A62 Inhibitor of growth protein 2; protein-peptide com 97.67
3v43_A112 Histone acetyltransferase KAT6A; MOZ, PHD finger, 97.59
3o70_A68 PHD finger protein 13; PHF13, structural genomics 97.56
2kwj_A114 Zinc finger protein DPF3; acetyl-lysine, transcrip 97.4
2lbm_A142 Transcriptional regulator ATRX; metal binding prot 97.28
1wew_A78 DNA-binding family protein; structural genomics, P 97.21
1x4i_A70 Inhibitor of growth protein 3; structural genomics 97.21
1wee_A72 PHD finger family protein; structural genomics, PH 97.16
2ri7_A174 Nucleosome-remodeling factor subunit BPTF; zinc fi 97.08
1wep_A79 PHF8; structural genomics, PHD domain, riken struc 97.07
3o7a_A52 PHD finger protein 13 variant; PHF13, zinc finger, 97.01
2rsd_A68 E3 SUMO-protein ligase SIZ1; E3 SUMO ligase, plant 96.96
1wem_A76 Death associated transcription factor 1; structura 96.92
3ql9_A129 Transcriptional regulator ATRX; zinc finger, trans 96.8
3kqi_A75 GRC5, PHD finger protein 2; metal-binding, zinc-fi 96.77
2xb1_A105 Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro; 96.62
2kgg_A52 Histone demethylase jarid1A; PHD finger, histone m 96.35
4bbq_A117 Lysine-specific demethylase 2A; oxidoreductase, ub 95.81
2vpb_A65 Hpygo1, pygopus homolog 1; gene regulation, WNT si 95.76
3lqh_A183 Histone-lysine N-methyltransferase MLL; PHD finger 95.67
1wil_A89 KIAA1045 protein; ring finger domain, structural g 94.61
3pur_A528 Lysine-specific demethylase 7 homolog; oxidoreduct 94.48
3kv5_D488 JMJC domain-containing histone demethylation prote 94.39
3kv4_A447 PHD finger protein 8; epigenetics, histone CODE, c 94.33
2ku7_A140 MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio 87.9
4gne_A107 Histone-lysine N-methyltransferase NSD3; zinc fing 81.16
>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2 Back     alignment and structure
Probab=99.25  E-value=2.1e-12  Score=97.05  Aligned_cols=50  Identities=34%  Similarity=0.822  Sum_probs=45.9

Q ss_pred             cccccccCcCCccceeeccCCCCCCcccccCCCCCCCCCCCCcccccCCCcC
Q 008908            3 TVCQQCGDKGFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEPK   54 (549)
Q Consensus         3 tvC~iCGd~GfeDkLLlCD~Cd~~A~HtYCL~~~l~~VPe~~~WyCp~C~s~   54 (549)
                      +.|.+||+.++++.|++||.|+ .+||+||+++++..+|+ ++|||+.|...
T Consensus         1 a~C~vC~~~~~~~~ll~Cd~C~-~~~H~~Cl~p~l~~~P~-g~W~C~~C~~~   50 (51)
T 1f62_A            1 ARCKVCRKKGEDDKLILCDECN-KAFHLFCLRPALYEVPD-GEWQCPACQPA   50 (51)
T ss_dssp             CCCTTTCCSSCCSCCEECTTTC-CEECHHHHCTTCCSCCS-SCCSCTTTSCC
T ss_pred             CCCCCCCCCCCCCCEEECCCCC-hhhCcccCCCCcCCCCC-CcEECcCcccc
Confidence            4799999999999999999998 69999999999999997 59999999763
>3shb_A E3 ubiquitin-protein ligase UHRF1; unmodified histone, methylation, UHRF1, PHD, ligase-NUCL protein complex; 1.80A {Homo sapiens} Back     alignment and structure
>2e6s_A E3 ubiquitin-protein ligase UHRF2; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>3asl_A E3 ubiquitin-protein ligase UHRF1; histone reader module, epigenetic regulation, LI binding protein complex; 1.41A {Homo sapiens} PDB: 3sou_A 3sow_A* 3sox_A 3zvy_A 2lgg_A 2lgk_A* 2lgl_A 3t6r_A 3zvz_B Back     alignment and structure
>2e6r_A Jumonji/ARID domain-containing protein 1D; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens} Back     alignment and structure
>1mm2_A MI2-beta; PHD, zinc finger, protein scaffold, DNA binding protein; NMR {Homo sapiens} SCOP: g.50.1.2 PDB: 2l75_A* 1mm3_A Back     alignment and structure
>1wev_A Riken cDNA 1110020M19; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: g.50.1.2 Back     alignment and structure
>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A Back     alignment and structure
>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2 Back     alignment and structure
>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens} Back     alignment and structure
>2yt5_A Metal-response element-binding transcription factor 2; zinc-regulated factor 1, ZIRF1, metal-response element DNA-binding protein M96; NMR {Mus musculus} Back     alignment and structure
>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens} Back     alignment and structure
>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens} Back     alignment and structure
>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A Back     alignment and structure
>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens} Back     alignment and structure
>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens} Back     alignment and structure
>2kwj_A Zinc finger protein DPF3; acetyl-lysine, transcription regulation, nucleus, metal BIND protein; HET: ALY; NMR {Homo sapiens} PDB: 2kwk_A 2kwn_A* 2kwo_A* Back     alignment and structure
>3o36_A Transcription intermediary factor 1-alpha; TRIM24, PHD finger, bromodomain, H4K16 acetylation, breast C transcription-protein binding complex; HET: ALY; 1.70A {Homo sapiens} PDB: 3o33_A* 3o34_A* 3o35_A* 3o37_A Back     alignment and structure
>3u5n_A E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, bromodomain, TGF-beta, epigenetics, methylation, K9ME3, K14AC, transcription; HET: M3L ALY; 1.95A {Homo sapiens} PDB: 3u5m_A* 3u5o_A* 3u5p_A* Back     alignment and structure
>2ro1_A Transcription intermediary factor 1-beta; KAP, TIF, PHD finger, bromodomain, SUMO, acetylation, alternative splicing, metal-binding, nucleus; NMR {Homo sapiens} Back     alignment and structure
>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A* Back     alignment and structure
>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens} Back     alignment and structure
>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens} Back     alignment and structure
>4gne_A Histone-lysine N-methyltransferase NSD3; zinc finger, transcription, nuclear protein, transf nuclear protein complex; 1.47A {Homo sapiens} PDB: 4gnd_A 4gnf_A 4gng_A* Back     alignment and structure
>1wen_A Inhibitor of growth family, member 4; ING1-like protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.50.1.2 PDB: 1wes_A Back     alignment and structure
>2vnf_A ING 4, P29ING4, inhibitor of growth protein 4; acetylation, alternative splicing, anti-oncogene, cell cycle, coiled C nucleus, zinc, zinc-finger, ING4; HET: M3L; 1.76A {Homo sapiens} SCOP: g.50.1.2 PDB: 2k1j_A 2jmq_A 2qic_A* Back     alignment and structure
>1weu_A Inhibitor of growth family, member 4; structural genomics, PHD domain, ING1-like protein, DNA binding protein, NPPSFA; NMR {Mus musculus} SCOP: g.50.1.2 Back     alignment and structure
>3c6w_A P28ING5, inhibitor of growth protein 5; chromatin, PHD, ING, epigenetics, alternative splicing, metal-binding, phosphoprotein, zinc; HET: M3L; 1.75A {Homo sapiens} PDB: 2pnx_A* Back     alignment and structure
>2jmi_A Protein YNG1, ING1 homolog 1; PHD, histone, recognition, yeast, protein binding; NMR {Saccharomyces cerevisiae} PDB: 2jmj_A* Back     alignment and structure
>1we9_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2 Back     alignment and structure
>2g6q_A Inhibitor of growth protein 2; protein-peptide complex, gene regulation, apoptosis; HET: M3L; 2.00A {Mus musculus} Back     alignment and structure
>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A Back     alignment and structure
>3o70_A PHD finger protein 13; PHF13, structural genomics consortium, SGC, structural genom type zinc finger, protein binding, zinc ION binding; 1.85A {Homo sapiens} Back     alignment and structure
>2kwj_A Zinc finger protein DPF3; acetyl-lysine, transcription regulation, nucleus, metal BIND protein; HET: ALY; NMR {Homo sapiens} PDB: 2kwk_A 2kwn_A* 2kwo_A* Back     alignment and structure
>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A Back     alignment and structure
>1wew_A DNA-binding family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2 Back     alignment and structure
>1x4i_A Inhibitor of growth protein 3; structural genomics, PHD domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>1wee_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2 Back     alignment and structure
>2ri7_A Nucleosome-remodeling factor subunit BPTF; zinc finger, alpha-helical bundle, dimethyl-lysine, bromodom chromatin regulator, metal-binding, nucleus; HET: MLY; 1.45A {Homo sapiens} PDB: 2fsa_A* 2f6n_A 2f6j_A* 3qzv_A* 3uv2_A* 3qzt_A* 3qzs_A* 2fui_A 2fuu_A* Back     alignment and structure
>1wep_A PHF8; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: g.50.1.2 Back     alignment and structure
>3o7a_A PHD finger protein 13 variant; PHF13, zinc finger, PHD domain, nuclear protein, structural structural genomics consortium, SGC, protein binding; HET: M3L; 1.67A {Homo sapiens} Back     alignment and structure
>2rsd_A E3 SUMO-protein ligase SIZ1; E3 SUMO ligase, plant homeodomain (PHD), histone binding; NMR {Oryza sativa japonica group} Back     alignment and structure
>1wem_A Death associated transcription factor 1; structural genomics, PHD domain, death inducer- obliterator 1(DIO-1); NMR {Mus musculus} SCOP: g.50.1.2 Back     alignment and structure
>3ql9_A Transcriptional regulator ATRX; zinc finger, transcription, lysine trimethylation, protein, histone-binding protein, transcription-structural complex; HET: M3L; 0.93A {Homo sapiens} PDB: 3qla_A* 3qlc_A 3qln_A 2jm1_A Back     alignment and structure
>3kqi_A GRC5, PHD finger protein 2; metal-binding, zinc-finger, histone-binding, NUC protein; HET: M3L; 1.78A {Homo sapiens} SCOP: g.50.1.2 Back     alignment and structure
>2xb1_A Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro; fusion protein, signal transduction, transcription, metal BI WNT proteins; 1.90A {Homo sapiens} Back     alignment and structure
>2kgg_A Histone demethylase jarid1A; PHD finger, histone modification, leukemia, alternative splicing, chromatin regulator, developmental protein; NMR {Homo sapiens} PDB: 2kgi_A* 3gl6_A* Back     alignment and structure
>4bbq_A Lysine-specific demethylase 2A; oxidoreductase, ubiquitin, ligase, ubiquitination, demethyla ZF-CXXC DNA binding domain, CPG island, chromatin; 2.24A {Homo sapiens} Back     alignment and structure
>2vpb_A Hpygo1, pygopus homolog 1; gene regulation, WNT signaling pathway, WNT signaling complex, chromosomal rearrangement, signaling protein; 1.59A {Homo sapiens} PDB: 2vpd_A 2yyr_A* 2dx8_A* 2vp7_A 2vpg_A* 2vpe_A* Back     alignment and structure
>3lqh_A Histone-lysine N-methyltransferase MLL; PHD finger, bromodomain, leukemia, apoptosis, chromati regulator, DNA-binding, isopeptide bond; 1.72A {Homo sapiens} PDB: 3lqi_A* 3lqj_A* 2kyu_A Back     alignment and structure
>1wil_A KIAA1045 protein; ring finger domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: g.50.1.3 Back     alignment and structure
>3pur_A Lysine-specific demethylase 7 homolog; oxidoreductase-oxidoreductase inhibitor complex; HET: 2HG; 2.10A {Caenorhabditis elegans} PDB: 3n9l_A 3n9m_A* 3n9o_A* 3n9p_A* 3n9q_A* 3n9n_A* 3puq_A* Back     alignment and structure
>3kv5_D JMJC domain-containing histone demethylation protein 1D; epigenetics, histone CODE, jumonji lysine demethylase, metal-binding, zinc, zinc-finger; HET: OGA; 2.39A {Homo sapiens} PDB: 3kv6_A* Back     alignment and structure
>3kv4_A PHD finger protein 8; epigenetics, histone CODE, covalent histone modifications, jumonji demethylase, mental retardation, metal-binding, zinc; HET: M3L MLY OGA; 2.19A {Homo sapiens} Back     alignment and structure
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Back     alignment and structure
>4gne_A Histone-lysine N-methyltransferase NSD3; zinc finger, transcription, nuclear protein, transf nuclear protein complex; 1.47A {Homo sapiens} PDB: 4gnd_A 4gnf_A 4gng_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 549
d1mm2a_61 g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens 4e-07
d1f62a_51 g.50.1.2 (A:) Williams-Beuren syndrome transcripti 1e-06
d1we9a_64 g.50.1.2 (A:) PHD finger protein At5g26210 {Thale 1e-06
d1weea_72 g.50.1.2 (A:) PHD finger protein At1g33420 {Thale 5e-06
d1wema_76 g.50.1.2 (A:) Death associated transcription facto 9e-06
d1fp0a170 g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF- 1e-05
d1wepa_79 g.50.1.2 (A:) PHD finger protein 8 {Mouse (Mus mus 2e-04
d1weva_88 g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus mu 0.001
>d1mm2a_ g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606]} Length = 61 Back     information, alignment and structure

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Mi2-beta (CHD4)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.9 bits (106), Expect = 4e-07
 Identities = 15/54 (27%), Positives = 22/54 (40%), Gaps = 5/54 (9%)

Query: 4  VCQQCGDKGFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEPKVAK 57
           C+ C D G    L+ C+ C + + HI+CL        +   W C  C     K
Sbjct: 11 FCRVCKDGGE---LLCCDTCPS-SYHIHCLNPPLPEIPNGE-WLCPRCTCPALK 59
>d1f62a_ g.50.1.2 (A:) Williams-Beuren syndrome transcription factor, WSTF {Human (Homo sapiens) [TaxId: 9606]} Length = 51 Back     information, alignment and structure
>d1we9a_ g.50.1.2 (A:) PHD finger protein At5g26210 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 64 Back     information, alignment and structure
>d1weea_ g.50.1.2 (A:) PHD finger protein At1g33420 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 72 Back     information, alignment and structure
>d1wema_ g.50.1.2 (A:) Death associated transcription factor 1, Datf1 (DIO-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 76 Back     information, alignment and structure
>d1fp0a1 g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo sapiens) [TaxId: 9606]} Length = 70 Back     information, alignment and structure
>d1wepa_ g.50.1.2 (A:) PHD finger protein 8 {Mouse (Mus musculus) [TaxId: 10090]} Length = 79 Back     information, alignment and structure
>d1weva_ g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus musculus) [TaxId: 10090]} Length = 88 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 ?
Query549
d1f62a_51 Williams-Beuren syndrome transcription factor, WST 99.09
d1fp0a170 Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo 98.92
d1mm2a_61 Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606 98.79
d1weva_88 PHD finger protein 22 {Mouse (Mus musculus) [TaxId 98.7
d1we9a_64 PHD finger protein At5g26210 {Thale cress (Arabido 98.28
d1wepa_79 PHD finger protein 8 {Mouse (Mus musculus) [TaxId: 98.2
d1wesa_71 PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mu 98.19
d1weea_72 PHD finger protein At1g33420 {Thale cress (Arabido 98.06
d2pnxa151 Inhibitor of growth protein 4, Ing4 {Homo sapiens 97.7
d1wema_76 Death associated transcription factor 1, Datf1 (DI 97.44
d1wewa_78 Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop 96.95
d1weqa_85 PHD finger protein 7 (NYD-SP6) {Mouse (Mus musculu 83.1
>d1f62a_ g.50.1.2 (A:) Williams-Beuren syndrome transcription factor, WSTF {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Williams-Beuren syndrome transcription factor, WSTF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.09  E-value=1.6e-11  Score=90.69  Aligned_cols=49  Identities=35%  Similarity=0.841  Sum_probs=45.2

Q ss_pred             cccccccCcCCccceeeccCCCCCCcccccCCCCCCCCCCCCcccccCCCc
Q 008908            3 TVCQQCGDKGFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEP   53 (549)
Q Consensus         3 tvC~iCGd~GfeDkLLlCD~Cd~~A~HtYCL~~~l~~VPe~~~WyCp~C~s   53 (549)
                      +.|.+|+..++++.+++||.|+ ..||++|+++++..+|. ++|||+.|+.
T Consensus         1 a~C~vC~~~~~~~~~i~Cd~C~-~~~H~~C~~p~~~~~p~-~~W~C~~C~~   49 (51)
T d1f62a_           1 ARCKVCRKKGEDDKLILCDECN-KAFHLFCLRPALYEVPD-GEWQCPACQP   49 (51)
T ss_dssp             CCCTTTCCSSCCSCCEECTTTC-CEECHHHHCTTCCSCCS-SCCSCTTTSC
T ss_pred             CCCcCcCCCCCCCCEEEcCCCC-CCCCCCCCCCCCCcCCC-CCEECcCCcC
Confidence            3699999999999999999998 68999999999999997 4899999985
>d1fp0a1 g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1mm2a_ g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1weva_ g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1we9a_ g.50.1.2 (A:) PHD finger protein At5g26210 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Back     information, alignment and structure
>d1wepa_ g.50.1.2 (A:) PHD finger protein 8 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1wesa_ g.50.1.2 (A:) PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1weea_ g.50.1.2 (A:) PHD finger protein At1g33420 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Back     information, alignment and structure
>d2pnxa1 g.50.1.2 (A:195-245) Inhibitor of growth protein 4, Ing4 {Homo sapiens [TaxId: 9606]} Back     information, alignment and structure
>d1wema_ g.50.1.2 (A:) Death associated transcription factor 1, Datf1 (DIO-1) {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1wewa_ g.50.1.2 (A:) Sumoylation ligase E3, SIZ1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Back     information, alignment and structure
>d1weqa_ g.50.1.2 (A:) PHD finger protein 7 (NYD-SP6) {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure