Citrus Sinensis ID: 005945

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-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------67

MQPSSCLNKPQQSSTLKDDSSTPHFGLAVSYASPSETNSQIGVSGSHLRPVVQPPLVKQFHGNLPNGADSLGETQVRNGRPRVDARGRSQLLPRYWPRFTDQDLQQISGDSNSVITPLFEKMLSASDAGRIGRLVLPKKCAEAYFPPISQPEGLPLKVQDSKGKEWIFQFRFWPNNNSRMYVLEGVTPCIQNMQLQAGDIVTFSRLEPEGKLVMGFRKASSASASDQDNEANKAGTGIPANGHAELADPSSWSKVDKSGYIATEALGAKSSISRKRKNTTLGSKSKRLKIENEDVIELKLTWEEAQGLLRPPPNNVPSVVVIEGYEFEEYEDAPILGKPTIFATDNVGEKIQWVQCEDCSKWRKVPANARLPSKWTCSGNLWDPERSVCSVAQELREEQLEDLIAPNNPASSKKLKAAKQEPDCVEALEGLDTLANLAILGEGEGLTASSQATTKHPRHRPGCSCIVCIQPPSGKGPKHKQTCTCNVCLTVKRRFHTLMLRREKKQSEKDAETSRKKQQQQKLPVPEKSADDDPLSCSKTGNNSPNEKKVVSEGSDDDSSRIKSSTSPFKGQIDLNIQPEREEELSPGSDSGSMIRLLQDATEKYLRQQRLSSSGVNTSSVDNEGLQGGVTGEKISNGITLDGSHQDTDEDHHGSLSVKASASISATG

cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHccccccccccccccccccccccccccHHHHHccccccccccccEEEEEccccccccccEEEEHHHHHHHcccccccccccEEEEcccccEEEEEEEEEccccccEEEEcccHHHHHccccccccEEEEEcccccccEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEccccccccccHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEccccccccccccccccccHHHHHHHccccccccHHHHHHccccccHHHccccHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc

cccccccccccccccccccccccccccccccccccccccccccccccccccccccccHccccccccccccccccccccccccccccccccccccccccccHHHHHHccccccccccHHHHEEccHccccccccEEEcHHHHHHHccccccccccEEEEEcccccEEEEEEEEcccccccEEEEccccHHHHHcccccccEEEEEEcccccEEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccHHHHHHHHHHHHHHHHcccccccccEEEEEEccEEEEcccccEEcccEEEEEccccccEEEEEcccccccccccccEEcccccccccccccccccccccHHHccHHHHHHHcccccHHHHHHHHHHccccHccccccHHHHHHHHHHHcccccccccccccccccccccccEEEEEEcccccccccccccccccHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccEEcccccccHHHccccccccHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccEEEccccccccccccccccccccccccccc

mqpssclnkpqqsstlkddsstphfglavsyaspsetnsqigvsgshlrpvvqpplvkqfhgnlpngadslgetqvrngrprvdargrsqllprywprftdqdlqqisgdsnsvITPLFEKMLsasdagrigrlvlpkkcaeayfppisqpeglplkvqdskgKEWIFQFrfwpnnnsrmyvLEGVTPCiqnmqlqagdivtfsrlepegklvmgfrkassasasdqdneankagtgipanghaeladpsswskvdksgyiaTEALgakssisrkrknttlgskskrlkieNEDVIELKLTWEEaqgllrpppnnvpsvvviegyefeeyedapilgkptifatdnvgekiqwvqcedcskwrkvpanarlpskwtcsgnlwdpersVCSVAQELREEQLEdliapnnpasskklkaakqepDCVEALEGLDTLANLAIlgegegltassqattkhprhrpgcscivciqppsgkgpkhkqtctcnvcltvKRRFHTLMLRREKKQSEKDAETSRKKQqqqklpvpeksadddplscsktgnnspnekkvvsegsdddssriksstspfkgqidlniqpereeelspgsdsgSMIRLLQDATEKYLRQQrlsssgvntssvdneglqggvtgekisngitldgshqdtdedhhgslsvkasaSISATG

mqpssclnkpqqsstlkddsstpHFGLAVSYASPSETNSQIGVSGSHLRPVVQPPLVKQFHGNLPngadslgetqvrngrprvdargrsqllprywPRFTDQDLQQISGDSNSVITPLFEKMLSASDAGRIGRLVLPKKCAEAyfppisqpeglPLKVQDSKGKEWIFQFRFWPNNNSRMYVLEGVTPCIQNMQLQAGDIVTFSRLEPEGKLVMGFRKAssasasdqdneaNKAGTGIPANGHAELADPSSWSKVDKSGYIATealgakssisrkrknttlgskskrlkienedvIELKLTWeeaqgllrpppnnvpsVVVIEGYEFEEYEDAPILGKPTIFATDNVGEKIQWVQCEDCSKWrkvpanarlpskwtcsgnlwdpeRSVCSVAQELREEQLedliapnnpasskklKAAKQEPDCVEALEGLDTLANLAILGEGEGLTASSQATTKHPRHRPGCSCIVCIQPpsgkgpkhkqtctcnvcltvkRRFHTLMLrrekkqsekdaetsrkkqqqqklpvpeksadddplscsktgnnspnekkvvsegsdddssriksstspfkgqidlniqpereeelspgsdsgSMIRLLQDATEKYLRQQRlsssgvntssvdneglqggvTGEKISNGITLDGSHQdtdedhhgslsvkasasisatg

MQPSSCLNKPQQSSTLKDDSSTPHFGLAVSYASPSETNSQIGVSGSHLRPVVQPPLVKQFHGNLPNGADSLGETQVRNGRPRVDARGRSQLLPRYWPRFTDQDLQQISGDSNSVITPLFEKMLSASDAGRIGRLVLPKKCAEAYFPPISQPEGLPLKVQDSKGKEWIFQFRFWPNNNSRMYVLEGVTPCIQNMQLQAGDIVTFSRLEPEGKLVMGFRKASSASASDQDNEANKAGTGIPANGHAELADPSSWSKVDKSGYIATEALGAKSSISRKRKNTTLGSKSKRLKIENEDVIELKLTWEEAQGLLRpppnnvpsvvvIEGYEFEEYEDAPILGKPTIFATDNVGEKIQWVQCEDCSKWRKVPANARLPSKWTCSGNLWDPERSVCSVAQELREEQLEDLIAPNNPASSKKLKAAKQEPDCVEALEGLDTLANLAILGEGEGLTASSQATTKHPRHRPGCSCIVCIQPPSGKGPKHKQTCTCNVCLTVKRRFHTLMLRREKKQSEKDAETSRKKQQQQKLPVPEKSADDDPLSCSKTGNNSPNEKKVVSEGSDDDSSRIKSSTSPFKGQIDLNIQPEREEELSPGSDSGSMIRLLQDATEKYLRQQRLSSSGVNTSSVDNEGLQGGVTGEKISNGITLDGSHQDTDEDHHGSLSVKASASISATG

******************************************************************************************LLPRYWPRFTDQDLQQI****NSVITPLFEKMLSASDAGRIGRLVLPKKCAEAYFPPISQPEGLPLKVQDSKGKEWIFQFRFWPNNNSRMYVLEGVTPCIQNMQLQAGDIVTFSRLEPEGKLV*******************************************************************************EDVIELKLTWEEAQGLLRPPPNNVPSVVVIEGYEFEEYEDAPILGKPTIFATDNVGEKIQWVQCEDCSKWRKVPANARLPSKWTCSGNLWDPERSVCSV********************************CVEALEGLDTLANLAILGE*******************GCSCIVCIQ*********KQTCTCNVCLTVKRRFHTLML************************************************************************************************************************************************************************

*********************************************************************************************************************LFEKMLSASDAGRIGRLVLPKKCAEAYFPPISQPEGLPLKVQDSKGKEWIFQFRFWPNNNSRMYVLEGVTPCIQNMQLQAGDIVTFSRLEPEGKLVMGF**********************PANGHAELADPSSWSKVDKSGYIATEA************************IENEDVIELKLTWEE*Q***********************************FATDNVGEKIQWVQCEDCSKWRKVPANARLPSKWTCSGNLWD***********************************************************************************************************************************************************************************************************************QDAT******************************************************************

*********************TPHFGLAVSYASPSETNSQIGVSGSHLRPVVQPPLVKQFHGNLPNGADSLGETQVRNGRPRVDARGRSQLLPRYWPRFTDQDLQQISGDSNSVITPLFEKMLSASDAGRIGRLVLPKKCAEAYFPPISQPEGLPLKVQDSKGKEWIFQFRFWPNNNSRMYVLEGVTPCIQNMQLQAGDIVTFSRLEPEGKLVMGF*****************AGTGIPANGHAELADPSSWSKVDKSGYIATEALGAKSSISRKRKNTTLGSKSKRLKIENEDVIELKLTWEEAQGLLRPPPNNVPSVVVIEGYEFEEYEDAPILGKPTIFATDNVGEKIQWVQCEDCSKWRKVPANARLPSKWTCSGNLWDPERSVCSVAQELREEQLEDLIAPNNPA***********PDCVEALEGLDTLANLAILGEGEGL**************PGCSCIVCIQPP*********TCTCNVCLTVKRRFHTLMLR*******************************************************************FKGQIDLNIQPE***********GSMIRLLQDATEKYLRQ*************DNEGLQGGVTGEKISNGITLDGS************************

*****************************************************************************************QLLPRYWPRFTDQDLQQIS*DSNSVITPLFEKMLSASDAGRIGRLVLPKKCAEAYFPPISQPEGLPLKVQDSKGKEWIFQFRFWPNNNSRMYVLEGVTPCIQNMQLQAGDIVTFSRLEPEGKLVMGFRKAS****************************************************************SKRLKIENEDVIELKLTWEEAQGLLRPPPNNVPSVVVIEGYEFEEYEDAPILGKPTIFATDNVGEKIQWVQCEDCSKWRKVPANARLPSKWTCSGNLWDPERSVCSVAQELREEQLEDLIAPNNPASSKKLK***********LEGLDTLANLAILGE*****************RPGCSCIVCIQPPSGKGPKHKQTCTCNVCLTVKRRFHTLMLRREKKQ*****************************************************************QI***IQPERE******SDSGSMIRLLQDATEKYLRQQRL*********************************************************

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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MQPSSCLNKPQQSSTLKDDSSTPHFGLAVSYASPSETNSQIGVSGSHLRPVVQPPLVKQFHGNLPNGADSLGETQVRNGRPRVDARGRSQLLPRYWPRFTDQDLQQISGDSNSVITPLFEKMLSASDAGRIGRLVLPKKCAEAYFPPISQPEGLPLKVQDSKGKEWIFQFRFWPNNNSRMYVLEGVTPCIQNMQLQAGDIVTFSRLEPEGKLVMGFRKASSASASDQDNEANKAGTGIPANGHAELADPSSWSKVDKSGYIATEALGAKSSISRKRKNTTLGSKSKRLKIENEDVIELKLTWEEAQGLLRPPPNNVPSVVVIEGYEFEEYEDAPILGKPTIFATDNVGEKIQWVQCEDCSKWRKVPANARLPSKWTCSGNLWDPERSVCSVAQELREEQLEDLIAPNNPASSKKLKAAKQEPDCVEALEGLDTLANLAILGEGEGLTASSQATTKHPRHRPGCSCIVCIQPPSGKGPKHKQTCTCNVCLTVKRRFHTLMLRxxxxxxxxxxxxxxxxxxxxxLPVPEKSADDDPLSCSKTGNNSPNEKKVVSEGSDDDSSRIKSSTSPFKGQIDLNIQPEREEELSPGSDSGSMIRLLQDATEKYLRQQRLSSSGVNTSSVDNEGLQGGVTGEKISNGITLDGSHQDTDEDHHGSLSVKASASISATG

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
Query		668	2.2.26 [Sep-21-2011]
Q0D5G4		955	B3 domain-containing prot	yes	no	0.853	0.596	0.571	0.0
Q5CCK4		780	B3 domain-containing tran	yes	no	0.784	0.671	0.464	1e-141
Q6Z3U3		949	B3 domain-containing prot	no	no	0.772	0.543	0.479	1e-136
Q8W4L5		790	B3 domain-containing tran	no	no	0.732	0.618	0.479	1e-127
O65420		713	B3 domain-containing tran	no	no	0.473	0.443	0.480	2e-71
Q7XKC4		438	Putative B3 domain-contai	no	no	0.160	0.244	0.444	1e-18
Q9LW31		313	B3 domain-containing tran	no	no	0.167	0.357	0.407	4e-18
Q7XKC5		433	B3 domain-containing prot	no	no	0.152	0.235	0.456	5e-18
Q6Z1Z3		362	B3 domain-containing prot	no	no	0.152	0.281	0.407	9e-16
A4LBC0		402	B3 domain-containing prot	no	no	0.161	0.268	0.381	2e-15

>sp\|Q0D5G4\|Y7633_ORYSJ B3 domain-containing protein Os07g0563300 OS=Oryza sativa subsp. japonica GN=Os07g0563300 PE=2 SV=2	Back alignment and function desciption

 Score =  652 bits (1681), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 352/616 (57%), Positives = 431/616 (69%), Gaps = 46/616 (7%)

Query: 14  STLKDDSSTPHFGLAVSYASPSETNSQIGVSGSHLRP-VVQPPLVKQFHGNLPNGADSLG 72
           S LKDD S    GL+ +++S +     I +  +  +  +    L KQF+ +  +  D+  
Sbjct: 349 SILKDDPSAVPAGLSSNFSSANGPKDHIRIGPTQQQQQMASSSLQKQFYSH--SVIDNDF 406

Query: 73  ETQVRNGRPRVDARGRSQLLPRYWPRFTDQDLQQISGDSNSVITPLFEKMLSASDAGRIG 132
           + Q+RNGRPR+DA+ RSQLLPRYWPR TDQ+LQ +SGDSNSVITPLFEKMLSASDAGRIG
Sbjct: 407 QAQLRNGRPRMDAKARSQLLPRYWPRITDQELQHLSGDSNSVITPLFEKMLSASDAGRIG 466

Query: 133 RLVLPKKCAEAYFPPISQPEGLPLKVQDSKGKEWIFQFRFWPNNNSRMYVLEGVTPCIQN 192
           RLVLPKKCAEAYFP ISQ EGLPLKVQD+ GKEW+FQFRFWPNNNSRMYVLEGVTPCIQ+
Sbjct: 467 RLVLPKKCAEAYFPAISQAEGLPLKVQDATGKEWVFQFRFWPNNNSRMYVLEGVTPCIQS 526

Query: 193 MQLQAGDIVTFSRLEPEGKLVMGFRKASSASASDQDNEANKAGTGIP---ANGHAELADP 249
           MQLQAGD VTFSR++PEGKLVMGFRKA++ SA +QD     A   +P   AN    + D 
Sbjct: 527 MQLQAGDTVTFSRIDPEGKLVMGFRKATNLSA-EQDQPTKPANGVLPPPEANNKVVVPDS 585

Query: 250 S------------------------SWSKVDKSGYIATEALGAKSS--ISRKRKNTTLGS 283
           S                        +  K+DK      E  G  SS  +  KRK T++G 
Sbjct: 586 SPNAAVPRPIKVNTESKSSSPVEQATACKIDKGALPQKEGPGTSSSSPLPVKRKATSVGP 645

Query: 284 KSKRLKIENEDVIELKLTWEEAQGLLRPPPNNVPSVVVIEGYEFEEYEDAPILGKPTIFA 343
           K KR  +++E+ +ELK+TWEEAQ LLRPPP   PS+VV++G+EFEEYE+ PILG+ T F 
Sbjct: 646 KIKRFHMDSEESMELKITWEEAQELLRPPP-KAPSIVVVDGHEFEEYEEPPILGRRTYFV 704

Query: 344 TDNVGEKIQWVQCEDCSKWRKVPANARLPSKWTCSGNLWDPERSVCSVAQELREEQLEDL 403
           TD  GE  QW QCEDCSKWRK+P +A LPSKWTCS N WD ERS C  AQE+  E+L ++
Sbjct: 705 TDQSGENHQWAQCEDCSKWRKLPVDALLPSKWTCSDNKWDSERSSCDSAQEINMEELGEM 764

Query: 404 IAPNNPASSKKLKAAKQEPDCVEALEGLDTLANLAILGEGEGLTASSQATTKHPRHRPGC 463
           I P  P ++KK K  K + D ++  +GLDTLANLAILGEGE L   SQ TT+HPRHRPGC
Sbjct: 765 I-PIKPGAAKKTK-GKVDTDNIDVSDGLDTLANLAILGEGESL--PSQPTTRHPRHRPGC 820

Query: 464 SCIVCIQPPSGKGPKHKQTCTCNVCLTVKRRFHTLMLRREKK-QSEKDAETSRKKQQ-QQ 521
           SCIVCIQPPSGKGPKHKQTCTCNVC+TV+RRF TLM+RREK+ QSEKD+   RK++  Q 
Sbjct: 821 SCIVCIQPPSGKGPKHKQTCTCNVCMTVRRRFRTLMMRREKRQQSEKDSGVPRKREPGQS 880

Query: 522 KLPVPEKSADDDPLSCSKTGNNSPNEKKVVS-EGSDDDSSRIKSSTSPFKGQIDLNIQPE 580
             PVP+  +   P S S     SP+++   + EG +D S   K ++SP K QIDLN QPE
Sbjct: 881 SEPVPQSGSGAHPTSTS-----SPHQRADTNGEGPEDMSIDNKRTSSPVKNQIDLNSQPE 935

Query: 581 REEELSPGSDSGSMIR 596
           RE+E SP SD+  ++R
Sbjct: 936 REDEQSPKSDATRLLR 951

Oryza sativa subsp. japonica (taxid: 39947)

>sp\|Q5CCK4\|VAL2_ARATH B3 domain-containing transcription repressor VAL2 OS=Arabidopsis thaliana GN=VAL2 PE=2 SV=1	Back alignment and function description

>sp\|Q6Z3U3\|Y7797_ORYSJ B3 domain-containing protein Os07g0679700 OS=Oryza sativa subsp. japonica GN=Os07g0679700 PE=2 SV=1	Back alignment and function description

>sp\|Q8W4L5\|VAL1_ARATH B3 domain-containing transcription repressor VAL1 OS=Arabidopsis thaliana GN=VAL1 PE=1 SV=1	Back alignment and function description

>sp\|O65420\|VAL3_ARATH B3 domain-containing transcription factor VAL3 OS=Arabidopsis thaliana GN=VAL3 PE=4 SV=3	Back alignment and function description

>sp\|Q7XKC4\|Y4765_ORYSJ Putative B3 domain-containing protein Os04g0676650 OS=Oryza sativa subsp. japonica GN=Os04g0676650 PE=3 SV=2	Back alignment and function description

>sp\|Q9LW31\|FUS3_ARATH B3 domain-containing transcription factor FUS3 OS=Arabidopsis thaliana GN=FUS3 PE=2 SV=2	Back alignment and function description

>sp\|Q7XKC5\|IDEFH_ORYSJ B3 domain-containing protein Os04g0676600 OS=Oryza sativa subsp. japonica GN=Os04g0676600 PE=2 SV=1	Back alignment and function description

>sp\|Q6Z1Z3\|IDEF1_ORYSJ B3 domain-containing protein IDEF1 OS=Oryza sativa subsp. japonica GN=IDEF1 PE=2 SV=1	Back alignment and function description

>sp\|A4LBC0\|LFL1_ORYSJ B3 domain-containing protein LFL1 OS=Oryza sativa subsp. japonica GN=LFL1 PE=2 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		668
224076806		918	predicted protein [Populus trichocarpa]	0.980	0.713	0.736	0.0
255560846		854	transcription factor, putative [Ricinus	0.965	0.755	0.739	0.0
449433878		896	PREDICTED: B3 domain-containing protein	0.995	0.742	0.702	0.0
357446313		888	B3 domain-containing transcription repre	0.970	0.729	0.730	0.0
449479362		899	PREDICTED: LOW QUALITY PROTEIN: B3 domai	0.995	0.739	0.704	0.0
224116220		842	predicted protein [Populus trichocarpa]	0.974	0.773	0.711	0.0
356549413		855	PREDICTED: B3 domain-containing protein	0.955	0.746	0.709	0.0
356549411		889	PREDICTED: B3 domain-containing protein	0.976	0.733	0.703	0.0
356555034		854	PREDICTED: B3 domain-containing protein	0.946	0.740	0.710	0.0
239983848		955	RecName: Full=B3 domain-containing prote	0.853	0.596	0.571	0.0

>gi\|224076806\|ref\|XP_002305001.1\| predicted protein [Populus trichocarpa] gi\|222847965\|gb\|EEE85512.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

 Score =  982 bits (2539), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 495/672 (73%), Positives = 552/672 (82%), Gaps = 17/672 (2%)

Query: 9   KPQQSSTLKDDSSTPHFGLAVSYASPSETNSQIGVSGSHLRPVVQPPLVKQFHGNLPNGA 68
           +PQ SS+L +D+S   FG+ + Y S SE+NSQI  S + L+P   PP  K FHG+L NG 
Sbjct: 252 QPQPSSSLMEDASGQQFGITIPYKSISESNSQIEGSVNALQPAPPPPFTKHFHGSLHNGV 311

Query: 69  DSLGETQVRNGRPRVDARGRSQLLPRYWPRFTDQDLQQISGDSNSVITPLFEKMLSASDA 128
           DS  +  +RNG+PR DARGRSQLLPRYWPRFTD +LQQISG+SNSVI PLFEKMLSASDA
Sbjct: 312 DSSVDGHIRNGKPRTDARGRSQLLPRYWPRFTDGELQQISGNSNSVIKPLFEKMLSASDA 371

Query: 129 GRIGRLVLPKKCAEAYFPPISQPEGLPLKVQDSKGKEWIFQFRFWPNNNSRMYVLEGVTP 188
           GRIGRLVLPKKCAEAYFPPISQPEGLPL+VQDSKGKEWIFQFRFWPNNNSRMYVLEGVTP
Sbjct: 372 GRIGRLVLPKKCAEAYFPPISQPEGLPLRVQDSKGKEWIFQFRFWPNNNSRMYVLEGVTP 431

Query: 189 CIQNMQLQAGDIVTFSRLEPEGKLVMGFRKASSASASDQDNEANKAGTGIPANGHAELAD 248
           CIQNMQLQAGDIVTFSRLEPEGKLVMGFRKA+SA  SDQDNE ++ G G+   G AEL D
Sbjct: 432 CIQNMQLQAGDIVTFSRLEPEGKLVMGFRKATSAPPSDQDNETSQTGNGVSTKGDAEL-D 490

Query: 249 PSSWSKVDKSGYIATEALGAKSSISRKRKNTTLGSKSKRLKIENEDVIELKLTWEEAQGL 308
           PS WSKVDKSGYIA E L  KSSI RKRK++TLGSKSKRL+IENED+IELKLTWEEAQGL
Sbjct: 491 PSPWSKVDKSGYIAKEVLEGKSSI-RKRKSSTLGSKSKRLRIENEDMIELKLTWEEAQGL 549

Query: 309 LRPPPNNVPSVVVIEGYEFEEYEDAPILGKPTIFATDNVGEKIQWVQCEDCSKWRKVPAN 368
           LRPPP++VPS+V IEG+EFEEYEDAP+LGKPTIFATDNVG+KIQWVQCEDC KWRK+PAN
Sbjct: 550 LRPPPDHVPSIVAIEGFEFEEYEDAPVLGKPTIFATDNVGQKIQWVQCEDCLKWRKLPAN 609

Query: 369 ARLPSKWTCSGNLWDPERSVCSVAQELREEQLEDLI-APNNPASSKKLKAAKQEPDCVEA 427
           A LPSKW CS N WDPERS CSVAQEL  EQLEDL+ + N   +SK+ K AK++ D VEA
Sbjct: 610 ALLPSKWACSSNTWDPERSSCSVAQELTAEQLEDLLPSCNLVVTSKRSKDAKKDIDRVEA 669

Query: 428 LEGLDTLANLAILGEGEGLTASSQATTKHPRHRPGCSCIVCIQPPSGKGPKHKQTCTCNV 487
           LEGLDTLANLAILGEGE   ASSQATTKHPRHRPGCSCIVCIQPPSGKGPKHKQTCTCNV
Sbjct: 670 LEGLDTLANLAILGEGEAFPASSQATTKHPRHRPGCSCIVCIQPPSGKGPKHKQTCTCNV 729

Query: 488 CLTVKRRFHTLMLRREK---------KQSEKDAETSRKKQQQQKLPVPEKSADDDPLSCS 538
           C TVKRRF TLM++REK         KQSEK+AET+RK+QQ+   P  EK  DD+P   S
Sbjct: 730 CQTVKRRFKTLMMKREKKQSEKEAETKQSEKEAETTRKRQQE---PSAEKLLDDEPSPSS 786

Query: 539 KTG--NNSPNEKKVVSEGSDDDSSRIKSSTSPFKGQIDLNIQPEREEELSPGSDSGSMIR 596
            TG  + SPN+KK VSEGSDDD SR+KSSTSPFKGQIDLNIQPERE+ELSPGSDSG M+R
Sbjct: 787 NTGSESGSPNKKKTVSEGSDDDPSRMKSSTSPFKGQIDLNIQPEREDELSPGSDSGGMMR 846

Query: 597 LLQDATEKYLRQQRLSSSGVNTSSVDNEGLQGGVTGEKISNGITLDGSHQDTDEDHHGSL 656
           +LQDATE YLR QR  SS  + +   N  L  G T EK+S+ I L  SHQD D+DH  + 
Sbjct: 847 MLQDATETYLRMQRFLSSDGDNNPSGNHMLSSGGTREKVSDVIMLGSSHQDADKDHPSAF 906

Query: 657 SVKASASISATG 668
           S+ ASAS  ATG
Sbjct: 907 SMNASASTPATG 918

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|255560846\|ref\|XP_002521436.1\| transcription factor, putative [Ricinus communis] gi\|223539335\|gb\|EEF40926.1\| transcription factor, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|449433878\|ref\|XP_004134723.1\| PREDICTED: B3 domain-containing protein Os07g0563300-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|357446313\|ref\|XP_003593434.1\| B3 domain-containing transcription repressor VAL2 [Medicago truncatula] gi\|355482482\|gb\|AES63685.1\| B3 domain-containing transcription repressor VAL2 [Medicago truncatula]	Back alignment and taxonomy information

>gi\|449479362\|ref\|XP_004155579.1\| PREDICTED: LOW QUALITY PROTEIN: B3 domain-containing protein Os07g0563300-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|224116220\|ref\|XP_002317242.1\| predicted protein [Populus trichocarpa] gi\|222860307\|gb\|EEE97854.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|356549413\|ref\|XP_003543088.1\| PREDICTED: B3 domain-containing protein Os07g0563300-like isoform 2 [Glycine max]	Back alignment and taxonomy information

>gi\|356549411\|ref\|XP_003543087.1\| PREDICTED: B3 domain-containing protein Os07g0563300-like isoform 1 [Glycine max]	Back alignment and taxonomy information

>gi\|356555034\|ref\|XP_003545844.1\| PREDICTED: B3 domain-containing protein Os07g0563300-like [Glycine max]	Back alignment and taxonomy information

>gi\|239983848\|sp\|Q0D5G4.2\|Y7633_ORYSJ RecName: Full=B3 domain-containing protein Os07g0563300	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
Query		668
TAIR\|locus:2116592		780	HSL1 "HSI2-like 1" [Arabidopsi	0.736	0.630	0.502	2.9e-133
TAIR\|locus:2064417		790	HSI2 "high-level expression of	0.817	0.691	0.451	1.7e-124
TAIR\|locus:2088439		313	FUS3 "FUSCA 3" [Arabidopsis th	0.166	0.354	0.412	2.8e-16
TAIR\|locus:2039165		244	ABS2 "ABNORMAL SHOOT 2" [Arabi	0.184	0.504	0.382	2e-15
UNIPROTKB\|Q6Z1Z3		362	IDEF1 "B3 domain-containing pr	0.282	0.522	0.326	2.4e-15
UNIPROTKB\|Q7XKC5		433	LOC_Os04g58000 "B3 domain-cont	0.152	0.235	0.456	3.1e-15
UNIPROTKB\|A4LBC0		402	LFL1 "B3 domain-containing pro	0.323	0.537	0.293	1.9e-14
UNIPROTKB\|P37398		727	VP1 "B3 domain-containing prot	0.199	0.182	0.357	1.2e-13
TAIR\|locus:2032170		363	LEC2 "LEAFY COTYLEDON 2" [Arab	0.269	0.495	0.308	1.7e-13
TAIR\|locus:2093166		720	ABI3 "AT3G24650" [Arabidopsis	0.232	0.215	0.331	2e-13

TAIR\|locus:2116592 HSL1 "HSI2-like 1" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1260 (448.6 bits), Expect = 2.9e-133, Sum P(2) = 2.9e-133
 Identities = 259/515 (50%), Positives = 341/515 (66%)

Query:    35 SETNS--QIGVSGSHL--RPVVQPPLVKQFHGNLPNGADSLGETQVRNGRPRVDARGRSQ 90
             S+TNS  Q+      L  +P    P+     G  P+G  SL  +Q+   RP  + RG++Q
Sbjct:   200 SKTNSIFQLAPRSRQLLPKPANSAPIAA---GMEPSG--SL-VSQIHVARPPPEGRGKTQ 253

Query:    91 LLPRYWPRFTDQDLQQISGD----SNSVITPLFEKMLSASDAGRIGRLVLPKKCAEAYFP 146
             LLPRYWPR TDQ+L Q+SG     SNS I PLFEK+LSASDAGRIGRLVLPK CAEAYFP
Sbjct:   254 LLPRYWPRITDQELLQLSGQYPHLSNSKIIPLFEKVLSASDAGRIGRLVLPKACAEAYFP 313

Query:   147 PISQPEGLPLKVQDSKGKEWIFQFRFWPNNNSRMYVLEGVTPCIQNMQLQAGDIVTFSRL 206
             PIS PEGLPLK+QD KGKEW+FQFRFWPNNNSRMYVLEGVTPCIQ+MQLQAGD VTFSR 
Sbjct:   314 PISLPEGLPLKIQDIKGKEWVFQFRFWPNNNSRMYVLEGVTPCIQSMQLQAGDTVTFSRT 373

Query:   207 EPEGKLVMGFRKASSASASDQDNEANKAGTGIPANGHAELADPSSWSKVDKSGYIATEAL 266
             EPEGKLVMG+RKA++++A+     +++    + +N         +WSK++KS  +A + L
Sbjct:   374 EPEGKLVMGYRKATNSTATQMFKGSSEPNLNMFSNSLNPGCGDINWSKLEKSEDMAKDNL 433

Query:   267 GAKSSISRKRKNT-TLGSKSKRLKIENEDVIELKLTWEEAQGLLRXXXXXXXXXXXIEGY 325
               +SS++  RK    +G+KSKRL I++ DV+ELK+TWEEAQ LLR           +E  
Sbjct:   434 FLQSSLTSARKRVRNIGTKSKRLLIDSVDVLELKITWEEAQELLRPPQSTKPSIFTLENQ 493

Query:   326 EFEEYEDAPILGKPTIFATDNVGEKIQWVQCEDCSKWRKVPANARLPSKWTCSGNLWDPE 385
             +FEEY++ P+ GK T+F +   GE+ QWVQC+ C KWR++P +  LP KW+CS NL DP 
Sbjct:   494 DFEEYDEPPVFGKRTLFVSRQTGEQEQWVQCDACGKWRQLPVDILLPPKWSCSDNLLDPG 553

Query:   386 RSVCSVAQELREEQLEDLIAPNNPASSKKLKAAKQEPDCVEALEGLDTLANLAILGEGEG 445
             RS CS   EL   + + L+  +     ++L ++ ++ +  +    L++L N  I   GE 
Sbjct:   554 RSSCSAPDELSPREQDTLVRQSKEFKRRRLASSNEKLNQSQDASALNSLGNAGITTTGEQ 613

Query:   446 LTASSQATTKHPRHRPGCSCIVCIQPPSGKGPKHKQTCTCNVCLTVKRRFHTLMLRREKK 505
                +  ATTKHPRHR GCSCIVC QPPSGKG KHK +CTC VC  VKRRF TLMLR+  K
Sbjct:   614 GEITVAATTKHPRHRAGCSCIVCSQPPSGKG-KHKPSCTCTVCEAVKRRFRTLMLRKRNK 672

Query:   506 ----QSEKDAETS---RKKQQQQKLPVPEKSADDD 533
                 Q+ + A++    R + + + +P  E +A ++
Sbjct:   673 GEAGQASQQAQSQSECRDETEVESIPAVELAAGEN 707

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0010030 "positive regulation of seed germination" evidence=IGI

GO:2000034 "regulation of seed maturation" evidence=IGI

GO:0007062 "sister chromatid cohesion" evidence=RCA

GO:0009630 "gravitropism" evidence=RCA

GO:0009790 "embryo development" evidence=RCA

GO:0009880 "embryonic pattern specification" evidence=RCA

GO:0010072 "primary shoot apical meristem specification" evidence=RCA

GO:0010162 "seed dormancy process" evidence=RCA

GO:0010431 "seed maturation" evidence=RCA

GO:0010564 "regulation of cell cycle process" evidence=RCA

GO:0043687 "post-translational protein modification" evidence=RCA

GO:0045595 "regulation of cell differentiation" evidence=RCA

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

GO:0048316 "seed development" evidence=RCA

GO:0048366 "leaf development" evidence=RCA

GO:0048825 "cotyledon development" evidence=RCA

GO:0051301 "cell division" evidence=RCA

GO:0005515 "protein binding" evidence=IPI

TAIR\|locus:2064417 HSI2 "high-level expression of sugar-inducible gene 2" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2088439 FUS3 "FUSCA 3" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2039165 ABS2 "ABNORMAL SHOOT 2" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

UNIPROTKB\|Q6Z1Z3 IDEF1 "B3 domain-containing protein IDEF1" [Oryza sativa Japonica Group (taxid:39947)]	Back alignment and assigned GO terms

UNIPROTKB\|Q7XKC5 LOC_Os04g58000 "B3 domain-containing protein Os04g0676600" [Oryza sativa Japonica Group (taxid:39947)]	Back alignment and assigned GO terms

UNIPROTKB\|A4LBC0 LFL1 "B3 domain-containing protein LFL1" [Oryza sativa Japonica Group (taxid:39947)]	Back alignment and assigned GO terms

UNIPROTKB\|P37398 VP1 "B3 domain-containing protein VP1" [Oryza sativa Japonica Group (taxid:39947)]	Back alignment and assigned GO terms

TAIR\|locus:2032170 LEC2 "LEAFY COTYLEDON 2" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2093166 ABI3 "AT3G24650" [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:
	eugene3.00040219	hypothetical protein (918 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
Query		668
cd10017		98	cd10017, B3_DNA, Plant-specific B3-DNA binding dom	2e-22
pfam02362		97	pfam02362, B3, B3 DNA binding domain	4e-20
smart01019		96	smart01019, B3, B3 DNA binding domain	2e-17
pfam07496		50	pfam07496, zf-CW, CW-type Zinc Finger	2e-12
cd10015		109	cd10015, BfiI_C_EcoRII_N_B3, DNA binding domains o	2e-08

>gnl\|CDD\|197383 cd10017, B3_DNA, Plant-specific B3-DNA binding domain	Back alignment and domain information

 Score = 92.0 bits (229), Expect = 2e-22
 Identities = 34/102 (33%), Positives = 54/102 (52%), Gaps = 4/102 (3%)

Query: 117 PLFEKMLSASDAGRIGRLVLPKKCAEAYFPPISQPEGLPLKVQDSKGKEWIFQFRFWPNN 176
           PLF K+L+ SD   +GRLVLPKK A+A+ PP    EG+ + ++D  GK+W  + +   N+
Sbjct: 1   PLFFKVLTPSDVSSLGRLVLPKKFAKAHLPP---KEGVEVTLEDPDGKKWTVKLKKRKNS 57

Query: 177 NSRMYVLEGVTPCIQNMQLQAGDIVTFSRLEPEGKLVMGFRK 218
             RM +  G    ++   L+ GD + F       K  +   +
Sbjct: 58  G-RMVLSGGWKEFVRANGLKEGDFLVFELDGRNSKFKVRIFR 98

The plant-specific B3 DNA binding domain superfamily includes the well-characterized auxin response factor (ARF) and the LAV (Leafy cotyledon2 [LEC2]-Abscisic acid insensitive3 [ABI3]-VAL) families, as well as the RAV (Related to ABI3 and VP1) and REM (REproductive Meristem) families. LEC2 and ABI3 have been shown to be involved in seed development, while other members of the LAV family seem to have a more general role, being expressed in many organs during plant development. Members of the ARF family bind to the auxin response element and depending on presence of an activation or repression domain, they activate or repress transcription. RAV and REM families are less studied B3 protein famillies. Length = 98

>gnl\|CDD\|216995 pfam02362, B3, B3 DNA binding domain	Back alignment and domain information

>gnl\|CDD\|214977 smart01019, B3, B3 DNA binding domain	Back alignment and domain information

>gnl\|CDD\|219431 pfam07496, zf-CW, CW-type Zinc Finger	Back alignment and domain information

>gnl\|CDD\|197381 cd10015, BfiI_C_EcoRII_N_B3, DNA binding domains of BfiI, EcoRII and plant B3 proteins	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		668
PF02362		100	B3: B3 DNA binding domain; InterPro: IPR003340 Two	99.65
PF07496		50	zf-CW: CW-type Zinc Finger; InterPro: IPR011124 Zi	99.62
PF03754		114	DUF313: Domain of unknown function (DUF313) ; Inte	98.11
PF09217		156	EcoRII-N: Restriction endonuclease EcoRII, N-termi	97.6
smart00249		47	PHD PHD zinc finger. The plant homeodomain (PHD) f	80.51

>PF02362 B3: B3 DNA binding domain; InterPro: IPR003340 Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species	Back alignment and domain information

Probab=99.65  E-value=7.4e-16  Score=132.00  Aligned_cols=97  Identities=24%  Similarity=0.434  Sum_probs=70.0

Q ss_pred             EEEecccccCCCCCcEEeehhhhcccCCCCCCCCCceEEEEeCCCCeEEEEEEEcCCCCCccccc-cCchhhhhccCCCC
Q 005945          119 FEKMLSASDAGRIGRLVLPKKCAEAYFPPISQPEGLPLKVQDSKGKEWIFQFRFWPNNNSRMYVL-EGVTPCIQNMQLQA  197 (668)
Q Consensus       119 F~KvLT~SDVgklgRLVIPK~~AE~~FPpL~~~~G~~L~v~D~~Gk~W~FRfsyw~nn~SR~YVL-~GWs~FVrsK~Lka  197 (668)
                      |.|+|+++|+.+.++|+||++.++.|.  +....++.|.+.|..|+.|.+++.++. +..+ |+| .||..||++++|++
T Consensus         1 F~K~l~~s~~~~~~~l~iP~~f~~~~~--~~~~~~~~v~l~~~~g~~W~v~~~~~~-~~~~-~~l~~GW~~Fv~~n~L~~   76 (100)
T PF02362_consen    1 FFKVLKPSDVSSSCRLIIPKEFAKKHG--GNKRKSREVTLKDPDGRSWPVKLKYRK-NSGR-YYLTGGWKKFVRDNGLKE   76 (100)
T ss_dssp             EEEE--TTCCCCTT-EEE-HHHHTTTS----SS--CEEEEEETTTEEEEEEEEEEC-CTTE-EEEETTHHHHHHHCT--T
T ss_pred             CEEEEEccCcCCCCEEEeCHHHHHHhC--CCcCCCeEEEEEeCCCCEEEEEEEEEc-cCCe-EEECCCHHHHHHHcCCCC
Confidence            899999999998889999999999982  112357899999999999999999883 3333 555 69999999999999


Q ss_pred             CCEEEEEEec-CCCeEEEEEEeC
Q 005945          198 GDIVTFSRLE-PEGKLVMGFRKA  219 (668)
Q Consensus       198 GDtVvF~R~e-~~GkL~IGVRRa  219 (668)
                      ||.|+|+... ...++.|.|.|+
T Consensus        77 GD~~~F~~~~~~~~~~~v~i~~~   99 (100)
T PF02362_consen   77 GDVCVFELIGNSNFTLKVHIFRK   99 (100)
T ss_dssp             T-EEEEEE-SSSCE-EEEEEE--
T ss_pred             CCEEEEEEecCCCceEEEEEEEC
Confidence            9999999975 345679999876

The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see IPR001471 from INTERPRO) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors []. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1WID_A 1YEL_A.

>PF07496 zf-CW: CW-type Zinc Finger; InterPro: IPR011124 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

>PF03754 DUF313: Domain of unknown function (DUF313) ; InterPro: IPR005508 This is a family of proteins from Arabidopsis thaliana (Mouse-ear cress) with uncharacterised function	Back alignment and domain information

>PF09217 EcoRII-N: Restriction endonuclease EcoRII, N-terminal; InterPro: IPR023372 There are four classes of restriction endonucleases: types I, II,III and IV	Back alignment and domain information

>smart00249 PHD PHD zinc finger	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
Query		668
1wid_A		130	Solution Structure Of The B3 Dna-Binding Domain Of		6e-14
2l7p_A		100	Ashh2 A Cw Domain Length = 100		2e-04

>pdb|1WID|A Chain A, Solution Structure Of The B3 Dna-Binding Domain Of Rav1 Length = 130

Back alignment and structure

Iteration: 1

Score = 76.3 bits (186), Expect = 6e-14, Method: Compositional matrix adjust. Identities = 47/116 (40%), Positives = 73/116 (62%), Gaps = 10/116 (8%) Query: 118 LFEKMLSASDAGRIGRLVLPKKCAEAYFP-PISQ--PEGLPLKVQDSKGKEWIFQFRFWP 174 LFEK ++ SD G++ RLV+PK AE +FP P S +G+ L +D GK W F++ +W Sbjct: 13 LFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYW- 71 Query: 175 NNNSRMYVL-EGVTPCIQNMQLQAGDIVTFSRLEPEG-KLVMGFRKASSASASDQD 228 N+S+ YVL +G + ++ L+AGD+V+FSR + +L +G++ S S SD D Sbjct: 72 -NSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQDQQLYIGWK---SRSGSDLD 123

PyMOL of 1wid

>pdb|2L7P|A Chain A, Ashh2 A Cw Domain Length = 100

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
Query		668
1wid_A		130	DNA-binding protein RAV1; DNA-binding domain, stru	2e-27
2l7p_A		100	Histone-lysine N-methyltransferase ASHH2; CW-domai	2e-15
2e61_A		69	Zinc finger CW-type PWWP domain protein 1; ZF-CW d	3e-14

>1wid_A DNA-binding protein RAV1; DNA-binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: b.142.1.2 Length = 130	Back alignment and structure

 Score =  106 bits (266), Expect = 2e-27
 Identities = 45/123 (36%), Positives = 72/123 (58%), Gaps = 7/123 (5%)

Query: 108 SGDSNSVITPLFEKMLSASDAGRIGRLVLPKKCAEAYFPPIS---QPEGLPLKVQDSKGK 164
           SG S      LFEK ++ SD G++ RLV+PK  AE +FP  S     +G+ L  +D  GK
Sbjct: 3   SGSSGRSAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGK 62

Query: 165 EWIFQFRFWPNNNSRMYVL-EGVTPCIQNMQLQAGDIVTFSRLE-PEGKLVMGFRKASSA 222
            W F++ +W  N+S+ YVL +G +  ++   L+AGD+V+FSR    + +L +G++  S +
Sbjct: 63  VWRFRYSYW--NSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQDQQLYIGWKSRSGS 120

Query: 223 SAS 225
              
Sbjct: 121 DLD 123

PyMOL of 1wid

>2l7p_A Histone-lysine N-methyltransferase ASHH2; CW-domain; NMR {Arabidopsis thaliana} Length = 100	Back alignment and structure

>2e61_A Zinc finger CW-type PWWP domain protein 1; ZF-CW domain, structural genomics, NPPSFA, national project protein structural and functional analyses; NMR {Homo sapiens} PDB: 2rr4_A* Length = 69	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		668
1wid_A		130	DNA-binding protein RAV1; DNA-binding domain, stru	99.95
2l7p_A		100	Histone-lysine N-methyltransferase ASHH2; CW-domai	99.76
2e61_A		69	Zinc finger CW-type PWWP domain protein 1; ZF-CW d	99.68
4i1k_A		146	B3 domain-containing transcription factor VRN1; B3	99.57
1yel_A		104	AT1G16640; CESG, protein structure initiative, str	99.4
4gut_A		776	Lysine-specific histone demethylase 1B; histone de	94.18
1na6_A		404	Ecorii, restriction endonuclease ecorii; site-spec	88.64
1we9_A		64	PHD finger family protein; structural genomics, PH	87.47
1wee_A		72	PHD finger family protein; structural genomics, PH	86.98
3kqi_A		75	GRC5, PHD finger protein 2; metal-binding, zinc-fi	84.35
3o70_A		68	PHD finger protein 13; PHF13, structural genomics	81.89
2lv9_A		98	Histone-lysine N-methyltransferase MLL5; zinc fing	81.86

>1wid_A DNA-binding protein RAV1; DNA-binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: b.142.1.2	Back alignment and structure

Probab=99.95  E-value=1.8e-27  Score=217.14  Aligned_cols=120  Identities=38%  Similarity=0.721  Sum_probs=100.9

Q ss_pred             cCCCCCcccceEEEecccccCCCCCcEEeehhhhcccCCCCCC---CCCceEEEEeCCCCeEEEEEEEcCCCCCccccc-
Q 005945          108 SGDSNSVITPLFEKMLSASDAGRIGRLVLPKKCAEAYFPPISQ---PEGLPLKVQDSKGKEWIFQFRFWPNNNSRMYVL-  183 (668)
Q Consensus       108 sgd~~s~~~~LF~KvLT~SDVgklgRLVIPK~~AE~~FPpL~~---~~G~~L~v~D~~Gk~W~FRfsyw~nn~SR~YVL-  183 (668)
                      ++..+.+..++|.|+||+|||++.+||+||+++|+.|||.++.   ..++.|.++|.+|++|+|+|+||  +.+++|+| 
T Consensus         3 ~~~~~~~~~~~F~K~Lt~SDv~~~~rL~iPk~~a~~~lP~~~~~~~~~~~~l~l~D~~Gk~W~fr~~~~--~~~~~~~Lt   80 (130)
T 1wid_A            3 SGSSGRSAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYW--NSSQSYVLT   80 (130)
T ss_dssp             -----CCCEEEEEEECCTTTTSSSCCEEECHHHHTTTSCCCSSCCSSCCEEEEEEETTTEEEEEEEEEE--TTTTEEEEE
T ss_pred             CCCCCCCCcceEEEEEehHHcCCCCEEEeCHHHHHhhCCccccccCCCcEEEEEEeCCCCEEEEEEEEE--CCCCceEEc
Confidence            3556677889999999999999889999999999999999874   57899999999999999999999  55678888 


Q ss_pred             cCchhhhhccCCCCCCEEEEEEec-CCCeEEEEEEeCCCCCCcccccc
Q 005945          184 EGVTPCIQNMQLQAGDIVTFSRLE-PEGKLVMGFRKASSASASDQDNE  230 (668)
Q Consensus       184 ~GWs~FVrsK~LkaGDtVvF~R~e-~~GkL~IGVRRa~~~~~s~q~~~  230 (668)
                      .||..||++|+|++||+|+|++.+ .+++|+|++||+.... ++|+++
T Consensus        81 ~GW~~FV~~~~L~~GD~~~F~~~~~~~~~l~I~~rr~~~~~-~~~~~~  127 (130)
T 1wid_A           81 KGWSRFVKEKNLRAGDVVSFSRSNGQDQQLYIGWKSRSGSD-LDASGP  127 (130)
T ss_dssp             SSHHHHHHHTTCCTTCEEEEEECCSSSCCEEEEEECCCSCS-SCC---
T ss_pred             CChHHHHHHcCCCCCCEEEEEEecCCCcEEEEEEEECCCCC-ccccCC
Confidence            599999999999999999999986 3468999999998654 465544

PyMOL of 1wid

>2l7p_A Histone-lysine N-methyltransferase ASHH2; CW-domain; NMR {Arabidopsis thaliana}	Back alignment and structure

>2e61_A Zinc finger CW-type PWWP domain protein 1; ZF-CW domain, structural genomics, NPPSFA, national project protein structural and functional analyses; NMR {Homo sapiens} PDB: 2rr4_A*	Back alignment and structure

>4i1k_A B3 domain-containing transcription factor VRN1; B3 domain beta-barrel, DNA binding protein; 1.60A {Arabidopsis thaliana}	Back alignment and structure

>1yel_A AT1G16640; CESG, protein structure initiative, structural genomics, center for eukaryotic structural genomics, unknown function; NMR {Arabidopsis thaliana} SCOP: b.142.1.2	Back alignment and structure

>4gut_A Lysine-specific histone demethylase 1B; histone demethylase; HET: FAD PGE; 2.00A {Homo sapiens} PDB: 4gur_A* 4gus_A* 4guu_A* 4fwe_A* 4fwf_A* 4fwj_A* 4gu1_A*	Back alignment and structure

>1na6_A Ecorii, restriction endonuclease ecorii; site-specific restriction, mutation, replication, hydrolase; 2.10A {Escherichia coli} SCOP: b.142.1.1 c.52.1.22 PDB: 3hqg_A 3hqf_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

>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

>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

>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

>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

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		668
d1wida_		117	b.142.1.2 (A:) DNA-binding protein RAV1 {Thale cre	7e-30
d1na6a1		175	b.142.1.1 (A:4-178) Restriction endonuclease EcoRI	2e-22
d1yela1		102	b.142.1.2 (A:1-102) At1g16640 {Thale cress (Arabid	7e-13

>d1wida_ b.142.1.2 (A:) DNA-binding protein RAV1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 117	Back information, alignment and structure


class: All beta proteins
fold: DNA-binding pseudobarrel domain
superfamily: DNA-binding pseudobarrel domain
family: B3 DNA binding domain
domain: DNA-binding protein RAV1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score =  111 bits (280), Expect = 7e-30
 Identities = 38/112 (33%), Positives = 66/112 (58%), Gaps = 5/112 (4%)

Query: 116 TPLFEKMLSASDAGRIGRLVLPKKCAEAYFPPISQ---PEGLPLKVQDSKGKEWIFQFRF 172
             LFEK ++ SD G++ RLV+PK  AE +FP  S     +G+ L  +D  GK W F++ +
Sbjct: 4   EALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSY 63

Query: 173 WPNNNSRMYVLEGVTPCIQNMQLQAGDIVTFSRLEPE-GKLVMGFRKASSAS 223
           W ++ S +   +G +  ++   L+AGD+V+FSR   +  +L +G++  S + 
Sbjct: 64  WNSSQSYVL-TKGWSRFVKEKNLRAGDVVSFSRSNGQDQQLYIGWKSRSGSD 114

PyMOL of d1wida_

>d1na6a1 b.142.1.1 (A:4-178) Restriction endonuclease EcoRII, N-terminal domain {Escherichia coli [TaxId: 562]} Length = 175	Back information, alignment and structure

>d1yela1 b.142.1.2 (A:1-102) At1g16640 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 102	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
Query		668
d1wida_		117	DNA-binding protein RAV1 {Thale cress (Arabidopsis	99.92
d1na6a1		175	Restriction endonuclease EcoRII, N-terminal domain	99.6
d1yela1		102	At1g16640 {Thale cress (Arabidopsis thaliana) [Tax	99.34
d1weea_		72	PHD finger protein At1g33420 {Thale cress (Arabido	80.44

>d1wida_ b.142.1.2 (A:) DNA-binding protein RAV1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}	Back information, alignment and structure

class: All beta proteins
fold: DNA-binding pseudobarrel domain
superfamily: DNA-binding pseudobarrel domain
family: B3 DNA binding domain
domain: DNA-binding protein RAV1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.92  E-value=2.9e-25  Score=195.26  Aligned_cols=107  Identities=38%  Similarity=0.752  Sum_probs=94.0

Q ss_pred             ccceEEEecccccCCCCCcEEeehhhhcccCCCCCC---CCCceEEEEeCCCCeEEEEEEEcCCCCCccccc-cCchhhh
Q 005945          115 ITPLFEKMLSASDAGRIGRLVLPKKCAEAYFPPISQ---PEGLPLKVQDSKGKEWIFQFRFWPNNNSRMYVL-EGVTPCI  190 (668)
Q Consensus       115 ~~~LF~KvLT~SDVgklgRLVIPK~~AE~~FPpL~~---~~G~~L~v~D~~Gk~W~FRfsyw~nn~SR~YVL-~GWs~FV  190 (668)
                      ..++|+|+||+|||++.+||+||+.+|++|||+++.   .+++.|.+.|.+|++|.|+|++|.  +.+.|++ .||..||
T Consensus         3 ~~~iF~K~Lt~sDv~~~~rL~iP~~~~~~~lp~~~~~~~~~~~~~~~~d~~g~~W~~~~~~~~--~~~~~~l~~GW~~Fv   80 (117)
T d1wida_           3 AEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYWN--SSQSYVLTKGWSRFV   80 (117)
T ss_dssp             CEEEEEEECCTTTTSSSCCEEECHHHHTTTSCCCSSCCSSCCEEEEEEETTTEEEEEEEEEET--TTTEEEEESSHHHHH
T ss_pred             CceEEEEEecchhcCCCCEEEECHHHHHHhCCccccccCCCcEEEEEEeCCCCEEEEEEEEEC--CCCceEEecCHHHHH
Confidence            467999999999999889999999999999999874   468999999999999999999994  3344555 7999999


Q ss_pred             hccCCCCCCEEEEEEec-CCCeEEEEEEeCCCCC
Q 005945          191 QNMQLQAGDIVTFSRLE-PEGKLVMGFRKASSAS  223 (668)
Q Consensus       191 rsK~LkaGDtVvF~R~e-~~GkL~IGVRRa~~~~  223 (668)
                      ++++|++||+|+|++.+ .+|+|+|++||+....
T Consensus        81 ~~~~Lk~GD~~~F~~~~~~~~~~~i~~r~~~~~~  114 (117)
T d1wida_          81 KEKNLRAGDVVSFSRSNGQDQQLYIGWKSRSGSD  114 (117)
T ss_dssp             HHTTCCTTCEEEEEECCSSSCCEEEEEECCCSCS
T ss_pred             HHcCCCCCCEEEEEEEeCCCCEEEEEEEECCCCC
Confidence            99999999999999986 4579999999997543

PyMOL of d1wida_

>d1na6a1 b.142.1.1 (A:4-178) Restriction endonuclease EcoRII, N-terminal domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1yela1 b.142.1.2 (A:1-102) At1g16640 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}	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