Citrus Sinensis ID: 002390

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-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780-------790-------800-------810-------820-------830-------840-------850-------860-------870-------880-------890-------900-------910-------920-------93

MNFIHSNPVLLGIPYKLDQIVLNFVLFFSLVMMLDNTKCRENFAGEKKCLNSELWHACAGPLVSLPPVGSRVVYFPQGHSEQVAASTNKEVDAHIPNYPNLPPQLICQLHNLTMHADVETDEVYAQMTLQPLSPQEQKDVYLLPAELGAPNKQPTNYFCKTLTASDTSTHGGFSVPRRAAEKVFPPLDYSQTPPAQELIARDLHDNEWKFRHIFRGQPKRHLLTTGWSVFVSAKRLVAGDSVLFIWNEKNQLLLGIRRATRPQTVMPSSVLSSDSMHIGLLAAAAHAAATNSRFTIFYNPRASPSEFVIPLAKYVKAVYHTRVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWPNSHWRSVKVGWDESTAGERQPRVSLWEIEPLTTFPMYSSPFPLRLKRPWPSGLPSFHGMKDGDMSINSPLMWLQGGVGDQGIQSLNFQGYGVTPWMQPRLDASIPGLQPDVYQAMAAAALQEMRTVDSSKLASQSLLQFQQSQNVSNGTASMIPRQMLQQSQAQNALLQSFQENQASAQAQLLQQQLQRQHSYNEQRQQQQQVQQSQQLHQLSVQPQISNVISTLPHLASSSQSQPPTLQTVASQCQQSNFSDSLGNPIASSDVSSMHTILGSLSQAGASHLLNSNASNPIISSSAMLTKQVTVDNHVPSAVSHCILPQVEQLGAQQSNVSELASLLPPFPGREYSSYHGSGDPQNNLLFGVSIDSSLMGQNGLPNLKNISSENESLSLPYAASNFTNNVGTDFPLNSDMTTSSCVDESGFLQSSENVDQVNPPTRTFVKVHKSGSFGRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLGDDPWQEFVNNVGYIKILSPLEVQQMGKGLSPVTSGPGQRLSSNNNFDDYVSRQELRSSSNGVASMGSINY

cccccccccccccccccHHHHHHHHHHHHHHHHHcccccccccccccccccHHHHHHcccccccccccccEEEEccccHHHHHcccccHHHHcccccccccccccEEEEEEEEEccccccccEEEEEEEEEcccccccccccccccccccccccccEEEEEEEcccccccccccccccccccccccccccccccccEEEEEEcccccEEEEEEEccccccccccccccccccccccccccEEEEEEcccccEEEEEEEcccccccccccccccccccccHHHHHHHHHHccccEEEEEccccccccEEEcHHHHHHHHHccccccccEEEEEEccccccEEEEEEEEEEEcccccccccccccccEEEEccccccccccccccccEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHcccccccEEEccccccHHHHHHHHHHHHccccccccccccccEEEEEcccccEEEcccccHHHHHHcccEEEEEcHHHHHccccccccccccccccccccccccccccccccccccccccccccccc

cccEccccEEEcccccccHHHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHcccccEccccccEEEEcccccHHHHHHHccccHHccccccccccccEEEEEEEEEEEccccccEEEEEEEEcccccccccccccccccccccccccccHHEEEEccccccccccccHHHHHHHHHcccccccccccHHHHHHHHHcccEEEEEEEEccccccEEEccccEEEEEccEEEcccEEEEEEcccccEEEEEEEcccccccccccEEccccHHHHHHHHHHHHHHccccEEEEEccccccccEEEEHHHHHHHHHcccEEEEEEEEEEEcccccccEEEEEEEEEccccccccccccccEEEEEEccccccccccccccccEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHcccccccHHHHcHcccHHcccccccccccccccHHHcccccccccccccccccccccccccccccccccccccccHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEcccccEEEEEEccccHHHHHHHHHHHHccccccccccccccEEEEEcccccEEEEccccHHHHHHHHEEEEEEcHHHHHHcccccccccccccccccccccccccccccccccccccccccccccc

mnfihsnpvllgipykldQIVLNFVLFFSLVMMLDntkcrenfagekkclnselwhacagplvslppvgsrvvyfpqghseqvaastnkevdahipnypnlppqlICQLhnltmhadvetDEVYAQmtlqplspqeqkdvyllpaelgapnkqptnyfcktltasdtsthggfsvprraaekvfppldysqtppaqeLIARDlhdnewkfrhifrgqpkrhlltTGWSVFVSAKRLVAGDSVLFIWNEKNQLLLGirratrpqtvmpssvlssdSMHIGLLAAAAHAAatnsrftifynpraspsefvIPLAKYVKAVYHTRVSVGMRFRMLFETEESSVRRYMGtitgisdldpvrwpnshwrsvkvgwdestagerqprvslweieplttfpmysspfplrlkrpwpsglpsfhgmkdgdmsinsplmwlqggvgdqgiqslnfqgygvtpwmqprldasipglqpDVYQAMAAAALQEMRTVDSSKLASQSLLQFQqsqnvsngtasmiprqmLQQSQAQNALLQSFQENQASAQAQLLQQQLQRQHSYNEQRQQQQQVQQSQQLHQLSVQPQISNVistlphlasssqsqpptlqtvasqcqqsnfsdslgnpiassdvssmHTILGSLSQAgashllnsnasnpiisssamltkqvtvdnhvpsavshcilpqveqlgaqqsNVSELasllppfpgreyssyhgsgdpqnnllfgvsidsslmgqnglpnlknisseneslslpyaasnftnnvgtdfplnsdmttsscvdesgflqssenvdqvnpptrTFVKVhksgsfgrsldiskfsSYDELRSELARMFglegqledpqrsgwqlVFVDRendvlllgddpwqefvnnvgyikilsplevqqmgkglspvtsgpgqrlssnnnfddyvsrqelrsssngvasmgsiny

MNFIHSNPVLLGIPYKLDQIVLNFVLFFSLVMMLDNTKCRENFAGEKKCLNSELWHACAGPLVSLPPVGSRVVYFPQGHSEQVAASTNKEVDAHIPNYPNLPPQLICQLHNLTMHADVETDEVYAQMTLQPLSPQEQKDVYLLPAELGAPNKQPTNYFCKTLTASDTSTHGGFSVPRRAAEKVFPPLDYSQTPPAQELIARDLHDNEWKFRHIFRGQPKRHLLTTGWSVFVSAKRLVAGDSVLFIWNEKNQLLLGIRRATRPQTVMPSSVLSSDSMHIGLLAAAAHAAATNSRFTIFYNPRASPSEFVIPLAKYVKAVYHTRVSVGMRFRMLFETEESSVRRYMGTItgisdldpvrwpNSHWRsvkvgwdestagerqprvslweiePLTTFPMYSSPFPLRLKRPWPSGLPSFHGMKDGDMSINSPLMWLQGGVGDQGIQSLNFQGYGVTPWMQPRLDASIPGLQPDVYQAMAAAALQEMRTVDSSKLASQSLLQFQQSQNVSNGTASMIPRQMLQQSQAQNALLQSFQENQASAQAQLLQQQLQRQHSYNEQRQQQQQVQQSQQLHQLSVQPQISNVISTLPHLASSSQSQPPTLQTVASQCQQSNFSDSLGNPIASSDVSSMHTILGSLSQAGASHLLNSNASNPIISSSAMLTKQVTVDNHVPSAVSHCILPQVEQLGAQQSNVSELASLLPPFPGREYSSYHGSGDPQNNLLFGVSIDSSLMGQNGLPNLKNISSENESLSLPYAASNFTNNVGTDFPLNSDMTTSSCVDESGFLQssenvdqvnppTRTFVKvhksgsfgrsldiskFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLGDDPWQEFVNNVGYIKILSPLEVQQMGKGLSPVtsgpgqrlssnnNFDDYVSRqelrsssngvasmgsiny

MNFIHSNPVLLGIPYKLDQIVLNFVLFFSLVMMLDNTKCRENFAGEKKCLNSELWHACAGPLVSLPPVGSRVVYFPQGHSEQVAASTNKEVDAHIPNYPNLPPQLICQLHNLTMHADVETDEVYAQMTLQPLSPQEQKDVYLLPAELGAPNKQPTNYFCKTLTASDTSTHGGFSVPRRAAEKVFPPLDYSQTPPAQELIARDLHDNEWKFRHIFRGQPKRHLLTTGWSVFVSAKRLVAGDSVLFIWNEKNQLLLGIRRATRPQTVMPSSVLSSDSMHIGLLaaaahaaaTNSRFTIFYNPRASPSEFVIPLAKYVKAVYHTRVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWPNSHWRSVKVGWDESTAGERQPRVSLWEIEPLTTFPMYSSPFPLRLKRPWPSGLPSFHGMKDGDMSINSPLMWLQGGVGDQGIQSLNFQGYGVTPWMQPRLDASIPGLQPDVYQAMAAAALQEMRTVDssklasqsllqfqqsqNVSNGTASMIPRqmlqqsqaqnallqsfqENqasaqaqllqqqlqrqhsyneqrqqqqqvqqsqqlhqlsvqpqISNVISTLPHLAsssqsqppTLQTVASQCQQSNFSDSLGNPIASSDVSSMHTILGSLSQAGASHLLnsnasnpiisssaMLTKQVTVDNHVPSAVSHCILPQVEQLGAQQSNVSELASLLPPFPGREYSSYHGSGDPQNNLLFGVSIDSSLMGQNGLPNLKNISSENESLSLPYAASNFTNNVGTDFPLNSDMTTSSCVDESGFLQSSENVDQVNPPTRTFVKVHKSGSFGRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLGDDPWQEFVNNVGYIKILSPLEVQQMGKGLSPVTSGPGQRLSSNNNFDDYVSRQELRSSSNGVASMGSINY

***IHSNPVLLGIPYKLDQIVLNFVLFFSLVMMLDNTKCRENFAGEKKCLNSELWHACAGPLVSLPPVGSRVVYFPQGH***********VDAHIPNYPNLPPQLICQLHNLTMHADVETDEVYAQMTL**********VYLLPAELG*****PTNYFCKTLTA********************************ELIARDLHDNEWKFRHIFRGQPKRHLLTTGWSVFVSAKRLVAGDSVLFIWNEKNQLLLGIRRATR*************SMHIGLLAAAAHAAATNSRFTIFYNPRASPSEFVIPLAKYVKAVYHTRVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWPNSHWRSVKVGWDESTAGERQPRVSLWEIEPLTTFPMYSSPFPLRLKRPWPSGLPSFHG****DMSINSPLMWLQGGVGDQGIQSLNFQGYGVTPWMQPRLDASIPGLQPDVYQAMAA*************************************************************************************************************************************************************************************TKQVTVDNHVPSAVSHCILPQVE************************************LLFGVS******************************************************************************************************LARMFGLEGQL***QRSGWQLVFVDRENDVLLLGDDPWQEFVNNVGYIKILSPLEV************************************************

*****SNPVLLGIPYKLDQIVLNFVLFFSL**********************ELWHACAGPLVSLPPVGSRVVYFPQGHSEQVA************NYPNLPPQLICQLHNLTMHADVETDEVYAQMTLQPLS***********************YFCKTLTASDTSTHGGFSVPRRAAEKVFPPLDYSQTPPAQELIARDLHDNEWKFRHIFRGQPKRHLLTTGWSVFVSAKRLVAGDSVLFIWNEKNQLLLGIRRAT********************LAAAAHAAATNSRFTIFYNPRASPSEFVIPLAKYVKAVYHTRVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWPNSHWRSVKVGWDESTAGERQPRVSLWEIEPLT*************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************HKSGSFGRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLGDDPWQEFVNNVGYIKIL*****************************************************

MNFIHSNPVLLGIPYKLDQIVLNFVLFFSLVMMLDNTKCRENFAGEKKCLNSELWHACAGPLVSLPPVGSRVVYFPQGHSEQVAASTNKEVDAHIPNYPNLPPQLICQLHNLTMHADVETDEVYAQMTLQPLSPQEQKDVYLLPAELGAPNKQPTNYFCKTLTASDTSTHGGFSVPRRAAEKVFPPLDYSQTPPAQELIARDLHDNEWKFRHIFRGQPKRHLLTTGWSVFVSAKRLVAGDSVLFIWNEKNQLLLGIRRATRPQTVMPSSVLSSDSMHIGLLAAAAHAAATNSRFTIFYNPRASPSEFVIPLAKYVKAVYHTRVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWPNSHWRSVKVGWDESTAGERQPRVSLWEIEPLTTFPMYSSPFPLRLKRPWPSGLPSFHGMKDGDMSINSPLMWLQGGVGDQGIQSLNFQGYGVTPWMQPRLDASIPGLQPDVYQAMAAAALQEMRTVDSSKLASQSLLQFQQSQNVSNGTASMIPRQMLQQSQAQNALLQSFQEN**************************************SVQPQISNVISTLP***********************NFSDSLGNPIASSDVSSMHTILGSLSQAGASHLLNSNASNPIISSSAMLTKQVTVDNHVPSAVSHCILPQVEQLGAQQSNVSELASLLPPFPGREYSSYHGSGDPQNNLLFGVSIDSSLMGQNGLPNLKNISSENESLSLPYAASNFTNNVGTDFPLNSDMTTSSCVDESGFLQSSENVDQVNPPTRTFVKVHKSGSFGRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLGDDPWQEFVNNVGYIKILSPLEVQQ***************LSSNNNFDDYVSRQELRSSSNGVASMGSINY

*NFIHSNPVLLGIPYKLDQIVLNFVLFFSLVMMLDN**********KKCLNSELWHACAGPLVSLPPVGSRVVYFPQGHSEQVAASTNKEVDAHIPNYPNLPPQLICQLHNLTMHADVETDEVYAQMTLQPLS******VYLLPAE****NKQPTNYFCKTLTASD****GGFSVPRRAAEKVFPPLDYSQTPPAQELIARDLHDNEWKFRHIFRGQPKRHLLTTGWSVFVSAKRLVAGDSVLFIWNEKNQLLLGIRRATRPQTVMPSSVLSSDSMHIGLLAAAAHAAATNSRFTIFYNPRASPSEFVIPLAKYVKAVYHTRVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWPNSHWRSVKVGWDESTAGERQPRVSLWEIEPLTTFPMYSSPFPLRLKRPWPSGLPSF***********************************VT**********I*GLQPDVYQAMAA************************************************************************************************************************************************************************************************************************************************L*F***IDSSLMGQN*************************************************************PTRTFVKVHKSGSFGRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLGDDPWQEFVNNVGYIKILSPLEVQQM*********************************************

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

iiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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oooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

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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		928	2.2.26 [Sep-21-2011]
Q6H6V4		908	Auxin response factor 6 O	yes	no	0.936	0.957	0.660	0.0
A2X1A1		908	Auxin response factor 6 O	N/A	no	0.936	0.957	0.660	0.0
A2YG67		917	Auxin response factor 17	N/A	no	0.931	0.942	0.649	0.0
Q653U3		917	Auxin response factor 17	no	no	0.931	0.942	0.649	0.0
Q2QM84		899	Auxin response factor 25	no	no	0.927	0.957	0.609	0.0
Q9FGV1		811	Auxin response factor 8 O	yes	no	0.829	0.949	0.583	0.0
Q9ZTX8		935	Auxin response factor 6 O	no	no	0.501	0.497	0.861	0.0
Q0J951		818	Auxin response factor 12	no	no	0.449	0.509	0.823	0.0
P93024		902	Auxin response factor 5 O	no	no	0.859	0.884	0.428	1e-170
A3B9A0		1055	Auxin response factor 16	no	no	0.492	0.433	0.628	1e-157

>sp\|Q6H6V4\|ARFF_ORYSJ Auxin response factor 6 OS=Oryza sativa subsp. japonica GN=ARF6 PE=1 SV=1	Back alignment and function desciption

 Score = 1100 bits (2846), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 597/904 (66%), Positives = 696/904 (76%), Gaps = 35/904 (3%)

Query: 44  AGEKKCLNSELWHACAGPLVSLPPVGSRVVYFPQGHSEQVAASTNKEVDAHIPNYPNLPP 103
           A E+KCLNSELWHACAGPLVSLP VGSRVVYFPQGHSEQVAASTNKE+++ IPNYPNLPP
Sbjct: 21  AEEQKCLNSELWHACAGPLVSLPAVGSRVVYFPQGHSEQVAASTNKEMESQIPNYPNLPP 80

Query: 104 QLICQLHNLTMHADVETDEVYAQMTLQPLSPQEQKDVYLLPAELGAPNKQPTNYFCKTLT 163
           QLICQLHN+TMHAD ETDEVYAQMTLQPLSPQE KD +L PAELG  +KQPTNYFCKTLT
Sbjct: 81  QLICQLHNVTMHADAETDEVYAQMTLQPLSPQELKDPFL-PAELGTASKQPTNYFCKTLT 139

Query: 164 ASDTSTHGGFSVPRRAAEKVFPPLDYSQTPPAQELIARDLHDNEWKFRHIFRGQPKRHLL 223
           ASDTSTHGGFSVPRRAAEKVFPPLD++Q PPAQEL+A+DLH NEWKFRHIFRGQPKRHLL
Sbjct: 140 ASDTSTHGGFSVPRRAAEKVFPPLDFTQQPPAQELMAKDLHGNEWKFRHIFRGQPKRHLL 199

Query: 224 TTGWSVFVSAKRLVAGDSVLFIWNEKNQLLLGIRRATRPQTVMPSSVLSSDSMHIGLLAA 283
           TTGWSVFVSAKRLVAGDSVLFIWN+ NQLLLGIRRA RPQTVMPSSVLSSDSMHIGLLAA
Sbjct: 200 TTGWSVFVSAKRLVAGDSVLFIWNDSNQLLLGIRRANRPQTVMPSSVLSSDSMHIGLLAA 259

Query: 284 AAHAAATNSRFTIFYNPRASPSEFVIPLAKYVKAVYHTRVSVGMRFRMLFETEESSVRRY 343
           AAHAA+TNSRFTIFYNPRASPSEFVIPLAKYVKAVYHTR+SVGMRFRMLFETEESSVRRY
Sbjct: 260 AAHAASTNSRFTIFYNPRASPSEFVIPLAKYVKAVYHTRISVGMRFRMLFETEESSVRRY 319

Query: 344 MGTITGISDLDPVRWPNSHWRSVKVGWDESTAGERQPRVSLWEIEPLTTFPMYSSPFPLR 403
           MGTITGISDLDPVRW NSHWRSVKVGWDESTAGERQPRVSLWEIEPLTTFPMY SPFPLR
Sbjct: 320 MGTITGISDLDPVRWMNSHWRSVKVGWDESTAGERQPRVSLWEIEPLTTFPMYPSPFPLR 379

Query: 404 LKRPWPSGLPSFHGMKDGDMSINSPLMWLQGGVGDQGIQSLNFQGYGVTPWMQPRLDASI 463
           LKRPWP+GLPS +G K+ D++  S LMWL+    + G QSLNF G G++PWMQPRLD+S+
Sbjct: 380 LKRPWPTGLPSLYGGKEDDLA--SSLMWLRDS-QNTGFQSLNFGGLGMSPWMQPRLDSSL 436

Query: 464 PGLQPDVYQAMAAAALQEMRTVDSSKLASQSLLQFQQSQNVSNGTASMIPRQMLQQSQAQ 523
            GLQPD+YQ +AAAA  +    +++K  S ++LQFQQ QN+  G +S++  Q+LQQ+Q Q
Sbjct: 437 LGLQPDMYQTIAAAAALQ----NTTKQVSPAMLQFQQPQNIV-GRSSLLSSQILQQAQPQ 491

Query: 524 NALL--QSFQEN--QASAQAQLLQQQLQRQHSYNE-------------QRQQQQQVQQSQ 566
              +  Q+   N  Q  +Q + LQQ LQ   S+NE               QQQ Q QQ Q
Sbjct: 492 FQQMYHQNINGNSIQGHSQPEYLQQPLQHCQSFNEQKPQLQPQQQQQESHQQQPQHQQMQ 551

Query: 567 QLHQLSVQPQISNVISTLPHLASSSQSQPPTLQTVASQCQQSNFSDSLGNPIASSDVSSM 626
           Q   LS    + N +S    L+S+ QS P TLQTV+   QQ NF D+  + ++ S+VSSM
Sbjct: 552 QQKHLSNFQTVPNALSVFSQLSSTPQSTPSTLQTVSPFSQQHNFPDTNISCLSPSNVSSM 611

Query: 627 HTILGSLSQAGASHLLNSNASNPIISSSAMLTKQVTVDNHVPSAVSHCILPQVEQLGAQQ 686
           H  L S     AS L       P+  S    +K+V V++ + S   H I  Q+E      
Sbjct: 612 HDTLRSFPSEAASDLPGVPRITPVPVSDPWSSKRVAVESTITSR-PHDISSQIENFDLTP 670

Query: 687 SNVSELASLLPPFPGRE-YSSYHGSGDPQNNLLFGVSIDS-SLMGQNGLPNLKNISSENE 744
           S++ +  S L P PGRE      GS DPQN+ LFGV+IDS SL+ Q+G+P+L N   EN 
Sbjct: 671 SSIPQ-NSTLAPLPGRECLVDQDGSSDPQNHFLFGVNIDSQSLLMQDGIPSLHN---ENS 726

Query: 745 SLSLPYAASNFTNNVGTDFPLNSDMTTSSCVDESGFLQSSENVDQVNPPTRTFVKVHKSG 804
           S ++PY+ SNF +    D+PL+  +TT  C+DESG++  S+N DQV  P  TFVKV+KSG
Sbjct: 727 SSTIPYSTSNFLSPSQDDYPLSQTLTTPGCLDESGYVPCSDNADQVKRPHATFVKVYKSG 786

Query: 805 SFGRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLGDDPWQE 864
           + GR LDI++FSSY ELRSE+ R+FGLEGQLEDP RSGWQLVFVDRE+DVLL+GDDPWQE
Sbjct: 787 TVGRLLDITRFSSYHELRSEVGRLFGLEGQLEDPLRSGWQLVFVDREDDVLLVGDDPWQE 846

Query: 865 FVNNVGYIKILSPLEVQQMGKGLSPVTSGPGQRLSSNNNFDDYVSRQELRSSSNGVASMG 924
           FVN+V  IKILSP EVQQMGK    + S   +RL   N+ D+Y+SRQE RS S G+AS+G
Sbjct: 847 FVNSVSCIKILSPQEVQQMGKPGIELFSTSARRL--GNSCDNYMSRQESRSLSTGIASVG 904

Query: 925 SINY 928
           S+ +
Sbjct: 905 SVEF 908

Auxin response factors (ARFs) are transcriptional factors that binds specifically to the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs).
Oryza sativa subsp. japonica (taxid: 39947)

>sp\|A2X1A1\|ARFF_ORYSI Auxin response factor 6 OS=Oryza sativa subsp. indica GN=ARF6 PE=2 SV=1	Back alignment and function description

>sp\|A2YG67\|ARFQ_ORYSI Auxin response factor 17 OS=Oryza sativa subsp. indica GN=ARF17 PE=2 SV=1	Back alignment and function description

>sp\|Q653U3\|ARFQ_ORYSJ Auxin response factor 17 OS=Oryza sativa subsp. japonica GN=ARF17 PE=2 SV=1	Back alignment and function description

>sp\|Q2QM84\|ARFY_ORYSJ Auxin response factor 25 OS=Oryza sativa subsp. japonica GN=ARF25 PE=2 SV=1	Back alignment and function description

>sp\|Q9FGV1\|ARFH_ARATH Auxin response factor 8 OS=Arabidopsis thaliana GN=ARF8 PE=2 SV=2	Back alignment and function description

>sp\|Q9ZTX8\|ARFF_ARATH Auxin response factor 6 OS=Arabidopsis thaliana GN=ARF6 PE=1 SV=2	Back alignment and function description

>sp\|Q0J951\|ARFL_ORYSJ Auxin response factor 12 OS=Oryza sativa subsp. japonica GN=ARF12 PE=2 SV=1	Back alignment and function description

>sp\|P93024\|ARFE_ARATH Auxin response factor 5 OS=Arabidopsis thaliana GN=ARF5 PE=1 SV=3	Back alignment and function description

>sp\|A3B9A0\|ARFP_ORYSJ Auxin response factor 16 OS=Oryza sativa subsp. japonica GN=ARF16 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		928
118486652		907	unknown [Populus trichocarpa]	0.950	0.972	0.808	0.0
356501413		896	PREDICTED: auxin response factor 6-like	0.943	0.977	0.803	0.0
356554039		866	PREDICTED: auxin response factor 6-like	0.909	0.974	0.813	0.0
359485334		891	PREDICTED: auxin response factor 6-like	0.929	0.968	0.779	0.0
225443952		908	PREDICTED: auxin response factor 6-like	0.950	0.971	0.739	0.0
302143499		836	unnamed protein product [Vitis vinifera]	0.834	0.925	0.737	0.0
296278602		889	ARF1 [Nicotiana benthamiana]	0.934	0.975	0.718	0.0
449466121		899	PREDICTED: auxin response factor 6-like	0.941	0.972	0.708	0.0
449515293		884	PREDICTED: LOW QUALITY PROTEIN: auxin re	0.940	0.987	0.706	0.0
222539816		891	ARF8 [Solanum melongena]	0.937	0.976	0.715	0.0

>gi\|118486652\|gb\|ABK95163.1\| unknown [Populus trichocarpa]	Back alignment and taxonomy information

 Score = 1439 bits (3726), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 720/891 (80%), Positives = 791/891 (88%), Gaps = 9/891 (1%)

Query: 45  GEKKCLNSELWHACAGPLVSLPPVGSRVVYFPQGHSEQVAASTNKEVDAHIPNYPNLPPQ 104
           G+KKCLNSELWHACAGPLVSLP VGSRVVYFPQGHSEQVAASTNKEVDAHIPNYP+LPPQ
Sbjct: 19  GDKKCLNSELWHACAGPLVSLPHVGSRVVYFPQGHSEQVAASTNKEVDAHIPNYPSLPPQ 78

Query: 105 LICQLHNLTMHADVETDEVYAQMTLQPLSPQEQKDVYLLPAELGAPNKQPTNYFCKTLTA 164
           LICQLHN+TMHADVETDEVYAQMTLQPLS  +QKD YLLPAELG  +KQPTNYFCKTLTA
Sbjct: 79  LICQLHNVTMHADVETDEVYAQMTLQPLSQDDQKDAYLLPAELGTASKQPTNYFCKTLTA 138

Query: 165 SDTSTHGGFSVPRRAAEKVFPPLDYSQTPPAQELIARDLHDNEWKFRHIFRGQPKRHLLT 224
           SDTSTHGGFSVPRRAAEKVFP LDYSQTPPAQELIARDLHDNEWKFRHIFRGQPKRHLLT
Sbjct: 139 SDTSTHGGFSVPRRAAEKVFPTLDYSQTPPAQELIARDLHDNEWKFRHIFRGQPKRHLLT 198

Query: 225 TGWSVFVSAKRLVAGDSVLFIWNEKNQLLLGIRRATRPQTVMPSSVLSSDSMHIGLLAAA 284
           TGWSVFVSAKRLVAGDSVLFIWNEKNQLLLGIRRA RPQT MPSSVLSSDSMHIGLLAAA
Sbjct: 199 TGWSVFVSAKRLVAGDSVLFIWNEKNQLLLGIRRANRPQTFMPSSVLSSDSMHIGLLAAA 258

Query: 285 AHAAATNSRFTIFYNPRASPSEFVIPLAKYVKAVYHTRVSVGMRFRMLFETEESSVRRYM 344
           AHAAATNSRFTIFYNPRASPSEFVIPL KY+KAVYHTRVSVGMRFRMLFETEESSVRRYM
Sbjct: 259 AHAAATNSRFTIFYNPRASPSEFVIPLVKYIKAVYHTRVSVGMRFRMLFETEESSVRRYM 318

Query: 345 GTITGISDLDPVRWPNSHWRSVKVGWDESTAGERQPRVSLWEIEPLTTFPMYSSPFPLRL 404
           GTITGISDLDPVRWPNSHWRSVKVGWDESTAGERQPRVSLWEIEPLTTFPMY S FP+RL
Sbjct: 319 GTITGISDLDPVRWPNSHWRSVKVGWDESTAGERQPRVSLWEIEPLTTFPMYPSAFPMRL 378

Query: 405 KRPWPSGLPSFHGMKDGDMSINSPLMWLQGGVGDQGIQSLNFQGYGVTPWMQPRLDASIP 464
           KRPWPSGLPSFHG++DGD++INSP+MWLQGGVGD G+QSLNFQ +GV PW+QPR D S+P
Sbjct: 379 KRPWPSGLPSFHGLQDGDLNINSPMMWLQGGVGDLGVQSLNFQSFGVAPWIQPRFDTSMP 438

Query: 465 GLQPDVYQAMAAAALQEMRTVDSSKLASQSLLQFQQSQNVSNGTASMIPRQMLQQSQAQN 524
            LQP++YQ MAAAALQEMRTV+SSKLASQS LQFQQSQNVSNG A++I RQMLQQS  Q+
Sbjct: 439 ALQPEMYQTMAAAALQEMRTVESSKLASQSHLQFQQSQNVSNGPAALIQRQMLQQSNLQH 498

Query: 525 ALLQSFQENQASAQAQLLQQQLQRQHSYN-----EQRQQQQQVQQSQQLHQLSVQPQISN 579
           ALLQ+FQENQAS QAQ LQQ LQ ++ Y      + + Q QQVQQ +QL++LS   QI N
Sbjct: 499 ALLQNFQENQASTQAQFLQQHLQHRNQYTGQQLQQHQPQLQQVQQPKQLNELSAPQQIPN 558

Query: 580 VISTLPHLASSSQSQPPTLQTVASQCQQSNFSDSLGNPIASSDVSSMHTILGSLSQAGAS 639
           VIS LPHL S + SQ P+LQ ++SQCQQ  FS+ LGN IA+SDVSSMH+++GSLSQ G S
Sbjct: 559 VISALPHLTSVAPSQSPSLQPISSQCQQQAFSEPLGNSIAASDVSSMHSVIGSLSQDGGS 618

Query: 640 HLLNSNASNPIISSSAMLTKQVTVDNHVPSAVSHCILPQVEQLGAQQSNVSELASLLPPF 699
           HLLNSN SNP+I S A+L+K+  +D  + S  +HC LPQVEQL   QS VS+LA+LL PF
Sbjct: 619 HLLNSNGSNPVI-SPALLSKRAAIDPQLSSGAAHCALPQVEQLRTTQSTVSDLATLLAPF 677

Query: 700 PGREYSSYHGSGDPQNNLLFGVSIDSS-LMGQNGLPNLKNISSENESLSLPYAASNFTNN 758
            GREYS+Y G+ DPQNNLLFGV+IDSS  M Q+G+PNL+NI +EN+ LS+P+AAS FT+ 
Sbjct: 678 SGREYSTYQGANDPQNNLLFGVNIDSSTFMLQHGIPNLRNIGTENDPLSMPFAASTFTSA 737

Query: 759 VGTDFPLNSDMTTSSCVDESGFLQSSENVDQVNPPTRTFVKVHKSGSFGRSLDISKFSSY 818
            G+D PLNSDMT SSCVDESGFLQSSENVDQVNP TRTFVKVHKSGS+GRSLDISKFSSY
Sbjct: 738 TGSDIPLNSDMTASSCVDESGFLQSSENVDQVNPSTRTFVKVHKSGSYGRSLDISKFSSY 797

Query: 819 DELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLGDDPWQEFVNNVGYIKILSPL 878
           DELRSELAR+F LEG LEDPQRSGWQLVF DRENDVLLLGDDPWQEFVNNV YIKILSPL
Sbjct: 798 DELRSELARLFCLEGLLEDPQRSGWQLVFGDRENDVLLLGDDPWQEFVNNVWYIKILSPL 857

Query: 879 EVQQMGK-GLSPVTSGPGQRLSSNNNFDDYVSRQELRSSSNGVASMGSINY 928
           EVQQMGK GLSP  S P Q+L SN+N D +++ Q  R+SSNG+ASMGS++Y
Sbjct: 858 EVQQMGKEGLSPAASVPCQKL-SNSNSDGHMNTQGFRNSSNGIASMGSLDY 907

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|356501413\|ref\|XP_003519519.1\| PREDICTED: auxin response factor 6-like [Glycine max]	Back alignment and taxonomy information

>gi\|356554039\|ref\|XP_003545357.1\| PREDICTED: auxin response factor 6-like [Glycine max]	Back alignment and taxonomy information

>gi\|359485334\|ref\|XP_002282830.2\| PREDICTED: auxin response factor 6-like [Vitis vinifera]	Back alignment and taxonomy information

>gi\|225443952\|ref\|XP_002279808.1\| PREDICTED: auxin response factor 6-like [Vitis vinifera]	Back alignment and taxonomy information

>gi\|302143499\|emb\|CBI22060.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|296278602\|gb\|ADH04265.1\| ARF1 [Nicotiana benthamiana]	Back alignment and taxonomy information

>gi\|449466121\|ref\|XP_004150775.1\| PREDICTED: auxin response factor 6-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449515293\|ref\|XP_004164684.1\| PREDICTED: LOW QUALITY PROTEIN: auxin response factor 6-like, partial [Cucumis sativus]	Back alignment and taxonomy information

>gi\|222539816\|gb\|ACM66271.1\| ARF8 [Solanum melongena]	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		928
TAIR\|locus:2204237		935	ARF6 "auxin response factor 6"	0.468	0.465	0.874	5.1e-296
TAIR\|locus:2152642		811	ARF8 "auxin response factor 8"	0.471	0.540	0.782	3.2e-232
TAIR\|locus:2202205		1086	ARF19 "auxin response factor 1	0.457	0.391	0.620	4e-177
TAIR\|locus:2035454		902	MP "MONOPTEROS" [Arabidopsis t	0.405	0.416	0.610	1.8e-160
TAIR\|locus:2174013		859	ARF2 "auxin response factor 2"	0.389	0.420	0.535	1.2e-125
TAIR\|locus:2175098		788	ARF4 "auxin response factor 4"	0.391	0.460	0.522	2.2e-120
TAIR\|locus:2025991		665	ARF1 "auxin response factor 1"	0.385	0.538	0.532	4.2e-117
TAIR\|locus:2039124		622	ARF11 "auxin response factor 1	0.405	0.604	0.479	2.2e-111
TAIR\|locus:2076765		602	ARF18 "auxin response factor 1	0.405	0.624	0.491	2.4e-108
TAIR\|locus:2138096		638	ARF9 "auxin response factor 9"	0.382	0.556	0.486	1.2e-104

TAIR\|locus:2204237 ARF6 "auxin response factor 6" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 2054 (728.1 bits), Expect = 5.1e-296, Sum P(2) = 5.1e-296
 Identities = 389/445 (87%), Positives = 408/445 (91%)

Query:    45 GEKKCLNSELWHACAGPLVSLPPVGSRVVYFPQGHSEQVAASTNKEVDAHIPNYPNLPPQ 104
             GEK+ LNSELWHACAGPLVSLPPVGSRVVYFPQGHSEQVAASTNKEVDAHIPNYP+L PQ
Sbjct:    17 GEKRVLNSELWHACAGPLVSLPPVGSRVVYFPQGHSEQVAASTNKEVDAHIPNYPSLHPQ 76

Query:   105 LICQLHNLTMHADVETDEVYAQMTLQPLSPQEQKDVYLLPAELGAPNKQPTNYFCKTLTA 164
             LICQLHN+TMHADVETDEVYAQMTLQPL+ QEQKD YL PAELG P++QPTNYFCKTLTA
Sbjct:    77 LICQLHNVTMHADVETDEVYAQMTLQPLNAQEQKDPYL-PAELGVPSRQPTNYFCKTLTA 135

Query:   165 SDTSTHGGFSVPRRAAEKVFPPLDYSQTPPAQELIARDLHDNEWKFRHIFRGQPKRHLLT 224
             SDTSTHGGFSVPRRAAEKVFPPLDYSQ PPAQEL+ARDLHDNEWKFRHIFRGQPKRHLLT
Sbjct:   136 SDTSTHGGFSVPRRAAEKVFPPLDYSQQPPAQELMARDLHDNEWKFRHIFRGQPKRHLLT 195

Query:   225 TGWSVFVSAKRLVAGDSVLFIWNEKNQLLLGIRRATRPQTVMPSSVLSSDSMHIGLLXXX 284
             TGWSVFVSAKRLVAGDSVLFIWN+KNQLLLGIRRA RPQTVMPSSVLSSDSMH+GLL   
Sbjct:   196 TGWSVFVSAKRLVAGDSVLFIWNDKNQLLLGIRRANRPQTVMPSSVLSSDSMHLGLLAAA 255

Query:   285 XXXXXTNSRFTIFYNPRASPSEFVIPLAKYVKAVYHTRVSVGMRFRMLFETEESSVRRYM 344
                  TNSRFTIFYNPRASPSEFVIPLAKYVKAVYHTRVSVGMRFRMLFETEESSVRRYM
Sbjct:   256 AHAAATNSRFTIFYNPRASPSEFVIPLAKYVKAVYHTRVSVGMRFRMLFETEESSVRRYM 315

Query:   345 GTITGISDLDPVRWPNSHWRSVKVGWDESTAGERQPRVSLWEIEPLTTFPMYSSPFPLRL 404
             GTITGI DLDP RW NSHWRSVKVGWDESTAGERQPRVSLWEIEPLTTFPMY SPFPLRL
Sbjct:   316 GTITGICDLDPTRWANSHWRSVKVGWDESTAGERQPRVSLWEIEPLTTFPMYPSPFPLRL 375

Query:   405 KRPWPSGLPSFHGMKDGDM--SINSPLMWLQGGVGDQGIQSLNFQGYGVTPWMQPRLDAS 462
             KRPWP GLPSFHG+K+ DM  S++SPLMW      D+G+QSLNFQG GV PWMQPRLD S
Sbjct:   376 KRPWPPGLPSFHGLKEDDMGMSMSSPLMW------DRGLQSLNFQGMGVNPWMQPRLDTS 429

Query:   463 -IPGLQPDVYQAMAAAALQEMRTVD 486
              + G+Q DVYQAMAAAALQ+MR +D
Sbjct:   430 GLLGMQNDVYQAMAAAALQDMRGID 454

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0009725 "response to hormone stimulus" evidence=IEA

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

GO:0009733 "response to auxin stimulus" evidence=IMP

GO:0009908 "flower development" evidence=IGI

GO:0005515 "protein binding" evidence=IPI

GO:0009855 "determination of bilateral symmetry" evidence=RCA

GO:0009886 "post-embryonic morphogenesis" evidence=RCA

GO:0009887 "organ morphogenesis" evidence=RCA

GO:0009909 "regulation of flower development" evidence=RCA

GO:0010014 "meristem initiation" evidence=RCA

GO:0010051 "xylem and phloem pattern formation" evidence=RCA

GO:0010073 "meristem maintenance" evidence=RCA

GO:0048439 "flower morphogenesis" evidence=RCA

GO:0048481 "ovule development" evidence=RCA

GO:0048507 "meristem development" evidence=RCA

GO:0048519 "negative regulation of biological process" evidence=RCA

TAIR\|locus:2152642 ARF8 "auxin response factor 8" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2202205 ARF19 "auxin response factor 19" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2035454 MP "MONOPTEROS" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2174013 ARF2 "auxin response factor 2" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2175098 ARF4 "auxin response factor 4" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2025991 ARF1 "auxin response factor 1" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2039124 ARF11 "auxin response factor 11" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2076765 ARF18 "auxin response factor 18" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2138096 ARF9 "auxin response factor 9" [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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
A2YG67	ARFQ_ORYSI	No assigned EC number	0.6498	0.9310	0.9422	N/A	no
Q9FGV1	ARFH_ARATH	No assigned EC number	0.5832	0.8297	0.9494	yes	no
Q6H6V4	ARFF_ORYSJ	No assigned EC number	0.6603	0.9364	0.9570	yes	no
A2X1A1	ARFF_ORYSI	No assigned EC number	0.6603	0.9364	0.9570	N/A	no

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:
	GSVIVG00018838001	SubName- Full=Chromosome chr12 scaffold_18, whole genome shotgun sequence; (830 aa)
		(Vitis vinifera)
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		928
pfam06507		83	pfam06507, Auxin_resp, Auxin response factor	6e-47
pfam02362		97	pfam02362, B3, B3 DNA binding domain	1e-26
smart01019		96	smart01019, B3, B3 DNA binding domain	1e-26
pfam02309		188	pfam02309, AUX_IAA, AUX/IAA family	8e-24
cd10017		98	cd10017, B3_DNA, Plant-specific B3-DNA binding dom	7e-22
pfam11498		476	pfam11498, Activator_LAG-3, Transcriptional activa	3e-04
pfam09606		768	pfam09606, Med15, ARC105 or Med15 subunit of Media	4e-04
cd10016		142	cd10016, EcoRII_N, N-terminal domain of type IIE r	8e-04
PRK10246		1047	PRK10246, PRK10246, exonuclease subunit SbcC; Prov	0.001
pfam09770		804	pfam09770, PAT1, Topoisomerase II-associated prote	0.001
COG3064		387	COG3064, TolA, Membrane protein involved in colici	0.003
pfam11498		476	pfam11498, Activator_LAG-3, Transcriptional activa	0.004
PRK00286		438	PRK00286, xseA, exodeoxyribonuclease VII large sub	0.004
PRK00286		438	PRK00286, xseA, exodeoxyribonuclease VII large sub	0.004
pfam03938		157	pfam03938, OmpH, Outer membrane protein (OmpH-like	0.004

>gnl\|CDD\|191545 pfam06507, Auxin_resp, Auxin response factor	Back alignment and domain information

 Score =  161 bits (410), Expect = 6e-47
 Identities = 57/84 (67%), Positives = 71/84 (84%), Gaps = 1/84 (1%)

Query: 284 AAHAAATNSRFTIFYNPRASPSEFVIPLAKYVKAVYHTRVSVGMRFRMLFETEESSVRRY 343
           AAHAA+T S F +FYNPRAS SEFV+P AKY+KA+ +   SVGMRF+M FETE+SS RR+
Sbjct: 1   AAHAASTGSPFHVFYNPRASTSEFVVPYAKYLKAMNN-PFSVGMRFKMRFETEDSSERRF 59

Query: 344 MGTITGISDLDPVRWPNSHWRSVK 367
            GTI+G+SDLDP+RWPNS WRS++
Sbjct: 60  SGTISGVSDLDPIRWPNSKWRSLQ 83

A conserved region of auxin-responsive transcription factors. Length = 83

>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\|216968 pfam02309, AUX_IAA, AUX/IAA family	Back alignment and domain information

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

>gnl\|CDD\|151935 pfam11498, Activator_LAG-3, Transcriptional activator LAG-3	Back alignment and domain information

>gnl\|CDD\|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex non-fungal	Back alignment and domain information

>gnl\|CDD\|197382 cd10016, EcoRII_N, N-terminal domain of type IIE restriction endonuclease EcoRII and similar proteins	Back alignment and domain information

>gnl\|CDD\|182330 PRK10246, PRK10246, exonuclease subunit SbcC; Provisional	Back alignment and domain information

>gnl\|CDD\|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1	Back alignment and domain information

>gnl\|CDD\|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]	Back alignment and domain information

>gnl\|CDD\|151935 pfam11498, Activator_LAG-3, Transcriptional activator LAG-3	Back alignment and domain information

>gnl\|CDD\|234714 PRK00286, xseA, exodeoxyribonuclease VII large subunit; Reviewed	Back alignment and domain information

>gnl\|CDD\|234714 PRK00286, xseA, exodeoxyribonuclease VII large subunit; Reviewed	Back alignment and domain information

>gnl\|CDD\|217803 pfam03938, OmpH, Outer membrane protein (OmpH-like)	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		928
PF06507		83	Auxin_resp: Auxin response factor; InterPro: IPR01	100.0
PF02309		215	AUX_IAA: AUX/IAA family; InterPro: IPR003311 The A	99.98
PF02362		100	B3: B3 DNA binding domain; InterPro: IPR003340 Two	99.72
KOG0644		1113	consensus Uncharacterized conserved protein, conta	99.18
PF09217		156	EcoRII-N: Restriction endonuclease EcoRII, N-termi	98.16
PF03754		114	DUF313: Domain of unknown function (DUF313) ; Inte	97.79
PF00564		84	PB1: PB1 domain; InterPro: IPR000270 The Phox and	97.01
smart00666		81	PB1 PB1 domain. Phox and Bem1p domain, present in	96.0
cd05992		81	PB1 The PB1 domain is a modular domain mediating s	95.98
cd06407		82	PB1_NLP A PB1 domain is present in NIN like protei	95.44
cd06396		81	PB1_NBR1 The PB1 domain is an essential part of NB	95.41
cd06398		91	PB1_Joka2 The PB1 domain is present in the Nicotia	94.75
cd06409		86	PB1_MUG70 The MUG70 protein is a product of the me	94.63
cd06403		80	PB1_Par6 The PB1 domain is an essential part of Pa	92.56
cd06404		83	PB1_aPKC PB1 domain is an essential modular domain	91.32
cd06401		81	PB1_TFG The PB1 domain found in TFG protein, an on	90.59
cd06402		87	PB1_p62 The PB1 domain is an essential part of p62	90.22
cd06397		82	PB1_UP1 Uncharacterized protein 1. The PB1 domain	87.32
cd06408		86	PB1_NoxR The PB1 domain is present in the Epichloe	81.42

>PF06507 Auxin_resp: Auxin response factor; InterPro: IPR010525 This pattern represents a conserved region of auxin-responsive transcription factors	Back alignment and domain information

Probab=100.00  E-value=4.5e-35  Score=262.59  Aligned_cols=83  Identities=66%  Similarity=1.100  Sum_probs=81.1

Q ss_pred             HHHHHHcCCcEEEEEcCCCCCCccccchHHHHHHHhcCCCccccEEEEeeeccccccceeeeEEEEeecCCCCCCCCCCc
Q 002390          284 AAHAAATNSRFTIFYNPRASPSEFVIPLAKYVKAVYHTRVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWPNSHW  363 (928)
Q Consensus       284 Aa~aaat~~~F~V~Y~PRas~sEFVVp~~kyvkA~~~~~ws~GMRFrM~fEtEdss~rry~GTI~gvsd~DP~rWP~S~W  363 (928)
                      |+|||+++++|+|+||||++++|||||++||++|+. ++|++||||||.||+||+++++|+|||+||+++||+|||+|+|
T Consensus         1 A~~aa~~~~~F~V~Y~PRa~~sEFVV~~~k~~~al~-~~~~~GmRfkM~fE~eds~~~~~~GtI~~v~~~dp~~w~~S~W   79 (83)
T PF06507_consen    1 AAHAAATGSPFEVFYYPRASPSEFVVPASKYDKALN-HPWSVGMRFKMRFETEDSSERRWQGTIVGVSDLDPIRWPGSKW   79 (83)
T ss_pred             ChhHhhcCCeEEEEECCCCCCcceEEEHHHHHHHhc-CCCCCCcEEEEEeccCCCccceeeeEEeEeeccCCCCCCCCCc
Confidence            689999999999999999999999999999999997 7999999999999999999999999999999999999999999


Q ss_pred             eeeE
Q 002390          364 RSVK  367 (928)
Q Consensus       364 R~Lq  367 (928)
                      ||||
T Consensus        80 R~Lq   83 (83)
T PF06507_consen   80 RMLQ   83 (83)
T ss_pred             ccCc
Confidence            9997

The plant hormone auxin (indole-3-acetic acid) can regulate the gene expression of several families, including Aux/IAA, GH3 and SAUR families. Two related families of proteins, Aux/IAA proteins (IPR003311 from INTERPRO) and the auxin response factors (ARF), are key regulators of auxin-modulated gene expression []. There are multiple ARF proteins, some of which activate, while others repress transcription. ARF proteins bind to auxin-responsive cis-acting promoter elements (AuxREs) using an N-terminal DNA-binding domain. It is thought that Aux/IAA proteins activate transcription by modifying ARF activity through the C-terminal protein-protein interaction domains (IPR011525 from INTERPRO) found in both Aux/IAA and ARF proteins. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0009725 response to hormone stimulus, 0005634 nucleus

>PF02309 AUX_IAA: AUX/IAA family; InterPro: IPR003311 The Aux/IAA family of genes are key regulators of auxin-modified gene expression []	Back alignment and domain information

>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

>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]	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

>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

>PF00564 PB1: PB1 domain; InterPro: IPR000270 The Phox and Bem1p domain, is present in many eukaryotic cytoplasmic signalling proteins	Back alignment and domain information

>smart00666 PB1 PB1 domain	Back alignment and domain information

>cd05992 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity	Back alignment and domain information

>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium)	Back alignment and domain information

>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62	Back alignment and domain information

>cd06398 PB1_Joka2 The PB1 domain is present in the Nicotiana plumbaginifolia Joka2 protein which interacts with sulfur stress inducible UP9 protein	Back alignment and domain information

>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain	Back alignment and domain information

>cd06403 PB1_Par6 The PB1 domain is an essential part of Par6 protein which in complex with Par3 and aPKC proteins is crucial for establishment of apical-basal polarity of animal cells	Back alignment and domain information

>cd06404 PB1_aPKC PB1 domain is an essential modular domain of the atypical protein kinase C (aPKC) which in complex with Par6 and Par3 proteins is crucial for establishment of apical-basal polarity of animal cells	Back alignment and domain information

>cd06401 PB1_TFG The PB1 domain found in TFG protein, an oncogenic gene product and fusion partner to nerve growth factor tyrosine kinase receptor TrkA and to the tyrosine kinase ALK	Back alignment and domain information

>cd06402 PB1_p62 The PB1 domain is an essential part of p62 scaffold protein (alias sequestosome 1,SQSTM) involved in cell signaling, receptor internalization, and protein turnover	Back alignment and domain information

>cd06397 PB1_UP1 Uncharacterized protein 1	Back alignment and domain information

>cd06408 PB1_NoxR The PB1 domain is present in the Epichloe festucae NoxR protein (NADPH oxidase regulator), a key regulator of NADPH oxidase isoform, NoxA	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		928
1wid_A		130	Solution Structure Of The B3 Dna-Binding Domain Of		9e-07

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

Back alignment and structure

Iteration: 1

Score = 52.8 bits (125), Expect = 9e-07, Method: Compositional matrix adjust. Identities = 30/87 (34%), Positives = 43/87 (49%) Query: 158 FCKTLTASDTSTHGGFSVPRRAAEKVFPPLDYSQTPPAQELIARDLHDNEWKFRHIFRGQ 217 F K +T SD +P+ AEK FP + + L D++ W+FR+ + Sbjct: 14 FEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYWNS 73 Query: 218 PKRHLLTTGWSVFVSAKRLVAGDSVLF 244 + ++LT GWS FV K L AGD V F Sbjct: 74 SQSYVLTKGWSRFVKEKNLRAGDVVSF 100

PyMOL of 1wid

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		928
1wid_A		130	DNA-binding protein RAV1; DNA-binding domain, stru	2e-43
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-09
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-05
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-04

>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 =  152 bits (386), Expect = 2e-43
 Identities = 37/126 (29%), Positives = 57/126 (45%)

Query: 148 GAPNKQPTNYFCKTLTASDTSTHGGFSVPRRAAEKVFPPLDYSQTPPAQELIARDLHDNE 207
           G+  +     F K +T SD        +P+  AEK FP    + +     L   D++   
Sbjct: 4   GSSGRSAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKV 63

Query: 208 WKFRHIFRGQPKRHLLTTGWSVFVSAKRLVAGDSVLFIWNEKNQLLLGIRRATRPQTVMP 267
           W+FR+ +    + ++LT GWS FV  K L AGD V F  +      L I   +R  + + 
Sbjct: 64  WRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQDQQLYIGWKSRSGSDLD 123

Query: 268 SSVLSS 273
           +S  SS
Sbjct: 124 ASGPSS 129

PyMOL of 1wid

>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

>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

>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 = 43.7 bits (102), Expect = 3e-04
 Identities = 114/669 (17%), Positives = 199/669 (29%), Gaps = 217/669 (32%)

Query: 15  YKLDQIVLNFVLFFSLVMMLDNTKCRENFAGEKKCLNS-ELWHACAGPLVSLPPVGSRVV 73
           Y+   I+  F   F  V   D   C++     K  L+  E+ H     ++      S  +
Sbjct: 16  YQYKDILSVFEDAF--VDNFD---CKDVQDMPKSILSKEEIDH-----IIMSKDAVSGTL 65

Query: 74  Y----FPQGHSEQVAASTNKEVDAHIPNY-------------PNLPPQLICQLHNLTMHA 116
                      E V        +    NY             P++  ++  +  +  ++ 
Sbjct: 66  RLFWTLLSKQEEMVQKFVE---EVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRD-RLYN 121

Query: 117 DVETDEVYAQMTLQPLSPQEQKDVYLLPAELGAPNKQPTNY--------FCKT-LTAS-- 165
           D +   V+A+  +  L P  +    LL  EL     +P             KT +     
Sbjct: 122 DNQ---VFAKYNVSRLQPYLKLRQALL--EL-----RPAKNVLIDGVLGSGKTWVALDVC 171

Query: 166 -DTSTHGGFSVP--------RRAAEKVFPPL---------DYSQTPPAQELIARDLHDNE 207
                                 + E V   L         +++        I   +H  +
Sbjct: 172 LSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQ 231

Query: 208 WKFRHIFRGQPKRHLLTTGWSVFVSAKRLVAGDSVLFIWNEKN--------QLLLGIRRA 259
            + R + + +P  + L            LV  +    + N K         ++LL     
Sbjct: 232 AELRRLLKSKPYENCL------------LVLLN----VQNAKAWNAFNLSCKILL----T 271

Query: 260 TRPQTVMPSSVLSSDSMHIGLLAAAAHAAATNSRFTIFYNPRASPSEFVIPLAKYVKAVY 319
           TR + V    + ++ + HI L     H + T    T        P E    L KY     
Sbjct: 272 TRFKQVT-DFLSAATTTHISL----DHHSMT---LT--------PDEVKSLLLKY----- 310

Query: 320 HTRVSVGMRFRML-FETEESSVRRYMGTITGISDL---DPVRWPNSHWRSVKVGWDESTA 375
                +  R + L  E   ++ R     ++ I++        W N  W+ V      +T 
Sbjct: 311 -----LDCRPQDLPREVLTTNPR----RLSIIAESIRDGLATWDN--WKHVNC-DKLTTI 358

Query: 376 GERQPRVSLWEIEP---------LTTFPMYSSPFPLR-LKRPWPSGLP--------SFH- 416
            E     SL  +EP         L+ FP  S+  P   L   W   +           H 
Sbjct: 359 IE----SSLNVLEPAEYRKMFDRLSVFP-PSAHIPTILLSLIWFDVIKSDVMVVVNKLHK 413

Query: 417 ------GMKDGDMSINSPLMWLQGGVGDQG------IQSLN----FQGYGVTPWMQPRLD 460
                   K+  +SI S  + L+  + ++       +   N    F    + P   P LD
Sbjct: 414 YSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIP---PYLD 470

Query: 461 ASIPGLQPDVYQAMAAAALQEMRTVDSSKLASQSLLQF---QQ----SQNVSNGTASMIP 513
                     Y  +    L+ +   +   L     L F   +Q         N + S++ 
Sbjct: 471 QYF-------YSHI-GHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILN 522

Query: 514 RQMLQQ---------------SQAQNAL---LQSFQEN-QASAQAQLLQQQLQRQHS--Y 552
              LQQ                +  NA+   L   +EN   S    LL+  L  +    +
Sbjct: 523 --TLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIF 580

Query: 553 NEQRQQQQQ 561
            E  +Q Q+
Sbjct: 581 EEAHKQVQR 589

PyMOL of 1vt4

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		928
1wid_A		130	DNA-binding protein RAV1; DNA-binding domain, stru	99.96
4i1k_A		146	B3 domain-containing transcription factor VRN1; B3	99.73
1yel_A		104	AT1G16640; CESG, protein structure initiative, str	99.54
1na6_A		404	Ecorii, restriction endonuclease ecorii; site-spec	95.25
1vd2_A		89	Protein kinase C, IOTA type; PB1 domain, OPCA moti	92.9
1wmh_B		86	Partitioning defective-6 homolog alpha; kinase, PB	92.14
2kkc_A		102	Sequestosome-1; P62, PB1, autophagy, ubiquitin-pro	91.7
2ktr_A		117	Sequestosome-1; autophagy, NF-KB signaling, HOMO-o	90.19
1q1o_A		98	Cell division control protein 24; PB1 domain, PCCR	85.6
1oey_J		107	P40-PHOX, neutrophil cytosol factor 4; immune syst	80.6

>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=99.96  E-value=5.8e-29  Score=236.55  Aligned_cols=115  Identities=29%  Similarity=0.479  Sum_probs=104.5

Q ss_pred             CCCCCCceeEEEeeccccCCCCCceeeecchhhhhCCCCCCCCCCCceEEEEEecCCCeEEEEEEEeCCCCceeEccchh
Q 002390          149 APNKQPTNYFCKTLTASDTSTHGGFSVPRRAAEKVFPPLDYSQTPPAQELIARDLHDNEWKFRHIFRGQPKRHLLTTGWS  228 (928)
Q Consensus       149 ~~~~~~~~~F~K~LT~SDV~~~GrfsVPk~~AE~~FP~Ld~s~~~p~q~L~~~Dl~Gk~W~FR~iyrg~pkrhlLTtGWs  228 (928)
                      ...+...++|+|+||+|||+++++|+||+++|++|||.++.++..++++|.++|.+|++|+|||+||+++++|+||+||+
T Consensus         5 ~~~~~~~~~F~K~Lt~SDv~~~~rL~iPk~~a~~~lP~~~~~~~~~~~~l~l~D~~Gk~W~fr~~~~~~~~~~~Lt~GW~   84 (130)
T 1wid_A            5 SSGRSAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYWNSSQSYVLTKGWS   84 (130)
T ss_dssp             ---CCCEEEEEEECCTTTTSSSCCEEECHHHHTTTSCCCSSCCSSCCEEEEEEETTTEEEEEEEEEETTTTEEEEESSHH
T ss_pred             CCCCCCcceEEEEEehHHcCCCCEEEeCHHHHHhhCCccccccCCCcEEEEEEeCCCCEEEEEEEEECCCCceEEcCChH
Confidence            34566788999999999999999999999999999999987766788999999999999999999999999999999999


Q ss_pred             hhhhccCCcCCCEEEEEEcc--CCeEEEEEEecCCCC
Q 002390          229 VFVSAKRLVAGDSVLFIWNE--KNQLLLGIRRATRPQ  263 (928)
Q Consensus       229 ~FVr~K~L~aGDsVvF~R~e--~GeL~VGIRRa~r~~  263 (928)
                      .||++|+|++||+|+|+|.+  +++|+|++||+.++.
T Consensus        85 ~FV~~~~L~~GD~~~F~~~~~~~~~l~I~~rr~~~~~  121 (130)
T 1wid_A           85 RFVKEKNLRAGDVVSFSRSNGQDQQLYIGWKSRSGSD  121 (130)
T ss_dssp             HHHHHTTCCTTCEEEEEECCSSSCCEEEEEECCCSCS
T ss_pred             HHHHHcCCCCCCEEEEEEecCCCcEEEEEEEECCCCC
Confidence            99999999999999999985  468999999998754

PyMOL of 1wid

>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

>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

>1vd2_A Protein kinase C, IOTA type; PB1 domain, OPCA motif, APKC, ZIP/P62, MEK5, molecular recognition, transferase; NMR {Homo sapiens} SCOP: d.15.2.2 PDB: 1wmh_A	Back alignment and structure

>1wmh_B Partitioning defective-6 homolog alpha; kinase, PB1 domain, OPCA motif, APKC, cell polarity, transferase/cell cycle complex; 1.50A {Homo sapiens} SCOP: d.15.2.2	Back alignment and structure

>2kkc_A Sequestosome-1; P62, PB1, autophagy, ubiquitin-proteasome system, NF-KB signaling, alternative splicing, apoptosis, cytoplasm, differentiation; NMR {Rattus norvegicus} PDB: 2ktr_B	Back alignment and structure

>2ktr_A Sequestosome-1; autophagy, NF-KB signaling, HOMO-oligomer, PB1 dimer, signaling protein, transport protein; NMR {Rattus norvegicus}	Back alignment and structure

>1q1o_A Cell division control protein 24; PB1 domain, PCCR, PC motif, OPCA motif, yeast, cell polarity, protein-protein interaction; NMR {Saccharomyces cerevisiae} SCOP: d.15.2.2 PDB: 2kfj_A 2kfk_B	Back alignment and structure

>1oey_J P40-PHOX, neutrophil cytosol factor 4; immune system, PB1 heterodimer/complex, NADPH oxidase, PB1 D heterodimerization; 2.0A {Homo sapiens} SCOP: d.15.2.2	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		928
d1wida_		117	b.142.1.2 (A:) DNA-binding protein RAV1 {Thale cre	2e-36
d1na6a1		175	b.142.1.1 (A:4-178) Restriction endonuclease EcoRI	2e-24
d1yela1		102	b.142.1.2 (A:1-102) At1g16640 {Thale cress (Arabid	4e-12

>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 =  130 bits (329), Expect = 2e-36
 Identities = 34/119 (28%), Positives = 54/119 (45%), Gaps = 4/119 (3%)

Query: 152 KQPTNYFCKTLTASDTSTHGGFSVPRRAAEKVFPPLDYSQTPPAQELIARDLHDNEWKFR 211
           +     F K +T SD        +P+  AEK FP    + +     L   D++   W+FR
Sbjct: 1   RSAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFR 60

Query: 212 HIFRGQPKRHLLTTGWSVFVSAKRLVAGDSVLFIW--NEKNQLLLGIRRATRPQTVMPS 268
           + +    + ++LT GWS FV  K L AGD V F     +  QL +G +   R  + + +
Sbjct: 61  YSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQDQQLYIGWKS--RSGSDLDA 117

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		928
d1wida_		117	DNA-binding protein RAV1 {Thale cress (Arabidopsis	99.94
d1na6a1		175	Restriction endonuclease EcoRII, N-terminal domain	99.8
d1yela1		102	At1g16640 {Thale cress (Arabidopsis thaliana) [Tax	99.44
d2bkfa1		85	Next to BRCA1 gene 1 protein, NBR1 (KIAA0049) {Hum	95.46
d1ip9a_		85	Bud emergence mediator Bemp1 {Baker's yeast (Sacch	92.34

>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=99.94  E-value=8.6e-27  Score=214.04  Aligned_cols=109  Identities=30%  Similarity=0.490  Sum_probs=102.5

Q ss_pred             CceeEEEeeccccCCCCCceeeecchhhhhCCCCCCCCCCCceEEEEEecCCCeEEEEEEEeCCCCceeEccchhhhhhc
Q 002390          154 PTNYFCKTLTASDTSTHGGFSVPRRAAEKVFPPLDYSQTPPAQELIARDLHDNEWKFRHIFRGQPKRHLLTTGWSVFVSA  233 (928)
Q Consensus       154 ~~~~F~K~LT~SDV~~~GrfsVPk~~AE~~FP~Ld~s~~~p~q~L~~~Dl~Gk~W~FR~iyrg~pkrhlLTtGWs~FVr~  233 (928)
                      ...+|.|+||+|||++++||+||+++|++|||+++...+.++++|.++|.+|++|+|+|+||++.++|+|++||..||++
T Consensus         3 ~~~iF~K~Lt~sDv~~~~rL~iP~~~~~~~lp~~~~~~~~~~~~~~~~d~~g~~W~~~~~~~~~~~~~~l~~GW~~Fv~~   82 (117)
T d1wida_           3 AEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFVKE   82 (117)
T ss_dssp             CEEEEEEECCTTTTSSSCCEEECHHHHTTTSCCCSSCCSSCCEEEEEEETTTEEEEEEEEEETTTTEEEEESSHHHHHHH
T ss_pred             CceEEEEEecchhcCCCCEEEECHHHHHHhCCccccccCCCcEEEEEEeCCCCEEEEEEEEECCCCceEEecCHHHHHHH
Confidence            36799999999999999999999999999999999888889999999999999999999999888899999999999999


Q ss_pred             cCCcCCCEEEEEEc--cCCeEEEEEEecCCC
Q 002390          234 KRLVAGDSVLFIWN--EKNQLLLGIRRATRP  262 (928)
Q Consensus       234 K~L~aGDsVvF~R~--e~GeL~VGIRRa~r~  262 (928)
                      |+|++||+|+|+|+  ++++++|++||+...
T Consensus        83 ~~Lk~GD~~~F~~~~~~~~~~~i~~r~~~~~  113 (117)
T d1wida_          83 KNLRAGDVVSFSRSNGQDQQLYIGWKSRSGS  113 (117)
T ss_dssp             TTCCTTCEEEEEECCSSSCCEEEEEECCCSC
T ss_pred             cCCCCCCEEEEEEEeCCCCEEEEEEEECCCC
Confidence            99999999999997  578999999988643

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

>d2bkfa1 d.15.2.2 (A:1-85) Next to BRCA1 gene 1 protein, NBR1 (KIAA0049) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1ip9a_ d.15.2.2 (A:) Bud emergence mediator Bemp1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure